To break the narrow diversity bottleneck of the wheat D genome, a set of Aegilops tauschii-wheat introgression(A-WI) lines was developed by crossing Ae. tauschii accession T015 with common wheat elite cultivar Zhoumai...To break the narrow diversity bottleneck of the wheat D genome, a set of Aegilops tauschii-wheat introgression(A-WI) lines was developed by crossing Ae. tauschii accession T015 with common wheat elite cultivar Zhoumai 18(Zhou18). A high-density genetic map was constructed based on Single Nucleotide Polymorphism(SNP) markers and 15 yield-related traits were evaluated in 11 environments for detecting quantitative trait loci(QTL). A total of 27 environmentally stable QTL were identified in at least five environments, 20 of which were derived from Ae. tauschii T015, explaining up to 24.27% of the phenotypic variations. The major QTL for kernel length(KL), QKl-2D.5, was delimited to a physical interval of approximately 2.6 Mb harboring 52 candidate genes. Three Kompetitive Allele Specific PCR(KASP)markers were successfully developed based on nonsynonymous nucleotide mutations of candidate gene AetT093_2Dv1G100900.1 and showed that A-WI lines with the T015 haplotype had significantly longer KL than the Zhou18 haplotype across all 11 environments. Four primary valuable A-WIs with good trait performance and carrying yield-related QTL were selected for breeding improvement. The results will facilitate the efficient transfer of beneficial genes from Ae. tauschii into wheat cultivars to improve wheat yield and other traits.展开更多
The diploid wild goat grass Aegilops tauschii(Ae. tauschii, 2 n = 14;DD), as the D-sub genome of common wheat, provides rich germplasm resources for many aspects of wheat breeding. Abscisic acid(ABA) is an essential p...The diploid wild goat grass Aegilops tauschii(Ae. tauschii, 2 n = 14;DD), as the D-sub genome of common wheat, provides rich germplasm resources for many aspects of wheat breeding. Abscisic acid(ABA) is an essential phytohormone that plays a pivotal role in plant adaptation to abiotic stresses. However,the gene regulation network of Ae. tauschii in response to ABA stress remains unclear. Here, we conducted a time-course strand-specific RNA-sequencing study to globally profile the transcriptome that responded to ABA treatment in Ae. tauschii. We identified 4818 differentially expressed transcription units/genes with time-point-specific induction/repression patterns. Using functional annotation, one-to-one ortholog and comparative transcriptome profiling analyses, we identified 319 ABA-responsive Ae. tauschii orthologs that were also induced/repressed under ABA treatment in hexaploid wheat. On the quantitative trait loci(QTL) used in wheat marker-assisted breeding, we found that the ABA-responsive expression patterns of eight Ae. tauschii orthologs were associated with drought stress tolerance, flowering process and/or grain quality. Of them, the ABA-responsive gene encoding sucrose:sucrose 1-fructosyltransferase in fructan and glucose metabolism pathways showed the most significant association with wheat drought tolerance. The characterization of ABA early-responsive genes in this study provides valuable information for exploring the molecular functions of the regulatory genes and will assist in wheat breeding.展开更多
Bread wheat(Triticum aestivum,AABBDD) is an allohexaploid species derived from two rounds of interspecific hybridizations.A high-quality genome sequence assembly of diploid Aegilops tauschii,the donor of the wheat D g...Bread wheat(Triticum aestivum,AABBDD) is an allohexaploid species derived from two rounds of interspecific hybridizations.A high-quality genome sequence assembly of diploid Aegilops tauschii,the donor of the wheat D genome,will provide a useful platform to study polyploid wheat evolution.A combined approach of BAC pooling and next-generation sequencing technology was employed to sequence the minimum tiling path(MTP) of 3176 BAC clones from the short arm of Ae.tauschii chromosome 3(At3DS).The final assembly of 135 super-scaffolds with an N50 of 4.2 Mb was used to build a247-Mb pseudomolecule with a total of 2222 predicted protein-coding genes.Compared with the orthologous regions of rice,Brachypodium,and sorghum,At3 DS contains 38.67%more genes.In comparison to At3 DS,the short arm sequence of wheat chromosome 3B(Ta3BS) is 95-Mb large in size,which is primarily due to the expansion of the non-centromeric region,suggesting that transposable element(TE) bursts in Ta3 B likely occurred there.Also,the size increase is accompanied by a proportional increase in gene number in Ta3 BS.We found that in the sequence of short arm of wheat chromosome 3D(Ta3DS),there was only less than 0.27%gene loss compared to At3 DS.Our study reveals divergent evolution of grass genomes and provides new insights into sequence changes in the polyploid wheat genome.展开更多
Aegilops tauschii,the wild progenitor of wheat D-genome and a valuable germplasm for wheat improvement,has a wide natural distribution from eastern Turkey to China.However,the phylogenetic relationship and dispersion ...Aegilops tauschii,the wild progenitor of wheat D-genome and a valuable germplasm for wheat improvement,has a wide natural distribution from eastern Turkey to China.However,the phylogenetic relationship and dispersion history of Ae.tauschii in China has not been scientifically clarified.In this study,we genotyped 208 accessions(with 104 in China)using dd RAD sequencing and 55K SNP array,and classified the population into six sublineages.Three possible spreading routes or events were identified,resulting in specific distribution patterns,with four sublineages found in Xinjiang,one in Qinghai,two in Shaanxi and one in Henan.We also established the correlation of SNP-based,karyotypebased and spike-morphology-based techniques to demonstrate the internal classification of Ae.tauschii,and developed consensus dataset with 1245 putative accessions by merging data previously published.Our analysis suggested that eight inter-lineage accessions could be assigned to the putative Lineage 3and these accessions would help to conserve the genetic diversity of the species.By developing the consensus phylogenetic relationships of Ae.tauschii,our work validated the hypothesis on the dispersal history of Ae.tauschii in China,and contributed to the efficient and comprehensive germplasm-mining of the species.展开更多
Wheat leaf rust is a prevalent foliar disease in wheat worldwide. Growing resistant cultivars is an effective strategy to minimize the impact of leaf rust on yield and grain quality. Lr42 is a leaf rust resistance gen...Wheat leaf rust is a prevalent foliar disease in wheat worldwide. Growing resistant cultivars is an effective strategy to minimize the impact of leaf rust on yield and grain quality. Lr42 is a leaf rust resistance gene identified from Aegilops tauschii and is still effective against current predominant leaf rust races in the United States and many other countries. In this study, we developed diagnostic DNA markers for Lr42 using the sequence polymorphisms of a differentially expressed gene(TaRPM1) encoding a putative NBARC protein in the Lr42 candidate region identified by RNA-sequencing of two near-isogenic lines contrasting in Lr42 alleles. Markers were designed based on a deletion mutation and a single nucleotide polymorphism(SNP) in the gene. Haplotype analyses of the newly developed markers in the three diversity panels demonstrated that they are diagnostic for Lr42, and superior to previously used markers in selection accuracy. These markers have the advantages of low cost and easy assay, and they are suitable for marker-assisted selection in breeding programs with either high-or low-throughput marker screening facilities.展开更多
基金financially supported by the National Natural Science Foundation of China (32230079, 32001492, 31871615, and31901547)Natural Science Foundation of Henan Province(222301420102)。
文摘To break the narrow diversity bottleneck of the wheat D genome, a set of Aegilops tauschii-wheat introgression(A-WI) lines was developed by crossing Ae. tauschii accession T015 with common wheat elite cultivar Zhoumai 18(Zhou18). A high-density genetic map was constructed based on Single Nucleotide Polymorphism(SNP) markers and 15 yield-related traits were evaluated in 11 environments for detecting quantitative trait loci(QTL). A total of 27 environmentally stable QTL were identified in at least five environments, 20 of which were derived from Ae. tauschii T015, explaining up to 24.27% of the phenotypic variations. The major QTL for kernel length(KL), QKl-2D.5, was delimited to a physical interval of approximately 2.6 Mb harboring 52 candidate genes. Three Kompetitive Allele Specific PCR(KASP)markers were successfully developed based on nonsynonymous nucleotide mutations of candidate gene AetT093_2Dv1G100900.1 and showed that A-WI lines with the T015 haplotype had significantly longer KL than the Zhou18 haplotype across all 11 environments. Four primary valuable A-WIs with good trait performance and carrying yield-related QTL were selected for breeding improvement. The results will facilitate the efficient transfer of beneficial genes from Ae. tauschii into wheat cultivars to improve wheat yield and other traits.
基金supported by the National Key Research and Development Program of China(2016YFD0101001)the Agricultural Science and Technology Innovation Program of CAAS。
文摘The diploid wild goat grass Aegilops tauschii(Ae. tauschii, 2 n = 14;DD), as the D-sub genome of common wheat, provides rich germplasm resources for many aspects of wheat breeding. Abscisic acid(ABA) is an essential phytohormone that plays a pivotal role in plant adaptation to abiotic stresses. However,the gene regulation network of Ae. tauschii in response to ABA stress remains unclear. Here, we conducted a time-course strand-specific RNA-sequencing study to globally profile the transcriptome that responded to ABA treatment in Ae. tauschii. We identified 4818 differentially expressed transcription units/genes with time-point-specific induction/repression patterns. Using functional annotation, one-to-one ortholog and comparative transcriptome profiling analyses, we identified 319 ABA-responsive Ae. tauschii orthologs that were also induced/repressed under ABA treatment in hexaploid wheat. On the quantitative trait loci(QTL) used in wheat marker-assisted breeding, we found that the ABA-responsive expression patterns of eight Ae. tauschii orthologs were associated with drought stress tolerance, flowering process and/or grain quality. Of them, the ABA-responsive gene encoding sucrose:sucrose 1-fructosyltransferase in fructan and glucose metabolism pathways showed the most significant association with wheat drought tolerance. The characterization of ABA early-responsive genes in this study provides valuable information for exploring the molecular functions of the regulatory genes and will assist in wheat breeding.
基金supported by funding from the National Natural Science Foundation of China(Nos.31290210,31210103902)the Unites States National Science Foundation grant(No.IOS 1238231)+1 种基金the USDA-Agricultural Research Service CRIS project(No.5325-21000-019)the Ministry of Education of China(111 project)
文摘Bread wheat(Triticum aestivum,AABBDD) is an allohexaploid species derived from two rounds of interspecific hybridizations.A high-quality genome sequence assembly of diploid Aegilops tauschii,the donor of the wheat D genome,will provide a useful platform to study polyploid wheat evolution.A combined approach of BAC pooling and next-generation sequencing technology was employed to sequence the minimum tiling path(MTP) of 3176 BAC clones from the short arm of Ae.tauschii chromosome 3(At3DS).The final assembly of 135 super-scaffolds with an N50 of 4.2 Mb was used to build a247-Mb pseudomolecule with a total of 2222 predicted protein-coding genes.Compared with the orthologous regions of rice,Brachypodium,and sorghum,At3 DS contains 38.67%more genes.In comparison to At3 DS,the short arm sequence of wheat chromosome 3B(Ta3BS) is 95-Mb large in size,which is primarily due to the expansion of the non-centromeric region,suggesting that transposable element(TE) bursts in Ta3 B likely occurred there.Also,the size increase is accompanied by a proportional increase in gene number in Ta3 BS.We found that in the sequence of short arm of wheat chromosome 3D(Ta3DS),there was only less than 0.27%gene loss compared to At3 DS.Our study reveals divergent evolution of grass genomes and provides new insights into sequence changes in the polyploid wheat genome.
基金supported by the National Natural Science Foundation of China(32001492)the Ministry of Agriculture of China(2016ZX08009)the Natural Science Foundation of Henan(202300410053)。
文摘Aegilops tauschii,the wild progenitor of wheat D-genome and a valuable germplasm for wheat improvement,has a wide natural distribution from eastern Turkey to China.However,the phylogenetic relationship and dispersion history of Ae.tauschii in China has not been scientifically clarified.In this study,we genotyped 208 accessions(with 104 in China)using dd RAD sequencing and 55K SNP array,and classified the population into six sublineages.Three possible spreading routes or events were identified,resulting in specific distribution patterns,with four sublineages found in Xinjiang,one in Qinghai,two in Shaanxi and one in Henan.We also established the correlation of SNP-based,karyotypebased and spike-morphology-based techniques to demonstrate the internal classification of Ae.tauschii,and developed consensus dataset with 1245 putative accessions by merging data previously published.Our analysis suggested that eight inter-lineage accessions could be assigned to the putative Lineage 3and these accessions would help to conserve the genetic diversity of the species.By developing the consensus phylogenetic relationships of Ae.tauschii,our work validated the hypothesis on the dispersal history of Ae.tauschii in China,and contributed to the efficient and comprehensive germplasm-mining of the species.
基金funded by the National Research Initiative Competitive Grants (2017-67007-25939) from US Department of Agriculture, the National Institute of Food and Agriculture。
文摘Wheat leaf rust is a prevalent foliar disease in wheat worldwide. Growing resistant cultivars is an effective strategy to minimize the impact of leaf rust on yield and grain quality. Lr42 is a leaf rust resistance gene identified from Aegilops tauschii and is still effective against current predominant leaf rust races in the United States and many other countries. In this study, we developed diagnostic DNA markers for Lr42 using the sequence polymorphisms of a differentially expressed gene(TaRPM1) encoding a putative NBARC protein in the Lr42 candidate region identified by RNA-sequencing of two near-isogenic lines contrasting in Lr42 alleles. Markers were designed based on a deletion mutation and a single nucleotide polymorphism(SNP) in the gene. Haplotype analyses of the newly developed markers in the three diversity panels demonstrated that they are diagnostic for Lr42, and superior to previously used markers in selection accuracy. These markers have the advantages of low cost and easy assay, and they are suitable for marker-assisted selection in breeding programs with either high-or low-throughput marker screening facilities.
