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Background: The blunt snout bream (Megalobrama amblycephala) is an important economic freshwater fish in China with tender flesh and high nutritional value. With the cultivation of superior new varieties and the expansion of breeding scale, it becomes imperative to employ sex-control technology to cultivate monosexual populations of M. amblycephala, thereby preventing the deterioration of desirable traits. The development of specific markers capable of accurately identifying the sex of M. amblycephala would facilitate the determination of the genetic sex of the breeding population before gonad maturation, thereby expediting the processes of sex-controlled breeding of M. amblycephala. Results: A whole-genome re-sequencing was performed for 116 females and 141 males M. amblycephala collected from nine populations. Seven candidate male-specific sequences were identified through comparative analysis of male and female genomes, which were further compared with the sequencing data of 257 individuals, and finally three male-specific sequences were generated. These three sequences were further validated by PCR amplification in 32 males and 32 females to confirm their potential as male-specific molecular markers for M. amblycephala. One of these markers showed potential applicability in M. pellegrini as well, enabling males to be identified using this specific molecular marker. Conclusions: The study provides a high-efficiency and cost-effective approach for the genetic sex identification in two species of Megalobrama. The developed markers in this study have great potential in facilitating sex-controlled breeding of M. amblycephala and M. pellegrini, while also contributing valuable insights into the underlying mechanisms of fish sex determination. [ABSTRACT FROM AUTHOR]

The size of peanut pods and seeds, which directly affects yield and quality, also has significant implications for mechanized production and market efficiency. Identifying relevant loci and mining candidate genes is crucial for cultivating high-yield peanut varieties. In this study, we employed advanced generation recombinant inbred lines developed by crossbreeding Huayu 44 and DF12 as the experimental material. Quantitative trait locus (QTL) mapping for traits related to pod and seed size was conducted across six environments. A total of 44 QTLs were detected, distributed on chromosomes A02, A05, B04, B08, and B10. An enrichment region for multiple QTLs was also identified on chromosome A05 (19.28~52.32 cm). In this region, 10 KASP markers were developed, narrowing the enrichment area to two candidate gene hotspot regions of 600.9 kb and 721.2 kb. By combining gene prediction and functional annotation within the intervals, 10 candidate genes, including those encoding cytochrome P450 protein, polyamine synthase, mannose-1-phosphate guanylyltransferase, pentatricopeptide repeat protein, and E2F transcription factor, were identified as regulators of pod and seed size. This study provides technical support for the genetic improvement and key gene identification of peanut pod and seed size. [ABSTRACT FROM AUTHOR]

Abstract Background The blunt snout bream (Megalobrama amblycephala) is an important economic freshwater fish in China with tender flesh and high nutritional value. With the cultivation of superior new varieties and the expansion of breeding scale, it becomes imperative to employ sex-control technology to cultivate monosexual populations of M. amblycephala, thereby preventing the deterioration of desirable traits. The development of specific markers capable of accurately identifying the sex of M. amblycephala would facilitate the determination of the genetic sex of the breeding population before gonad maturation, thereby expediting the processes of sex-controlled breeding of M. amblycephala. Results A whole-genome re-sequencing was performed for 116 females and 141 males M. amblycephala collected from nine populations. Seven candidate male-specific sequences were identified through comparative analysis of male and female genomes, which were further compared with the sequencing data of 257 individuals, and finally three male-specific sequences were generated. These three sequences were further validated by PCR amplification in 32 males and 32 females to confirm their potential as male-specific molecular markers for M. amblycephala. One of these markers showed potential applicability in M. pellegrini as well, enabling males to be identified using this specific molecular marker. Conclusions The study provides a high-efficiency and cost-effective approach for the genetic sex identification in two species of Megalobrama. The developed markers in this study have great potential in facilitating sex-controlled breeding of M. amblycephala and M. pellegrini, while also contributing valuable insights into the underlying mechanisms of fish sex determination.

Sorghum is an important C4 crop with various food and nonfood uses. Although improvements through hybridization and selection have been exploited, the introduction of genetic variation and the development of new genotypes in sorghum are still limited. Fast-neutron (FN) mutagenesis is a very effective method for gene functional studies and to create genetic variability. However, the full spectrum of FN-induced mutations in sorghum is poorly understood. To address this, we generated an FN-induced mutant population from the inbred line 'BTx623' and sequenced 40 M1 seedlings to evaluate the mutagenic effects of FNs on sorghum. The results show that each line had an average of 43.7 single-base substitutions (SBSs), 3.7 InDels and 35.15 structural variations (SVs). SBSs accounted for approximately 90.0% of the total number of small mutations. Among the eight treatment groups, FN irradiation at a dose of 19 Gy generated the highest number of mutations. The ratio of transition/transversion ranged from 1.77 to 2.21, and the G/C to A/T transition was the most common substitution in all mutant lines. The distributions of the identified SBSs and InDels were similar and uneven across the genome. An average of 3.63 genes were mutated in each mutant line, indicating that FN irradiation resulted in a suitable density of mutated genes, which can be advantageous for improving elite material for one specific or a few traits. These results provide a basis for the selection of the suitable dose of mutagen and new genetic resources for sorghum breeding. [ABSTRACT FROM AUTHOR]

, Henan 450046;2. The Shennong Laboratory, Zhengzhou, Henan 450046) Abstract [Objective] This study aims to analyze the population structure and conservation priorities of local chicken breeds in China to promote sustainable and healthy development of animal husbandry. [Method] The study collected whole-genome re-sequencing data of 96 individuals from eight breeds. The population structure was analyzed by principal component analysis (PCA), constructing a phylogenetic tree, and analyzing inbreeding and genetic distances. The increase or decrease in overall gene and allele diversity was calculated by removing each breed, and the contribution of each breed to the synthesis of a population with maximum gene and allele diversity was simulated to systematically evaluate breed conservation priorities. [Result] The results showed that the eight breeds were divided into four clusters, with the highest differentiation between the Tibetan chicken and other breeds, which was further divided into two subclusters. The other breeds were divided into two clusters, northern and southern. The contribution of Tibetan chicken to genetic diversity is the highest; followed by Wenchang chicken and Yao chicken, these three should be considered as the priority conservation breeds. [Conclusion] The results of this study will provide a reference for the protection, development and utilization of local chicken breeds. [ABSTRACT FROM AUTHOR]

The size of peanut pods and seeds, which directly affects yield and quality, also has significant implications for mechanized production and market efficiency. Identifying relevant loci and mining candidate genes is crucial for cultivating high-yield peanut varieties. In this study, we employed advanced generation recombinant inbred lines developed by crossbreeding Huayu 44 and DF12 as the experimental material. Quantitative trait locus (QTL) mapping for traits related to pod and seed size was conducted across six environments. A total of 44 QTLs were detected, distributed on chromosomes A02, A05, B04, B08, and B10. An enrichment region for multiple QTLs was also identified on chromosome A05 (19.28~52.32 cm). In this region, 10 KASP markers were developed, narrowing the enrichment area to two candidate gene hotspot regions of 600.9 kb and 721.2 kb. By combining gene prediction and functional annotation within the intervals, 10 candidate genes, including those encoding cytochrome P450 protein, polyamine synthase, mannose-1-phosphate guanylyltransferase, pentatricopeptide repeat protein, and E2F transcription factor, were identified as regulators of pod and seed size. This study provides technical support for the genetic improvement and key gene identification of peanut pod and seed size.

Abstract Lumpfish, Cyclopterus lumpus, have historically been harvested throughout Atlantic Canada and are increasingly in demand as a solution to controlling sea lice in Atlantic salmon farms—a process which involves both the domestication and the transfer of lumpfish between geographic regions. At present, little is known regarding population structure and diversity of wild lumpfish in Atlantic Canada, limiting attempts to assess the potential impacts of escaped lumpfish individuals from salmon pens on currently at‐risk wild populations. Here, we characterize the spatial population structure and genomic‐environmental associations of wild populations of lumpfish throughout the Northwest Atlantic using both 70K SNP array data and whole‐genome re‐sequencing data (WGS). At broad spatial scales, our results reveal a large environmentally associated genetic break between the southern populations (Gulf of Maine and Bay of Fundy) and northern populations (Newfoundland and the Gulf of St. Lawrence), linked to variation in ocean temperature and ice cover. At finer spatial scales, evidence of population structure was also evident in a distinct coastal group in Newfoundland and significant isolation by distance across the northern region. Both evidence of consistent environmental associations and elevated genome‐wide variation in FST values among these three regional groups supports their biological relevance. This study represents the first extensive description of population structure of lumpfish in Atlantic Canada, revealing evidence of broad and fine geographic scale environmentally associated genomic diversity. Our results will facilitate the commercial use of lumpfish as a cleaner fish in Atlantic salmon aquaculture, the identification of lumpfish escapees, and the delineation of conservation units of this at‐risk species throughout Atlantic Canada.

Lumpfish, Cyclopterus lumpus, have historically been harvested throughout Atlantic Canada and are increasingly in demand as a solution to controlling sea lice in Atlantic salmon farms—a process which involves both the domestication and the transfer of lumpfish between geographic regions. At present, little is known regarding population structure and diversity of wild lumpfish in Atlantic Canada, limiting attempts to assess the potential impacts of escaped lumpfish individuals from salmon pens on currently at‐risk wild populations. Here, we characterize the spatial population structure and genomic‐environmental associations of wild populations of lumpfish throughout the Northwest Atlantic using both 70K SNP array data and whole‐genome re‐sequencing data (WGS). At broad spatial scales, our results reveal a large environmentally associated genetic break between the southern populations (Gulf of Maine and Bay of Fundy) and northern populations (Newfoundland and the Gulf of St. Lawrence), linked to variation in ocean temperature and ice cover. At finer spatial scales, evidence of population structure was also evident in a distinct coastal group in Newfoundland and significant isolation by distance across the northern region. Both evidence of consistent environmental associations and elevated genome‐wide variation in FST values among these three regional groups supports their biological relevance. This study represents the first extensive description of population structure of lumpfish in Atlantic Canada, revealing evidence of broad and fine geographic scale environmentally associated genomic diversity. Our results will facilitate the commercial use of lumpfish as a cleaner fish in Atlantic salmon aquaculture, the identification of lumpfish escapees, and the delineation of conservation units of this at‐risk species throughout Atlantic Canada. [ABSTRACT FROM AUTHOR]

BACKGROUND: We have previously developed a rice-based oral vaccine against cholera diarrhea, MucoRice-CTB. Using Agrobacterium-mediated co-transformation, we produced the selection marker-free MucoRice-CTB line 51A, which has three copies of the cholera toxin B subunit (CTB) gene and two copies of an RNAi cassette inserted into the rice genome. We determined the sequence and location of the transgenes on rice chromosomes 3 and 12. The expression of alpha-amylase/trypsin inhibitor, a major allergen protein in rice, is lower in this line than in wild-type rice. Line 51A was self-pollinated for five generations to fix the transgenes, and the seeds of the sixth generation produced by T5 plants were defined as the master seed bank (MSB). T6 plants were grown from part of the MSB seeds and were self-pollinated to produce T7 seeds (next seed bank; NSB). NSB was examined and its whole genome and proteome were compared with those of MSB. RESULTS: We re-sequenced the transgenes of NSB and MSB and confirmed the positions of the three CTB genes inserted into chromosomes 3 and 12. The DNA sequences of the transgenes were identical between NSB and MSB. Using whole-genome sequencing, we compared the genome sequences of three NSB with three MSB samples, and evaluated the effects of SNPs and genomic structural variants by clustering. No functionally important mutations (SNPs, translocations, deletions, or inversions of genic regions on chromosomes) between NSB and MSB samples were detected. Analysis of salt-soluble proteins from NSB and MSB samples by shot-gun MS/MS detected no considerable differences in protein abundance. No difference in the expression pattern of storage proteins and CTB in mature seeds of NSB and MSB was detected by immuno-fluorescence microscopy. CONCLUSIONS: All analyses revealed no considerable differences between NSB and MSB samples. Therefore, NSB can be used to replace MSB in the near future.

Hollyhock (Alcea rosea (Linn). Cavan) is an herbaceous flowering plant with significant applications in urban greening, soil remediation, and traditional medicine. However, its genetic diversity and molecular characteristics at the population level have not been explored yet. Here, the phenotypic and genetic diversity of 162 hollyhock accessions from China revealed extensive variation among 11 traits and strong correlations between several quantitative traits. Whole-genome re-sequencing of 32 randomly chosen accessions identified 10,468,760 core single-nucleotide polymorphisms (SNPs) distributed evenly across the genome, except for on chromosome 21, and the average nucleotide diversity (π) was calculated to be 0.00397. Principal component analysis showed that these 32 accessions could be divided into four subpopulations, which was in agreement with the population structure analysis, and the subpopulations were strongly correlated with geographic location. A neighbor-joining dendrogram displayed similar clusters, except for accessions HuB25 and HLJ28, which formed two separate clusters. Our findings illuminate the genetic diversity in hollyhock and provide valuable information for hollyhock breeding. [ABSTRACT FROM AUTHOR]

Identifying alleles associated with adaptation to new environments will advance our understanding of evolution from the molecular level. Previous studies have found that the Populus davidiana southwest population in East Asia has differentiated from other populations in the range. We aimed to evaluate the contributions of the ancestral-state bases (ASBs) relative to derived bases (DBs) in the local adaptation of P. davidiana in the Yunnan–Guizhou Plateau from a quantitative perspective using whole-genome re-sequencing data from 90 P. davidiana samples from three regions across the species range. Our results showed that the uplift of the Qinghai–Tibet Plateau during the Neogene and associated climate fluctuations during the Middle Pleistocene were likely an important factor in the early divergence of P. davidiana. Highly differentiated genomic regions between populations were inferred to have undergone strong linked natural selection, and ASBs are the chief means by which populations of P. davidiana adapt to novel environmental conditions; however, when adapting to regions with high environmental differences relative to the ancestral range, the proportion of DBs was significantly higher than that of background regions, as ASBs are insufficient to cope with these environments. Finally, a number of genes were identified in the outlier region. [ABSTRACT FROM AUTHOR]

Tartary buckwheat (Fagopyrum tataricum Garetn.), a dicotyledonous herbaceous crop, has good adaptation to low nitrogen (LN) condition. The plasticity of roots drives the adaption of Tartary buckwheat under LN, but the detailed mechanism behind the response of TB roots to LN remains unclear. In this study, the molecular mechanism of two Tartary buckwheat genotypes' roots with contrasting sensitivity in response to LN was investigated by integrating physiological, transcriptome and whole-genome re-sequencing analysis. LN improved primary and lateral root growth of LN-sensitive genotype, whereas the roots of LN-insensitive genotype showed no response to LN. 2, 661 LN-responsive differentially expressed genes (DEGs) were identified by transcriptome analysis. Of these genes, 17 N transport and assimilation-related and 29 hormone biosynthesis and signaling genes showed response to LN, and they may play important role in Tartary buckwheat root development under LN. The flavonoid biosynthetic genes' expression was improved by LN, and their transcriptional regulations mediated by MYB and bHLH were analyzed. 78 transcription factors, 124 small secreted peptides and 38 receptor-like protein kinases encoding genes involved in LN response. 438 genes were differentially expressed between LN-sensitive and LN-insensitive genotypes by comparing their transcriptome, including 176 LN-responsive DEGs. Furthermore, nine key LN-responsive genes with sequence variation were identified, including FtNRT2.4 , FtNPF2.6 and FtMYB1R1. This paper provided useful information on the response and adaptation of Tartary buckwheat root to LN, and the candidate genes for breeding Tartary buckwheat with high N use efficiency were identified. • Nitrogen deficiency improved root growth of low nitrogen (LN)-sensitive genotype. • Flavonoid biosynthetic genes' expression was improved by LN, and their transcriptional regulations were analyzed. • Nine key LN-responsive genes with sequence variation were identified, such as FtNRT2.4 , FtNPF2.6 and FtMYB1R1. [ABSTRACT FROM AUTHOR]

Soil salinization is detrimental to the growth and development of flax and ultimately leads to a decrease in yield. However, the molecular mechanism of linseed response to salt stress is still unclear. In this study, a salt-tolerant (ST) linseed variety STS and a salt-sensitive (SS) variety DYM were selected as experiment materials. Bulk segregation analysis and whole-genome resequencing technologies were performed to map salt tolerance quantitative trait loci (QTL). A total of 38,625 QTL loci were identified. Fifteen genes (which were not annotated in the reference genome) were identified within a 2.597 ​Mb region in chromosome 1. Two salt tolerance candidate genes Lus.o.m.scaffold91.141 and Lus.o.m. Scaffold1.14 encoding WD40 and cytochrome P450 were identified by predicting protein functions. Previous studies showed that WD40 and cytochrome P450 could significantly improve plant salt stress tolerance. In this paper, results showed that Lus.o.m.scaffold91.141 and Lus.o.m. Scaffold1.14 might be involved in response to salt stress in lineseed. The fine mapping and functional analysis of these genes provide a molecular breeding basis for the genetic improvement of high salt-tolerant linseed varieties.

Hollyhock (Alcea rosea (Linn). Cavan) is an herbaceous flowering plant with significant applications in urban greening, soil remediation, and traditional medicine. However, its genetic diversity and molecular characteristics at the population level have not been explored yet. Here, the phenotypic and genetic diversity of 162 hollyhock accessions from China revealed extensive variation among 11 traits and strong correlations between several quantitative traits. Whole-genome re-sequencing of 32 randomly chosen accessions identified 10,468,760 core single-nucleotide polymorphisms (SNPs) distributed evenly across the genome, except for on chromosome 21, and the average nucleotide diversity (π) was calculated to be 0.00397. Principal component analysis showed that these 32 accessions could be divided into four subpopulations, which was in agreement with the population structure analysis, and the subpopulations were strongly correlated with geographic location. A neighbor-joining dendrogram displayed similar clusters, except for accessions HuB25 and HLJ28, which formed two separate clusters. Our findings illuminate the genetic diversity in hollyhock and provide valuable information for hollyhock breeding.

Main conclusion: SmANS deletion leads to white flower mutation in Salvia miltiorrhiza. SmANS deletion leads to white flower mutation in Salvia miltiorrhiza. Abstract Salvia miltiorrhiza is an essential traditional Chinese medicine (TCM) with purple flowers, and S. miltiorrhiza Bge. f. alba is a unique intraspecific variation with white flowers. The molecular mechanism of flower color formation in S. miltiorrhiza will provide vital information for the variation and evolution. Here, we performed HPLC, transcriptomic, and re-sequencing analyses of purple-flowered S. miltiorrhiza line ‘Zihua105’ (ZH105) and white-flowered S. miltiorrhiza Bge. f. alba line ‘Baihua18’ (BH18). Delphinidin was the most anthocyanidin in ZH105, which become the main different between ZH105 vs. BH18 flowers. Transcriptome analysis revealed 299 differentially expressed genes (DEGs). SmANS, the anthocyanidin synthase gene in the down-stream anthocyanin biosynthesis pathway, was significantly expressed in ZH105 corollas, suggesting it might play a key role in white petal formation. Whole-genome re-sequencing revealed that a 6.75 kb segment located on chromosome 5, which contains the complete sequence of the SmANS genes, was lost in BH18 and another S. miltiorrhiza Bge. f. alba line. In contrast, the other five purple-flowered S. miltiorrhiza lines both possessed this segment. Further molecular marker identification also confirmed that wild S. miltiorrhiza Bge. f. alba lines lost regions that contained a complete or important part of SmANS sequences. Subsequently, the research showed that the deletion mutant of SmANS genes resulted in the natural white flower color variant of S. miltiorrhiza. [ABSTRACT FROM AUTHOR]

Drought tolerance is one of the most important targets for wheat breeding. Previous population genetics studies have uncovered 20 large-effect quantitative trait loci (QTLs) that contribute to stress-responsive agronomic traits. Here, we identified 19,035,814 single nucleotide polymorphisms and 719,049 insertion/deletion variations in the genomes of two popular winter wheat cultivars, Lu-Mai 14 and Han-Xuan 10, using a whole-genome re-sequencing assay. There were 4972 loss-of-function mutations carried by protein-coding genes, such as CCA1/LHY, AGO1, ABI3/VP1, EIN3, TPP, and ARFs. We carried out a time-course abscisic acid (ABA)-treatment experiment and profiled 61,251 expressed genes in the roots using a strand-specific RNA sequencing approach. A large number of genes showed time-point specific and/or cultivar-preferential responsive expression patterns. Gene ontology enrichment analysis revealed that ABA-responsive genes were associated with stress-related functions. Among the 20 QTLs, we uncovered 306 expressed genes with high- and/or moderate-effect variations and 472 differentially expressed genes. Detailed analysis and verification of the homozygous genomic variations in the candidate genes encoding sulfotransferase, proteinase, kinase, nitrate transporter, and transcription factors suggested previously unexpected pathways associated with abiotic stress responses in wheat. [ABSTRACT FROM AUTHOR]

1. To evaluate the inbreeding of yellow-feathered chickens (YFCs) and identify genes related to their unique characteristics, whole-genome re-sequencing data were applied to detect runs of homozygosity (ROH) in the genomes of 10 YFC chickens from each of 10 different YFC breeds. The number, length, distribution of ROH, and inbreeding coefficient in different YFC populations were calculated. Genomic regions with high frequency in ROH were annotated. 2. In total, 25,547 ROH with an average length of 335 kb were detected, with most being <1 Mb. The domination of short ROH reflected the long breeding history of this chicken. The number, length, frequency, and distribution of ROH varied among chicken populations, and high genetic diversity was maintained. 3. Numerous genes related to YFC characteristics were identified in the high-frequency ROH regions. Among these, IFNA, IFNB, IL11 RA, IL22 RA1, IFNLR1, and TRIF genes were involved in disease resistance. The AMY, G6PC, SDHB, GCNT4, and ACO genes were associated with energy material metabolism; and FABPL, AQP7, ACAA2, and RYR2 were related to meat quality and flavour. The KITLG, CREB3, RYR2, and LGR4 genes, related to pigmentation, were detected. 4. This ROH-based inbreeding evaluation lays the foundation for breeding and conservation of YFC populations, and the candidate genes identified can be used for marker-assisted selection. [ABSTRACT FROM AUTHOR]

Characterization of genetic variants is crucial for understanding the molecular mechanisms behind selected traits and enhancing the rate of genetic gain through artificial selection. This study explored the genetic diversity and population structure of blunt snout bream Megalobrama amblycephala , a key freshwater fish in Chinese aquaculture. We conducted whole-genome re-sequencing of individuals from six populations, comprising three natural and three genetically improved strains, to assess genetic diversity, population structure and the impacts of selective breeding. We identified 17,009,590 high-quality biallelic single nucleotide polymorphism (SNP) loci. Genetic diversity assessments revealed low levels of polymorphism across populations, with genetically improved strains showing moderate to high genetic differentiation from their source populations. The study also highlighted runs of homozygosity (ROH) and analyzed linkage disequilibrium (LD) decay, indicating minimal recent inbreeding and diverse recombination events among populations. Selective sweep analyses uncovered significant selection loci associated with growth and hypoxia tolerance traits. Enrichment analyses identified genes involved in olfactory signal transduction, immune response, and metabolism pathways, which are closely related to these selective traits. These findings offer insights into the genetic basis of critical traits in M. amblycephala , contributing to the conservation of germplasm resources and supporting ongoing selective breeding efforts. • Whole-genome re-sequencing revealed genetic differentiation in natural and improved populations of M. amblycephala. • Selective sweep analysis identified key genes associated with growth and hypoxia tolerance. • Genetic diversity and linkage disequilibrium analysis showed minimal inbreeding, supporting sustainable genetic improvement. [ABSTRACT FROM AUTHOR]

[Display omitted] • Paleo-rivers on the Sunda Shelf have shaped the evolution of Mixornis tit-babblers. • Populations from Natuna and Anambas Islands are genetically and phenotypically embedded in M. gularis. • Taxon woodi from Palawan deserves elevation to species status. Rivers constitute an important biogeographic divide in vast areas of tropical rainforest, such as the Amazon and Congo Basins. Southeast Asia's rainforests are currently fragmented across islands divided by sea, which has long obscured their extensive history of terrestrial connectivity as part of a vast (but now submerged) subcontinent – Sundaland – during most of the Quaternary. The role of paleo-rivers in determining population structure in Sundaic rainforests at a time when these forests were connected remains little understood. We examined the coloration of museum skins and used the genomic DNA of museum samples and freshly-collected blood tissue of a pair of Sundaic songbird species, the pin-striped and bold-striped tit-babblers (Mixornis gularis and M. bornensis , respectively), to assess the genetic affinity of populations on small Sundaic islands that have largely been ignored by modern research. Our genomic and morphological results place the populations from the Anambas and Natuna Islands firmly within M. gularis from the Malay Peninsula in western Sundaland, even though some of these islands are geographically much closer to Borneo, where M. bornensis resides. Our results reveal genetic structure consistent with the course of Sundaic paleo-rivers and the location of the interfluvia they formed, and add to a small but growing body of evidence that rivers would have been of equal biogeographic importance in Sundaland's former connected forest landscape as they are in Amazonia and the Congo Basin today. [ABSTRACT FROM AUTHOR]

Chinese cabbage (Brassica rapa L.) is one of the most important and highly nutritious vegetables in China belonging to the Brassicaceae family. Flowering or bolting is one of the most critical developmental stages in flowering plants. For the spring-sown Chinese cabbage, late-bolting is desirable over early-bolting according to consumer preferences. We determined the inheritance pattern of the late-bolting trait using F1 and F2 generated from a cross between 'SY2004' (late-bolting) and 'CX14-1' (early-bolting). The genetic analysis revealed that the late-bolting to early-bolting trait was controlled by an incomplete dominant gene that we named BrLb-1. Furthermore, we performed bulked segregant analysis (BSA) via whole genome re-sequencing and the results showed that this gene was harbored on the chromosome A07 at the intersections of 20,070,000 to 25,290,000 bp and 20,330,000 to 25,220,000, an interval distance of 4.89 Mb. In this candidate interval, totals of 2321 and 1526 SNPs with non-synonymous mutations, and 229 and 131 InDels with frameshift mutations, were found between the parents and the bulked pools, respectively. Furthermore, we identified three putative candidate genes for the late-bolting trait, including BraA07g029500, BraA07g029530 and BraA07g030360, which code for the AGAMOUS-like MADS-box protein AGL12, a pentatricopeptide repeat-containing protein and NAC transcription factor 29, respectively; however, further functional analysis is required. These genetic variants could be utilized for the further development of molecular markers for marker-assisted breeding in Chinese cabbage. [ABSTRACT FROM AUTHOR]

Abstract Background We have previously developed a rice-based oral vaccine against cholera diarrhea, MucoRice-CTB. Using Agrobacterium-mediated co-transformation, we produced the selection marker–free MucoRice-CTB line 51A, which has three copies of the cholera toxin B subunit (CTB) gene and two copies of an RNAi cassette inserted into the rice genome. We determined the sequence and location of the transgenes on rice chromosomes 3 and 12. The expression of alpha-amylase/trypsin inhibitor, a major allergen protein in rice, is lower in this line than in wild-type rice. Line 51A was self-pollinated for five generations to fix the transgenes, and the seeds of the sixth generation produced by T5 plants were defined as the master seed bank (MSB). T6 plants were grown from part of the MSB seeds and were self-pollinated to produce T7 seeds (next seed bank; NSB). NSB was examined and its whole genome and proteome were compared with those of MSB. Results We re-sequenced the transgenes of NSB and MSB and confirmed the positions of the three CTB genes inserted into chromosomes 3 and 12. The DNA sequences of the transgenes were identical between NSB and MSB. Using whole-genome sequencing, we compared the genome sequences of three NSB with three MSB samples, and evaluated the effects of SNPs and genomic structural variants by clustering. No functionally important mutations (SNPs, translocations, deletions, or inversions of genic regions on chromosomes) between NSB and MSB samples were detected. Analysis of salt-soluble proteins from NSB and MSB samples by shot-gun MS/MS detected no considerable differences in protein abundance. No difference in the expression pattern of storage proteins and CTB in mature seeds of NSB and MSB was detected by immuno-fluorescence microscopy. Conclusions All analyses revealed no considerable differences between NSB and MSB samples. Therefore, NSB can be used to replace MSB in the near future.

Summary: Bohai Black (BHB) cattle, one of eight representative indigenous breeds in China, is well known for its high resistance to disease, endurance under unfavorable feeding conditions and excellent meat quality. Over recent, the number of BHB cattle has decreased sharply. To investigate the population structure and genetic diversity of this breed, the whole‐genome data of 35 individuals from a conservation farm were obtained using the Illumina 150 bp paired‐end platform. The results of the genetic structure and diversity analyses showed that BHB cattle had mixed Bos taurus and Bos indicus ancestry, close phylogenic relationships with Jiaxian Red and Luxi cattle and abundant genetic diversity. The bulls tested here could be divided into six families. This study presents a comprehensive evaluation of the genetic structure and diversity of the BHB cattle, and lays the theoretical basis for conservation and utilization of the valuable germplasm resource. [ABSTRACT FROM AUTHOR]

Potato, (Solanum tuberosum), is one of the most common and important food sources for humans. It is not only essential as a food source but also has many benefits for human health. Potato is ranked as the world's third non-cereal crop after rice and wheat. Biotic stress, such as viruses, is a common stress in potato-growing areas, leading to reduced tuber yield and quality. This review begins with a description of resistance mechanisms to viruses, historical perspective on potato improvement for virus resistance based on classic and next-generation sequencing (NGS) techniques. Classical breeding has been exploited for improving virus resistant potato. In recent years, plant breeding has quickly changed from phenotypic selection to genotype selection, facilitating the selection process both in terms of time and accuracy. The next-generation sequencing techniques have valuable potential to study the genotype selection through whole-genome re-sequencing (WGRS) and genome-wide association study (GWAS), and RNA-seq has been used to identify markers in virus-resistance potato, facilitating potato breeding for virus resistance. Identification of molecular markers based on new generation sequencing methods and in particular NGS along with bioinformatics tools has facilitated the identification of related markers. The objectives of this review were to better understand virus resistance genes and to recommend the most effective technique and/ or combination approaches for identification of molecular markers in order to breed potato plants resistant to viruses. [ABSTRACT FROM AUTHOR]

Despite the global biodiversity of terrestrial gastropods and their ecological and economic importance, the genomic basis of ecological adaptation and speciation in land snail taxa is still largely unknown. Here, we combined whole-genome re-sequencing with population genomics to evaluate the historical demography and the speciation process of two closely related species of land snails from western Europe, Candidula unifasciata and C. rugosiuscula. Historical demographic analysis indicated fluctuations in the size of ancestral populations, probably driven by Pleistocene climatic fluctuations. Although the current population distributions of both species do not overlap, our approximate Bayesian computation model selection approach on several speciation scenarios suggested that gene flow has occurred throughout the divergence process until recently. Positively selected genes diverging early in the process were associated with intragenomic and cyto-nuclear incompatibilities, respectively, potentially fostering reproductive isolation as well as ecological divergence. Our results suggested that the speciation between species entails complex processes involving both gene flow and ecological speciation, and that further research based on whole-genome data can provide valuable understanding on species divergence. This article is part of the Theo Murphy meeting issue 'Molluscan genomics: broad insights and future directions for a neglected phylum'. [ABSTRACT FROM AUTHOR]

An integrative approach of adaptive laboratory evolution, whole-genome sequencing and single-cell analysis was used to explore mechanisms related to establishment and maintenance of syntrophic interaction between sulfate-reducing Desulfovibrio vulgaris and methanogen Methanosarcina barkeri. Adaptive laboratory evolution of the D. vulgaris and M. barkeri dual-cultures under two different concentrations of electron donor lactate (38 mM and 50 mM) was conducted by propagating continuously for 50 transfers (~200 generations). Physiological analysis showed that, compared with the initial dual-cultures, the adapted dual-cultures (E38 and E50) have increased growth rates (1.1-fold and 1.2 -fold) and higher biomass yields (3.0-fold and 3.8-fold) on 38 mM and 50 mM lactate, respectively. Whole-genome re-sequencing of D. vulgaris in the adapted dualcultures revealed 11 and 12 mutations in the D. vulgaris genomes of E38 and E50 dual-cultures, respectively, among which 4 mutations were found in both adapted dual-cultures. RT-qPCR analysis showed that the expression levels of 8 mutated genes were gradually up-regulated in D. vulgaris along with the evolution process. In addition, their heterogeneity was found decreased along with the evolution, as revealed by singlecell RT-qPCR analysis, reflecting adjustments of both gene expression and gene heterogeneity to the gradually established syntrophic relationship. [ABSTRACT FROM AUTHOR]

Oogenesis involves a series of biochemical and physiological transformations and numerous regulated genes. The autotetraploid Carassius auratus (4nRR) originated from whole-genome duplication of Carassius auratus red var. (RCC), which produces diploid eggs through pairing of diploid-like chromosome during female meiosis. To explore the molecular mechanisms underlying oogenesis in 4nRR, we used the Illumina sequencing platform to characterize the ovaries of 4nRR and RCC. Transcriptome and whole-genome re-sequencing were performed to uncover the key genes and potential genetic mutations related to oogenesis. Each sample produced paired-end reads in the range of 66.97 to 98.36 million via Illumina HiSeq™ 2500. After comparing of the transcriptome profiles between the 4nRR and RCC, we uncovered 8562 differentially expressed genes (DEGs). The DEGs were enriched in oogenesis-related processes, including oogenesis, oocyte development, ubiquitin-mediated proteolysis, the signaling pathways of MAPK and calcium, and oocyte meiosis as investigated by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. Additionally, whole-genome re-sequencing revealed 34,058,834 SNPs and 6,153,711 InDels, including 6,677,638 non-synonymous variations (SNPs) and 706,210 frame-shift InDels in the 8510 DEGs of 4nRR fish. Subsequently, whole-genome re-sequencing and transcriptomatic analyses revealed the genes that participate in oogenesis associated processes. Specifically, genes involved in ubiquitin-mediated proteolysis (SMURF1, UBE2I), calcium transport (CALM3, CAMK4), and meiosis (MAPK3, GRB2, CPEB1, CCNB2, YWHAE) were related to oogenesis in 4nRR. These findings enrich our understanding of oogenesis in the autopolyploid fish. [ABSTRACT FROM AUTHOR]

Mungbean [Vigna radiata (L.) R. Wilczek var. radiata] is vital grain legume having nutritional and socio-economic importance, especially in the developing countries. We performed whole-genome re-sequencing of three accessions representing the wild progenitor species, released and landrace of mungbean to identify SNPs with relevance to genetic relationships analysis. Approximately 9.3 million raw reads were obtained using Ion Torrent PGM™ platform and more than 92% of the reads were mapped to the reference mungbean genome. We identified a total of 233,799 single-nucleotide polymorphisms in relation to the reference genome (SNPs: 103,341 in wild, 93,078 in released and 37,380 in landrace accessions) and 9544 insertions and deletions (InDels: 4742 in wild, 3608 in released and 1194 in landrace accessions) in the coding and non-coding regions. In all accessions, genomic variants were unevenly distributed within and across the mungbean chromosomes. Among these 5339, 4739 and 1795 SNPs were non-synonymous in 815, 790 and 317 genes of wild, released and landrace accessions, respectively. These polymorphisms might contribute to the variation in important pathways of genes for abiotic and biotic stress tolerance and important agronomic traits, such as seed dormancy, flowering time and seed size in mungbean. Among the randomly selected SNPs, a selected subset was validated using Sanger sequencing technique. The genomic variations among mungbean wild, released and landrace accessions constitute a powerful tool to support genetic research and molecular breeding of mungbean. [ABSTRACT FROM AUTHOR]

Drought tolerance is one of the most important targets for wheat breeding. Previous population genetics studies have uncovered 20 large-effect quantitative trait loci (QTLs) that contribute to stress-responsive agronomic traits. Here, we identified 19,035,814 single nucleotide polymorphisms and 719,049 insertion/deletion variations in the genomes of two popular winter wheat cultivars, Lu-Mai 14 and Han-Xuan 10, using a whole-genome re-sequencing assay. There were 4972 loss-of-function mutations carried by protein-coding genes, such as CCA1/LHY, AGO1, ABI3/VP1, EIN3, TPP, and ARFs. We carried out a time-course abscisic acid (ABA)-treatment experiment and profiled 61,251 expressed genes in the roots using a strand-specific RNA sequencing approach. A large number of genes showed time-point specific and/or cultivar-preferential responsive expression patterns. Gene ontology enrichment analysis revealed that ABA-responsive genes were associated with stress-related functions. Among the 20 QTLs, we uncovered 306 expressed genes with high- and/or moderate-effect variations and 472 differentially expressed genes. Detailed analysis and verification of the homozygous genomic variations in the candidate genes encoding sulfotransferase, proteinase, kinase, nitrate transporter, and transcription factors suggested previously unexpected pathways associated with abiotic stress responses in wheat.

Chinese cabbage (Brassica rapa L.) is one of the most important and highly nutritious vegetables in China belonging to the Brassicaceae family. Flowering or bolting is one of the most critical developmental stages in flowering plants. For the spring-sown Chinese cabbage, late-bolting is desirable over early-bolting according to consumer preferences. We determined the inheritance pattern of the late-bolting trait using F1 and F2 generated from a cross between ‘SY2004’ (late-bolting) and ‘CX14-1’ (early-bolting). The genetic analysis revealed that the late-bolting to early-bolting trait was controlled by an incomplete dominant gene that we named BrLb-1. Furthermore, we performed bulked segregant analysis (BSA) via whole genome re-sequencing and the results showed that this gene was harbored on the chromosome A07 at the intersections of 20,070,000 to 25,290,000 bp and 20,330,000 to 25,220,000, an interval distance of 4.89 Mb. In this candidate interval, totals of 2321 and 1526 SNPs with non-synonymous mutations, and 229 and 131 InDels with frameshift mutations, were found between the parents and the bulked pools, respectively. Furthermore, we identified three putative candidate genes for the late-bolting trait, including BraA07g029500, BraA07g029530 and BraA07g030360, which code for the AGAMOUS-like MADS-box protein AGL12, a pentatricopeptide repeat-containing protein and NAC transcription factor 29, respectively; however, further functional analysis is required. These genetic variants could be utilized for the further development of molecular markers for marker-assisted breeding in Chinese cabbage.

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The Chongming white goat (CM) is an indigenous goat breed exhibits unique traits that are adapted to the local environment and artificial selection. By performing whole-genome re-sequencing, we generated 14–20× coverage sequences from 10 domestic goat breeds to explore the genomic characteristics and selection signatures of the CM breed. We identified a total of 23,508,551 single-nucleotide polymorphisms (SNPs) and 2,830,800 insertion–deletion mutations (indels) after read mapping and variant calling. We further specifically identified 1.2% SNPs (271,713) and 0.9% indels (24,843) unique to the CM breed in comparison with the other nine goat breeds. Missense (SIFT < 0.05), frameshift, splice-site, start-loss, stop-loss, and stop-gain variants were identified in 183 protein-coding genes of the CM breed. Of the 183, 36 genes, including AP4E1, FSHR, COL11A2, and DYSF, are involved in phenotype ontology terms related to the nervous system, short stature, and skeletal muscle morphology. Moreover, based on genome-wide FST and pooled heterozygosity (Hp) calculation, we further identified selection signature genes between the CM and the other nine goat breeds. These genes are significantly associated with the nervous system (C2CD3, DNAJB13, UCP2, ZMYND11, CEP126, SCAPER, and TSHR), growth (UCP2, UCP3, TSHR, FGFR1, ERLIN2, and ZNF703), and coat color (KITLG, ASIP, AHCY, RALY, and MC1R). Our results suggest that the CM breed may be differentiated from other goat breeds in terms of nervous system owing to natural or artificial selection. The whole-genome analysis provides an improved understanding of genetic diversity and trait exploration for this indigenous goat breed.

Genetic variations are an important source of germplasm diversity, as it provides an allele resource that contributes to the development of new traits for plant breeding. Gamma rays have been widely used as a physical agent for mutation creation in plants, and their mutagenic effect has attracted extensive attention. However, few studies are available on the comprehensive mutation profile at both the large-scale phenotype mutation screening and whole-genome mutation scanning. In this study, biological effects on M1 generation, large-scale phenotype screening in M2 generation, as well as whole-genome re-sequencing of seven M3 phenotype-visible lines were carried out to comprehensively evaluate the mutagenic effects of gamma rays on Arabidopsis thaliana. A total of 417 plants with visible mutated phenotypes were isolated from 20,502 M2 plants, and the phenotypic mutation frequency of gamma rays was 2.03% in Arabidopsis thaliana. On average, there were 21.57 single-base substitutions (SBSs) and 11.57 small insertions and deletions (InDels) in each line. Single-base InDels accounts for 66.7% of the small InDels. The genomic mutation frequency was 2.78 × 10−10/bp/Gy. The ratio of transition/transversion was 1.60, and 64.28% of the C > T events exhibited the pyrimidine dinucleotide sequence; 69.14% of the small InDels were located in the sequence with 1 to 4 bp terminal microhomology that was used for DNA end rejoining, while SBSs were less dependent on terminal microhomology. Nine genes, on average, were predicted to suffer from functional alteration in each re-sequenced line. This indicated that a suitable mutation gene density was an advantage of gamma rays when trying to improve elite materials for one certain or a few traits. These results will aid the full understanding of the mutagenic effects and mechanisms of gamma rays and provide a basis for suitable mutagen selection and parameter design, which can further facilitate the development of more controlled mutagenesis methods for plant mutation breeding.

The Chongming white goat (CM) is an indigenous goat breed exhibits unique traits that are adapted to the local environment and artificial selection. By performing whole-genome re-sequencing, we generated 14–20× coverage sequences from 10 domestic goat breeds to explore the genomic characteristics and selection signatures of the CM breed. We identified a total of 23,508,551 single-nucleotide polymorphisms (SNPs) and 2,830,800 insertion–deletion mutations (indels) after read mapping and variant calling. We further specifically identified 1.2% SNPs (271,713) and 0.9% indels (24,843) unique to the CM breed in comparison with the other nine goat breeds. Missense (SIFT < 0.05), frameshift, splice-site, start-loss, stop-loss, and stop-gain variants were identified in 183 protein-coding genes of the CM breed. Of the 183, 36 genes, including AP4E1 , FSHR , COL11A2 , and DYSF , are involved in phenotype ontology terms related to the nervous system, short stature, and skeletal muscle morphology. Moreover, based on genome-wide F ST and pooled heterozygosity (Hp) calculation, we further identified selection signature genes between the CM and the other nine goat breeds. These genes are significantly associated with the nervous system (C2CD3 , DNAJB13 , UCP2 , ZMYND11 , CEP126 , SCAPER , and TSHR), growth (UCP2 , UCP3 , TSHR , FGFR1 , ERLIN2 , and ZNF703), and coat color (KITLG , ASIP , AHCY , RALY , and MC1R). Our results suggest that the CM breed may be differentiated from other goat breeds in terms of nervous system owing to natural or artificial selection. The whole-genome analysis provides an improved understanding of genetic diversity and trait exploration for this indigenous goat breed. [ABSTRACT FROM AUTHOR]

Considerable genetic variation in agronomic nitrogen (N) use efficiency (NUE) has been reported among genotypes of Brassica napus. However, the physiological and molecular mechanisms underpinning these differences remain poorly understood. In this study, physiological and genetic factors impacting NUE were identified in field trials and hydroponic experiments using two B. napus genotypes with contrasting NUE. The results showed that the N‐efficient genotype (D4‐15) had greater N uptake and utilization efficiencies, more root tips, larger root surface and root volume, and higher N assimilation and photosynthesis capacity than the N‐inefficient genotype (D2‐1). Genomic analysis revealed that D4‐15 had a greater genome diversity related to NUE than D2‐1. By combining genomic and transcriptomic analysis, genes involved in photosynthesis and C/N metabolism were implicated in conferring NUE. Co‐expression network analysis of genes that differed between the two genotypes suggested gene clusters impacting NUE. A nitrate transporter gene BnaA06g04560D (NRT2.1) and two vacuole nitrate transporter CLC genes (BnaA02g11800D and BnaA02g28670D) were up‐regulated by N starvation in D4‐15 but not in D2‐1. The study revealed that high N uptake and utilization efficiencies, maintained photosynthesis and coordinated C/N metabolism confer high NUE in B. napus, and identified candidate genes that could facilitate breeding for enhanced NUE in B. napus. In the study, the N‐efficient B. napus genotype (D4‐15) had greater yield, N uptake and utilization efficiencies, better root architecture, and more N assimilation and photosynthesis than the N‐inefficient genotype (D2‐1). Genomic analysis revealed that D4‐15 had a greater genome diversity related to NUE, than D2‐1. By integrating genomic and transcriptomic analyses, 11 genes in shoots and 14 genes in roots involved in photosynthesis and C/N metabolism. Co‐expression network analysis suggested a high affinity nitrate transporter gene BnaA06g04560D (NRT2.1) and two vacuole nitrate transporter CLC genes (BnaA02g11800D and BnaA02g28670D) impacting NUE in B. napus. The study revealed that high N uptake and utilization efficiencies, together with maintained photosynthesis and coordinated C/N metabolism confer high NUE in B. napus, and identified candidate genes for these processes that could facilitate breeding for enhanced NUE in B. napus. [ABSTRACT FROM AUTHOR]

Yield loss in the economically important hazelnut (Corylus spp.) occurs through the frequent formation of blank nuts. Although the condition is associated with embryo abortion, we have not yet identified the regulatory genes involved. Therefore, this study aimed to determine the genes related to embryo abortion in hazel. We performed whole-genome re-sequencing and single-nucleotide polymorphism (SNP) analysis on four mutant hazelnut trees (Empty1 to Empty4, C. heterophylla) bearing blank nuts and four wild-type trees (Full1 to Full4, C. heterophylla). A paired comparison of Empty1 vs. Full1, Empty2 vs. Full2, Empty3 vs. Full3, and Empty4 vs. Full4, along with the intersection of Empty1 to Empty4, revealed 3 081 common SNPs in the four blank-nut mutants. Of these, 215 synonymous SNPs in exonic regions were distributed across 178 candidate genes. Heterozygosity analysis showed that average homozygous and heterozygous SNP ratios were respectively 0.409 and 0.591 in the samples. According to Gene Ontology classification, candidate genes were enriched in the categories of binding, catalysis, molecular transducer, transporter, and molecular function regulator. Among these, 18 of 178 genes had homozygous SNPs in Empty1–4. Cis elements in the promoter region of starch synthase 4 (SS4) contain the RY-element, implying seed-specific expression. Starch granules were absent from Empty1–4 cotyledon cells, but abundantly present in Full1–Full4 cotyledon cells. The blank-nut phenotype has heavier nut shells. Overall, we conclude that single-nucleotide variants of Acetyl-CoA carboxylase 1 (ACC1), intracellular sodium/hydrogen exchanger 2 (NHX2), UDP-glycosyltransferase 74E2 (UGT74E2), DEFECTIVE IN MERISTEM SILENCING 3 (DMS3), DETOXIFICATION 43 (FRD3), and SS4 may induce embryo abortion, leading to blank-nut formation. Our results will benefit future research on how the gain or loss of candidate genes influences seed development. Moreover, our study provides novel prospects for seedless cultivar development.

Yield loss in the economically important hazelnut (Corylus spp.) occurs through the frequent formation of blank nuts. Although the condition is associated with embryo abortion, we have not yet identified the regulatory genes involved. Therefore, this study aimed to determine the genes related to embryo abortion in hazel. We performed whole-genome re-sequencing and single-nucleotide polymorphism (SNP) analysis on four mutant hazelnut trees (Empty1 to Empty4, C. heterophylla) bearing blank nuts and four wild-type trees (Full1 to Full4, C. heterophylla). A paired comparison of Empty1 vs. Full1, Empty2 vs. Full2, Empty3 vs. Full3, and Empty4 vs. Full4, along with the intersection of Empty1 to Empty4, revealed 3 081 common SNPs in the four blank-nut mutants. Of these, 215 synonymous SNPs in exonic regions were distributed across 178 candidate genes. Heterozygosity analysis showed that average homozygous and heterozygous SNP ratios were respectively 0.409 and 0.591 in the samples. According to Gene Ontology classification, candidate genes were enriched in the categories of binding, catalysis, molecular transducer, transporter, and molecular function regulator. Among these, 18 of 178 genes had homozygous SNPs in Empty1–4. Cis elements in the promoter region of starch synthase 4 (SS4) contain the RY-element, implying seed-specific expression. Starch granules were absent from Empty1–4 cotyledon cells, but abundantly present in Full1–Full4 cotyledon cells. The blank-nut phenotype has heavier nut shells. Overall, we conclude that single-nucleotide variants of Acetyl-CoA carboxylase 1 (ACC1), intracellular sodium/hydrogen exchanger 2 (NHX2), UDP-glycosyltransferase 74E2 (UGT74E2), DEFECTIVE IN MERISTEM SILENCING 3 (DMS3), DETOXIFICATION 43 (FRD3), and SS4 may induce embryo abortion, leading to blank-nut formation. Our results will benefit future research on how the gain or loss of candidate genes influences seed development. Moreover, our study provides novel prospects for seedless cultivar development. [ABSTRACT FROM AUTHOR]

Key message: Genome-wide insertions/deletions were identified in Bt transgenic poplar through whole-genome re-sequencing, revealing the molecular mechanisms underlying changes in the growth and wood characteristics of Bt transgenic poplar.Abstract: Poplar is a fast-growing tree that relieves the wood demand in China. Previously, we found growth and wood characteristics differed in some lines of insect-resistant Bt transgenic poplar. Here, we selected five Bt transgenic lines (#12, #153, #172, #208 and #209), one untransformed control (CK2), one comparable control (CK3), and one native cultivar (JY, Populus × euramericana ‘Robusta’) in Xinjiang, China, for further study. Based on breast diameter, tree height, chemical content, and fibre morphology analyses, these transgenic lines showed fast growth and high-lignin and low-cellulose contents in the cell wall. In addition, genome-wide insertions/deletions (InDels) were compared between two transgenic lines (#12 and #153) and the untransformed control via whole-genome re-sequencing. GO enrichment and protein-protein interaction networks indicated the genes affected by differential InDels were related to programmed cell death and defence responses. This study provides new insight into the molecular mechanisms underlying changes in biomass characteristics in Bt transgenic poplar. [ABSTRACT FROM AUTHOR]

Nitrogen (N) is a non-mineral macronutrient essential for plant growth and development. Oilseed rape (AnAnCnCn, 2n = 4x = 38) has a high requirement for N nutrients whereas showing the lowest N use efficiency (NUE) among crops. The mechanisms underlying NUE regulation in Brassica napus remain unclear because of genome complexity. In this study, we performed high-depth and -coverage wholegenome re-sequencing (WGS) of an N-efficient (higher NUE) genotype "XY15" and an N-inefficient (lower NUE) genotype "814" of rapeseed. More than 687 million 150-bp paired-end reads were generated, which provided about 93% coverage and 503 depth of the rapeseed genome. Applying stringent parameters, we identified a total of 1,449,157 single-nucleotide polymorphisms (SNPs), 335,228 InDels, 175,602 structure variations (SVs) and 86,280 copy number variations (CNVs) between the N-efficient and -inefficient genotypes. The largest proportion of various DNA polymorphisms occurred in the inter-genic regions. Unlike CNVs, the SNP/InDel and SV polymorphisms showed variation bias of the An and Cn subgenomes, respectively. Gene ontology analysis showed the genetic variants were mapped onto the genes involving N compound transport and ATPase complex metabolism, but not including N assimilation-related genes. On basis of identification of N-starvation responsive genes through high-throughput expression profiling, we also mapped these variants onto some key NUE-regulating genes, and validated their significantly differential expression between the N-efficient and -inefficient genotypes through qRT-PCR assays. Our data provide genome-wide high resolution DNA variants underlying NUE divergence in allotetraploid rapeseed genotypes, which would expedite the effective identification and functional validation of key NUE-regulating genes through genomics-assisted improvement of crop nutrient efficiency. [ABSTRACT FROM AUTHOR]

The direct use of industrial flue gas in microalgae production is desired for mitigating CO 2 emissions, but the low pH resulting from the inflow of acidic gases (mainly CO 2 , NO x, and SO x) imposes detrimental effects on microalgal growth and is considered the main technical challenge for simultaneous biomass production and CO 2 sequestration. In this study, we investigated the adaptive responses of the model marine diatom Phaeodactylum tricornutum to acidic stress at pH 6.0. Gradual changes in the ratio of morphotypes, chlorophyll content, and photosynthetic efficiency were observed as a result of adaptive laboratory evolution (ALE) under constant acidic stress. The evolved strains showed a significant increase in growth rate in acidic conditions after ALE, and phenotypic characterization demonstrated a stable trait of acid tolerance with an average increase in growth by 110.4%, 46.1%, and 27.5% at pH 5.5, 6.0, and 6.5, respectively compared with the parental wild-type strain. Furthermore, RNA sequencing and whole-genome re-sequencing analyses revealed that core pathways, including photosynthesis, pH regulation/ion transport, and carbohydrate and fatty acid metabolism, were upregulated across all three evolved strains, though they exhibited different evolutionary trajectories. This study demonstrated the feasibility of recovering photosynthetic capability after acidic stress in the marine diatom P. tricornutum through ALE and provided molecular data to reveal essential alterations in genetic regulations that could enable cells to tolerate low environmental pH. [Display omitted] • Acidic pH significantly impaired the photosynthesis and growth of P. tricornutum. • Low-pH tolerance in P. tricornutum was improved through the adaptive laboratory evolution process. • Photosynthesis, pH regulation/ion transport, carbohydrate and fatty acid metabolism were upregulated in acid-adapted diatoms. • Whole genome resequencing showed distinct evolutionary trajectories among the evolved strains. [ABSTRACT FROM AUTHOR]

[Display omitted] • Historical DNA from museum specimens is a valuable source for phylogenomics. • Low-coverage WGS generates both mito- & nuclear-genome data from historical samples. • Large variation in data quality among modern and historical avian samples. • Agapornis ancestor colonized Madagascar from Australasia by trans -oceanic dispersal. • The common ancestor of Agapornis species was granivorous. Natural history collections contain specimens that provide important insights into studies of ecology and evolution. With the advancement of high-throughput sequencing, historical DNA (hDNA) from museum specimens has become a valuable source of genomic data to study the evolutionary history of organisms. Low-coverage whole genome sequencing (WGS) has been increasingly applied to museum specimens for analyzing organelle genomes, but is still uncommon for genotyping the nuclear DNA fraction. In this study, we applied low-coverage WGS to phylogenomic analyses of parrots in the genus Agapornis by including both modern samples and historical specimens of ∼100-year-old. Agapornis are small-sized African and Malagasy parrots with diverse characters. Earlier phylogenetic studies failed to resolve the positions of some key lineages, prohibiting a robust interpretation of the biogeography and evolution of these African parrots. Here, we demonstrated the use of low-coverage WGS for generating both mitochondrial and nuclear genomic data, and evaluated data quality differences between modern and historical samples. Our resolved Agapornis phylogeny indicates the ancestor of Agapornis likely colonized Madagascar from Australasia by trans -oceanic dispersal events before dispersing to the African continent. Genome-wide SNPs also allowed us to identify the parental origins of hybrid Agapornis individuals. This study demonstrates the potential of applying low-coverage WGS to phylogenomics and population genomics analyses and illustrates how including historical museum specimens can address outstanding questions regarding the evolutionary history of contemporary lineages. [ABSTRACT FROM AUTHOR]

• A weak phylogeographic sub-structure was observed within Colletotrichum acutatum species complex from rubber trees in China. • Genetic recombination is main patterns of genetic variation within Colletotrichum acutatum species complex from rubber trees in China. • Morphological characters and levels of aggressiveness between populations show significant differences. The Colletotrichum acutatum species complex possesses a diverse number of important traits, such as a wide host range and host preference, different modes of reproduction, and different strategies of host infection. Research using comparative genomics has attempted to find correlations between these traits. Here, we used multi-locus techniques and gene genealogical concordance analysis to investigate the phylogenetic relationships and taxonomic status of the Colletotrichum acutatum species complex using field isolates obtained from rubber trees. The results revealed that the dominant species was C. australisinense , followed by C. bannaense , while strain YNJH17109 was identified as C. laticiphilum. The taxonomic status of strains YNLC510 and YNLC511 was undetermined. Using whole-genome single nucleotide polymorphism data to analyze population structure, 18 strains of C. australisinense were subsequently divided into four populations, one of which was derived from an admixture of two populations. In addition, the strains LD1687, GD1628, and YNLC516, did not belong to any populations, and were considered to be admixtures of two or more populations. A split decomposition network analysis also provided evidence for genetic recombination within Colletotrichum acutatum species complex from rubber trees in China. Overall, a weak phylogeographic sub-structure was observed. Analysis also revealed significant differences in morphological characters and levels of virulence between populations. [ABSTRACT FROM AUTHOR]

The petal color of B. napus is usually yellow, but white, cream, golden yellow, orange, and other colors have also been reported. The pigmentation mechanisms and evolutionary processes of petal color in B. napus remain elusive. An analysis of the inheritance of the orange petal color (OPC) trait indicated that this trait was controlled by two recessive genes, termed Bnpc1 and Bnpc2. For fine mapping of the Bnpc1 gene, two backcrossing populations, BC4 and BC5, were developed from the cross between an OPC parent, X118, and a yellow petal color parent, R258. Whole-genome re-sequencing with bulked segregation analysis using BC4 individuals was conducted, and as a result, two major candidate intervals of Bnpc1 were identified on chromosome C09 of B. napus (C09: 1.000–5.464 and 6.491–7.777 Mb). Subsequently, the genetic and physical linkage maps were constructed for the BC5 population using 10 simple sequence repeat, two sequencecharacterized amplified region and 12 insertiondeletion (InDel) markers. The Bnpc1 gene was located in scaffold_38 on C09 of B. napus and flanked by Indel-31 and Indel-5, with genetic distances of 0.083 and 0.042 cM, respectively. The interval distance between the two markers was 151 kb (4.624–4.775 Mb) and was included in the first re-sequenced candidate region (C09: 1.000–5.464 Mb). The present study may facilitate cloning of the Bnpc1 gene as well as markerassisted selection for developing OPC B. napus varieties and revealing the mechanism of petal color formation in B. napus. [ABSTRACT FROM AUTHOR]

Heading date is one of the most important traits in rice breeding. It is governed by multiple genes, including known quantitative trait loci (QTLs). In general, almost all japonica cultivars, including Nipponbare, head early under short-day (SD) conditions, but some indica cultivars, including Kasalath, head late. To explain this difference, we identified QTLs controlling heading date under SD conditions. We used NILs, CSSLs, and BILs from a cross between Nipponbare and Kasalath, and evaluated days to heading (DTH) under SD conditions. No NILs or CSSLs showed late heading, but two BILs (BIL-55 and BIL-78) had almost the same DTH as Kasalath. We developed an F2 population from a cross between BIL-55 and Nipponbare and performed QTL analysis using SSR markers. The late-heading phenotype was controlled by two known genes and at least two novel QTLs on chromosomes 4 and 6, named qDTH4.5 and qDTH6.3. These QTLs were confirmed by QTL-seq. The QTLs and polymorphisms detected here will provide useful information for further genetic studies and breeding under SD conditions at lower latitudes. [ABSTRACT FROM AUTHOR]

Purple plants with higher anthocyanin content have attracted increasing attention in recent years due to their advantageous biological functions and nutritional value. A spontaneous mutant with purple leaves, designated 1280-1, was discovered in Brassica juncea line 1280. A previous genetic analysis indicated that the purple leaf trait in 1280-1 was controlled by a dominant gene (BjPl1). In the present study, an analysis of total anthocyanin content further indicated that the purple leaf trait was controlled by a complete dominance gene. According to a survey of 426 primers available from public resources, BjPl1 was assigned to linkage group B2 of B. juncea. In the early stage of this research, based on comparative mapping in Brassica, two simple sequence repeat (SSR) markers developed from A2 of B. rapa delimited the BjPl1 gene to a 0.7-cM genetic interval in the corresponding linkage map. According to information on the B. juncea genome released recently, the location of BjPl1 was further narrowed to a 225-kb interval (17.74–17.97 Mb). Within the target region, whole-genome re-sequencing identified two candidate regions (17.74–17.78 Mb and 17.93–17.96 Mb). Through Blast analysis of the two candidate intervals, four homologous anthocyanin biosynthetic genes were identified and localized to a 17.93–17.96 Mb interval of B2 (approximately 27 kb), which might include BjPl1. This work lays the foundation for the isolation of BjPl1 and will further improve our understanding of the molecular mechanisms of the anthocyanin metabolic pathway in Brassica. [ABSTRACT FROM AUTHOR]

Background: Microsatellite markers are widely used for estimating genetic diversity within and differentiation among populations. However, it has rarely been tested whether such estimates are useful proxies for genome-wide patterns of variation and differentiation. Here, we compared microsatellite variation with genome-wide single nucleotide polymorphisms (SNPs) to assess and quantify potential marker-specific biases and derive recommendations for future studies. Overall, we genotyped 180 Arabidopsis halleri individuals from nine populations using 20 microsatellite markers. Twelve of these markers were originally developed for Arabidopsis thaliana (cross-species markers) and eight for A. halleri (species-specific markers). We further characterized 2 million SNPs across the genome with a pooled whole-genome re-sequencing approach (Pool-Seq). Results: Our analyses revealed that estimates of genetic diversity and differentiation derived from cross-species and species-specific microsatellites differed substantially and that expected microsatellite heterozygosity (SSR-He) was not significantly correlated with genome-wide SNP diversity estimates (SNP-He and θWatterson) in A. halleri. Instead, microsatellite allelic richness (Ar) was a better proxy for genome-wide SNP diversity. Estimates of genetic differentiation among populations (FST) based on both marker types were correlated, but microsatellite-based estimates were significantly larger than those from SNPs. Possible causes include the limited number of microsatellite markers used, marker ascertainment bias, as well as the high variance in microsatellite-derived estimates. In contrast, genomewide SNP data provided unbiased estimates of genetic diversity independent of whether genome- or only exome-wide SNPs were used. Further, we inferred that a few thousand random SNPs are sufficient to reliably estimate genome-wide diversity and to distinguish among populations differing in genetic variation. Conclusions: We recommend that future analyses of genetic diversity within and differentiation among populations use randomly selected high-throughput sequencing-based SNP data to draw conclusions on genome-wide diversity patterns. In species comparable to A. halleri, a few thousand SNPs are sufficient to achieve this goal. [ABSTRACT FROM AUTHOR]

Detection of mutations at the whole-genome level is now possible by the use of high-throughput sequencing. However, determining mutations is a time-consuming process due to the number of false positives provided by mutation-detecting programs. AMAP (automated mutation analysis pipeline) was developed to overcome this issue. AMAP integrates a set of well-validated programs for mapping (BWA), removal of potential PCR duplicates (Picard), realignment (GATK) and detection of mutations (SAMtools, GATK, Pindel, BreakDancer and CNVnator). Thus, all types of mutations such as base substitution, deletion, insertion, translocation and chromosomal rearrangement can be detected by AMAP. In addition, AMAP automatically distinguishes false positives by comparing lists of candidate mutations in sequenced mutants. We tested AMAP by inputting already analyzed read data derived from three individual Arabidopsis thaliana mutants and confirmed that all true mutations were included in the list of candidate mutations. The result showed that the number of false positives was reduced to 12% of that obtained in a previous analysis that lacked a process of reducing false positives. Thus, AMAP will accelerate not only the analysis of mutation induction by individual mutagens but also the process of forward genetics. [ABSTRACT FROM AUTHOR]