Table 1_Discovery and development of single-nucleotide polymorphism markers for resistance to Striga gesnerioides in cowpea (Vigna unguiculata).xlsx

IntroductionThe parasitic weed [Striga gesnerioides (Willd.) Vatke] is a principal biotic constraint to cowpea [Vigna unguiculata (L.) Walp.] production in West and Central Africa, causing severe yield reductions. Multiple races of S. gesnerioides exist across the cowpea-growing areas of the sub-region. Past efforts identified some resistant sources and race-specific genes underpinning Striga resistance, but deployment of associated markers in breeding is limited. Here, we utilized a 51K cowpea iSelect single-nucleotide polymorphisms (SNPs) to decipher genomic regions underlying Striga resistance and explore marker conversion and validation for easy deployment.
MethodThe study used two-year phenotypic data on a minicore panel of 368 cowpea genotypes screened at two sites in Northern Nigeria. SNPs performances were verified and validated using two independent sets of 60 and 20 diverse genotypes respectively.
ResultsThe minicore displayed apparent differences in response to the S. gesnerioides attack. A genome-wide scan uncovered a primary gene effect signal on chromosome Vu11 and minor regions on chromosomes Vu02, Vu03, Vu07, Vu09 and Vu10. The major effect region on Vu11 harbored a coil-coil nucleotide-binding site leucine-rich repeat (CC-NBS-LRR) protein, encoded by the RSG3–301 gene, previously implicated in race-specific resistance to S. gesnerioides in cowpea. The associated SNPs were successfully converted into Kompetitive Allele-Specific PCR (KASP) assays and validated using 20 independent diverse cowpea genotypes. Five KASP markers, snpVU00075, snpVU00076, snpVU00077, snpVU00078, and snpVU00079, depicted consistent and significant associations with the phenotype in the validation set.
DiscussionThe markers provide valuable tools for efficient marker-assisted selection (MAS) in breeding programs focused on developing Striga-resistant cowpea varieties.

引言：寄生性杂草列当（Striga gesnerioides (Willd.) Vatke）是西非与中非地区豇豆[Vigna unguiculata (L.) Walp.]生产的主要生物胁迫因子，可造成严重的产量损失。该次区域的豇豆种植区域内存在多个该列当物种的生理小种。过往研究已鉴定出部分抗源及调控列当抗性的生理小种特异性基因，但相关分子标记在育种中的应用仍较为有限。本研究采用51K豇豆iSelect单核苷酸多态性（single-nucleotide polymorphisms, SNPs）标记芯片，解析介导列当抗性的基因组区域，并探索标记转化与验证方案以推动其便捷应用。
材料与方法：本研究使用了尼日利亚北部两个试验点对368份豇豆核心微集合（minicore panel）基因型进行两年表型鉴定获得的数据。研究利用两组独立的多样化豇豆基因型群体（分别包含60份与20份材料）对单核苷酸多态性标记的性能进行验证。
结果：该核心微集合对S. gesnerioides侵染的响应表现出显著差异。全基因组扫描鉴定到11号染色体（Vu11）上存在主效基因效应信号，同时在Vu02、Vu03、Vu07、Vu09及Vu10号染色体上存在次要效应区域。Vu11染色体上的主效区域包含一个由RSG3–301基因编码的卷曲螺旋-核苷酸结合位点-富亮氨酸重复（coil-coil nucleotide-binding site leucine-rich repeat, CC-NBS-LRR）蛋白，该基因此前被报道参与调控豇豆对S. gesnerioides的生理小种特异性抗性。关联的单核苷酸多态性标记已成功转化为竞争性等位基因特异性PCR（Kompetitive Allele-Specific PCR, KASP）检测体系，并通过20份独立的多样化豇豆基因型群体完成验证。其中5个KASP标记，即snpVU00075、snpVU00076、snpVU00077、snpVU00078与snpVU00079，在验证群体中与表型呈现出稳定且显著的关联。
讨论：上述标记可为聚焦培育抗列当豇豆品种的育种项目中高效开展标记辅助选择（marker-assisted selection, MAS）提供极具价值的工具。