Bread wheat(Triticum aestivum)is an important crop and serves as a significant source of protein and calories for humans,worldwide.Nevertheless,its large and allopolyploid genome poses constraints on genetic improveme...Bread wheat(Triticum aestivum)is an important crop and serves as a significant source of protein and calories for humans,worldwide.Nevertheless,its large and allopolyploid genome poses constraints on genetic improvement.The complex reticulate evolutionary history and the intricacy of genomic resources make the deciphering of the functional genome considerably more challenging.Recently,we have developed a comprehensive list of versatile computational tools with the integration of statistical models for dissecting the polyploid wheat genome.Here,we summarize the methodological innovations and applications of these tools and databases.A series of step-by-step examples illustrates how these tools can be utilized for dissecting wheat germplasm resources and unveiling functional genes associated with important agronomic traits.Furthermore,we outline future perspectives on new advanced tools and databases,taking into consideration the unique features of bread wheat,to accelerate genomic-assisted wheat breeding.展开更多
Dear Editor,Gene cloning has a fundamental role in crop research but has long been hindered by high costs and labor requirements,which have limited the numbers of genes that have been functionally characterized,especi...Dear Editor,Gene cloning has a fundamental role in crop research but has long been hindered by high costs and labor requirements,which have limited the numbers of genes that have been functionally characterized,especially in wheat(Liang et al.,2021).Quantitative trait locus(QTL)mapping is the first step in gene cloning,enabling the localization of genomic loci that show significant associations with quantitative traits.One commonly used strategy is based on single-nucleotide polymorphism(SNP)arrays(Sun et al.,2020).展开更多
Bread wheat(Triticum aestivum)became a globally dominant crop after incorporating the D genome from the donor species Aegilops tauschii,but the evolutionary history that shaped the D genome during this process remains...Bread wheat(Triticum aestivum)became a globally dominant crop after incorporating the D genome from the donor species Aegilops tauschii,but the evolutionary history that shaped the D genome during this process remains to be clarified.Here,we propose a renewed evolutionary model linking Ae.tauschii and the hexaploid wheat D genome by constructing an ancestral haplotype map covering 762 Ae.tauschii and hexaploid wheat accessions.We dissected the evolutionary trajectories of Ae.tauschii lineages and reported a few independent intermediate accessions,demonstrating that low-frequency intersublineage gene flow had enriched the diversity of Ae.tauschii.We discovered that the D genome of hexaploid wheat was inherited from a unified ancestral template,but with a mosaic composition that was highly mixed and derived mainly from three Ae.tauschii L2 sublineages located in the Caspian coastal region.This result suggests that early agricultural activities facilitated innovations in D-genome composition and finalized the success of hexaploidization.We found that the majority(51.4%)of genetic diversity was attributed to novel mutations absent in Ae.tauschii,and we identified large Ae.tauschii introgressions from various lineages,which expanded the diversity of the wheat D genome and introduced beneficial alleles.This work sheds light on the process of wheat hexaploidization and highlights the evolutionary significance of the multi-layered genetic diversity of the bread wheat D genome.展开更多
基金supported by the National Natural Science Foundation of China (32322059 and 32272124)China Postdoctoral Science Foundation (2023M733807)+2 种基金Frontiers Science Center for Molecular Design Breeding (2022TC152)Pinduoduo-China Agricultural University Research Fund (PC2023B01016)the 2115 Talent Development Program of China Agricultural University.
文摘Bread wheat(Triticum aestivum)is an important crop and serves as a significant source of protein and calories for humans,worldwide.Nevertheless,its large and allopolyploid genome poses constraints on genetic improvement.The complex reticulate evolutionary history and the intricacy of genomic resources make the deciphering of the functional genome considerably more challenging.Recently,we have developed a comprehensive list of versatile computational tools with the integration of statistical models for dissecting the polyploid wheat genome.Here,we summarize the methodological innovations and applications of these tools and databases.A series of step-by-step examples illustrates how these tools can be utilized for dissecting wheat germplasm resources and unveiling functional genes associated with important agronomic traits.Furthermore,we outline future perspectives on new advanced tools and databases,taking into consideration the unique features of bread wheat,to accelerate genomic-assisted wheat breeding.
基金supported by the STI 2030-Major Projects(2023ZD 0407501)the National Key Research and Development Program of China(2023YFF1000100)supported by the High-performance Computing Platform of China Agricultural University.
文摘Dear Editor,Gene cloning has a fundamental role in crop research but has long been hindered by high costs and labor requirements,which have limited the numbers of genes that have been functionally characterized,especially in wheat(Liang et al.,2021).Quantitative trait locus(QTL)mapping is the first step in gene cloning,enabling the localization of genomic loci that show significant associations with quantitative traits.One commonly used strategy is based on single-nucleotide polymorphism(SNP)arrays(Sun et al.,2020).
基金supported by the National Natural Science Foundation of China(32322059,32401798)the China National Postdoctoral Program for Innovative Talents(BX20230414)+1 种基金the Chinese Universities Scientific Fund(no.2024TC162)supported by the Highperformance Computing Platform of China Agricultural University.
文摘Bread wheat(Triticum aestivum)became a globally dominant crop after incorporating the D genome from the donor species Aegilops tauschii,but the evolutionary history that shaped the D genome during this process remains to be clarified.Here,we propose a renewed evolutionary model linking Ae.tauschii and the hexaploid wheat D genome by constructing an ancestral haplotype map covering 762 Ae.tauschii and hexaploid wheat accessions.We dissected the evolutionary trajectories of Ae.tauschii lineages and reported a few independent intermediate accessions,demonstrating that low-frequency intersublineage gene flow had enriched the diversity of Ae.tauschii.We discovered that the D genome of hexaploid wheat was inherited from a unified ancestral template,but with a mosaic composition that was highly mixed and derived mainly from three Ae.tauschii L2 sublineages located in the Caspian coastal region.This result suggests that early agricultural activities facilitated innovations in D-genome composition and finalized the success of hexaploidization.We found that the majority(51.4%)of genetic diversity was attributed to novel mutations absent in Ae.tauschii,and we identified large Ae.tauschii introgressions from various lineages,which expanded the diversity of the wheat D genome and introduced beneficial alleles.This work sheds light on the process of wheat hexaploidization and highlights the evolutionary significance of the multi-layered genetic diversity of the bread wheat D genome.
