Identification and validation of QTLs for green plant percentage in barley (Hordeum vulgare L.) anther culture

The original version is available at: http://www.springerlink.com/content/688481281g18035q/fulltext.pdfIn cereals, albinism is a major obstacle to produce doubled haploids (DH) for breeding programs. In order to identify QTLs for green plant percentage in barley anther culture, a specific population was developed. This population, consisting of 100 DH lines, was generated by crossing the model cultivar for anther culture “Igri” with an albino-producing DH line (DH46) selected from Igri x Dobla, in search of a maximum segregation for the trait and minimum for the other anther culture variables. A combination of bulked segregant analysis and AFLP methodology was used to identify markers linked to the trait. A linkage map was constructed using these AFLPs, together with RAPD, STS and SSR markers. This study identified a new QTL for green plant percentage on chromosome 3H and confirmed the previously reported one on chromosome 5H. Up to 65.2% of the phenotypic variance for this trait was explained by the additive effects of these two QTLs. Thirty elite cultivars of barley from different origin, row type, growth habit and end use, were selected to validate these QTLs. Since two of the markers linked to the QTLs were AFLPs, we successfully converted them into simple PCR-based SCAR markers. Only the SSR HVM60, on chromosome 3H, was significantly associated with the trait, explaining near 20% of the phenotypic variance. Among the allelic variants identified for this marker, HVM60-120bp was associated with the highest values of green plant percentage.M. Muñoz-Amatriaín and X-W Chen were recipients of a fellowship from Ministry of Education and Science of Spain. The research was supported by Projects AGL2001-1631 and AGL2004-03396 from Plan Nacional de Recursos y Tecnologías Agroalimentarias of Spain.Peer reviewe

Transcriptome analysis of barley anthers: effect of mannitol treatment on microspore embryogenesis

The definitive version is available at: http://www.blackwell-synergy.com/doi/full/10.1111/j.1399-3054.2006.00729.xCarbohydrate starvation is an efficient stress treatment for induction of microspore embryogenesis. Transcriptome analysis of anthers response to mannitol treatment using the 22k Barley1 GeneChip revealed large changes in gene expression. Statistical analysis and filtering for 4-fold or greater changes resulted in 2,673 genes, of which 887 were up-regulated and 1,786 down-regulated. Great differences in some metabolic pathways, accompanied by a multi-dimensional stress response were found. Analysis of transcription factors showed that most of the down-regulated transcription factors were related to growth and development, and the up-regulated with abiotic and biotic stress responses and changes in developmental programs. Interestingly, the expression of most cell cycle related genes did not change significantly. Transcriptome analysis provided a successful approach to identify genes involved in mannitol treatment, essential for triggering microspore embryogenesis.María Muñoz-Amatriaín is recipient of a FPI fellowship and a Short-term Scientific Mission to UCR, from Ministerio de Educación y Ciencia of Spain. The research was supported by Projects AGL-2001-1631 and AGL-2004-03396, from Plan Nacional I+D+I, Ministerio de Educación y Ciencia of Spain.Peer reviewe

Genomic regions, cellular components and gene regulatory basis underlying pod length variations in cowpea (V. unguiculata L. Walp).

Cowpea (V. unguiculata L. Walp) is a climate resilient legume crop important for food security. Cultivated cowpea (V. unguiculata L) generally comprises the bushy, short-podded grain cowpea dominant in Africa and the climbing, long-podded vegetable cowpea popular in Asia. How selection has contributed to the diversification of the two types of cowpea remains largely unknown. In the current study, a novel genotyping assay for over 50 000 SNPs was employed to delineate genomic regions governing pod length. Major, minor and epistatic QTLs were identified through QTL mapping. Seventy-two SNPs associated with pod length were detected by genome-wide association studies (GWAS). Population stratification analysis revealed subdivision among a cowpea germplasm collection consisting of 299 accessions, which is consistent with pod length groups. Genomic scan for selective signals suggested that domestication of vegetable cowpea was accompanied by selection of multiple traits including pod length, while the further improvement process was featured by selection of pod length primarily. Pod growth kinetics assay demonstrated that more durable cell proliferation rather than cell elongation or enlargement was the main reason for longer pods. Transcriptomic analysis suggested the involvement of sugar, gibberellin and nutritional signalling in regulation of pod length. This study establishes the basis for map-based cloning of pod length genes in cowpea and for marker-assisted selection of this trait in breeding programmes

Identification of QTL controlling domestication-related traits in cowpea (Vigna unguiculata L. Walp)

[EN] Cowpea (Vigna unguiculata L. Walp) is a warm-season legume with a genetically diverse gene-pool composed of wild and cultivated forms. Cowpea domestication involved considerable phenotypic changes from the wild progenitor, including reduction of pod shattering, increased organ size, and changes in flowering time. Little is known about the genetic basis underlying these changes. In this study, 215 recombinant inbred lines derived from a cross between a cultivated and a wild cowpea accession were used to evaluate nine domestication-related traits (pod shattering, peduncle length, flower color, days to flowering, 100-seed weight, pod length, leaf length, leaf width and seed number per pod). A high-density genetic map containing 17,739 single nucleotide polymorphisms was constructed and used to identify 16 quantitative trait loci (QTL) for these nine traits. Based on annotations of the cowpea reference genome, genes within these regions are reported. Four regions with clusters of QTL were identified, including one on chromosome 8 related to increased organ size. This study provides new knowledge of the genomic regions controlling domestication-related traits in cowpea as well as candidate genes underlying those QTL. This information can help to exploit wild relatives in cowpea breeding programsSIThis work was supported by grants from the Generation Challenge Program (TL1), the Feed the Future Innovation Lab for Climate Resilient Cowpea (Cooperative Agreement AID-OAA-A-13-00070), and the NSF BREAD project “Advancing the Cowpea Genome for Food Security’’ (Award #1543963)’’. Partial support was also provided by the Hatch Project CA-R-BPS-5306-H. Sassoum Lo was supported by funds from the West Africa Agricultural Productivity Program. We thank the International Institute of Tropical Agriculture for the RIL population. We also thank Abdou Souleymane (INRA, Niger) for helping to identify the wild parent, Stefano Lonardi and Steve Wanamaker (University of California Riverside, USA) for the cowpea genome sequence and annotations, and Dr. Paul Gepts (University of California Davis, USA) for his valuable input

Distribution, functional impact, and origin mechanisms of copy number variation in the barley genome

BACKGROUND There is growing evidence for the prevalence of copy number variation (CNV) and its role in phenotypic variation in many eukaryotic species. Here we use array comparative genomic hybridization to explore the extent of this type of structural variation in domesticated barley cultivars and wild barleys. RESULTS A collection of 14 barley genotypes including eight cultivars and six wild barleys were used for comparative genomic hybridization. CNV affects 14.9% of all the sequences that were assessed. Higher levels of CNV diversity are present in the wild accessions relative to cultivated barley. CNVs are enriched near the ends of all chromosomes except 4H, which exhibits the lowest frequency of CNVs. CNV affects 9.5% of the coding sequences represented on the array and the genes affected by CNV are enriched for sequences annotated as disease-resistance proteins and protein kinases. Sequence-based comparisons of CNV between cultivars Barke and Morex provided evidence that DNA repair mechanisms of double-strand breaks via single-stranded annealing and synthesis-dependent strand annealing play an important role in the origin of CNV in barley. CONCLUSIONS We present the first catalog of CNVs in a diploid Triticeae species, which opens the door for future genome diversity research in a tribe that comprises the economically important cereal species wheat, barley, and rye. Our findings constitute a valuable resource for the identification of CNV affecting genes of agronomic importance. We also identify potential mechanisms that can generate variation in copy number in plant genomes.This work was financially supported by the following grants: project GABI-BARLEX, German Federal Ministry of Education and Research (BMBF), #0314000 to MP, US, KFXM and NS; Triticeae Coordinated Agricultural Project, USDA-NIFA #2011-68002-30029 to GJM; and Agriculture and Food Research Initiative Plant Genome, Genetics and Breeding Program of USDA’s Cooperative State Research and Extension Service, #2009-65300- 05645 to GJM

Genetic diversity and structure of Iberian Peninsula cowpeas compared to world-wide cowpea accessions using high density SNP markers

Cowpea (Vigna unguiculata L. Walp) is an important legume crop due to its high protein content, adaptation to heat and drought and capacity to fix nitrogen. Europe has a deficit of cowpea production. Knowledge of genetic diversity among cowpea landraces is important for the preservation of local varieties and is the basis to obtain improved varieties. The aims of this study were to explore diversity and the genetic structure of a set of Iberian Peninsula cowpea accessions in comparison to a worldwide collection and to infer possible dispersion routes of cultivated cowpea.This study was supported by EUROLEGUME project. This project has received funding from the European Union’s Seventh Framework Programme for research, technological development and demonstration under grant agreement no 613781. European Investment Funds by FEDER/COMPETE/ POCI – Operational Competitiveness and Internationalization Programme, under Project POCI-01-0145-FEDER-006958 and National Funds by FCT – Portuguese Foundation for Science and Technology, under the project UID/AGR/04033/2013. MMA was partially supported by the Feed the Future Innovation Lab for Climate Resilient Cowpea (USAID Cooperative Agreement AID-OAA-A-13-00070), which is directed by TJC. The funding entities had no role in the design of the study, collection, analysis and interpretation of data, or in writing the manuscript.info:eu-repo/semantics/publishedVersio

Distribution, functional impact, and origin mechanisms of copy number variation in the barley genome

BACKGROUND: There is growing evidence for the prevalence of copy number variation (CNV) and its role in phenotypic variation in many eukaryotic species. Here we use array comparative genomic hybridization to explore the extent of this type of structural variation in domesticated barley cultivars and wild barleys. RESULTS: A collection of 14 barley genotypes including eight cultivars and six wild barleys were used for comparative genomic hybridization. CNV affects 14.9% of all the sequences that were assessed. Higher levels of CNV diversity are present in the wild accessions relative to cultivated barley. CNVs are enriched near the ends of all chromosomes except 4H, which exhibits the lowest frequency of CNVs. CNV affects 9.5% of the coding sequences represented on the array and the genes affected by CNV are enriched for sequences annotated as disease-resistance proteins and protein kinases. Sequence-based comparisons of CNV between cultivars Barke and Morex provided evidence that DNA repair mechanisms of double-strand breaks via single-stranded annealing and synthesis-dependent strand annealing play an important role in the origin of CNV in barley. CONCLUSIONS: We present the first catalog of CNVs in a diploid Triticeae species, which opens the door for future genome diversity research in a tribe that comprises the economically important cereal species wheat, barley, and rye. Our findings constitute a valuable resource for the identification of CNV affecting genes of agronomic importance. We also identify potential mechanisms that can generate variation in copy number in plant genomes

Genetic basis of barley contributions to beer flavor

13 Pags.- 1 Fig.- 3 Tabls. © 2022 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY-NC-ND license.Barley malt is critical for the malting, brewing, and distilling industries, as it is one of the main ingredients of beer and some types of spirits. There is growing evidence that barley genotype - via malt - can impact the flavors of beers and spirits. However, information on the barley genes involved in these flavors is lacking. Therefore, we used quantitative trait locus (QTL) mapping of malt quality traits, beer sensory descriptors and metabolic compounds on a biparental population of doubled haploids derived from the cross of the cultivars Golden Promise and Full Pint. Putative candidate genes for QTLs were identified by alignment with the reference barley genome sequence. There were thirty-seven QTLs across all chromosomes except 4H, with three QTL clusters located on 3H (1 cluster) and 5H (2 clusters: mid-5H and end-5H). Those “hotspots” contained QTLs for multiple phenotypes. Several candidate genes that regulate plant metabolism were identified within the QTLs and included HvAlaAT, HvDep1, HvMKK3, HvGA20ox1 and HvGA20ox2. These genes are involved in seed dormancy and plant height. Alleles at these loci, and perhaps at physically linked loci, can have key downstream effects on malting quality, beer flavor, and abundance of volatile metabolites.Research at Oregon State University was supported by the Agricultural Research Foundation Barley Progress Fund. At Colorado State University, research was supported by CSU's College of Agricultural Sciences, with partial support from the American Malting Barley Association.Peer reviewe