Pre-harvest sprouting(PHS) adversely affects wheat quality and yield, and grain color(GC) is associated with PHS resistance. However, the genetic relationship between GC and PHS resistance remains unclear. In this stu...Pre-harvest sprouting(PHS) adversely affects wheat quality and yield, and grain color(GC) is associated with PHS resistance. However, the genetic relationship between GC and PHS resistance remains unclear. In this study, 168 wheat varieties(lines) with significant differences in GC and PHS resistance were genotyped using an Illumina 90K iSelect SNP array. Genome-wide association study(GWAS) based on a mixed linear model showed that 67 marker-trait associations(MTAs) assigned to 29 loci, including 17 potentially novel loci, were significantly associated with GC, which explained 1.1–17.0% of the phenotypic variation. In addition, 100 MTAs belonging to 54 loci, including 31 novel loci, were significantly associated with PHS resistance, which accounted for 1.1–14.7% of the phenotypic variation. Subsequently, two cleaved amplified polymorphic sequences(CAPS) markers, 2B-448 on chromosome 2B and 5B-301 on chromosome 5B,were developed from the representative SNPs of the major common loci Qgc.ahau-2B.3/Qphs.ahau-2B.4controlling GC/PHS resistance and PHS resistance locus Qphs.ahau-5B.4, respectively. Further validation in 171 Chinese mini-core collections confirmed significant correlations of the two CAPS markers with GC and PHS resistance phenotypes under different environments(P<0.05). Furthermore, the wheat public expression database, transcriptomic sequencing, and gene allelic variation analysis identified TraesCS5B02G545100, which encodes glutaredoxin, as a potential candidate gene linked to Qphs.ahau-5B.4. The new CAPS marker CAPS-356 was then developed based on the SNP(T/C) in the coding sequences(CDS) region of TraesCS5B02G545100. The high-density linkage map of the Jing 411/Hongmangchun 21 recombinant inbred lines(RILs) constructed based on specific locus amplified fragment sequencing markers showed that CAPS-356 collocated with a novel QTL for PHS resistance, supporting the role of TraesCS5B02G545100 as the potential candidate gene linked to Qphs.ahau-5B.4. These results provide valuable information for the map-based cloning of Qphs.ahau-5B.4 and breeding of PHS resistant white-grained varieties.展开更多
Common wheat(Triticum aestivum L.)is the most important crop in the world and a typical allopolyploid with a large and complex genome.Pre-harvest sprouting(PHS)leads to a significant reduction in grain quality worldwi...Common wheat(Triticum aestivum L.)is the most important crop in the world and a typical allopolyploid with a large and complex genome.Pre-harvest sprouting(PHS)leads to a significant reduction in grain quality worldwide.PHS is a complex trait with related QTL located on different chromosomes.However,the study of markers and genes related to PHS resistance is limited especially for whitegrained wheat.Four pairs of near isogenic lines(NILs)from a white-grained wheat cross of CharaDM5637B*8 targeting a major QTL for PHS resistance(Qphs.ccsu-3A.1)on wheat chromosme 3AL were genotyped using the 90K SNP Illumina iSelect array.Ten SNPs were identified,with a 75%-100%consistency between genotype and phenotype in the resistant or susceptible isolines.The 10 SNPs were converted to cost-effective kompetitive allele-specific PCR(KASP)markers.Screening of 48 wheat cultivars with different phenotypes of PHS identified four KASP markers with 81.3%-85.4%conformity between genotype and phenotype.Further investigation revealed that the four SNPs(BS00022245_51,Kukri_c49927_151,BS00022884_51 and BS00110550_51)corresponding to the four validated KASP markers are residing in three independent genes(TraesCS3A03G1072800,TraesCS3A03G1072400,TraesCS3A03G1071800)close to each other with a distance of 4.28-4.48 Mb to the targeted QTL.These three annotated genes have potential functions related to PHS resistance.Our study revealed that combined use of NILs and the 90K SNP chip is a powerful approach for developing KASP markers and mining functional genes in wheat.The KASP markers for PHS resistance on chromosome 3AL are useful for high-throughput evaluation and marker-assisted selection,and the three identified genes could lead to a better understanding of the genetic pathways controlling PHS.展开更多
籽粒硬度是小麦品质评价的重要指标。为挖掘控制小麦籽粒硬度的重要基因/位点,以国内外171个小麦品种组成的自然群体为材料,在4个环境下利用小麦90K SNP芯片对籽粒硬度进行全基因组关联分析(genome-wide association study,GWAS)。171...籽粒硬度是小麦品质评价的重要指标。为挖掘控制小麦籽粒硬度的重要基因/位点,以国内外171个小麦品种组成的自然群体为材料,在4个环境下利用小麦90K SNP芯片对籽粒硬度进行全基因组关联分析(genome-wide association study,GWAS)。171个小麦品种籽粒硬度变异系数为56.59%~66.80%,相关系数为0.88~0.92。GWAS结果表明,共检测到20个与小麦籽粒硬度显著相关的SNPs,其中,14个SNPs(7个位点)在2个及以上环境中能被检测到,分别位于1A、1B、1D、2A、5A和7A染色体上,可解释6.76%~11.79%的表型变异。表型贡献率超过10%的SNPs有4个(3个位点),分布在1D、2A和5A染色体上,其中,1D染色体上的标记wsnp_Ku_c19622_29138795在3个环境中能被检测到,可解释9.08%~11.79%的表型变异;2A染色体上的标记Excalibur_c12675_1789在4个环境中均能被检测到,可解释9.10%~10.86%的表型变异;5A染色体上的标记wsnp_Ra_c24707_34262900和BS00041219_51在2个环境中能被检测到,可解释6.76%~10.35%的表型变异。在所有环境下均与小麦籽粒硬度显著相关的位点有4个,分别位于1A、1B、2A和7A染色体上。展开更多
[目的]小麦遗传图谱是进行小麦染色体分析和研究表型变异的遗传基础。通过利用传统分子标记和现代基因芯片技术相结合,构建高密度遗传图谱,重点开展主要产量主要构成要素——粒重的初级基因定位,确定影响粒重的主效QTL位点,为开发粒重C...[目的]小麦遗传图谱是进行小麦染色体分析和研究表型变异的遗传基础。通过利用传统分子标记和现代基因芯片技术相结合,构建高密度遗传图谱,重点开展主要产量主要构成要素——粒重的初级基因定位,确定影响粒重的主效QTL位点,为开发粒重CAPS分子标记及在分子标记辅助育种提供依据和指导,并为利用小麦粒重次级群体进行精细定位和基因挖掘奠定基础。[方法]利用90 K小麦SNP基因芯片、DArt芯片技术及传统的分子标记技术,以包含173个家系的RIL群体(F9:10重组自交系)为材料,构建高密度遗传图谱,并利用QTL network2.0进行了3年共4环境粒重QTL分析。[结果]构建了覆盖小麦21条染色体的高密度遗传图谱,该图谱共含有6 244个多态性标记,其中SNP标记6 001个、DAr T标记216个、SSR标记27个,覆盖染色体总长度4 875.29 c M,标记间平均距离0.78 c M。A、B、D染色体组分别有2 390、3 386和468个标记,分别占总标记数的38.3%、54.3%和7.5%;3个染色体组标记间平均距离分别为0.80、0.75和0.80 c M。用该分子遗传图谱对4个环境下粒重进行QTL分析,检测到位于1B、4B、5B、6A染色体上9个加性QTL,效应值大于10%的QTL位点有QGW4B-17、QGW4B-5、QGW4B-2、QGW6A-344、QGW6A-137;其中QGW4B-17在多个环境下检测到,其贡献率为16%—33.3%,可增加粒重效应值2.30-2.97g,该位点是稳定表达的主效QTL。9个QTL的加性效应均来自大粒母本山农01-35,单个QTL位点加性效应可增加千粒重1.09—2.97 g。[结论]构建的覆盖小麦21条染色体的分子遗传图谱共含有6 241个多态性标记,标记间平均距离为0.77 c M。利用该图谱检测到位于1B、4B、5B、6A染色体上9个控制粒重的加性QTL,其中QGW4B-17是稳定表达的主效QTL位点,贡献率为16.5%—33%,可增加粒重效应值2.30—2.97 g。展开更多
Vitamin B is essential for maintaining normal life activities in humans and animals who have to intake the microelement from the outside, especially from cereal products. In the present study 166 Chinese and foreign w...Vitamin B is essential for maintaining normal life activities in humans and animals who have to intake the microelement from the outside, especially from cereal products. In the present study 166 Chinese and foreign wheat cultivars planted in two environments were characterized for variation in vitamin B1 and B2 contents. A genome-wide association study(GWAS) using the wheat 90 K SNP assay identified 17 loci for vitamin B1 and 7 for vitamin B2 contents. Linear regression analysis showed a significantly positive correlation of the number of favorable alleles with vitamin B1 and B2 contents. Marker-trait associations(MTAs) at IWB43809(6AS, 0cM) and IWB69903(6AS, 13cM) were new and stable, and significantly associated with vitamin B1 content across two environments. The loci identified in this study and associated SNP markers could be used for improvement of vitamin B1 and B2 contents to obtain superior quality along with grain yield in wheat.展开更多
小麦遗传图谱是进行小麦染色体分析和表型研究的遗传基础.构建高密度遗传图谱,针对小麦重要农艺性状进行初级定位,确定相关性状主效数量性状位点(Quantitative Trait Loci,QTL),有助于开发辅助选择的实用性标记,并为利用次级群体进行精...小麦遗传图谱是进行小麦染色体分析和表型研究的遗传基础.构建高密度遗传图谱,针对小麦重要农艺性状进行初级定位,确定相关性状主效数量性状位点(Quantitative Trait Loci,QTL),有助于开发辅助选择的实用性标记,并为利用次级群体进行精细定位和基因挖掘奠定基础.本研究以H461×CN16的重组自交系(Recombinant Inbred Line,RIL)为作图群体,利用90k小麦SNP基因芯片技术,对包含188个家系的RIL群体(F7)进行多态性分析,构建高密度遗传图谱,并利用Map QTL5.0的多QTL模型(MQM),对旗叶长、穗粒数等8个重要农艺性状进行QTL定位分析.构建了包括43个连锁群的分子遗传图谱,成功连锁到除2D、5D、6D外的18条染色体.该图谱共含有6 573个多态性SNP标记,覆盖的遗传距离长2 647.02 c M,标记间平均距离仅为0.4 c M.A、B、D三个染色体组分别含有标记2 696、3 094和684个;覆盖染色长度分别为1 130.92 c M、1 164.82 c M和330.44 c M;分别建立19、18和5个连锁群.对8种重要田间农艺性状进行QTL分析,共检测到66个重要农艺性状QTL,其中包括26个主效QTL,包含未见报道的新位点7个.全部QTL分布于2A、4A、6A、2B、4B、5B、2D、4D、7D 9条染色体上,单个QTL可解释表型变异率7.4%-19.5%,其中62个QTL加性效应来自母本H461,其余来自父本CN16.以上结果为小麦重要农艺性状QTL精细定位打下了基础,也为分子标记辅助育种提供了参考.展开更多
基金supported by grants from the University Synergy Innovation Program of Anhui Province,China(GXXT-2021-058)the National Natural Science Foundation of China(Joint Fund Projects,U20A2033)+3 种基金the Natural Science Foundation of Anhui Province,China(2108085MC98)the Jiangsu Collaborative Innovation Center for Modern Crop Production,China(JCIC-MCP)the key scientific and technological breakthroughs of Anhui Province(2021d06050003)the joint key project of improved wheat variety of Anhui Province,China(21803003).
文摘Pre-harvest sprouting(PHS) adversely affects wheat quality and yield, and grain color(GC) is associated with PHS resistance. However, the genetic relationship between GC and PHS resistance remains unclear. In this study, 168 wheat varieties(lines) with significant differences in GC and PHS resistance were genotyped using an Illumina 90K iSelect SNP array. Genome-wide association study(GWAS) based on a mixed linear model showed that 67 marker-trait associations(MTAs) assigned to 29 loci, including 17 potentially novel loci, were significantly associated with GC, which explained 1.1–17.0% of the phenotypic variation. In addition, 100 MTAs belonging to 54 loci, including 31 novel loci, were significantly associated with PHS resistance, which accounted for 1.1–14.7% of the phenotypic variation. Subsequently, two cleaved amplified polymorphic sequences(CAPS) markers, 2B-448 on chromosome 2B and 5B-301 on chromosome 5B,were developed from the representative SNPs of the major common loci Qgc.ahau-2B.3/Qphs.ahau-2B.4controlling GC/PHS resistance and PHS resistance locus Qphs.ahau-5B.4, respectively. Further validation in 171 Chinese mini-core collections confirmed significant correlations of the two CAPS markers with GC and PHS resistance phenotypes under different environments(P<0.05). Furthermore, the wheat public expression database, transcriptomic sequencing, and gene allelic variation analysis identified TraesCS5B02G545100, which encodes glutaredoxin, as a potential candidate gene linked to Qphs.ahau-5B.4. The new CAPS marker CAPS-356 was then developed based on the SNP(T/C) in the coding sequences(CDS) region of TraesCS5B02G545100. The high-density linkage map of the Jing 411/Hongmangchun 21 recombinant inbred lines(RILs) constructed based on specific locus amplified fragment sequencing markers showed that CAPS-356 collocated with a novel QTL for PHS resistance, supporting the role of TraesCS5B02G545100 as the potential candidate gene linked to Qphs.ahau-5B.4. These results provide valuable information for the map-based cloning of Qphs.ahau-5B.4 and breeding of PHS resistant white-grained varieties.
基金funded by Global Innovation Linkage program (GIL53853) from Australian Department of Industry, Science, Energy and ResourcesAustralian Government RTP Scholarship (International)University Postgraduate Awards (UPA)
文摘Common wheat(Triticum aestivum L.)is the most important crop in the world and a typical allopolyploid with a large and complex genome.Pre-harvest sprouting(PHS)leads to a significant reduction in grain quality worldwide.PHS is a complex trait with related QTL located on different chromosomes.However,the study of markers and genes related to PHS resistance is limited especially for whitegrained wheat.Four pairs of near isogenic lines(NILs)from a white-grained wheat cross of CharaDM5637B*8 targeting a major QTL for PHS resistance(Qphs.ccsu-3A.1)on wheat chromosme 3AL were genotyped using the 90K SNP Illumina iSelect array.Ten SNPs were identified,with a 75%-100%consistency between genotype and phenotype in the resistant or susceptible isolines.The 10 SNPs were converted to cost-effective kompetitive allele-specific PCR(KASP)markers.Screening of 48 wheat cultivars with different phenotypes of PHS identified four KASP markers with 81.3%-85.4%conformity between genotype and phenotype.Further investigation revealed that the four SNPs(BS00022245_51,Kukri_c49927_151,BS00022884_51 and BS00110550_51)corresponding to the four validated KASP markers are residing in three independent genes(TraesCS3A03G1072800,TraesCS3A03G1072400,TraesCS3A03G1071800)close to each other with a distance of 4.28-4.48 Mb to the targeted QTL.These three annotated genes have potential functions related to PHS resistance.Our study revealed that combined use of NILs and the 90K SNP chip is a powerful approach for developing KASP markers and mining functional genes in wheat.The KASP markers for PHS resistance on chromosome 3AL are useful for high-throughput evaluation and marker-assisted selection,and the three identified genes could lead to a better understanding of the genetic pathways controlling PHS.
文摘籽粒硬度是小麦品质评价的重要指标。为挖掘控制小麦籽粒硬度的重要基因/位点,以国内外171个小麦品种组成的自然群体为材料,在4个环境下利用小麦90K SNP芯片对籽粒硬度进行全基因组关联分析(genome-wide association study,GWAS)。171个小麦品种籽粒硬度变异系数为56.59%~66.80%,相关系数为0.88~0.92。GWAS结果表明,共检测到20个与小麦籽粒硬度显著相关的SNPs,其中,14个SNPs(7个位点)在2个及以上环境中能被检测到,分别位于1A、1B、1D、2A、5A和7A染色体上,可解释6.76%~11.79%的表型变异。表型贡献率超过10%的SNPs有4个(3个位点),分布在1D、2A和5A染色体上,其中,1D染色体上的标记wsnp_Ku_c19622_29138795在3个环境中能被检测到,可解释9.08%~11.79%的表型变异;2A染色体上的标记Excalibur_c12675_1789在4个环境中均能被检测到,可解释9.10%~10.86%的表型变异;5A染色体上的标记wsnp_Ra_c24707_34262900和BS00041219_51在2个环境中能被检测到,可解释6.76%~10.35%的表型变异。在所有环境下均与小麦籽粒硬度显著相关的位点有4个,分别位于1A、1B、2A和7A染色体上。
文摘[目的]小麦遗传图谱是进行小麦染色体分析和研究表型变异的遗传基础。通过利用传统分子标记和现代基因芯片技术相结合,构建高密度遗传图谱,重点开展主要产量主要构成要素——粒重的初级基因定位,确定影响粒重的主效QTL位点,为开发粒重CAPS分子标记及在分子标记辅助育种提供依据和指导,并为利用小麦粒重次级群体进行精细定位和基因挖掘奠定基础。[方法]利用90 K小麦SNP基因芯片、DArt芯片技术及传统的分子标记技术,以包含173个家系的RIL群体(F9:10重组自交系)为材料,构建高密度遗传图谱,并利用QTL network2.0进行了3年共4环境粒重QTL分析。[结果]构建了覆盖小麦21条染色体的高密度遗传图谱,该图谱共含有6 244个多态性标记,其中SNP标记6 001个、DAr T标记216个、SSR标记27个,覆盖染色体总长度4 875.29 c M,标记间平均距离0.78 c M。A、B、D染色体组分别有2 390、3 386和468个标记,分别占总标记数的38.3%、54.3%和7.5%;3个染色体组标记间平均距离分别为0.80、0.75和0.80 c M。用该分子遗传图谱对4个环境下粒重进行QTL分析,检测到位于1B、4B、5B、6A染色体上9个加性QTL,效应值大于10%的QTL位点有QGW4B-17、QGW4B-5、QGW4B-2、QGW6A-344、QGW6A-137;其中QGW4B-17在多个环境下检测到,其贡献率为16%—33.3%,可增加粒重效应值2.30-2.97g,该位点是稳定表达的主效QTL。9个QTL的加性效应均来自大粒母本山农01-35,单个QTL位点加性效应可增加千粒重1.09—2.97 g。[结论]构建的覆盖小麦21条染色体的分子遗传图谱共含有6 241个多态性标记,标记间平均距离为0.77 c M。利用该图谱检测到位于1B、4B、5B、6A染色体上9个控制粒重的加性QTL,其中QGW4B-17是稳定表达的主效QTL位点,贡献率为16.5%—33%,可增加粒重效应值2.30—2.97 g。
基金supported by National Key Research and Development Programs of China(2016YFD0101802,2016YFE0108600,2014CB1381050)Gene Transformation Projects(2016ZX08002003–003)Core Research Budget of the Non–profit Governmental Research Institutions(Y2016XT06)
文摘Vitamin B is essential for maintaining normal life activities in humans and animals who have to intake the microelement from the outside, especially from cereal products. In the present study 166 Chinese and foreign wheat cultivars planted in two environments were characterized for variation in vitamin B1 and B2 contents. A genome-wide association study(GWAS) using the wheat 90 K SNP assay identified 17 loci for vitamin B1 and 7 for vitamin B2 contents. Linear regression analysis showed a significantly positive correlation of the number of favorable alleles with vitamin B1 and B2 contents. Marker-trait associations(MTAs) at IWB43809(6AS, 0cM) and IWB69903(6AS, 13cM) were new and stable, and significantly associated with vitamin B1 content across two environments. The loci identified in this study and associated SNP markers could be used for improvement of vitamin B1 and B2 contents to obtain superior quality along with grain yield in wheat.
文摘小麦遗传图谱是进行小麦染色体分析和表型研究的遗传基础.构建高密度遗传图谱,针对小麦重要农艺性状进行初级定位,确定相关性状主效数量性状位点(Quantitative Trait Loci,QTL),有助于开发辅助选择的实用性标记,并为利用次级群体进行精细定位和基因挖掘奠定基础.本研究以H461×CN16的重组自交系(Recombinant Inbred Line,RIL)为作图群体,利用90k小麦SNP基因芯片技术,对包含188个家系的RIL群体(F7)进行多态性分析,构建高密度遗传图谱,并利用Map QTL5.0的多QTL模型(MQM),对旗叶长、穗粒数等8个重要农艺性状进行QTL定位分析.构建了包括43个连锁群的分子遗传图谱,成功连锁到除2D、5D、6D外的18条染色体.该图谱共含有6 573个多态性SNP标记,覆盖的遗传距离长2 647.02 c M,标记间平均距离仅为0.4 c M.A、B、D三个染色体组分别含有标记2 696、3 094和684个;覆盖染色长度分别为1 130.92 c M、1 164.82 c M和330.44 c M;分别建立19、18和5个连锁群.对8种重要田间农艺性状进行QTL分析,共检测到66个重要农艺性状QTL,其中包括26个主效QTL,包含未见报道的新位点7个.全部QTL分布于2A、4A、6A、2B、4B、5B、2D、4D、7D 9条染色体上,单个QTL可解释表型变异率7.4%-19.5%,其中62个QTL加性效应来自母本H461,其余来自父本CN16.以上结果为小麦重要农艺性状QTL精细定位打下了基础,也为分子标记辅助育种提供了参考.
