Despite the large number of genomic and transcriptomic resources in maize, there is still much to learn about the function of genes in developmental and biochemical processes. Some maize mutants that were generated by...Despite the large number of genomic and transcriptomic resources in maize, there is still much to learn about the function of genes in developmental and biochemical processes. Some maize mutants that were generated by gamma-irradiation showed clear segregation for the kernel phenotypes in B73 ? Mo17 F2 ears. To better understand the functional genomics of kernel development,we developed a mapping and gene identi?cation pipeline, bulked segregant exome sequencing(BSEx-seq), to map mutants with kernel phenotypes including opaque endosperm and reduced kernel size. BSEx-seq generates and compares the sequence of the exon fraction from mutant and normal plant F2 DNA pools. The comparison can derive mapping peaks, identify deletions within the mapping peak, and suggest candidate genes within the deleted regions. We then used the public kernel-speci?c expression data to narrow down the list of candidate genes/mutations and identi?ed deletions ranging from several kb to more than 1 Mb. A full deletion allele of the Opaque-2 gene was identi?ed in mutant 531, which occurs within a $200-kb deletion. Opaque mutant 1486 has a 6248-bp deletion in the mapping interval containing two candidate genes encoding RNA-directed DNA methylation 4(RdDM4) and AMP-binding protein, respectively. This study demonstrates the ef?-ciency and cost-effectiveness of BSEx-seq for causal mutation mapping and candidate gene selection,providing a new option in mapping-by-sequencing for maize functional genomics studies.展开更多
Barley(Hordeum vulgare ssp.vulgare)is one of the first crops to be domesticated and is adapted to a wide range of environments.Worldwide barley germplasm collections possess valuable allelic variations that could furt...Barley(Hordeum vulgare ssp.vulgare)is one of the first crops to be domesticated and is adapted to a wide range of environments.Worldwide barley germplasm collections possess valuable allelic variations that could further improve barley productivity.Although barley genomics has offered a global picture of allelic variation among varieties and its association with various agronomic traits,polymorphisms from East Asian varieties remain scarce.In this study,we analyze exome polymorphisms in a panel of 274 barley varieties collected worldwide,including 137 varieties from East Asian countries and Ethiopia.We reveal the underlying population structure and conduct genome-wide association studies for 10 agronomic traits.Moreover,we examin genome-wide associations for traits related to grain size such as awn length and glume length.Our results demonstrate the value of diverse barley germplasm panels containing Eastern varieties,highlighting their distinct genomic signatures relative to Western subpopulations.展开更多
基金supported by the Agriculture and Food Research Initiative competitive grant (Grant No.2013-02278)the United States Department of Agriculture,National Institute of Food and Agriculture (USDA-NIFA)Center for Plant Science Innovation Program of Excellence and Department of Agronomy and Horticulture,University of NebraskaLincoln,United States
文摘Despite the large number of genomic and transcriptomic resources in maize, there is still much to learn about the function of genes in developmental and biochemical processes. Some maize mutants that were generated by gamma-irradiation showed clear segregation for the kernel phenotypes in B73 ? Mo17 F2 ears. To better understand the functional genomics of kernel development,we developed a mapping and gene identi?cation pipeline, bulked segregant exome sequencing(BSEx-seq), to map mutants with kernel phenotypes including opaque endosperm and reduced kernel size. BSEx-seq generates and compares the sequence of the exon fraction from mutant and normal plant F2 DNA pools. The comparison can derive mapping peaks, identify deletions within the mapping peak, and suggest candidate genes within the deleted regions. We then used the public kernel-speci?c expression data to narrow down the list of candidate genes/mutations and identi?ed deletions ranging from several kb to more than 1 Mb. A full deletion allele of the Opaque-2 gene was identi?ed in mutant 531, which occurs within a $200-kb deletion. Opaque mutant 1486 has a 6248-bp deletion in the mapping interval containing two candidate genes encoding RNA-directed DNA methylation 4(RdDM4) and AMP-binding protein, respectively. This study demonstrates the ef?-ciency and cost-effectiveness of BSEx-seq for causal mutation mapping and candidate gene selection,providing a new option in mapping-by-sequencing for maize functional genomics studies.
基金supported by a Grant-in-Aid for Scientific Research(B)(grant no.15KT0038 to K.M.)a Grant-in-Aid for Scientific Research(C)(grant no.19K11861 to K.M.and R.N.)of the Japan Society for the Promotion of Scienceby CREST(grant no.JPMJCR16O4 to K.M.)of the Japan Science and Technology Agency。
文摘Barley(Hordeum vulgare ssp.vulgare)is one of the first crops to be domesticated and is adapted to a wide range of environments.Worldwide barley germplasm collections possess valuable allelic variations that could further improve barley productivity.Although barley genomics has offered a global picture of allelic variation among varieties and its association with various agronomic traits,polymorphisms from East Asian varieties remain scarce.In this study,we analyze exome polymorphisms in a panel of 274 barley varieties collected worldwide,including 137 varieties from East Asian countries and Ethiopia.We reveal the underlying population structure and conduct genome-wide association studies for 10 agronomic traits.Moreover,we examin genome-wide associations for traits related to grain size such as awn length and glume length.Our results demonstrate the value of diverse barley germplasm panels containing Eastern varieties,highlighting their distinct genomic signatures relative to Western subpopulations.
