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As a desirable agricultural trait, multi-inflorescence (MI) fulfills the requirement of mechanized harvesting and yield increase in rapeseed (Brassica napus L.). However, the genetic mechanism underlying the multi-inflorescence trait remain poorly understood. We previously identified a difference of one pair of dominant genes between the two mapping parental materials. In this study, phenotype and expression analysis indicated that the imbalance of the CLAVATA (CLV)-WUSCHEL (WUS) feedback loop may contribute to the abnormal development of the shoot apical meristem (SAM). BnaMI was fine-mapped to a 55 kb genomic region combining with genotype and phenotype of 5768 BCF1 individuals using a traditional mapping approach. Through comparative and expression analyses, combined with the annotation in Arabidopsis, five genes in this interval were identified as candidate genes. The present findings may provide assistance in functional analysis of the mechanism associated with multi-inflorescence and yield increase in rapeseed. [ABSTRACT FROM AUTHOR]

Sexual reproduction involves meiotic recombination and the creation of crossing over between homologous chromosomes, which leads to new allele combinations. We present a new approach that uses the allele frequency differences and the physical distance of neighboring polymorphisms to estimate the recombination rate from pool genotyping or sequencing. This allows a considerable cost reduction compared to conventional mapping based on genotyping or sequencing data of single individuals. We evaluated the approach based on computer simulations at various genotyping depths and population sizes as well as applied it to experimental data of 45 barley populations, comprising 4182 RIL. High correlations between the recombination rates from this new pool genetic mapping approach and conventional mapping in simulated and experimental barley populations were observed. The proposed method therefore provides a reliable genetic map position and recombination rate estimation in defined genomic windows. [ABSTRACT FROM AUTHOR]

Pineapple is the most important economic plant in the family Bromeliaceae and the third-most economically important tropical fruit in the world. It has become an important tropical fruit in Guangdong, Hainan, and Guangxi, which are suitable areas for its cultivation. However, modern and well-organized breeding systems have not yet been established for pineapple. In this review, we describe the current status of the geographical distribution, industrial development, and breeding of pineapple in China. The current status of pineapple breeding is introduced, including traditional breeding methods, such as crossbreeding, mutagenesis breeding, and biotechnology breeding, combining cell engineering and gene engineering. In addition, the research progress on assisted breeding technology based on genetic map construction and molecular marker development is presented. New challenges and perspectives for obtaining high fruit quality are discussed in the context of breeding programs for pineapple. [ABSTRACT FROM AUTHOR]

Summary: We had the fortune of starting our scientific/research careers in the Molecular Biology and Crop Biotechnology Laboratory of Professor P.K. Gupta at Ch. Charan Singh University, Meerut, UP, India. Here, we describe the most important scientific contributions of our beloved mentor in the area of cytotaxonomy, cytogenetics, mutation breeding, quantitative genetics, molecular biology, crop biotechnology and plant genomics, on his 85th birthday. Important contributions made in the development and use of genomics resources including the development and use of different kinds of molecular markers, genetic and physical mapping, quantitative trait locus (QTL) interval mapping, genome‐wide association mapping and molecular breeding including marker‐assisted selection have been briefly summarized. Efforts have been also made to give readers a glimpse of important contributions in the study of cytology/apomixis of grasses, cytotaxonomic studies in asteraceae/fabaceae, nuclear/repetitive DNA content in Lolium, interspecific/intergeneric relationships involving the genus Hordeum and re‐examining taxonomy of the tribe Triticeae. [ABSTRACT FROM AUTHOR]

Foxtail millet (Setaria italica) is an ideal model of genetic system for functional genomics of the Panicoideae crop. Identification of QTL responsible for morpho-agronomic and yield-related traits facilitates dissection of genetic control and breeding in cereal crops. Here, based on a Yugu1 × Longgu7 RIL population and genome-wide resequencing data, an updated linkage map harboring 2297 bin and 74 SSR markers was constructed, spanning 1315.1 cM with an average distance of 0.56 cM between adjacent markers. A total of 221 QTL for 17 morpho-agronomic and yield-related traits explaining 5.5 ~ 36% of phenotypic variation were identified across multi-environments. Of these, 109 QTL were detected in two to nine environments, including the most stable qLMS6.1 harboring a promising candidate gene Seita.6G250500, of which 70 were repeatedly identified in different trials in the same geographic location, suggesting that foxtail millet has more identical genetic modules under the similar ecological environment. One hundred-thirty QTL with overlapping intervals formed 22 QTL clusters. Furthermore, six superior recombinant inbred lines, RIL35, RIL48, RIL77, RIL80, RIL115 and RIL125 with transgressive inheritance and enrichment of favorable alleles in plant height, tiller, panicle morphology and yield related-traits were screened by hierarchical cluster. These identified QTL, QTL clusters and superior lines lay ground for further gene-trait association studies and breeding practice in foxtail millet. [ABSTRACT FROM AUTHOR]

Key message: The candidate recessive gene AhRt2 responsible for red testa of peanut was identified through combined BSA-seq and linkage mapping approaches. The testa color of peanuts (Arachis hypogaea L.) is an important trait, and those with red testa are particularly popular owing to the high-anthocyanin content. However, the identification of genes underlying the regulation of the red testa trait in peanut are rarely reported. In order to fine map red testa gene, two F2:4 populations were constructed through the cross of YZ9102 (pink testa) with ZH12 (red testa) and ZH2 (red testa). Genetic analysis indicated that red testa was controlled by a single recessive gene named as AhRt2 (Red testa gene 2). Using BSA-seq approach, AhRt2 was preliminary identified on chromosome 12, which was further mapped to a 530-kb interval using 220 recombinant lines through linkage mapping. Furthermore, functional annotation, expression profiling, and the analyses of sequence variation confirmed that the anthocyanin reductase namely (Arahy.IK60LM) was the most likely candidate gene for AhRt2. It was found that a SNP in the third exon of AhRt2 altered the encoding amino acids, and was associated with red testa in peanut. In addition, a closely linked molecular marker linked with red testa trait in peanut was also developed for future studies. Our results provide valuable insight into the molecular mechanism underlying peanut testa color and present significant diagnostic marker resources for marker-assisted selected breeding in peanut. [ABSTRACT FROM AUTHOR]

Genetic linkage maps based on single nucleotide polymorphisms (SNPs) represent an essential tool for a variety of genomic analyses. Today, next-generation sequencing (NGS) enables rapid genotyping of different mapping populations based on thousands of SNPs and the construction of highly saturated linkage maps. Nevertheless, missing data in the genotyping of the parental lines creates a bottleneck that determines the number of SNPs that can be used for the linkage map. As a proof of concept, a highly saturated genetic linkage map was constructed using the imputed genotypic data of a recombinant inbred line (RIL) population and the limited genotypic information of its parental lines. Two ABH genotype files were created from a pseudo-parental genotypic data set that includes all the SNPs present in the RIL population. In the first ABH file pseudo-parental 1 was considered parental A, while in the second pseudo-parental 1 was considered parental B. These two duplicate ABH genotype files were merged by chromosome and subjected to linkage map analysis. Since the ABH data were duplicated, two mirrored linkage groups were generated per chromosome. The correct linkage map was identified and selected based on the partial genotypic data of the parental lines. This strategy was effective for constructing a highly saturated linkage map of 33,421 SNPs based on the genotyping of 205 RILs and a limited number of 100 SNPs present in the parental lines. This strategy enables the use of all the NGS SNP data obtained from a low-coverage sequencing experiment in the mapping population. [ABSTRACT FROM AUTHOR]

Winter field survival (WFS) in autumn-seeded winter cereals is a complex trait associated with low temperature tolerance (LTT), prostrate growth habit (PGH), and final leaf number (FLN). WFS and the three sub-traits were analyzed by a genome-wide association study of 96 rye (Secale cereal L.) genotypes of different origins and winter-hardiness levels. A total of 10,244 single nucleotide polymorphism (SNP) markers were identified by genotyping by sequencing and 259 marker-trait-associations (MTAs; p < 0.01) were revealed by association mapping. The ten most significant SNPs (p < 1.49e−04) associated with WFS corresponded to nine strong candidate genes: Inducer of CBF Expression 1 (ICE1), Cold-regulated 413-Plasma Membrane Protein 1 (COR413-PM1), Ice Recrystallization Inhibition Protein 1 (IRIP1), Jasmonate-resistant 1 (JAR1), BIPP2C1-like protein phosphatase, Chloroplast Unusual Positioning Protein-1 (CHUP1), FRIGIDA-like 4 (FRL4-like) protein, Chalcone Synthase 2 (CHS2), and Phenylalanine Ammonia-lyase 8 (PAL8). Seven of the candidate genes were also significant for one or several of the sub-traits supporting the hypothesis that WFS, LTT, FLN, and PGH are genetically interlinked. The winter-hardy rye genotypes generally carried additional allele variants for the strong candidate genes, which suggested allele diversity was a major contributor to cold acclimation efficiency and consistent high WFS under varying field conditions. [ABSTRACT FROM AUTHOR]

Key message: A major QTL, qBWA12, was fine mapped to a 216.68 kb physical region, and A12.4097252 was identified as a useful KASP marker for breeding peanut varieties resistant to bacterial wilt. Bacterial wilt, caused by Ralstonia solanacearum, is a major disease detrimental to peanut production in China. Breeding disease-resistant peanut varieties is the most economical and effective way to prevent the disease and yield loss. Fine mapping the QTLs for bacterial wilt resistance is critical for the marker-assisted breeding of disease-resistant varieties. A recombinant inbred population comprising 521 lines was used to construct a high-density genetic linkage map and to identify QTLs for bacterial wilt resistance following restriction-site-associated DNA sequencing. The genetic map, which included 5120 SNP markers, covered a length of 3179 cM with an average marker distance of 0.6 cM. Four QTLs for bacterial wilt resistance were mapped on four chromosomes. One major QTL, qBWA12, with LOD score of 32.8–66.0 and PVE of 31.2–44.8%, was stably detected in all four development stages investigated over the 3 trial years. Additionally, qBWA12 spanned a 2.7 cM region, corresponding to approximately 0.4 Mb and was fine mapped to a 216.7 kb region by applying KASP markers that were polymorphic between the two parents based on whole-genome resequencing data. In a large collection of breeding and germplasm lines, it was proved that KASP marker A12.4097252 can be applied for the marker-assisted breeding to develop peanut varieties resistant to bacterial wilt. Of the 19 candidate genes in the region covered by qBWA12, nine NBS-LRR genes should be further investigated regarding their potential contribution to the resistance of peanut against bacterial wilt. [ABSTRACT FROM AUTHOR]

Key message: Comparative sequence analysis was used to design a SNP marker that aided in the identification of new sources of oat stem rust resistance. New races of Puccinia graminis f. sp. avenae (Pga) threaten global oat production. An A. strigosa accession known to carry the broadly effective oat stem rust resistance gene, Pg6, was crossed with two susceptible A. strigosa accessions to generate 198 F2:3 families and 190 F5:6 RILs. The RIL population was used to determine that Pg6 was a single dominant gene located between 475 and 491 Mbp on diploid chromosome AA2 of the A. atlantica genome. This region was further refined by identifying SNPs associated with Pg6 resistance in a panel of previously sequenced A-genome accessions. Twenty-four markers were developed from SNPs that showed perfect association between the Pg6 phenotype and 11 sequenced Avena diploid accessions. These markers were validated in the RILs and F2:3 families, and the markers most closely linked with resistance were tested in a diverse panel of 253 accessions consisting of oat stem rust differentials, all available diploid Avena spp. accessions, and 41 A. vaviloviana accessions from the National Small Grains Collection. One SNP marker located at 483, 439, 497 bp on AA2, designated as AA2_483439497, was perfectly associated with the Pg6 phenotype in Avena strigosa diploids and was within several Kb of a resistance gene analog, RPP13. The marker results and seedling testing against Pga races DBD, KBD, TJS, and TQL enabled the postulation of Pg6 and potential new sources of resistance in the Avena panel. These results will be used to infer Pg6 presence in other germplasm collections and breeding programs and can assist with introgression, gene pyramiding, and cloning of Pg6. [ABSTRACT FROM AUTHOR]

Watermelon possesses diverse ovary, fruit, and seed morphological traits and the successful identification of QTLs/genes controlling these traits are of great significance to breeders. Whole-genome re-sequencing using next-generation sequencing technology was employed to detect SNPs in the parental lines P1 (ZXG1553) and P2 (W1-17), for CAPS marker and linkage map development. The linkage map was developed by genotyping of 138 polymorphic CAPS markers with 191-F2 mapping population that covered all 11 chromosomes with a total length of 1853.34 cM. A total of thirty QTLs (2 Ovary weight, 2 Ovary length, 3 Ovary width, 4 Ovary hairiness, 2 Fruit weight, 1 Fruit length, 1 Fruit width, 1 Brix, 1 Rind thickness, 1 Seed length, 2 Seed width, 4 Rind chlorophyll a, 3 Rind chlorophyll b, and 3 Rind total chlorophyll) were detected for 14 significant ovary, fruit, and seed morphological traits. The QTLs exhibited different LOD score range (2.50 ~ 20.97) and phenotypic explained variance (3.30 ~ 25.91%) for all morphological traits. These detected QTLs and corresponding flanking CAPS markers could be valuable data to facilitate the further investigation in watermelon breeding programs and in-depth genetic basis studies. [ABSTRACT FROM AUTHOR]

Finding the quantitative trait loci (QTLs) and uncovering the genes controlling early flowering in pumpkin are the basic needs to select appropriate varieties for cultivation. Two QTLs related to first female flowering node (FFFN) and four QTLs related to first male flowering node (FMFN) were detected based on high‐density genetic map of pumpkin. Based on annotation information, two candidate genes, flowering locus T‐like protein (FLT) associated with FFFN on chr10 and flowering locus T‐like 2 (FLT2) associated with FMFN on chr11, were identified which were the homologues of flowering time switching gene, flowering Locus T (FT), in different crops. Seven different insertion–deletions (InDels) in promoter regions of FLT and FLT2 were identified by the analysis of wholegenome resequencing data of parental lines. Our results suggested that FLT and FLT2 are candidate genes for controlling FFFN and FMFN traits in pumpkin, respectively. Two insertion–deletion molecular markers were developed to distinguish the lower flowering node F2 individuals. This research will provide the theoretical and practical basis for the selection and cultivation of early flowering pumpkin varieties. [ABSTRACT FROM AUTHOR]

Meagre (Argyrosomus regius), is a benthopelagic species rapidly emerging in aquaculture, due to its low food to biomass conversion rate, good fillet yield and ease of production. Tracing a species genomic background along with describing the genetic basis of important traits can greatly influence both conservation strategies and production perspectives. In this study, we employed ddRAD sequencing of 266 fish from six F1 meagre families, to construct a high-density genetic map comprising 4529 polymorphic SNP markers. The QTL mapping analysis provided a genomic appreciation for the weight trait identifying a statistically significant QTL on linkage group 15 (LG15). The comparative genomics analysis with six teleost species revealed an evolutionarily conserved karyotype structure. The synteny observed, verified the already well-known fusion events of the three-spine stickleback genome, reinforced the evidence of reduced evolutionary distance of Sciaenids with the Sparidae family, reflected the evolutionary proximity with Dicentrarchus labrax, traced several putative chromosomal rearrangements and a prominent putative fusion event in meagre's LG17. This study presents novel elements concerning the genome evolutionary history of a non-model teleost species recently adopted in aquaculture, starts to unravel the genetic basis of the species growth-related traits, and provides a high-density genetic map as a tool that can help to further establish meagre as a valuable resource for research and production. [ABSTRACT FROM AUTHOR]

Growth directly influences production rate and therefore is one of the most important and well-studied traits in animal breeding. However, understanding the genetic basis of growth has been hindered by its typically complex polygenic architecture. Here, we performed quantitative trait locus mapping and genome-wide association studies for 10 growth traits that were observed over 2 years in 1,100 F1 captive-bred trevally (Pseudocaranx georgianus). We constructed the first high-density linkage map for trevally, which included 19,861 single nucleotide polymorphism markers, and discovered 8 quantitative trait loci for height, length, and weight on linkage groups 3, 14, and 18. Using genome-wide association studies, we further identified 113 single nucleotide polymorphism-trait associations, uncovering 10 genetic hot spots involved in growth. Two of the markers found in the genome-wide association studies colocated with the quantitative trait loci previously mentioned, demonstrating that combining quantitative trait locus mapping and genome-wide association studies represents a powerful approach for the identification and validation of loci controlling complex traits. This is the first study of its kind for trevally. Our findings provide important insights into the genetic architecture of growth in this species and supply a basis for fine mapping quantitative trait loci, genomic selection, and further detailed functional analysis of the genes underlying growth in trevally. [ABSTRACT FROM AUTHOR]

This study investigated genetic linkage, recombination fractions and mutation rates of 16 X chromosomal short tandem repeat (X-STR) markers using a recently developed multiplex PCR assay for Sinhalese population of Sri Lanka, by analyzing 81 three-generation families including 81 grandfathers with daughters and 162 grandsons. In addition, 31 two generation families involving mother father daughter trios were included for mutation analysis. The analysis of recombination fractions between marker pairs identified two linkage blocks (maximum LOD scores > 3.0) each spanning a physical distance of 44.35 Mb and 6.04 Mb respectively. Though recombination events are usually rare among closely linked markers, crossovers were observed for markers located < 1.0 Mb apart. The recombination fractions observed are not fully concordant with those reported earlier, including the second-generation Rutgers combined linkage-physical map. This suggests that linkage is not uniform among different populations. However, the overall and marker-specific mutation rates of the present study did not differ from previous reports, though it needs confirmation with a much larger sample set. The findings presented here will provide the baseline information required for biostatistical calculations conducted using X-STR markers, in complex kinship analysis of Sinhalese population. [ABSTRACT FROM AUTHOR]

Grape ( Vitis vinifera),is one of the most important fruit trees, and the genetic breeding of grape has been paid much attention. Due to the long childhood and high genetic heterozygosity, traditional cross breeding takes a long time and low efficiency. Therefore, by constructing grape genetic linkage map and locating quantitative traits loci (QTL), we can analyze the relationship between molecular markers and phenotype in grape hybrid population, select breeding parents more pertinently, early identify future hybrid population, carry out marker assisted selectio (MAS), and speed up the breeding process. With the development of molecular biology and genome sequencing technology, more and more QTL had been analyzed since gene mapping was carried out in 2000. This paper reviewed the QTL mapping of important genes found in grape in recent 20 years, such as downy mildew resistance, powdery mildew resistance, phylloxera resistance, berry size, seedless, skin color and so on, and focused on the mapping of Myb gene related to grape color traits and its application in MAS, in order to explore the key genes related to the formation and regulation of resistance and quality traits in grape germplasm resources, promote the progress of grape molecular designed breeding, which would contribute to the rapid improvement of grape breeding level in China. [ABSTRACT FROM AUTHOR]

Phalaenopsis spp. represent the most popular orchids worldwide. Both P. equestris and P. aphrodite are the two important breeding parents with the whole genome sequence available. However, marker–trait association is rarely used for floral traits in Phalaenopsis breeding. Here, we analyzed markers associated with aesthetic traits of Phalaenopsis orchids by using genome-wide association study (GWAS) with the F1 population P. Intermedia of 117 progenies derived from the cross between P. aphrodite and P. equestris. A total of 113,517 single nucleotide polymorphisms (SNPs) were identified in P. Intermedia by using genotyping-by-sequencing with the combination of two different restriction enzyme pairs, Hinp1 I/Hae III and Apek I/Hae III. The size-related traits from flowers were negatively related to the color-related traits. The 1191 SNPs from Hinp1 I/ Hae III and 23 simple sequence repeats were used to establish a high-density genetic map of 19 homolog groups for P. equestris. In addition, 10 quantitative trait loci were highly associated with four color-related traits on chromosomes 2, 5 and 9. According to the sequence within the linkage disequilibrium regions, 35 candidate genes were identified and related to anthocyanin biosynthesis. In conclusion, we performed marker-assisted gene identification of aesthetic traits with GWAS in Phalaenopsis orchids. [ABSTRACT FROM AUTHOR]

Background: Wheat powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), is an important disease affecting wheat production. Planting resistant cultivars is an effective, safe, and economical method to control the disease. Map construction using next-generation sequencing facilitates gene cloning based on genetic maps and high-throughput gene expression studies. In this study, specific-locus amplified fragment sequencing (SLAF) was used to analyze Huixianhong (female parent), Hongyoumai (male parent) and two bulks (50 homozygous resistant and 50 susceptible F2:3 segregating population derived from Huixianhong × Hongyoumai to determine a candidate gene region for resistance to powdery mildew on the long arm of chromosome 7B in wheat landrace Hongyoumai. Gene expressions of candidate regions were obtained using bulked segregant RNA-seq in 10 homozygous resistant and 10 susceptible progeny inoculated by Bgt.. Candidate genes were obtained using homology-based cloning in two parents. Results: A 12.95 Mb long candidate region in chromosome 7BL was identified, and five blocks in SLAF matched the scaffold of the existing co-segregation marker Xmp1207. In the candidate region, 39 differentially expressed genes were identified using RNA-seq, including RGA4 (Wheat_Chr_Trans_newGene_16173)—a disease resistance protein whose expression was upregulated in the resistant pool at 16 h post inoculation with Bgt. Quantitative reverse transcription (qRT)-PCR was used to further verify the expression patterns in Wheat_Chr_Trans_newGene_16173 that were significantly different in the two parents Hongyoumai and Huixianhong. Two RGA4 genes were cloned based on the sequence of Wheat_Chr_Trans_newGene_16173, respectively from two parent and there was one amino acid mutation: S to G in Huixianhong on 510 loci. Conclusion: The combination of SLAF and BSR-seq methods identified a candidate region of pmHYM in the chromosome 7BL of wheat landrace cultivar Hongyoumai. Comparative analysis between the scaffold of co-segregating marker Xmp1207 and SLAF-seq showed five matching blocks. qRT-PCR showed that only the resistant gene Wheat_Chr_Trans_newGene_16173 was significantly upregulated in the resistant parent Hongyoumai after inoculation with Bgt, and gene cloning revealed a difference in one amino acid between the two parent genes, indicating it was involved in the resistance response and may be the candidate resistance gene pmHYM. [ABSTRACT FROM AUTHOR]

Key message: A tiller inhibition gene, TIN4, was mapped to an approximately 311 kb genomic interval on chromosome arm 2DL of wheat. The tiller is one of the key components of plant morphological architecture and a central agronomic trait affecting spike number in wheat. Low tiller number has been proposed as a major component of crop ideotypes for high yield potential. In this study, we characterized the development of tillering in near-isogenic lines (NIL7A and NIL7B), indicating that the TIN4 gene inhibited the growth of tillering buds and negatively regulated tiller number. Low-tillering was controlled by a single gene (TIN4) located on chromosome 2DL by genetic analysis and bulked segregant RNA-seq analysis. A total of 17 new polymorphic markers were developed in this study, and 61 recombinants were identified in the secondary F2 population containing 4,266 individuals. TIN4 was finally mapped on a 0.35 cM interval, co-segregated with molecular marker M380, within a 311 kb genomic interval of the wheat cultivar Chinese Spring reference genome sequence that contained twelve predicted genes. Yield experiments showed that the yield of low-tillering lines was higher than that of high-tillering lines at a higher density. Overall, this study provides a foundation for the construction of a low-tillering ideotype for improving wheat yield and further cloning TIN4 by map-based cloning approach. [ABSTRACT FROM AUTHOR]

Einkorn harbours a wide range of genetic diversity for agronomically important traits. Heading date is one of the important traits for the adaptation of wheat species to various climatic conditions and the cultivation in diverse regions and seasons. In this study, DArTseq and SSR marker‐based linkage map of einkorn wheat was constructed using 150 recombinant inbred lines (RILs) derived from a cross between ID1623 and MONLIS. The linkage map involved 865 SNP, 787 Silico‐DArT and 16 SSR DNA markers mapped to 741 loci in seven linkage groups and covered 1158.54 cM with an average density of 1.56 cM/locus. Four QTLs associated with heading date, detected in all environments by composite interval mapping (CIM), were positioned across the 2A, 5A and 7A einkorn wheat chromosomes. Two major and stable QTLs, QThd‐2A.2 and QThd 5A.1, were identified on chromosomes 2A and 5A, respectively. These QTLs probably coincide with photoperiod and vernalization genes in accordance with previously published maps. The new map will facilitate quantitative trait locus mapping, map‐based cloning and comparative genomics in wheat species. [ABSTRACT FROM AUTHOR]

As genotyping-by-sequencing (GBS) is widely used in barley genetic studies, the translation of the physical position of GBS-derived SNPs into accurate genetic positions has become relevant. The main aim of this study was to develop a high-resolution consensus linkage map based on GBS-derived SNPs. The construction of this integrated map involved 11 bi-parental populations composed of 3743 segregating progenies. We adopted a uniform set of SNP-calling and filtering conditions to identify 50 875 distinct SNPs segregating in at least one population. These SNPs were grouped into 18 580 non-redundant SNPs (bins). The resulting consensus linkage map spanned 1050.1 cM, providing an average density of 17.7 bins and 48.4 SNPs per cM. The consensus map is characterized by the absence of large intervals devoid of marker coverage (significant gaps), the largest interval between bins was only 3.7 cM and the mean distance between adjacent bins was 0.06 cM. This high-resolution linkage map will contribute to several applications in genomic research, such as providing useful information on the recombination landscape for QTLs/genes identified via GWAS or ensuring a uniform distribution of SNPs when developing low-cost genotyping tools offering a limited number of markers. [ABSTRACT FROM AUTHOR]

Recombination is a major force that shapes genetic diversity. Determination of recombination rate is important and can theoretically be improved by increasing the sample size. However, it is nearly impossible to estimate recombination rates using traditional population genetics methods when the sample size is large because these methods are highly computationally demanding. In this study, we used a refined machine learning approach to estimate the recombination rate of the human genome using the UK10K human genomic dataset with 7,562 genomic sequences and its three subsets with 200, 400 and 2,000 genomic sequences. The estimation was performed under the human Out-of-Africa demographic model. We not only obtained an accurate human genetic map, but also found that the fluctuation of estimated recombination rate is reduced along the human genome when the sample size increases. The estimated UK10K recombination rate heterogeneity is less than that estimated from its subsets. Our results demonstrate how the sample size affects the estimated recombination rate, and analyses of a larger number of genomes result in a more precise estimation of recombination rate. The accurate genetic map based on UK10K data set is also expected to benefit other human biology researches. [ABSTRACT FROM AUTHOR]

Submerged germination ability is a key trait of rice (Oryza sativa L.) in the success of water direct seeding. Therefore, mining submerged germination‐related loci and seeking high tolerant rice germplasms are important for developing rice direct seeding breeding strategies. Here, we treated 272 recombinant inbred lines (RILs, F15) from a cross from Luohui 9 (indica) and RPY geng (japonica) with simulated submergence for 7 days. We successfully bred several superior homozygous RILs with high submergence resistance, namely, R53, R137, R148, R176, and R180, via indica and japonica hybridization strategies. Then, the QTL mapping of coleoptile length trait was performed by R/qtl and IciMapping softwares based on the high‐density bin marker genetic map and two QTLs responsible for coleoptile length were detected in chromosomes 1 (qCL‐1.1) and 3 (qCL‐3.1). The haplotype results of RILs showed that the aggregation of elite alleles of these two QTLs in an individual was beneficial to improving the rice submergence tolerance. According to contrasting genotype of qCL‐1.1 and qCL‐3.1 with different coleoptile lengths, RIL07 (R07) and R180 were selected to further RNA‐seq analysis for analyzing the possible molecular mechanisms of rice under submergence stress. Finally, LOC_Os01g04430, LOC_Os01g04530, and LOC_Os03g22720 for qCL‐1.1 and qCL‐3.1 were characterized to affect submergence stress by the overlapped analysis of two independent sets of RNA‐seq data, qRT‐PCR verification, and gene sequence alignments. In this study, the submerged germination‐related QTLs/genes and high submergence‐tolerant RILs provided new genetic resources for breeding rice varieties suitable for direct seeding via molecular breeding strategies in the immediate future. [ABSTRACT FROM AUTHOR]

Coffee production has been limited by the coffee leaf rust (CLR) disease. Genetic markers linked to resistance have been utilized for molecular breeding programs. Some of these markers have been linked specifically to a hypothetical SH3 gene that confers resistance against CLR. Using PrimerBLAST, the binding sites of these SH3 markers have been localized to a region in chromosome 3 of the coffee genome. Protein-coding genes were obtained from the Ensembl Plants website and filtered using the Orange software according to the gene annotations of their predicted products. The candidate resistance and resistance-associated genes were then datamined and physical maps were constructed to visualize their locations. The data generated by this study may help guide future investigations regarding SH3-conferred resistance. [ABSTRACT FROM AUTHOR]

Downy mildew (DM) is one of the most serious diseases in sunflower-growing regions worldwide, often significantly reducing sunflower yields. The causal agent of sunflower DM, the oomycete pathogen Plasmopara halstedii, is highly virulent and aggressive. Studying regional disease spread and virulence evolution in the DM pathogen population is important for the development of new sunflower inbred lines with resistance to the existing DM pathogen. The sunflower line 803–1, as one of nine international differential hosts, has been used in the identification of P. halstedii virulent pathotypes in sunflower since 2000. The DM resistance gene in 803–1 was temporally designated Pl5 + based on allelic analysis but has not been molecularly characterized. In the present study, bulked segregant analysis and genetic mapping confirmed the presence of the Pl gene within a large gene cluster on sunflower chromosome 13 in 803–1, as previously reported. Subsequent saturation mapping in the gene target region with single nucleotide polymorphism (SNP) markers placed this gene at an interval of 3.4 Mb in the XRQ reference genome assembly, a location different from that of Pl5. Therefore, the Pl gene in 803–1 was re-designated Pl36 because it is not allelic with Pl5. Four SNP markers co-segregated with Pl36, and SNP SFW05743 was 1.1 cM proximal to Pl36. The relationship of eight Pl genes in the cluster is discussed based on their origin, map position, and specificity of resistance/susceptibility to DM infection. [ABSTRACT FROM AUTHOR]

G. barbadense is renowned for its high-quality fiber and is highly regarded as a natural material in the textile industry. However, research on cotton has mainly focused on G. hirsutum , and progress in sea island cotton has been relatively slow. There was limited understanding of the genetic loci and transcriptional regulatory mechanisms of important traits, and the genetic basis for the development of superior traits remains unclear. In this study, a recombinant inbred line (RIL) population was constructed using two sea island cotton parents from different cotton regions. The phenotypic characteristics of the two parents and the RIL population, as well as the phenotypic correlations, heritability, and genetic models of the RIL population, were comprehensively analyzed. The RIL population was genotyped using whole-genome resequencing technology, and a high-density intraspecific linkage map was constructed, consisting of 5295 bin markers and a total genetic map distance of 2721.79 centimorgans (cM). Phenotypic data collected from five different environments were used to detect 169 quantitative trait loci (QTLs) using the composite interval mapping method. Among these QTLs, 30 were related to agronomic traits, 61 were related to yield traits, and 78 were related to fiber quality traits. Additionally, 17 QTL clusters were detected, and the additive effects of these clusters explained the correlation between different phenotypic traits. Candidate genes for stable QTLs related to agronomic and yield traits were identified through variant annotation and functional prediction. Two bin markers associated with lint percentage (LP) were validated as potential breeding markers. Furthermore, using RNA-seq data of cotton fiber from the RIL population parents, the dynamic changes in gene expression during different developmental stages of cotton fiber were revealed, and important differentially expressed genes in the secondary cell wall development and metabolism network of fibers were identified. Importantly, through the combined analysis of fiber trait QTLs and transcriptomes, eight candidate genes involved in regulating fiber quality traits were predicted, and the genetic basis of the excellent allele site qFL_D04_1 in the breeding history of Chinese sea island cotton was elucidated. In summary, this study provides new genetic resources and potential breeding markers for cotton variety improvement, valuable theoretical information for understanding the genetic basis of important traits in sea island cotton, and effectively promotes the development of cotton biotechnology breeding. • A high-density intraspecific genetic map was built with 2721.79 cM total genetic distance and 5295 bin markers. • Identified 169 QTLs related to agronomic, yield, and fiber quality traits, including 31 stable QTLs and 17 QTL clusters. • Discovered 106 key genes linked to fiber development, and clarified the genetic basis of the qFL-D04–1 locus. [ABSTRACT FROM AUTHOR]

• 17 SCAR markers linked to double flower trait of petunia hybrida was developed. • A high-density genetic map was constructed with 4474 SNP markers. • The double flower genes in petunia were first mapped to a genomic region of 1.82 Mb. Double flower (DF) is one of the important ornamental traits of horticultural plants, but the molecular mechanism of its formation is still unclear. In this study, forward genetic approaches were applied to explore the key genes involved in the DF formation in petunia. We developed a total of 17 SCAR markers linked to DF, and initially mapped the DF genes onto 9 scaffolds (totally 13.3 Mb) in the genome of the DF petunia. We also constructed a genetic linkage map of petunia, which contained 4474 SNP markers, with a total genetic distance of 2022.786 cM and an average genetic distance of 0.758 cM. In QTL analysis, a QTL associated with DF trait was detected. The LOD value of the marker was 3.82–12.71, and the contribution rate was 16.0 %–44.0 %. To further shorten the mapping interval of the DF genes, we constructed a near-isogenic line (NIL) population containing 2757 plants, and used these 17 SCAR markers to screen the recombinant plants, and located the DF genes within a 2.2 Mb interval. Combined with Bacterial Artificial Chromosome (BAC) library screening, the mapping interval of the DF genes was ultimately shortened from 2.2 Mb to 1.82 Mb. Presently, research on the DF trait of petunia mainly focused on the ABC(D)E model. The fine mapping results of petunia DF genes obtained in this study provide a new idea for revealing the molecular mechanism of DF formation in petunia. [ABSTRACT FROM AUTHOR]

Melon (Cucumis melo L., 2n = 24) belongs to the family Cucurbitaceae and is an important vegetable crop. This study aimed to investigate the quantitative trait loci (QTL) of flowering‐related traits to understand the genetic inheritance and candidate gene of flowering‐related traits. The specific length amplified fragment sequencing (SLAF‐seq) technology was used to construct a genetic map of 115 individual plants in the melon F2 population. A total of 82.6 Gb of data were generated using SLAF‐seq. A genetic map was constructed with 10,596 specific length amplified fragment markers in 12 linkage groups, which spanned 1,383.88 cM with an average distance of 0.13 cM between markers. Ten QTL of flowering‐related traits were detected, which explained 2.16–19.34% of the phenotypic variance. The logarithm of the odds (LOD) values ranged from 3.5 to 24.9. Ninety‐four F2:3 families were used for mapping mft and fft in candidate regions by simple sequence repeat (SSR) and cleaved amplified polymorphic sequences (CAPS) markers. The mapping results showed that mft2.1 and fft2.1 were located in the same region, between CmSSR07071 and CmSSR07102. By gene annotation, 36 candidate genes were detected in this region, 26 of which were annotated. Quantitative reverse transcription–polymerase chain reaction (PCR) showed that candidate genes, including WRKY transcription factor and AP2/ERF and B3 domain‐containing transcription factor, were differentially expressed in female and male flowers in the flower budding stages. These genes may provide the theoretical foundation for gene cloning and genetic transformation in melons. Core Ideas: A high‐density genetic map spanning 1,383.88 cM was constructed.A total of 10 QTL was located in five linkage groups.Using gene alignment, 26 candidate genes were detected in this region. [ABSTRACT FROM AUTHOR]

Cotton is the most important fiber crop in the world. Asiatic cotton (Gossypium arboreum, genome A2) is a diploid cotton species producing spinnable fibers and important germplasm for cotton breeding and a significant model for fiber biology. However, the genetic map of Asiatic cotton has been lagging behind tetraploid cottons, as well as other stable crops. This study aimed to construct a high-density SNP genetic map and to map QTLs for important yield and fiber quality traits. Using a recombinant inbred line (RIL) population and genome resequencing technology, we constructed a high-density genetic map that covered 1980.17 cM with an average distance of 0.61 cM between adjacent markers. QTL analysis revealed a total of 297 QTLs for 13 yield and fiber quality traits in three environments, explaining 5.0–37.4% of the phenotypic variance, among which 75 were stably detected in two or three environments. Besides, 47 QTL clusters, comprising 131 QTLs for representative traits, were identified. Our works laid solid foundation for fine mapping and cloning of QTL for yield and fiber quality traits in Asiatic cotton. [ABSTRACT FROM AUTHOR]

Background The helmeted honeyeater (Lichenostomus melanops cassidix) is a Critically Endangered bird endemic to Victoria, Australia. To aid its conservation, the population is the subject of genetic rescue. To understand, monitor, and modulate the effects of genetic rescue on the helmeted honeyeater genome, a chromosome-length genome and a high-density linkage map are required. Results We used a combination of Illumina, Oxford Nanopore, and Hi-C sequencing technologies to assemble a chromosome-length genome of the helmeted honeyeater, comprising 906 scaffolds, with length of 1.1 Gb and scaffold N50 of 63.8 Mb. Annotation comprised 57,181 gene models. Using a pedigree of 257 birds and 53,111 single-nucleotide polymorphisms, we obtained high-density linkage and recombination maps for 25 autosomes and Z chromosome. The total sex-averaged linkage map was 1,347 cM long, with the male map being 6.7% longer than the female map. Recombination maps revealed sexually dimorphic recombination rates (overall higher in males), with average recombination rate of 1.8 cM/Mb. Comparative analyses revealed high synteny of the helmeted honeyeater genome with that of 3 passerine species (e.g. 32 Hi-C scaffolds mapped to 30 zebra finch autosomes and Z chromosome). The genome assembly and linkage map suggest that the helmeted honeyeater exhibits a fission of chromosome 1A into 2 chromosomes relative to zebra finch. PSMC analysis showed a ∼15-fold decline in effective population size to ∼60,000 from mid- to late Pleistocene. Conclusions The annotated chromosome-length genome and high-density linkage map provide rich resources for evolutionary studies and will be fundamental in guiding conservation efforts for the helmeted honeyeater. [ABSTRACT FROM AUTHOR]

Stripe rust, caused by Puccinia striiformis Westend. f.sp. tritici Erikss. (Pst), is one of the most devastating diseases of wheat (Triticum aestivum L.) globally. Exploring and utilizing new sources of resistance is essential for breeding resistant wheat cultivars. Thus, a doubled haploid population (n = 291) derived from the cross 'AAC Innova'/'AAC Proclaim' was evaluated to dissect the genetics of resistance in the cultivar 'AAC Innova'. This population was evaluated for stripe rust severity in disease nurseries at Creston, British Columbia (in 2016 and 2020), and Lethbridge, Alberta (in 2016, 2017 and 2020), and genotyped using the wheat 90 K SNP assay. A high-density genetic map was constructed which consisted of 7112 SNP markers with an average marker interval of 2.3 cM. Quantitative trait loci (QTL) mapping identified one major (QYr.lrdc-2A) and 10 minor effect (QYr.lrdc-2B.1, QYr.lrdc-2B.2, QYr.lrdc-2B.3, QYr.lrdc-2B.4, QYr.lrdc-2D, QYr.lrdc-3B, QYr.lrdc-5A, QYr.lrdc-5B, QYr.lrdc-5D and QYr.lrdc-7D) loci. The QTL QYr.lrdc-2A was consistently effective against Pst races across all environments and explained up to 33.0% of the phenotypic variation. Other QTLs were either less consistent or environment specific. 'AAC Innova' contributed stripe rust resistance alleles for most of the QTLs except for QYr.lrdc-2D, QYr.lrdc-5A and QYr.lrdc-7D. The QTLs identified in this study should be valuable for diversifying the sources of genetic resistance against current and new virulent races of Pst. In particular, the 'AAC Innova'-derived QTL QYr.lrdc-2A could be a valuable source of resistance to incorporate into commercial cultivars and combine with other genes using the associated SNP markers identified in this study. [ABSTRACT FROM AUTHOR]

Spot form net blotch (SFNB), caused by the necrotrophic fungal pathogen Pyrenophora teres f. maculata (Ptm), is a foliar disease of barley that results in significant yield losses in major growing regions worldwide. Understanding the host-parasite interactions between pathogen virulence/avirulence genes and the corresponding host susceptibility/resistance genes is important for the deployment of genetic resistance against SFNB. Two recombinant inbred mapping populations were developed to characterize genetic resistance/susceptibility to the Ptm isolate 13IM8.3, which was collected from Idaho (ID). An Illumina Infinium array was used to produce a genome-wide marker set. Quantitative trait loci (QTL) analysis identified ten significant resistance/susceptibility loci, with two of the QTL being common to both populations. One of the QTL on 5H appears to be novel, while the remaining loci have been reported previously. Single nucleotide polymorphisms (SNPs) closely linked to or delimiting the significant QTL have been converted to user-friendly markers. Loci and associated molecular markers identified in this study will be useful in genetic mapping and deployment of the genetic resistance to SFNB in barley. [ABSTRACT FROM AUTHOR]

Prunus persica “Mihong” cultivar is a domesticated white peach that was generated from the crossing between “Yumyeong” and “Chiyomaru” cultivars in the Republic of Korea in 1995. We launched “Mihong” genome sequencing in 2018 and “Mihong” reached to 200 scaffold and 241 Mb sequences using long-read sequencing and Hi-C technology. F1 populations of ”Kawanakajima Hakuto,” “Mihong,” “Changhowon Hwangdo,” and “Yumi” were developed in NIHHS. These four cultivars were sequenced and assembled using the SOAPdenovo version 2.04. First, we surveyed the SSRs in “Mihong” assembly sequences and extracted the ±300 bp flanking sequences containing SSRs. Second, the assembly sequences of three cultivars were aligned and mapped against “Mihong” ±300 bp flanking sequences using BLASTn (version 2.2.29+). We anticipated the differential length in SSRs among the four cultivars. We sorted the primers with a standard deviation over 4.5 (STEV > 4.5) among the four cultivars. In addition, we surveyed the primers having difference in over 10 bp with “Kawanakajima Hakuto” and “Mihong” for polymorphic markers in the mapping population. All primer pairs were designed to generate amplicons of 150-200 bp in coating SSR regions using primer3 (version 3-2.2.3). We selected 260 SSR markers with a physical distance of average per 1 Mb. These SSR markers accounted for 74% polymorphism in the four genotypes. Finally, a F1 population of “Kawanakajima Hakuto” and “Mihong” covered 884.5 cM with 465 SNPs and 86 SSRs and this genetic map matched correctly to the HI-C pseudomolecule of P. persica. [ABSTRACT FROM AUTHOR]

Rice production relies on large amounts of synthetic nitrogen fertilizer to meet crop nutritional demands. However, the current fertilizer use efficiency is poor, with an average of 30–50% of total applied nitrogen (N) recovered in grains. Consequently, optimizing N availability and N use efficiency (NUE) has become a major target for rice yield improvement, and looking for quantitative trait loci (QTL) associated with NUE can provide useful information for developing nitrogen efficient rice genotypes. The present study aims to identify QTLs associated with NUE and its two components, agronomic NUE (agNUE) and grain nitrogen increase rate (GIR). A recombinant inbred line population (RIL) derived from a cross between Nipponbare and OM052, consisting of 159 F3 individuals was developed and cultivated in low-N (8 kg N/0.67 ha, N8) and high-N (18 kg N/0.67 ha, N18) conditions. Specific length amplified fragment sequencing (SLAF) was used to genotype the RILs and construct a high-density linkage map spanning 1587.70 cM, consisting 2707 SLAF markers with an average interval of 0.59 cM between adjacent marker loci. QTL analysis confirmed four significant QTLs distributed among chromosome 1, 6, and 11, with the proportion of phenotypic variance explained by each QTL ranging from 2.96 to 11.11% and LOD scores from 1.67 to 3.75. Functional annotation of genes located within the QTL intervals revealed NUE putative candidate genes. Overall, the QTLs identified in this study contribute information that could be useful for NUE improvement in rice. [ABSTRACT FROM AUTHOR]

Key message: Two major QTL associated with resistance to Fusarium wilt (FW) were identified using whole-genome resequencing. Sequence variations and gene expression level differences suggest that TIR-NBS and LRR-RLK are candidate genes associated with FW-resistance. Fusarium wilt (FW) caused by Fusarium oxysporum f. sp. raphani is an important disease in radish, leading to severe decrease in yield and quality. YR4 as a novel genetic source to resistant to FW was confirmed through screening with five pathogen isolates. We have generated F2 and F2:3 populations segregated with FW resistance using YR4 and YR18 inbred lines. The disease symptom was evaluated in F2:3 population (n = 180) in three independent studies over two years. We identified 4 QTL including the two major QTL (FoRsR7.159A and FoRsR9.359A). FoRsR7.159A and FoRsR9.359A were detected in three replicated experiments. FoRsR7.159A was delimited to the 2.18-Mb physical interval on chromosome R07, with a high LOD value (5.17–12.84) and explained phenotypic variation (9.34%–27.97%). The FoRsR9.359A represented relatively low LOD value (3.38–4.52) and explained phenotypic variation (6.24%–8.82%). On the basis of the re-sequencing data for the parental lines, we identified five putative resistance-related genes and 13 unknown genes with sequence variations at the gene and protein levels. A semi-quantitative RT-PCR analysis revealed that Rs382940 (TIR-NBS) and Rs382200 (RLK) were expressed only in 'YR4' from 0 to 6 days after the inoculation. Moreover, Rs382950 (TIR-NBS-LRR) was more highly expressed in 'YR4' from 3 to 6 days after the inoculation. These three genes might be important for FW-resistance in radish. We identified several markers based on these potential candidate genes. The marker set should be useful for breeding system to introduce the FW resistance loci from 'YR4' to improve tolerance to FW. [ABSTRACT FROM AUTHOR]

Tobacco (Nicotiana tabacum L.) is an economic crop and a model organism for studies of plant biology and genetics. As an allotetraploid plant generated from interspecific hybridization, tobacco has a massive genome (4.5 Gb). Recently, a genetic map with 45,081 single nucleotide polymorphism (SNP) markers was constructed using whole-genome sequencing data for a tobacco population including 274 individuals. This provides a basis for quantitative trait locus (QTL) mapping and genomic selection, which have been widely applied to other crops but have not been feasible in tobacco. Based on this high-density genetic map, we identified QTLs associated with important agronomic traits, chemical compounds in dry leaves, and hazardous substances in processed cigarettes. The LOD values for major QTLs were highest for agronomic traits, followed by chemical compounds and hazardous substances. In addition to the identification of molecular markers, we evaluated genomic selection models and found that BayesB had the highest prediction accuracy for the recombinant inbred line population. Our results offer new insights into the genetic mechanism underlying important traits, such as agronomic traits and quality-related chemical compounds in tobacco, and will be able to support the application of molecular breeding to tobacco. [ABSTRACT FROM AUTHOR]

Barley mild mosaic virus (BaMMV), transmitted by the soil-borne protist Polymyxa graminis, has a serious impact on winter barley production. Previously, the BaMMV resistance gene rym15 was mapped on chromosome 6HS, but the order of flanking markers was non-collinear between different maps. To resolve the position of the flanking markers and to enable map-based cloning of rym15, two medium-resolution mapping populations Igri (susceptible) × Chikurin Ibaraki 1 (resistant) (I × C) and Chikurin Ibaraki 1 × Uschi (susceptible) (C × U), consisting of 342 and 180 F2 plants, respectively, were developed. Efficiency of the mechanical inoculation of susceptible standards varied from 87.5 to 100% and in F2 populations from 90.56 to 93.23%. Phenotyping of F2 plants and corresponding F3 families revealed segregation ratios of 250 s:92r (I × C, χ2 = 0.659) and 140 s:40r (C × U, χ2 = 0.741), suggesting the presence of a single recessive resistance gene. After screening the parents with the 50 K Infinium chip and anchoring corresponding SNPs to the barley reference genome, 8 KASP assays were developed and used to remap the gene. Newly constructed maps revealed a collinear order of markers, thereby allowing the identification of high throughput flanking markers. This study demonstrates how construction of medium-resolution mapping populations in combination with robust phenotyping can efficiently resolve conflicting marker ordering and reduce the size of the target interval. In the reference genome era and genome-wide genotyping era, medium-resolution mapping will help accelerate candidate gene identification for traits where phenotyping is difficult. [ABSTRACT FROM AUTHOR]

White strains of Hypsizygus marmoreus are more difficult to cultivate than are brown strains; therefore, new white strain breeding strategies are required. Accordingly, we constructed the genetic map of H. marmoreus with 1996 SNP markers on 11 linkage groups (LGs) spanning 1380.49 cM. Prior to analysis, 82 backcrossed strains (HM8 lines) were generated by mating between KMCC03106-31 and the progenies of the F1 hybrid (Hami-18-KMCC03106-93). Using HM8, the first 23 quantitative trait loci (QTLs) of yield-related traits were detected with high limit of detection (LOD) scores (1.98-9.86). The length, thickness, and hardness of the stipe were colocated on LG 1. Especially, length of stipe and thickness of stipe were highly correlated given that the correlation coefficients were negative (-0.39, p value = .01). And a typical biomodal distribution was observed for lightness of the pileus and the lightness of the pileus trait belonged to the LG 8, as did traits of earliness and mycelial growth in potato dextrose agar (PDA) medium. Therefore, results for color traits can be suggested that color is controlled by a multi-gene of one locus. The yield trait was highly negatively correlated with the traits for thickness of the stipe (-0.45, p value = .01). Based on additive effects, the white strain was confirmed as recessive; however, traits of mycelial growth, lightness, and quality were inherited by backcrossed HM8 lines. This new genetic map, finely mapped QTLs, and the strong selection markers could be used in molecular breeding of H. marmoreus. [ABSTRACT FROM AUTHOR]

Understanding dynamic changes in the genetic architecture of quantitative traits is crucial in developmental genetics. Functional mapping is an appropriate method that passes a mathematical equation to describe a biological developmental process with the genetic mapping framework. Appropriate genetic model and applicable mapping population are indispensable condition for functional mapping of important agronomic traits in plants. Based on the Wang–Lan–Ding model, we ever applied a DH population to carry out functional mapping QTLs underlying growth trajectory on tiller number. However, inconsistent genetic background among the DH lines might disturb the mapping results. With the advent of innovative research materials, single segment substitution lines, allows us to do more precise genetic analyses. Thus functional mapping was again conducted on tiller number using the Wang–Lan–Ding model and a single segment substitution line population with the genetic background of Huajingxian 74 so as to explore QTL dynamic mechanism to regulate developmental traits. We detected that all five single segment substitution lines harbored tillering QTLs with additives and/or dominances to influence the four functional parameters, the optimum tillering time (t0), the maximum tiller number (K), the tillering increased rate (r) and the tillering decreased rate (c), which were estimated from the Wang–Lan–Ding model and with some biological meaning. They mainly brought the inflexion point (t0) delay, the peak increase (K) and the degradation (c) acceleration, while the growth (r) slow down. Moreover, epistatic interactions among these QTLs were confirmed to be prevalent. A total of 39 significant epistatic effects were detected to associate with the four parameters, occupying 34.8% of 112 pairs of epistatic interactions investigated. Contrary to the QTL effects, these epistatic effects largely decreased t0, K and c, while increased r. Our results indicated that the five QTL effects and their epistatic effects significantly changed the shape and trajectory of tiller number via influence of the four functional parameters. Rational use of these QTLs is expected to improve tillering number of rice by molecular design breeding. [ABSTRACT FROM AUTHOR]

Key Message: AhRt1 controlling red testa color in peanut was fine-mapped to an interval of 580 kb on chromosome A03, and one gene encoding bHLH transcriptional factor was identified as the putative candidate gene. Peanut with red testa has higher nutritional and economic value than the traditional pink testa varieties. Identification of genes controlling red testa color will accelerate the breeding program and facilitate uncovering the genetic mechanism. In this study, in order to identify gene underlying the red testa color in peanut, a F2 population derived from a cross between a pink testa peanut variety "Fuhua 8" and a red testa variety "Quanhonghua 1" was constructed. The genetic analysis for the F2 population revealed that the red testa color was controlled by one single dominant locus. This locus, named as AhRt1 (Arachis hypogaea Red Testa 1), was preliminary identified in chromosome A03 by BSA-sequencing analysis. Using a segregation mapping population, AhRt1 was fine-mapped to a 580-kb genomic region by substitution mapping strategy. Gene candidate analysis suggested that one predicted gene encoding bHLH transcriptional factor may be the possible candidate gene for AhRt1. A diagnostic marker closely linked to candidate gene has been developed for validating the fine-mapping result in different populations and peanut germplasm. Our findings will benefit the breeding program for developing new varieties with red testa color and laid foundation for map-based cloning gene responsible for red testa in peanut. [ABSTRACT FROM AUTHOR]

Key Message: Linkage and association mapping identified nine candidate intervals for wheat GPC, and large-scale association mapping based on 9 corresponding KASP markers and 1163 F4 breeding lines revealed 3 significant markers. Wheat grain protein content (GPC) is an important quality indicator. The GPC of wheat grown in the middle and lower reaches of the Yangtze River is often low. Marker-assisted selection (MAS) is an effective tool for improving quantitative traits; however, most markers have not been effectively applied in GPC improvement except Gpc-B1, although many loci associated with GPC were identified. In this study, linkage analysis using a recombinant inbred line population from the cross of core parents of Ningmai 9 and Yangmai 158 and association mapping using the local cultivated varieties were performed and nine candidate intervals were identified. The appropriate kompetitive allele-specific PCR (KASP) markers associated with GPC were successfully developed and screened in 1163 F4 breeding lines. Three markers, Kgpc-2B, Kgpc-2D, and Kgpc-4A, were validated to be significantly related to GPC by large-scale association mapping, and they were combined to achieve the highest efficiency to enhance GPC. We applied these markers in 164 F6 breeding lines and obtained 15 lines with high GPC, indicating their high selective efficiency. Further, strategies for gene exploration in the three significant intervals were proposed. These results were expected to provide a novel route for improving GPC in wheat quality breeding. [ABSTRACT FROM AUTHOR]

Background: Leaf shape is an important agronomic trait in ornamental kale (Brassica oleracea L. var. acephala). Although some leaf shape-related genes have been reported in ornamental kale, the detailed mechanism underlying leaf shape formation is still unclear. Here, we report a lobed-leaf trait in ornamental kale, aiming to analyze its inheritance and identify the strong candidate gene. Results: Genetic analysis of F2 and BC1 populations demonstrate that the lobed-leaf trait in ornamental kale is controlled by a single dominant gene, termed BoLl-1 (Brassica oleracea lobed-leaf). By performing whole-genome resequencing and linkage analyses, the BoLl-1 gene was finely mapped to a 127-kb interval on chromosome C09 flanked by SNP markers SL4 and SL6, with genetic distances of 0.6 cM and 0.6 cM, respectively. Based on annotations of the genes within this interval, Bo9g181710, an orthologous gene of LATE MERISTEM IDENTITY 1 (LMI1) in Arabidopsis, was predicted as the candidate for BoLl-1, and was renamed BoLMI1a. The expression level of BoLMI1a in lobed-leaf parent 18Q2513 was significantly higher compared with unlobed-leaf parent 18Q2515. Sequence analysis of the parental alleles revealed no sequence variations in the coding sequence of BoLMI1a, whereas a 1737-bp deletion, a 92-bp insertion and an SNP were identified within the BoLMI1a promoter region of parent 18Q2513. Verification analyses with BoLMI1a-specific markers corresponding to the promoter variations revealed that the variations were present only in the lobed-leaf ornamental kale inbred lines. Conclusions: This study identified a lobed-leaf gene BoLMI1a, which was fine-mapped to a 127-kb fragment. Three variations were identified in the promoter region of BoLMI1a. The transcription level of BoLMI1a between the two parents exhibited great difference, providing new insight into the molecular mechanism underlying leaf shape formation in ornamental kale. [ABSTRACT FROM AUTHOR]

Understanding genetic diversity in target populations is of great importance in breeding and a prerequisite for association mapping of traits. In this study, 57 cross species simple sequence repeat (SSR) markers were screened for amplification in China aster. Twenty six polymorphic markers were used to estimate the genetic diversity in forty two China aster genotypes. The observed and expected heterozygosities within the genotypes were ranged from 0.00 to 0.80 and 0.17 to 0.50, respectively. Weighted Neighbor Joining method, grouped China aster genotypes into five major clusters which coincided for morphological traits mostly flower color and form, but not correlated for their geographical locations. The results suggested that, population may be useful for the genome-wide marker–trait association mapping. These set of cross species transferable SSR markers would enable the application of the SSR technique in China aster crop improvement. [ABSTRACT FROM AUTHOR]

Cytoplasmic male-sterility (CMS) has been exclusively used to produce F1 hybrid seeds of onion (Allium cepa L.). A single nuclear locus, Ms, is known to restore male-fertility of CMS in onions. Unstable male-sterile onions producing a small amount of pollen grains have been identified in a previous study. When such unstable male-sterile onions were crossed with stable male-sterile onions containing CMS-R cytoplasm, male-fertility was completely restored, although genotypes of the Ms locus were homozygous recessive. Inheritance patterns indicated that male-fertility restoration was controlled by a single locus designated as Ms2. A combined approach of bulked segregant analysis and RNA-seq was used to identify candidate genes for the Ms2 locus. High resolution melting markers were developed based on single nucleotide polymorphisms (SNPs) detected by RNA-Seq. Comparative mapping of the Ms2 locus showed that Ms2 was positioned at the end of chromosome 2 with a distance of approximately 70 cM away from the Ms locus. Although 38 contigs containing reliable SNPs were analyzed using recombinants selected from 1344 individuals, no contig showed perfect linkage to Ms2. Interestingly, transcription levels of orf725, a CMS-associated gene in onions, were significantly reduced in male-fertile individuals of segregating populations. However, no significant change in its transcription level was observed in individuals of a segregating population with male-fertility genotypes determined by the Ms locus, suggesting that male-fertility restoration mechanism of Ms2 might be different from that of the Ms locus. [ABSTRACT FROM AUTHOR]

This study used SSR and AFLP markers to construct the genetic linkage map of Reyan5-11×PR107 population, integrated the published genetic linkage map and utilised the integrated map to perform QTL mapping of rubber yield-related traits. A genetic map consisting of 132 molecular markers (88 SSR and 44 AFLP markers) was constructed, and a joint map consisting of 143 molecular markers (99 SSR and 44 AFLP markers), which contained 19 linkage groups covering the rubber tree genome of 1298.5 cM, each linkage group containing 2–40 Mark, the average distance between the marks is 9.08 cM. Under the conditions of LOD ≥ 2.5, it was detected 2 QTLs related to girth, 3 QTLs related to dry rubber content, and 3 QTLs related to dry rubber yield per tree, 4 QTLs related to the unit secant length dry rubber yield, 5 QTLs related to the number of conducting phloem laticifer and 4 QTLs related to the number of yellow phloem laticifer. [ABSTRACT FROM AUTHOR]

Improving fiber quality and yield are major research objectives for cotton breeders in the United States. Identifying broadly existing and stable quantitative trait loci (QTLs) related to fiber quality is critical to properly utilizing genomic resources in cotton improvement programs. An F6 recombinant inbred line (RIL) population derived from the cross of NC05AZ21 × TX‐2324 was used to develop linkage maps and for QTL analysis of six fiber quality traits and lint percentage. The Illumina 63K single nucleotide polymorphism (SNP) array was used to genotype the RIL population. Analysis of variance of phenotypic trait data showed significant differences among lines and years for all traits tested. The heritability for tested traits ranged from 0.56 to 0.91. Genetic mapping was performed using 3,009 polymorphic SNP markers on the RILs. We constructed a genetic map with a total length of 4,983.73 cM and an average distance of 1.66 cM between markers. The linkage map corresponded well with the Upland cotton (Gossypium hirsutum L.) sequence‐based physical map. Thirty‐two QTLs with additive effects for lint percentage and fiber quality traits were identified on 15 chromosomes, explaining 7.9–22.2% of the phenotypic variance. The majority of these QTLs were mapped in the D subgenome, indicating that functional mutations in the D subgenome are responsible for the major fiber quality improvements in Upland cotton. Furthermore, five QTL clusters were located on four chromosomes (Chr.05, Chr.18, Chr.19, and Chr.26), which may explain the strong correlation between fiber quality traits measured. The QTLs identified in the current study could be targeted for marker‐assisted selection and map‐based cloning of fiber quality traits in Upland cotton. Core Ideas: QTL mapping using a SNP array on a recombinant inbred line population was performed.The genetic map of SNPs corresponded well with the sequence‐based physical map.Thirty‐two QTLs for six fiber quality traits and lint percentage were identified.The D subgenome harbored the majority of QTLs for fiber quality in Upland cotton.QTLs for fiber quality traits clustered on a handful of chromosomal regions. [ABSTRACT FROM AUTHOR]

This study aimed to identify quantitative trait loci (QTLs) for growth-related traits by constructing a genetic linkage map based on single nucleotide polymorphism (SNP) markers in Japanese quail. A QTL mapping population of 277 F2 birds was obtained from an intercross between a male of a large-sized strain and three females of a normal-sized strain. Body weight (BW) was measured weekly from hatching to 16 weeks of age. Non-linear regression growth models of Weibull, Logistic, Gompertz, Richards, and Brody were analyzed, and growth curve parameters of Richards was selected as the best model to describe the quail growth curve of the F2 birds. Restriction-site associated DNA sequencing developed 125 SNP markers that were informative between their parental strains. The SNP markers were distributed on 16 linkage groups that spanned 795.9 centiMorgan (cM) with an average marker interval of 7.3 cM. QTL analysis of phenotypic traits revealed four main-effect QTLs. Detected QTLs were located on chromosomes 1 and 3 and were associated with BW from 4 to 16 weeks of age and asymptotic weight of Richards model at genome-wide significant at 1% or 5% level. No QTL was detected for BW from 0 to 3 weeks of age. This is the first report identified QTLs for asymptotic weight of the Richards parameter in Japanese quail. These results highlight that the combination of QTL studies and the RAD-seq method will aid future breeding programs identify genes underlying the QTL and the application of marker-assisted selection in the poultry industry, particularly the Japanese quail. [ABSTRACT FROM AUTHOR]

Key message: Stably expressed type I and type II resistance QTL were identified using two Yangmai 158-derived RIL populations, and plant-height and flowering-time QTL intervals detected did not contribute to the FHB resistance variations. Yangmai 158 (Y158) is an elite wheat cultivar widely grown in China with stable Fusarium head blight (FHB) resistance. To enrich the genetic basis underlying FHB resistance, QTL mapping was conducted using two recombinant inbred line (RIL) populations derived from crosses of Y158 with susceptible lines Annong 8455 and Veery. Survey with makers linked to Fhb1, Fhb2, Fhb4 and Fhb5 in resistance cultivar Wangshuibai indicated that both Y158 and the susceptible lines do not contain these QTL. The RIL populations were surveyed with 65 PCR markers and 55 K chip, which generated 23,159 valid marker data, to produce genetic maps for whole genome scanning of quantitative trait loci (QTL). A total of six QTL, all with the Y158 alleles for better resistance and including one stably expressed QTL for type I resistance (Qfhi.nau-2D) and one stably expressed QTL for type II resistance (Qfhs.nau-2A), were identified. Moreover, taking advantage of the great genetic variations in plant height and flowering time, QTL conditioning these two traits were determined. Of six plant-height QTL and three flowering-time QTL intervals detected, none were associated with FHB resistance. The FHB resistance QTL in Y158 were shown to be useful alternatives in FHB resistance breeding programs. The SNP markers flanking Qfhs.nau-2A and Qfhi.nau-2D have been converted to breeder-friendly PCR-based markers to facilitate their applications. [ABSTRACT FROM AUTHOR]

Facial morphology is highly variable, both within and among human populations, and a sizable portion of this variation is attributable to genetics. Previous genome scans have revealed more than 100 genetic loci associated with different aspects of normal-range facial variation. Most of these loci have been detected in Europeans, with few studies focusing on other ancestral groups. Consequently, the degree to which facial traits share a common genetic basis across diverse sets of humans remains largely unknown. We therefore investigated the genetic basis of facial morphology in an East African cohort. We applied an open-ended data-driven phenotyping approach to a sample of 2,595 3D facial images collected on Tanzanian children. This approach segments the face into hierarchically arranged, multivariate features that capture the shape variation after adjusting for age, sex, height, weight, facial size and population stratification. Genome scans of these multivariate shape phenotypes revealed significant (p < 2.5 × 10−8) signals at 20 loci, which were enriched for active chromatin elements in human cranial neural crest cells and embryonic craniofacial tissue, consistent with an early developmental origin of the facial variation. Two of these associations were in highly conserved regions showing craniofacial-specific enhancer activity during embryological development (5q31.1 and 12q21.31). Six of the 20 loci surpassed a stricter threshold accounting for multiple phenotypes with study-wide significance (p < 6.25 × 10−10). Cross-population comparisons indicated 10 association signals were shared with Europeans (seven sharing the same associated SNP), and facilitated fine-mapping of causal variants at previously reported loci. Taken together, these results may point to both shared and population-specific components to the genetic architecture of facial variation. Author summary: Genetic factors play an important role in shaping human facial features. Over the last decade, studies have identified numerous genes associated with various facial traits. The vast majority of these studies have focused on European or Asian populations, while African populations have been underrepresented. Increasing the diversity of these analyses can reveal novel associations and cross-population analyses can help deepen our understanding of known genetic associations. We therefore performed a genome scan of 3D facial features in African children from Tanzania and then compared our results to Europeans. We found 20 regions of the genome associated with facial shape in Tanzanian children, 10 of which were also present in Europeans, indicating evidence for a partly shared genetic basis for human facial shape across populations. In addition, about half of the genetic associations observed in Tanzanians were not present in Europeans, and some of the shared signals differed between populations in the specific genetic variants associated or specific facial traits affected. These results shed light on the shared and population-specific genetic contributors to normal-range facial variation. [ABSTRACT FROM AUTHOR]

Key message: This is the first identification of QTLs underlying resistance to Pseudoperonospora cubensis in Cucumis melo using a genetically characterized isolate. Pseudoperonospora cubensis, causal organism of cucurbit downy mildew (CDM), is one of the largest threats to cucurbit production in the eastern USA. Currently, no Cucumis melo (melon) cultivars have significant levels of resistance. Additionally, little is understood about the genetic basis of resistance in C. melo. Recombinant inbred lines (RILs; N = 169) generated from a cross between the resistant melon breeding line MR-1 and susceptible cultivar Ananas Yok'neam were phenotyped for CDM resistance in both greenhouse and growth chamber studies. A high-density genetic linkage map with 5,663 binned SNPs created from the RIL population was utilized for QTL mapping. Nine QTLs, including two major QTLs, were associated with CDM resistance. Of the major QTLs, qPcub-10.1 was stable across growth chamber and greenhouse tests, whereas qPcub-8.2 was detected only in growth chamber tests. qPcub-10.1 co-located with an MLO-like protein coding gene, which has been shown to confer resistance to powdery mildew and Phytophthora in other plants. This is the first screening of C. melo germplasm with a genetically characterized P. cubensis isolate. [ABSTRACT FROM AUTHOR]