Despite recent progress in crop genomics studies,the genomic changes brought about by modern breeding selection are still poorly understood,thus hampering genomics-assisted breeding,especially in polyploid crops with ...Despite recent progress in crop genomics studies,the genomic changes brought about by modern breeding selection are still poorly understood,thus hampering genomics-assisted breeding,especially in polyploid crops with compound genomes such as common wheat(Triticum aestivum).In this work,we constructed genome resources for the modern elite common wheat variety Aikang 58(AK58).Comparative genomics between AK58 and the landrace cultivar Chinese Spring(CS)shed light on genomic changes that occurred through recent varietal improvement.We also explored subgenome diploidization and divergence in common wheat and developed a homoeologous locus-based genome-wide association study(HGWAS)approach,which was more effective than single homoeolog-based GWAS in unraveling agronomic trait-associated loci.A total of 123 major HGWAs loci were detected using a genetic population derived from AK58 and cs.Elite homoeologous haplotypes(HHs),formed by combinations of subgenomic homoeologs of the associated loci,were found in both parents and progeny,and many could substantially improve wheat yield and related traits.We built a website where users can download genome assembly sequence and annotation data for AK58,perform blast analysis,and run JBrowse.Our work enriches genome resources for wheat,provides new insights into genomic changes during modern wheat improve-.ment,and suggests that efficientmining of elite HHs can make a substantial contribuutionto genomics-assisted breeding in common wheat and other polyploid crops.展开更多
The centromere is the region of a chromosome that directs its separation and plays an important role in cell division and reproduction of organisms.Elucidating the dynamics of centromeres is an alternative strategy fo...The centromere is the region of a chromosome that directs its separation and plays an important role in cell division and reproduction of organisms.Elucidating the dynamics of centromeres is an alternative strategy for exploring the evolution of wheat.Here,we comprehensively analyzed centromeres from the de novoassembled common wheat cultivar Aikang58(AK58),Chinese Spring(CS),and all sequenced diploid and tetraploid ancestors by chromatin immunoprecipitation sequencing,whole-genome bisulfite sequencing,RNA sequencing,assay for transposase-accessible chromatin using sequencing,and comparative genomics.We found that centromere-associated sequences were concentrated during tetraploidization and hexaploidization.Centromeric repeats of wheat(CRWs)have undergone expansion during wheat evolution,with strong interweaving between the A and B subgenomes post tetraploidization.We found that CENH3 prefers to bind with younger CRWs,as directly supported by immunocolocalization on two chromosomes(1A and 2A)of wild emmer wheat with dicentromeric regions,only one of which bound with CENH3.In a comparison of AK58 with CS,obvious centromere repositioning was detected on chromosomes 1B,3D,and 4D.The active centromeres showed a unique combination of lower CG but higher CHH and CHG methylation levels.We also found that centromeric chromatin was more open than pericentromeric chromatin,with higher levels of gene expression but lower gene density.Frequent introgression between tetraploid and hexaploid wheat also had a strong influence on centromere position on the same chromosome.This study also showed that active wheat centromeres were genetically and epigenetically determined.展开更多
基金the Collaborative Innovation Center for Henan Grain Crops,the Ministry of Science and Technology of the People's Republic of China(2021YFF1000200)the National Natural Science Foundation of China(Major Program,31991213)+4 种基金the Central Publicinterest Scientific Institution Basal Research Fund(Y2021YJ01)the Major Public Welfare Projects of Henan Province(201300110800)the Key Research and Development Program of China(2016YFD0100102)the CAAS Agricultural Science and Technology Innovation Program(CAASZDRW202002)the seed innovation program of the Ministry of Agriculture and Rural Affairs of China,and the Henan Provincial R&D Projects of Interregional Cooperation for Local Scientific and Technological Development Guided by the Central Government(YDZX20214100004191).
文摘Despite recent progress in crop genomics studies,the genomic changes brought about by modern breeding selection are still poorly understood,thus hampering genomics-assisted breeding,especially in polyploid crops with compound genomes such as common wheat(Triticum aestivum).In this work,we constructed genome resources for the modern elite common wheat variety Aikang 58(AK58).Comparative genomics between AK58 and the landrace cultivar Chinese Spring(CS)shed light on genomic changes that occurred through recent varietal improvement.We also explored subgenome diploidization and divergence in common wheat and developed a homoeologous locus-based genome-wide association study(HGWAS)approach,which was more effective than single homoeolog-based GWAS in unraveling agronomic trait-associated loci.A total of 123 major HGWAs loci were detected using a genetic population derived from AK58 and cs.Elite homoeologous haplotypes(HHs),formed by combinations of subgenomic homoeologs of the associated loci,were found in both parents and progeny,and many could substantially improve wheat yield and related traits.We built a website where users can download genome assembly sequence and annotation data for AK58,perform blast analysis,and run JBrowse.Our work enriches genome resources for wheat,provides new insights into genomic changes during modern wheat improve-.ment,and suggests that efficientmining of elite HHs can make a substantial contribuutionto genomics-assisted breeding in common wheat and other polyploid crops.
基金supported by funding from the National Key Research and Development Program of China(2022YFF1003402)the China Natural Science Foundation(31371622)the CAAS Innovation Program.
文摘The centromere is the region of a chromosome that directs its separation and plays an important role in cell division and reproduction of organisms.Elucidating the dynamics of centromeres is an alternative strategy for exploring the evolution of wheat.Here,we comprehensively analyzed centromeres from the de novoassembled common wheat cultivar Aikang58(AK58),Chinese Spring(CS),and all sequenced diploid and tetraploid ancestors by chromatin immunoprecipitation sequencing,whole-genome bisulfite sequencing,RNA sequencing,assay for transposase-accessible chromatin using sequencing,and comparative genomics.We found that centromere-associated sequences were concentrated during tetraploidization and hexaploidization.Centromeric repeats of wheat(CRWs)have undergone expansion during wheat evolution,with strong interweaving between the A and B subgenomes post tetraploidization.We found that CENH3 prefers to bind with younger CRWs,as directly supported by immunocolocalization on two chromosomes(1A and 2A)of wild emmer wheat with dicentromeric regions,only one of which bound with CENH3.In a comparison of AK58 with CS,obvious centromere repositioning was detected on chromosomes 1B,3D,and 4D.The active centromeres showed a unique combination of lower CG but higher CHH and CHG methylation levels.We also found that centromeric chromatin was more open than pericentromeric chromatin,with higher levels of gene expression but lower gene density.Frequent introgression between tetraploid and hexaploid wheat also had a strong influence on centromere position on the same chromosome.This study also showed that active wheat centromeres were genetically and epigenetically determined.