Table_1_A robust SNP-haplotype assay for Bct gene region conferring resistance to beet curly top virus in common bean (Phaseolus vulgaris L.).xlsx

Beet curly top virus (BCTV), which is synonymous with curly top virus (CTV), causes significant yield loss in common bean (snap and dry beans) cultivars and several other important crops. Common bean cultivars have been found to be resistant to CTV, but screening for resistance is challenging due to the cyclical nature of epidemics and spotty feeding by the leafhopper that vectors the virus. We used an SNP dataset for the Snap Bean Association Panel (SnAP) agro-inoculated with CTV-Logan (CA/Logan) strain to locate the Bct gene region to a 1.7-Mb interval on chromosome Pv07 using genome-wide association study (GWAS) analysis. Recombinant lines from the SnAP were used to further narrow the Bct region to a 58.0-kb interval. A missense SNP (S07_2970381) in candidate gene Phvul.007G036300 Exonuclease V (EXO5) was identified as the most likely causal mutation, and it was the most significant SNP detected by GWAS in a dry bean population (DBP) naturally infected by the CTV-Worland (Wor) strain. Tm-shift assay markers developed for SNP S07_2970381 and two linked SNPs, S07_2970276 and S07_2966197, were useful for tracking different origins of the Bct EXO5 candidate gene resistance to CTV in common bean. The three SNPs identified four haplotypes, with haplotype 3-1 (Haplo3-1) of Middle American origin associated with the highest levels of CTV resistance. This SNP-haplotype assay will enable breeders to track resistance sources and to develop cultivars with better CTV resistance.

甜菜曲顶病毒（Beet curly top virus, BCTV），又名曲顶病毒（curly top virus, CTV），可对普通菜豆（食荚菜豆与干粮菜豆）品种及其他多种重要作物造成显著产量损失。已有研究发现部分普通菜豆品种对CTV具有抗性，但由于病害流行呈周期性，且传毒媒介叶蝉的取食分布不均，抗病性筛选工作极具挑战性。本研究利用经CTV-Logan（CA/Logan）株系农杆菌介导接种的食荚菜豆关联作图群体（Snap Bean Association Panel, SnAP）的单核苷酸多态性（Single Nucleotide Polymorphism, SNP）数据集，通过全基因组关联分析（genome-wide association study, GWAS）将Bct基因区域定位至菜豆第7号染色体（Pv07）上1.7兆碱基的区间内。利用SnAP群体中的重组自交系，研究人员进一步将Bct区域缩小至58.0千碱基区间。在候选基因Phvul.007G036300（核酸外切酶V, Exonuclease V, EXO5）中鉴定到的错义SNP位点S07_2970381，被确定为最可能的赋予CTV抗性的因果突变位点；同时该位点也是在自然感染CTV-Worland（Wor）株系的干粮菜豆群体（dry bean population, DBP）中，GWAS检测到的最显著SNP位点。针对S07_2970381及其两个连锁SNP位点S07_2970276、S07_2966197开发的Tm位移（Tm-shift）检测标记，可用于追踪普通菜豆中抗CTV的Bct EXO5候选基因的不同起源。上述三个SNP位点可区分四种单倍型，其中源自中美洲的单倍型3-1（Haplo3-1）与最高水平的CTV抗性相关。该SNP-单倍型检测方法可助力育种者追踪抗源材料，培育出抗CTV性能更优的菜豆品种。