利用集群分离分析结合高密度芯片快速定位小麦成株期抗条锈病基因YrC271

Rapid identification of adult plant wheat stripe rust resistance gene YrC271 using high-throughput SNP array-based bulked segregant analysis

由国际玉米小麦改良中心(CIMMYT)培育的春小麦高代选系C271对小麦条锈病保持抗性近40年。为明确C271的抗条锈病遗传组分,利用感病品种晋麦79与C271杂交构建含有229个F_(2:3)家系的遗传群体,并于2019年在陕西杨凌和四川江油进行成株期病害调查。运用集群分离分析(BSA)结合高密度660K芯片策略在3B染色体短臂上快速挖掘出大量的与抗病关联的SNP,利用等位基因特异的定量PCR标记(AQP)进行验证并作图,成功检测到一个效应值较大的QTL,可解释表型变异为22.7%~30.8%,暂命名为YrC271,位于标记AX-109001377和AX-111087256之间,约1.9 cM,对应的物理距离1.9 Mb。利用已公布的小麦基因组信息对该区间进行比较基因组分析,结果表明,与中国春基因组相比,不同材料间存在小片段的插入以及倒位现象,但总体共线性良好。同时利用1484份小麦660K分型数据对该区间进行单倍型分析,总体可分为5种区间单倍型,其中C271所在的单倍型组的抗性优于其他组。虽然C271不含有Yr30和Yr58连锁标记的阳性片段,但从相对遗传位置、条锈病抗性表现以及育种系谱看,YrC271与Yr30和Yr58都很类似,其关系需要进一步确认。对主效QTL定位来讲,芯片结合BSA策略可快速锁定目标QTL区域,再应用AQP技术既提高了作图效率,也降低了标记分析的成本,为高通量基因/QTL定位工作提供了借鉴。

Wheat cultivar C271 registered as PI 210904 in the USDA National Small Grains Collection was developed from Pun-jab Pakistan in 1953 and it confers adult plant resistance(APR)to stripe rust both in the United States and China for many years.In the present study,we dissected the genetic basis of stripe rust resistance on 229 F_(2:3) populations produced by crossing Jinmai 79 and C271 in the fields of Yangling and Jiangyou.Bulked segregant analysis coupled with wheat 660K SNP array placed the ma-jority of SNPs differences on chromosome arm 3BS.After using allele-specific quantitative PCR based genotyping assay(AQP)to confirm the SNPs,a linkage map was constructed and a major locus was detected across all environments based on IciMapping v4.1 software.The QTL,designated as YrC271,was flanked by SNP markers AX-109001377 and AX-111087256 with a genetic interval of 1.9 cM corresponding to a physical distance of 1.9 Mb in RefSeq v.1.0(positions 6.1–8.0 Mb).Comparative genomics analysis was performed to detect the collinear genomic regions of different hexaploid wheat accessions(Triticum aestivum),T.dicoccoides,and T.turgidum.More than 340 SNPs in the physical region were extracted for haplotype analysis in a panel of over 1484 worldwide common wheat accessions,and five major haplotypes(Hap1,Hap2,Hap3,Hap4,and Hap5)were identified.And the favorable haplotype Hap1 was highly associated with stripe rust resistance.YrC271 appeared to be similar to YrC271 based on comparison of relative distance,stripe rust responses,and pedigree analyses,but allelism tests,cloning or precise phenotypic comparisons would be needed for confirmation.The YrC271 region provided the opportunity for further map-based cloning and haplotypes analysis enabled pyramiding favorable alleles into commercial cultivars by marker-assisted selection.