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Flower color plays a crucial role in the appeal and selection of ornamental plants, directly influencing breeding strategies and the broader horticulture industry. Lantana camara , a widely favored flowering shrub, presents a rich palette of flower colors. Yet, the intricate molecular mechanisms governing this color variation in the species have remained largely unidentified. With the aim of filling this gap, this study embarked on a comprehensive de novo transcriptome assembly and differential gene expression analysis across 3 distinct lantana accessions, each showcasing a unique flower color. By harnessing the capabilities of both PacBio and Illumina sequencing platforms, a robust transcriptome assembly, encompassing 123,492 gene clusters and boasting 94.2% BUSCO completeness, was developed. The differential expression analysis unveiled 72,862 unique gene clusters that exhibited varied expression across different flower stages. A pronounced upregulation of 8 candidate core anthocyanin biosynthesis genes in the red-flowered accession was uncovered. This was further complemented by an upregulation of candidate MYB75 (PAP1) and bHLH42 (TT8) transcription factors. A candidate carotenoid cleavage dioxygenase (CCD4a) gene cluster also manifested a marked upregulation in white flowers. The study unveils the molecular groundwork of lantana's flower color variation, offering insights for future research and potential applications in breeding ornamental plants with desired color traits. [ABSTRACT FROM AUTHOR]

Legumes such as peanut (Arachis hypogea) can fulfill most of their nitrogen requirement by symbiotic association with nitrogen-fixing bacteria, rhizobia. Nutrient availability is largely determined by microbial diversity and activity in the rhizosphere that influences plant health, nutrition, and crop yield, as well as soil quality and soil fertility. However, our understanding of the complex effects of microbial diversity and rhizobia inoculation on crop yields of different peanut cultivars under organic versus conventional farming systems is extremely limited. In this research, we studied the impacts of conventional vs. organic cultivation practices and inoculation with commercial vs. single strain inoculum on peanut yield and soil microbial diversity of five peanut cultivars. The experiment was set up in the field following a split-split-plot design. Our results from the 16 S microbiome sequencing showed considerable variations of microbial composition between the cultivation types and inoculum, indicating a preferential association of microbes to peanut roots with various inoculum and cropping system. Alpha diversity indices (chao1, Shannon diversity, and Simpson index) of soil microbiome were generally higher in plots with organic than conventional inorganic practices. The cultivation type and inoculum explained significant differences among bacterial communities. Taxonomic classification revealed two phyla, TM6 and Firmicutes were significantly represented in inorganic as compared to organic soil, where significant phyla were Armatimonadetes, Gemmatimonadetes, Nitrospirae, Proteobacteria, Verrucomicrobia, and WS3. Yields in the organic cultivation system decreased by 10–93% of the yields in the inorganic cultivation system. Cultivar G06 and T511 consistently showed relative high yields in both organic and inorganic trials. Our results show significant two-way interactions between cultivation type and genotype for most of the trait data collected. Therefore, it is critical for farmers to choose varieties based on their cultivation practices. Our results showed that bacterial structure was more uniform in organic fields and microbial diversity in legumes was reduced in inorganic fields. This research provided guides for farmers and scientists to improve peanut yield while promoting microbial diversity and increasing sustainability. [ABSTRACT FROM AUTHOR]

Jatropha (Jatropha curcas L.) is an economically important species with a great potential for biodiesel production. To enrich the jatropha genomic databases and resources for microgravity studies, we sequenced and annotated the transcriptome of jatropha and developed SSR and SNP markers from the transcriptome sequences. In total 1,714,433 raw reads with an average length of 441.2 nucleotides were generated. De novo assembling and clustering resulted in 115,611 uniquely assembled sequences (UASs) including 21,418 full-length cDNAs and 23,264 new jatropha transcript sequences. The whole set of UASs were fully annotated, out of which 59,903 (51.81%) were assigned with gene ontology (GO) term, 12,584 (10.88%) had orthologs in Eukaryotic Orthologous Groups (KOG), and 8,822 (7.63%) were mapped to 317 pathways in six different categories in Kyoto Encyclopedia of Genes and Genome (KEGG) database, and it contained 3,588 putative transcription factors. From the UASs, 9,798 SSRs were discovered with AG/CT as the most frequent (45.8%) SSR motif type. Further 38,693 SNPs were detected and 7,584 remained after filtering. This UAS set has enriched the current jatropha genomic databases and provided a large number of genetic markers, which can facilitate jatropha genetic improvement and many other genetic and biological studies. [ABSTRACT FROM AUTHOR]

Abstract: Cotton fiber maturity, degree of secondary cell wall thickening relative to the perimeter, is one of the most important fiber quality and processing parameters of cotton. Immature fibers result in low dye uptake, increased fiber breakage, fabric defects, and waste. Because of that, breeders, cotton producers, spinners, and textile manufacturers desire cotton lint that is mature. However, fast and reliable methods to quantify maturity that fit into the current breeding and marketing systems are not available. The reference method to measure fiber maturity is the cross-section method, where 1μm thick fiber cross-sections are evaluated under a microscope. It is time consuming, tedious, and impractical for high volume measurement of fiber maturity. Interest is rising toward rapid routine instruments to measure fiber maturity such as the Advanced Fiber Information System (AFIS) and the cottonscope. The AFIS instrument individualizes and presents individual fibers to electro-optical sensors in order to measure fiber maturity while the cottonscope uses polarized light microscopy and image analysis to measure the maturity of fiber snippets. 104 reference cotton samples were tested with these three methods to assess the potential of these maturity measurements. Both AFIS and cottonscope maturity measurements show good correlations with the reference method. At this stage of our investigations it appears that the cottonscope may be faster than the AFIS and that its dynamic range is similar to that of the reference method. Both AFIS and cottonscope require a very small sample size (500mg for AFIS and 50mg for cottonscope). Therefore, both can be used in various cases where we only have access to a small sample (single boll sample for example). Nevertheless, obtaining a representative sample of the lint to be tested could be challenging. [Copyright &y& Elsevier]

Cowpea (Vigna unguiculata L. Walp) is a multipurpose crop widely cultivated in tropical and subtropical regions around the world. Characterizing cowpea phenotypes in germplasm collections is a crucial step to ensure future breeding efforts in the species. In this study, we estimated variance components and calculated genetic parameters for eight traits in 292 accessions from the University of California Riverside cowpea mini‐core collection, along with three lines released by the USDA, and seven cultivars. Broad‐sense heritability (H2) ranged from.21 to.83 for all accessions evaluated in Year 1, and from.16 to.83 for traits evaluated in 100 accessions during Year 2. Genotype × year correlations ranged from.45 to.99, illustrating consistency in phenotypic performance for some traits. Positive trait correlations were estimated for plant height and days to flowering, biomass at flowering (R1), and biomass at pod maturity (R6). Biomass at R1 and R6 were highly positively correlated. The USDA line US‐1137 showed high biomass production and can be used as forage and cover crop, whereas US‐1136, US 1138, and the cultivar Iron Clay showed superior traits as dual‐purpose (grain and/or fodder). Several accessions from the mini‐core outperformed cultivars and represent valuable genetic resources that can contribute to cowpea improvement. Moreover, these results showed that multiyear and/or multienvironment studies are needed to reliable select improved germplasm for agronomic traits. This study will provide cowpea breeders and geneticists with valuable phenotypic data to start new breeding efforts, and/or opportunities for gene discovery for key phenological and agronomic traits. Core Ideas: The UC‐Riverside mini‐core cowpea collection was phenotyped in Florida.Genetic parameters revealed large phenotypic diversity in this germplasm.Grain, forage, and multipurpose types were identified and selected.Accessions showed greater diversity than cowpea cultivars.The collection holds broad genetic diversity to improve cowpea productivity. [ABSTRACT FROM AUTHOR]

Napier grass is a tropical perennial C4 grass with superior biomass yield and quality. It is an important forage crop and a promising feedstock for lignocellulosic biofuel production. However, precise phenotyping and genotyping data to support the molecular breeding of Napier grass are scarce. A Napier grass F1 mapping population (segregating pseudo‐F2 population) was generated by hybridizing genetically distant parents (N190 × N122) with contrasting flowering‐time‐ and biomass‐related traits. True F1 hybrids were confirmed with a simple sequence repeat marker, vegetatively propagated, and phenotyped in replicate field plots for 2 years (2 harvests per year) in Citra, FL, USA (29.40N). Near‐normal distributions were observed for flowering date, plant height, number of tillers, stem diameter, and leaf width, confirming the quantitative nature of these traits. The annual dry biomass yield of F1 hybrids varied between 21.0 and 41.1 t ha−1. The highest‐yielding F1 hybrids showed remarkable hybrid vigor exceeding the annual biomass production of the highest‐yielding parental accession (26.9 t ha−1) by 52% and the biomass yield of the control "Merkeron" cultivar (29.2 t ha−1) by 41% over 2 years. F1 hybrids with delayed flowering time along with significantly increased biomass yield were also identified. Late‐flowering accessions allowed maximum biomass harvest before formation and dispersal of seeds, reducing invasion risk. The developed mapping population will be an excellent resource for identifying quantitative trait loci and candidate genes for flowering‐ and biomass‐related traits in Napier grass that will accelerate the improvement of this non‐domesticated bioenergy crop. [ABSTRACT FROM AUTHOR]

Fruit size is an important fruit quality trait that influences the production and commodity values of loquats (Eriobotrya japonica Lindl.). The Small Auxin Upregulated RNA (SAUR) gene family has proven to play a vital role in the fruit development of many plant species. However, it has not been comprehensively studied in a genome-wide manner in loquats, and its role in regulating fruit size remains unknown. In this study, we identified 95 EjSAUR genes in the loquat genome. Tandem duplication and segmental duplication contributed to the expansion of this gene family in loquats. Phylogenetic analysis grouped the SAURs from Arabidopsis, rice, and loquat into nine clusters. By analyzing the transcriptome profiles in different tissues and at different fruit developmental stages and comparing two sister lines with contrasting fruit sizes, as well as by functional predictions, a candidate gene (EjSAUR22) highly expressed in expanding fruits was selected for further functional investigation. A combination of Indoleacetic acid (IAA) treatment and virus-induced gene silencing revealed that EjSAUR22 was not only responsive to auxin, but also played a role in regulating cell size and fruit expansion. The findings from our study provide a solid foundation for understanding the molecular mechanisms controlling fruit size in loquats, and also provide potential targets for manipulation of fruit size to accelerate loquat breeding. [ABSTRACT FROM AUTHOR]

An interspecific peanut hybrid population was generated from a cross between Arachis diogoi, a wild species with resistance to spotted wilt, and "Gregory", a susceptible cultivar. The objectives of the study are to identify successful introgression of A. diogoi's genome and to evaluate the spotted wilt resistance in the introgression population. Sixty‐three putative introgression lines were genotyped using 137 polymorphic simple sequence repeat markers, out of which 14 markers located on seven of the 20 peanut chromosomes showed introgression of A. diogoi genome into at least one of the introgression lines. In addition, genotyping by sequencing of a subset of the population revealed SNP loci displaying introgression of A. diogoi genome on every chromosome of the A sub‐genome of the introgression lines, with the most introgressed loci on chromosome A05. Several introgression lines showed consistent spotted wilt resistance, suggesting successful genomic introgression of A. diogoi contributing to the resistance. [ABSTRACT FROM AUTHOR]

Summary: Sugarcane (Saccharum spp.) is a highly energy‐efficient crop primarily for sugar and bio‐ethanol production. Sugarcane genetics and cultivar improvement have been extremely challenging largely due to its complex genomes with high polyploidy levels. In this study, we deeply sequenced the coding regions of 307 sugarcane germplasm accessions. Nearly five million sequence variations were catalogued. The average of 98× sequence depth enabled different allele dosages of sequence variation to be differentiated in this polyploid collection. With selected high‐quality genome‐wide SNPs, we performed population genomic studies and environmental association analysis. Results illustrated that the ancient sugarcane hybrids, S. barberi and S. sinense, and modern sugarcane hybrids are significantly different in terms of genomic compositions, hybridization processes and their potential ancestry contributors. Linkage disequilibrium (LD) analysis showed a large extent of LD in sugarcane, with 962.4 Kbp, 2739.2 Kbp and 3573.6 Kbp for S. spontaneum, S. officinarum and modern S. hybrids respectively. Candidate selective sweep regions and genes were identified during domestication and historical selection processes of sugarcane in addition to genes associated with environmental variables at the original locations of the collection. This research provided an extensive amount of genomic resources for sugarcane community and the in‐depth population genomic analyses shed light on the breeding and evolution history of sugarcane, a highly polyploid species. [ABSTRACT FROM AUTHOR]

Enabled by the next generation sequencing, target enrichment sequencing (TES) is a powerful method to enrich genomic regions of interest and to identify sequence variations. The objective of this study was to explore the feasibility of probe design from transcript sequences for TES application in calling sequence variants in peanut, an important allotetraploid crop with a large genome size. In this study, we applied an in-solution hybridization method to enrich DNA sequences of seven peanut genotypes. Our results showed that it is feasible to apply TES with probes designed from transcript sequences in polyploid peanut. Using a set of 31,123 probes, a total of 5131 and 7521 genes were targeted in peanut A and B genomes, respectively. For each genotype used in this study, the probe target capture regions were efficiently covered with high depth. The average on-target rate of sequencing reads was 42.47%, with a significant amount of off-target reads coming from genomic regions homologous to target regions. In this study, when given predefined genomic regions of interest and the same amount of sequencing data, TES provided the highest coverage of target regions when compared to whole genome sequencing, RNA sequencing, and genotyping by sequencing. Single nucleotide polymorphism (SNP) calling and subsequent validation revealed a high validation rate (85.71%) of homozygous SNPs, providing valuable markers for peanut genotyping. This study demonstrated the success of applying TES for SNP identification in peanut, which shall provide valuable suggestions for TES application in other non-model species without a genome reference available. [ABSTRACT FROM AUTHOR]

Background: Sugarcane (Saccharum spp.) is one of the most important economic crops because of its high sugar production and biofuel potential. Due to the high polyploid level and complex genome of sugarcane, it has been a huge challenge to investigate genomic sequence variations, which are critical for identifying alleles contributing to important agronomic traits. In order to mine the genetic variations in sugarcane, genotyping by sequencing (GBS), was used to genotype 14 representative Saccharum complex accessions. GBS is a method to generate a large number of markers, enabled by next generation sequencing (NGS) and the genome complexity reduction using restriction enzymes. Results: To use GBS for high throughput genotyping highly polyploid sugarcane, the GBS analysis pipelines in 14 Saccharum complex accessions were established by evaluating different alignment methods, sequence variants callers, and sequence depth for single nucleotide polymorphism (SNP) filtering. By using the established pipeline, a total of 76,251 non-redundant SNPs, 5642 InDels, 6380 presence/absence variants (PAVs), and 826 copy number variations (CNVs) were detected among the 14 accessions. In addition, non-reference based universal network enabled analysis kit and Stacks de novo called 34,353 and 109,043 SNPs, respectively. In the 14 accessions, the percentages of single dose SNPs ranged from 38.3% to 62.3% with an average of 49.6%, much more than the portions of multiple dosage SNPs. Concordantly called SNPs were used to evaluate the phylogenetic relationship among the 14 accessions. The results showed that the divergence time between the Erianthus genus and the Saccharum genus was more than 10 million years ago (MYA). The Saccharum species separated from their common ancestors ranging from 0.19 to 1.65 MYA. Conclusions: The GBS pipelines including the reference sequences, alignment methods, sequence variant callers, and sequence depth were recommended and discussed for the Saccharum complex and other related species. A large number of sequence variations were discovered in the Saccharum complex, including SNPs, InDels, PAVs, and CNVs. Genome-wide SNPs were further used to illustrate sequence features of polyploid species and demonstrated the divergence of different species in the Saccharum complex. The results of this study showed that GBS was an effective NGS-based method to discover genomic sequence variations in highly polyploid and heterozygous species. [ABSTRACT FROM AUTHOR]

The molecular mechanisms of symbiosis in cultivated peanut with a 'crack entry' infection process are largely understudied. In this study, we investigated the root transcriptional profiles of two pairs of non-nodulating (nod−) and nodulating (nod+) sister inbred peanut lines, E4/E5 and E7/E6, and their nod+ parents, F487A and PI262090 during rhizobial infection and nodule initiation by using RNA-seq technology. A total of 143, 101, 123, 215, 182, and 289 differentially expressed genes (DEGs) were identified in nod− E4, E7 and nod+ E5, E6, F487A, and PI262090 after inoculation with Bradyrhizobium sp. Different deficiencies at upstream of symbiotic signaling pathway were revealed in the two nod− genotypes. DEGs specific in nod+ genotypes included orthologs to some known symbiotic signaling pathway genes, such as NFR5, NSP2, NIN, ERN1, and many other novel and/or functionally unknown genes. Gene ontology (GO) enrichment analysis of nod+ specific DEGs revealed 54 significantly enriched GO terms, including oxidation-reduction process, metabolic process, and catalytic activity. Genes related with plant defense systems, hormone biosynthesis and response were particularly enriched. To our knowledge, this is the first report revealing symbiosis-related genes in a genome-wide manner in peanut representative of the 'crack entry' species. [ABSTRACT FROM AUTHOR]