Wheat crops in China are constantly challenged by stripe rust. Deployment of cultivars with diverse resistances is the best strategy to control the disease. A recombinant inbred line(RIL) population derived from a cro...Wheat crops in China are constantly challenged by stripe rust. Deployment of cultivars with diverse resistances is the best strategy to control the disease. A recombinant inbred line(RIL) population derived from a cross between the resistant cultivar Chakwal 86 and susceptible landrace Mingxian 169 was studied in multiple environments to examine the underlying genetics and to identify quantitative trait loci(QTL) for stripe rust resistance.One hundred and twenty-eight RILs were genotyped with wheat 35 K SNP array and a genome-wide linkage map with 1480 polymorphic SNP markers, or bins, was constructed.Two major QTL on chromosomes 1BL and 3BS, and one minor QTL on 6BS had significant effects in reducing stripe rust severity. The QTL were validated using composite interval mapping(CIM) and inclusive composite interval mapping(ICIM). These methods explained59.0%–74.1% of the phenotype variation in disease response. The QTL on chromosome 1 BL was confirmed to be Yr29/Lr46 and the one on 3BS was the resistance allele identified in CIMMYT germplasm but was not Yr30/Sr2. The QTL on 6BS probably corresponded to previously known QTL. RILs with combined QTL were more resistant than those with single or no QTL. Kompetitive allele-specific PCR(KASP) assays for the QTL with largest effect QTL on chromosome 3BS were performed on a subset of RILs and 150 unrelated wheat lines. The QTL on 3BS with its linked KASP markers can be used in marker-assisted selection to improve stripe rust resistance in breeding programs.展开更多
Single-nucleotide polymorphisms(SNPs)arewidely used asmolecularmarkers for constructing genetic linkage maps in wheat.Compared with available SNP-based genotyping platforms,a genotyping by target sequencing(GBTS)syste...Single-nucleotide polymorphisms(SNPs)arewidely used asmolecularmarkers for constructing genetic linkage maps in wheat.Compared with available SNP-based genotyping platforms,a genotyping by target sequencing(GBTS)system with capture-in-solution(liquid chip)technology has become the favored genotyping technology because it is less demanding and more cost effective,flexible,and user-friendly.In this study,a new GenoBaits WheatSNP16K(GBW16K)GBTS array was designed using datasets generated by the wheat 660K SNP array and resequencing platforms in our previous studies.The GBW16K array contains 14868 target SNP regions that are evenly distributed across the wheat genome,and 37669 SNPs in these regions can be identified in a diversity panel consisting of 239wheat accessions from around theworld.Principal component and neighbor-joining analyses using the called SNPs are consistent with the pedigree information and geographic distributions or ecological environments of the accessions.For the GBW16K marker panel,the average genetic diversity among the 239 accessions is 0.270,which is sufficient for linkage map construction and preliminary mapping of targeted genes or quantitative trait loci(QTLs).A genetic linkage map,constructed using the GBW16K array-based genotyping of a recombinant inbred line population derived from a cross of the CIMMYT wheat line Yaco“S”and the Chinese landrace Mingxian169,enables the identification of Yr27,Yr30,and QYr.nwafu-2BL.4 for adult-plant resistance to stripe rust from Yaco“S”and of Yr18 from Mingxian169.QYr.nwafu-2BL.4 is different from any previously reported gene/QTL.Three haplotypes and six candidate genes have been identified for QYr.nwafu-2BL.4 on the basis of haplotype analysis,micro-collinearity,gene annotation,RNA sequencing,and SNP data.This array provides a new tool for wheat genetic analysis and breeding studies and for achieving durable control of wheat stripe rust.展开更多
基金financially supported by the National Science Foundation for Young Scientists of China(31701421)the National Key Research and Development Program of China(2016YFE0108600)+2 种基金the China Agriculture Research System(CARS-3-1-11)the Genetically Modified Organisms Breeding Major Project(2016ZX08002001)the Key Project of Science and Technology of Tibetan Autonomous Region,China(XZ201702NB15)
文摘Wheat crops in China are constantly challenged by stripe rust. Deployment of cultivars with diverse resistances is the best strategy to control the disease. A recombinant inbred line(RIL) population derived from a cross between the resistant cultivar Chakwal 86 and susceptible landrace Mingxian 169 was studied in multiple environments to examine the underlying genetics and to identify quantitative trait loci(QTL) for stripe rust resistance.One hundred and twenty-eight RILs were genotyped with wheat 35 K SNP array and a genome-wide linkage map with 1480 polymorphic SNP markers, or bins, was constructed.Two major QTL on chromosomes 1BL and 3BS, and one minor QTL on 6BS had significant effects in reducing stripe rust severity. The QTL were validated using composite interval mapping(CIM) and inclusive composite interval mapping(ICIM). These methods explained59.0%–74.1% of the phenotype variation in disease response. The QTL on chromosome 1 BL was confirmed to be Yr29/Lr46 and the one on 3BS was the resistance allele identified in CIMMYT germplasm but was not Yr30/Sr2. The QTL on 6BS probably corresponded to previously known QTL. RILs with combined QTL were more resistant than those with single or no QTL. Kompetitive allele-specific PCR(KASP) assays for the QTL with largest effect QTL on chromosome 3BS were performed on a subset of RILs and 150 unrelated wheat lines. The QTL on 3BS with its linked KASP markers can be used in marker-assisted selection to improve stripe rust resistance in breeding programs.
基金financially supported by the National Key R&D Program of China(2021YFD1200600)International Cooperation and Exchange of the National Natural Science Foundation of China(grant no.31961143019)+2 种基金the National Science Foundation for Young Scientists in China(grant no.32302377)the National Natural Science Foundation of China(grant nos.32272088 and 32372562)the Major Program of the National Natural Science Foundation of China(32293240).
文摘Single-nucleotide polymorphisms(SNPs)arewidely used asmolecularmarkers for constructing genetic linkage maps in wheat.Compared with available SNP-based genotyping platforms,a genotyping by target sequencing(GBTS)system with capture-in-solution(liquid chip)technology has become the favored genotyping technology because it is less demanding and more cost effective,flexible,and user-friendly.In this study,a new GenoBaits WheatSNP16K(GBW16K)GBTS array was designed using datasets generated by the wheat 660K SNP array and resequencing platforms in our previous studies.The GBW16K array contains 14868 target SNP regions that are evenly distributed across the wheat genome,and 37669 SNPs in these regions can be identified in a diversity panel consisting of 239wheat accessions from around theworld.Principal component and neighbor-joining analyses using the called SNPs are consistent with the pedigree information and geographic distributions or ecological environments of the accessions.For the GBW16K marker panel,the average genetic diversity among the 239 accessions is 0.270,which is sufficient for linkage map construction and preliminary mapping of targeted genes or quantitative trait loci(QTLs).A genetic linkage map,constructed using the GBW16K array-based genotyping of a recombinant inbred line population derived from a cross of the CIMMYT wheat line Yaco“S”and the Chinese landrace Mingxian169,enables the identification of Yr27,Yr30,and QYr.nwafu-2BL.4 for adult-plant resistance to stripe rust from Yaco“S”and of Yr18 from Mingxian169.QYr.nwafu-2BL.4 is different from any previously reported gene/QTL.Three haplotypes and six candidate genes have been identified for QYr.nwafu-2BL.4 on the basis of haplotype analysis,micro-collinearity,gene annotation,RNA sequencing,and SNP data.This array provides a new tool for wheat genetic analysis and breeding studies and for achieving durable control of wheat stripe rust.
