纯度是玉米种子质量的重要指标之一,尤其杂交种自交株是影响田间产量的关键因素。KASP(kompetitive allele specific PCR)技术具有高通量、低成本的优点,适用于种子纯度检测。本研究基于12套杂交种及其父母本的三联体样本及335份玉米杂...纯度是玉米种子质量的重要指标之一,尤其杂交种自交株是影响田间产量的关键因素。KASP(kompetitive allele specific PCR)技术具有高通量、低成本的优点,适用于种子纯度检测。本研究基于12套杂交种及其父母本的三联体样本及335份玉米杂交种国家审定标准样品SNP指纹,从384个SNP基础位点筛选获得60个候选位点,位点转化为KASP引物的成功率为95%。综合考虑引物双亲互补率、多态性、稳定性和分型效果等多项指标,最终确定20个引物作为玉米杂交种纯度鉴定的核心引物,能够有效鉴定99.7%供试样品纯度。对于待测样品京科968通过SNP-DNA指纹数据库查询,并选择双亲互补型引物进行纯度鉴定。在检测的110个个体中,共检出1个自交苗和2个异型株,纯度为97.3%。同时,基于纯度核心引物对批量样品检测建立高通量纯度检测方案,具有快捷、准确、高通量和低成本的特点,为政府监管和企业提供了更多纯度鉴定方案的选择。展开更多
Fusarium head blight(FHB)is one of the prevalent fungal diseases of wheat worldwide.Exploring new FHB resistance quantitative trait loci(QTL)in adapted wheat cultivars is a critical step for breeding new FHB-resistant...Fusarium head blight(FHB)is one of the prevalent fungal diseases of wheat worldwide.Exploring new FHB resistance quantitative trait loci(QTL)in adapted wheat cultivars is a critical step for breeding new FHB-resistant cultivars.In this study,we developed a population of 236 F5:7 recombinant inbred lines(RILs)using two popular Chinese wheat cultivars,Yangmai 158 and Zhengmai 9023,with moderate FHB resistance to identify the QTL for FHB type II resistance.This population was evaluated for percentage of symptomatic spikelets per spike(PSS)using single floret injection in repeated greenhouse experiments.Mean PSSs were 33.2%for Yangmai 158 and 30.3%for Zhengmai 9023.A genetic linkage map of 1002 single nucleotide polymorphisms(SNPs)generated by genotyping-by-sequencing(GBS)was constructed for the RIL population.Six QTL were identified for FHB resistance,and three of them were repeatable in the both experiments.Zhengmai 9023 contributed the resistance allele at one repeatable QTL,designated as Qfhb.7D,whereas Yangmai 158 contributed the resistance alleles at the other two repeatable QTL,Qfhb.3AL and Qfhb.2DS.The additional QTL,Qfhb.4AS was significant in the mean PSS,and Qfhb.2DL and Qfhb.7AS were significant in only one experiment.Replacement of each allele individually at the three repeatable QTL significantly changed PSSs.Qfhb.3AL,Qfhb.2DS,and Qfhb.7D explained 8.35%to 9.89%,5.13%to 7.43%,and 6.15%to 9.32%of the phenotypic variations,respectively.The three repeatable QTL contributed by the two parents were additive and stacking the resistance alleles from all the three repeatable QTL showed the highest level of resistance in the current RIL population.Ten SNPs in the QTL regions of Qfhb.3AL,Qfhb.2DS,and Qfhb.7D were converted into KBioscience competitive allele-specific PCR(KASP)assays.One KASP marker for Qfhb.3AL was validated in a panel of wheat cultivars from China.Some of these KASP markers could be useful for marker-assisted selection to stack these QTL.展开更多
Starch is the most important component in endosperm of sorghum grain.Usually,two types of starch are present:amylose(AM)and amylopectin(AP).The levels of AM and AP contents play a significant role in the appearance,st...Starch is the most important component in endosperm of sorghum grain.Usually,two types of starch are present:amylose(AM)and amylopectin(AP).The levels of AM and AP contents play a significant role in the appearance,structure,and quality of sorghum grains and in marketing applications.In the present study,a panel of 634 sorghum(Sorghum bicolor(L.)Moench)accessions were evaluated for starch,AM,and AP contents of grain,which included a mini core collection of 242 accessions from the International Crops Research Institute for the Semi-Arid Tropics(ICRISAT)in India,and 252 landraces and 140 cultivars from China.The average starch content was 67.64%and the average AM and AP contents were 20.19 and 79.81%,respectively.We developed a total of 260000 high-confidence single nucleotide polymorphism(SNP)markers in the panel of 634 accessions of S.bicolor using specific locus amplified fragment sequencing(SLAF-seq).We performed genome-wide association studies(GWAS)of starch,AM,and AM/AP of grain and SNP markers based on a mixed linear model(MLM).In total,70 significant association signals were detected for starch,AM,and AM/AP ratio of grain with P<4.452×10^-7,of which 10 SNPs were identified with significant starch,51 SNPs were associated with AM,and nine SNPs were associated with the AM/AP ratio.The Gene Ontology(GO)analysis identified 12 candidate genes at five QTLs associated with starch metabolism within the 200-kb intervals,located on chromosomes 1,5,6,and 9.Of these genes,Sobic.006G036500.1 encodes peptidyl-prolyl cis-trans-isomerase CYP38 responsible for hexose monophosphate shunt(HMS)and Sobic.009G071800 encodes 6-phospho-fructokinase(PFK),which is involved in the embden-meyerhof pathway(EMP).Kompetitive allele specific PCR(KASP)markers were developed to validate the GWAS results.The C allele is correlated with a high starch content,while the T allele is linked with a low level of starch content,and provides reliable haplotypes for MAS in sorghum quality improvement.展开更多
Grain number per spikelet (GNS) is a key determinant of grain yield in wheat.A recombinant inbred line population comprising 300 lines was developed from a cross between a high GNS variety H461 and Chinese Spring from...Grain number per spikelet (GNS) is a key determinant of grain yield in wheat.A recombinant inbred line population comprising 300 lines was developed from a cross between a high GNS variety H461 and Chinese Spring from which the reference genome assembly of bread wheat was obtained.Both parents and the recombinant inbred lines were genotyped using the wheat 55K single nucleotide polymorphism(SNP) array.A high-density genetic map containing 21,197 SNPs was obtained.These markers covered each of the 21 chromosomes with a total linkage distance of 3792.71 c M.Locations of these markers in this linkage map were highly consistent with their physical locations in the genome assembly of Chinese Spring.The two parents and the whole RIL population were assessed for GNS in two consecutive years at two different locations.Based on multi-environment phenotype data and best liner unbiased prediction values,three quantitative trait loci (QTL) for GNS were identified.One of them located on chromosomes 2B and the other two on 2D.Phenotypic variation explained by these loci varied from 3.07%to26.57%.One of these QTL,QGns.sicau-2D-2,was identified in each of all trials conducted.Based on the best linear unbiased prediction values,this locus explained 19.59%–26.57%of phenotypic variation.A KASP(Kompetitive Allele-Specific PCR) marker closely linked with this locus was generated and used to validate the effects of this locus in three different genetic backgrounds.The identified QTL and the KASP marker developed for it will be highly valuable in fine-mapping the locus and in exploiting it for markerassisted selection in wheat breeding programs.展开更多
Pod shattering causes severe yield loss in rapeseed(Brassica napus L.)under modern agricultural practice.Identification of highly shatter-resistant germplasm is desirable for the development of rapeseed cultivars for ...Pod shattering causes severe yield loss in rapeseed(Brassica napus L.)under modern agricultural practice.Identification of highly shatter-resistant germplasm is desirable for the development of rapeseed cultivars for mechanical harvesting.In the present study,an elite line OR88 with strong shatter resistance and a lignified-layer bridge(LLB)structure was identified.The LLB structure was unique to OR88 and co-segregated with high pod-shatter resistance.The LLB structure is differentiated at stage 12 of gynoecium development without any gynoecium defects.Genetic analysis showed that LLB is controlled by a single recessive gene.By BSA-Seq and map-based cloning,the resistance gene location was delimited to a0.688 Mb region on chromosome C09.Transcriptome analysis suggested Bn TCP8.C09 as the gene responsible for LLB.The expression of Bn TCP.C09 was strongly downregulated in OR88,suppressing cell proliferation in the pod valve margin.KASP markers linked to the candidate gene were developed.This pod shatter-resistant line could be used in rapeseed breeding programs by direct transfer of the gene with the assistance of the DNA markers.展开更多
文摘纯度是玉米种子质量的重要指标之一,尤其杂交种自交株是影响田间产量的关键因素。KASP(kompetitive allele specific PCR)技术具有高通量、低成本的优点,适用于种子纯度检测。本研究基于12套杂交种及其父母本的三联体样本及335份玉米杂交种国家审定标准样品SNP指纹,从384个SNP基础位点筛选获得60个候选位点,位点转化为KASP引物的成功率为95%。综合考虑引物双亲互补率、多态性、稳定性和分型效果等多项指标,最终确定20个引物作为玉米杂交种纯度鉴定的核心引物,能够有效鉴定99.7%供试样品纯度。对于待测样品京科968通过SNP-DNA指纹数据库查询,并选择双亲互补型引物进行纯度鉴定。在检测的110个个体中,共检出1个自交苗和2个异型株,纯度为97.3%。同时,基于纯度核心引物对批量样品检测建立高通量纯度检测方案,具有快捷、准确、高通量和低成本的特点,为政府监管和企业提供了更多纯度鉴定方案的选择。
基金supported partially by the US Wheat and Barley Scab Initiative,the National Research Initiative Competitive Grants(2017-67007-25939)from the National Institute of Food and Agriculture,U.S.Department of Agriculturethe National Natural Science Foundation of China(31671690)+1 种基金the Natural Science Foundation of Jiangsu Province(BK20161375)the National Key Research and Development Program of China(2016YFD0100502)。
文摘Fusarium head blight(FHB)is one of the prevalent fungal diseases of wheat worldwide.Exploring new FHB resistance quantitative trait loci(QTL)in adapted wheat cultivars is a critical step for breeding new FHB-resistant cultivars.In this study,we developed a population of 236 F5:7 recombinant inbred lines(RILs)using two popular Chinese wheat cultivars,Yangmai 158 and Zhengmai 9023,with moderate FHB resistance to identify the QTL for FHB type II resistance.This population was evaluated for percentage of symptomatic spikelets per spike(PSS)using single floret injection in repeated greenhouse experiments.Mean PSSs were 33.2%for Yangmai 158 and 30.3%for Zhengmai 9023.A genetic linkage map of 1002 single nucleotide polymorphisms(SNPs)generated by genotyping-by-sequencing(GBS)was constructed for the RIL population.Six QTL were identified for FHB resistance,and three of them were repeatable in the both experiments.Zhengmai 9023 contributed the resistance allele at one repeatable QTL,designated as Qfhb.7D,whereas Yangmai 158 contributed the resistance alleles at the other two repeatable QTL,Qfhb.3AL and Qfhb.2DS.The additional QTL,Qfhb.4AS was significant in the mean PSS,and Qfhb.2DL and Qfhb.7AS were significant in only one experiment.Replacement of each allele individually at the three repeatable QTL significantly changed PSSs.Qfhb.3AL,Qfhb.2DS,and Qfhb.7D explained 8.35%to 9.89%,5.13%to 7.43%,and 6.15%to 9.32%of the phenotypic variations,respectively.The three repeatable QTL contributed by the two parents were additive and stacking the resistance alleles from all the three repeatable QTL showed the highest level of resistance in the current RIL population.Ten SNPs in the QTL regions of Qfhb.3AL,Qfhb.2DS,and Qfhb.7D were converted into KBioscience competitive allele-specific PCR(KASP)assays.One KASP marker for Qfhb.3AL was validated in a panel of wheat cultivars from China.Some of these KASP markers could be useful for marker-assisted selection to stack these QTL.
基金supported by the earmarked fund for China Agriculture Research System (CARS-06)
文摘Starch is the most important component in endosperm of sorghum grain.Usually,two types of starch are present:amylose(AM)and amylopectin(AP).The levels of AM and AP contents play a significant role in the appearance,structure,and quality of sorghum grains and in marketing applications.In the present study,a panel of 634 sorghum(Sorghum bicolor(L.)Moench)accessions were evaluated for starch,AM,and AP contents of grain,which included a mini core collection of 242 accessions from the International Crops Research Institute for the Semi-Arid Tropics(ICRISAT)in India,and 252 landraces and 140 cultivars from China.The average starch content was 67.64%and the average AM and AP contents were 20.19 and 79.81%,respectively.We developed a total of 260000 high-confidence single nucleotide polymorphism(SNP)markers in the panel of 634 accessions of S.bicolor using specific locus amplified fragment sequencing(SLAF-seq).We performed genome-wide association studies(GWAS)of starch,AM,and AM/AP of grain and SNP markers based on a mixed linear model(MLM).In total,70 significant association signals were detected for starch,AM,and AM/AP ratio of grain with P<4.452×10^-7,of which 10 SNPs were identified with significant starch,51 SNPs were associated with AM,and nine SNPs were associated with the AM/AP ratio.The Gene Ontology(GO)analysis identified 12 candidate genes at five QTLs associated with starch metabolism within the 200-kb intervals,located on chromosomes 1,5,6,and 9.Of these genes,Sobic.006G036500.1 encodes peptidyl-prolyl cis-trans-isomerase CYP38 responsible for hexose monophosphate shunt(HMS)and Sobic.009G071800 encodes 6-phospho-fructokinase(PFK),which is involved in the embden-meyerhof pathway(EMP).Kompetitive allele specific PCR(KASP)markers were developed to validate the GWAS results.The C allele is correlated with a high starch content,while the T allele is linked with a low level of starch content,and provides reliable haplotypes for MAS in sorghum quality improvement.
基金supported by the National Natural Science Foundation of China (31771794)the National Key Research and Development Program of China (2016YFD0101004 and 2017YFD0100900)the International Science & Technology Cooperation Program of the Bureau of Science and Technology of Chengdu China (2015DFA306002015-GH03-00008-HZ)。
文摘Grain number per spikelet (GNS) is a key determinant of grain yield in wheat.A recombinant inbred line population comprising 300 lines was developed from a cross between a high GNS variety H461 and Chinese Spring from which the reference genome assembly of bread wheat was obtained.Both parents and the recombinant inbred lines were genotyped using the wheat 55K single nucleotide polymorphism(SNP) array.A high-density genetic map containing 21,197 SNPs was obtained.These markers covered each of the 21 chromosomes with a total linkage distance of 3792.71 c M.Locations of these markers in this linkage map were highly consistent with their physical locations in the genome assembly of Chinese Spring.The two parents and the whole RIL population were assessed for GNS in two consecutive years at two different locations.Based on multi-environment phenotype data and best liner unbiased prediction values,three quantitative trait loci (QTL) for GNS were identified.One of them located on chromosomes 2B and the other two on 2D.Phenotypic variation explained by these loci varied from 3.07%to26.57%.One of these QTL,QGns.sicau-2D-2,was identified in each of all trials conducted.Based on the best linear unbiased prediction values,this locus explained 19.59%–26.57%of phenotypic variation.A KASP(Kompetitive Allele-Specific PCR) marker closely linked with this locus was generated and used to validate the effects of this locus in three different genetic backgrounds.The identified QTL and the KASP marker developed for it will be highly valuable in fine-mapping the locus and in exploiting it for markerassisted selection in wheat breeding programs.
基金the National Natural Science Foundation of China(U19A2029)the National Key Research and Development Program of China(2018YFE0108000)+1 种基金Science and Technology Innovation Project of the Chinese Academy of Agricultural Sciences(CAAS-ZDRW202105)China Agriculture Research System of MOF and MARA。
文摘Pod shattering causes severe yield loss in rapeseed(Brassica napus L.)under modern agricultural practice.Identification of highly shatter-resistant germplasm is desirable for the development of rapeseed cultivars for mechanical harvesting.In the present study,an elite line OR88 with strong shatter resistance and a lignified-layer bridge(LLB)structure was identified.The LLB structure was unique to OR88 and co-segregated with high pod-shatter resistance.The LLB structure is differentiated at stage 12 of gynoecium development without any gynoecium defects.Genetic analysis showed that LLB is controlled by a single recessive gene.By BSA-Seq and map-based cloning,the resistance gene location was delimited to a0.688 Mb region on chromosome C09.Transcriptome analysis suggested Bn TCP8.C09 as the gene responsible for LLB.The expression of Bn TCP.C09 was strongly downregulated in OR88,suppressing cell proliferation in the pod valve margin.KASP markers linked to the candidate gene were developed.This pod shatter-resistant line could be used in rapeseed breeding programs by direct transfer of the gene with the assistance of the DNA markers.
