Understanding the role of heterotic genes in contributing to heterosis is essential for advancing hybrid breeding.We analyzed plant height(PH),ear height(EH),and transcriptomic data from a maize hybrid pop-ulation.Gen...Understanding the role of heterotic genes in contributing to heterosis is essential for advancing hybrid breeding.We analyzed plant height(PH),ear height(EH),and transcriptomic data from a maize hybrid pop-ulation.Genome-wide association studies(GWASs)revealed that dominance effects of quantitative trait loci(QTLs)play a significant role in hybrid traits and mid-parent heterosis.By integrating GWAS,expression GWAS(eGWAS),and module eGWAS analysis,we prioritized six candidate heterotic genes underlying six QTLs,including one QTL that spans the bZIP29 gene.In the hybrid population,bZIP29 exhibits additive expression and dominance effects for both hybrid traits and mid-parent heterosis,with its favorable allele correlating positively with PH and EH.bZIP29 demonstrates dominance or over-dominance patterns in hy-brids derived from crosses between transgenic and wild-type lines,contingent upon its expression.A tsCUT&Tag assay revealed that bZIP29 protein binds directly to a gene regulated by its associated expres-sion QTL(eQTL)and six genes within expression modules governed by its associated module-eQTLs(meQTLs).Regulatory networks involving bZIP29 are more extensive in hybrid subpopulations than in the parental population.This study offers insights into key heterotic genes and networks that underpin the robust growth of hybrid maize.展开更多
Innovations in genomics have enabled the development of low-cost,high-resolution,single nucleotide polymorphism(SNP)genotyping arrays that accelerate breeding progress and support basic research in crop science.Here,w...Innovations in genomics have enabled the development of low-cost,high-resolution,single nucleotide polymorphism(SNP)genotyping arrays that accelerate breeding progress and support basic research in crop science.Here,we developed and validated the Soy SNP618 K array(618,888 SNPs)for the important crop soybean.The SNPs were selected from whole-genome resequencing data containing 2,214 diverse soybean accessions;29.34%of the SNPs mapped to genic regions representing 86.85%of the 56,044annotated high-confidence genes.Identity-by-state analyses of 318 soybeans revealed 17 redundant accessions,highlighting the potential of the Soy SNP618 K array in supporting gene bank management.The patterns of population stratification and genomic regions enriched through domestication were highly consistent with previous findings based on resequencing data,suggesting that the ascertainment bias in the Soy SNP618 K array was largely compensated for.Genome-wide association mapping in combination with reported quantitative trait loci enabled fine-mapping of genes known to influence flowering time,E2 and Gm PRR3 b,and of a new candidate gene,Gm VIP5.Moreover,genomic prediction of flowering and maturity time in 502 recombinant inbred lines was highly accurate(>0.65).Thus,the Soy SNP618 K array is a valuable genomic tool that can be used to address many questions in applied breeding,germplasm management,and basic crop research.展开更多
基金supported by the National Key R&D Program of China(2023YFF1000400)the Biological Breeding-National Science and Technology Major Project(2023ZD04076)+1 种基金the China Agriculture Research System of Maize(CARS-02-13)the Innovation Program of the Chinese Academy of Agricultural Sciences.
文摘Understanding the role of heterotic genes in contributing to heterosis is essential for advancing hybrid breeding.We analyzed plant height(PH),ear height(EH),and transcriptomic data from a maize hybrid pop-ulation.Genome-wide association studies(GWASs)revealed that dominance effects of quantitative trait loci(QTLs)play a significant role in hybrid traits and mid-parent heterosis.By integrating GWAS,expression GWAS(eGWAS),and module eGWAS analysis,we prioritized six candidate heterotic genes underlying six QTLs,including one QTL that spans the bZIP29 gene.In the hybrid population,bZIP29 exhibits additive expression and dominance effects for both hybrid traits and mid-parent heterosis,with its favorable allele correlating positively with PH and EH.bZIP29 demonstrates dominance or over-dominance patterns in hy-brids derived from crosses between transgenic and wild-type lines,contingent upon its expression.A tsCUT&Tag assay revealed that bZIP29 protein binds directly to a gene regulated by its associated expres-sion QTL(eQTL)and six genes within expression modules governed by its associated module-eQTLs(meQTLs).Regulatory networks involving bZIP29 are more extensive in hybrid subpopulations than in the parental population.This study offers insights into key heterotic genes and networks that underpin the robust growth of hybrid maize.
基金supported by the Agricultural Science and Technology Innovation Program(ASTIP)of Chinese Academy of Agricultural Sciences(CAAS-ZDRW20210)the National Key Research and Development Program of China(nos.2020YFE0202300 and 2021YFD1201600)the Platform of National Crop Germplasm Resources of China(nos.2016-004 and 2017-004)。
文摘Innovations in genomics have enabled the development of low-cost,high-resolution,single nucleotide polymorphism(SNP)genotyping arrays that accelerate breeding progress and support basic research in crop science.Here,we developed and validated the Soy SNP618 K array(618,888 SNPs)for the important crop soybean.The SNPs were selected from whole-genome resequencing data containing 2,214 diverse soybean accessions;29.34%of the SNPs mapped to genic regions representing 86.85%of the 56,044annotated high-confidence genes.Identity-by-state analyses of 318 soybeans revealed 17 redundant accessions,highlighting the potential of the Soy SNP618 K array in supporting gene bank management.The patterns of population stratification and genomic regions enriched through domestication were highly consistent with previous findings based on resequencing data,suggesting that the ascertainment bias in the Soy SNP618 K array was largely compensated for.Genome-wide association mapping in combination with reported quantitative trait loci enabled fine-mapping of genes known to influence flowering time,E2 and Gm PRR3 b,and of a new candidate gene,Gm VIP5.Moreover,genomic prediction of flowering and maturity time in 502 recombinant inbred lines was highly accurate(>0.65).Thus,the Soy SNP618 K array is a valuable genomic tool that can be used to address many questions in applied breeding,germplasm management,and basic crop research.
