Wiersma Andrew T, Hamilton John P, Vaillancourt Brieanne, Brose Julia, Awale Halima E, Wright Evan M, Kelly James D, Buell C Robin
Archer Daniels Midland Company, New Plymouth, Idaho, USA.
Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan, USA.
Plant Genome. 2024 Dec;17(4):e20523. doi: 10.1002/tpg2.20523. Epub 2024 Oct 13.
Access to broad genomic resources and closely linked marker-trait associations for common beans (Phaseolus vulgaris L.) can facilitate development of improved varieties with increased yield, improved market quality traits, and enhanced disease resistance. The emergence of virulent races of anthracnose (caused by Colletotrichum lindemuthianum) and bean common mosaic virus (BCMV) highlight the need for improved methods to identify and incorporate pan-genomic variation in breeding for disease resistance. We sequenced the P. vulgaris Andean Diversity Panel (ADP) and performed a genome-wide association study (GWAS) to identify associations for resistance to BCMV and eight races of anthracnose. Historical single nucleotide polymorphism (SNP)-chip and phenotypic data enabled a three-way comparison between SNP-chip, reference-based whole genome shotgun sequence (WGS)-SNP, and reference-free k-mer (short nucleotide subsequence) GWAS. Across all traits, there was excellent concordance between SNP-chip, WGS-SNP, and k-mer GWAS results-albeit at a much higher marker resolution for the WGS data sets. Significant k-mer haplotype variation revealed selection of the linked I-gene and Co-u traits in North American breeding lines and cultivars. Due to structural variation, only 9.1 to 47.3% of the significantly associated k-mers could be mapped to the reference genome. Thus, to determine the genetic context of cis-associated k-mers, we generated draft whole genome assemblies of four ADP accessions and identified an expanded local repertoire of disease resistance genes associated with resistance to anthracnose and BCMV. With access to variant data in the context of a pan-genome, high resolution mapping of agronomic traits for common bean is now feasible.
获得广泛的基因组资源以及与普通菜豆（Phaseolus vulgaris L.）紧密连锁的标记-性状关联，有助于培育产量更高、市场品质性状更好且抗病性更强的改良品种。炭疽病（由Colletotrichum lindemuthianum引起）和菜豆普通花叶病毒（BCMV）的毒性小种的出现，凸显了改进方法以识别并将泛基因组变异纳入抗病育种的必要性。我们对普通菜豆安第斯多样性面板（ADP）进行了测序，并开展了全基因组关联研究（GWAS），以确定对BCMV和八种炭疽病小种的抗性关联。历史单核苷酸多态性（SNP）芯片和表型数据实现了SNP芯片、基于参考基因组的全基因组鸟枪法测序（WGS）-SNP和无参考基因组的k-mer（短核苷酸子序列）GWAS之间的三方比较。在所有性状上，SNP芯片、WGS-SNP和k-mer GWAS结果之间具有极好的一致性——尽管WGS数据集的标记分辨率要高得多。显著的k-mer单倍型变异揭示了北美育种系和品种中连锁的I基因和Co-u性状的选择。由于结构变异，只有9.1%至47.3%的显著关联k-mer能够定位到参考基因组上。因此，为了确定顺式关联k-mer的遗传背景，我们生成了四个ADP种质的全基因组草图组装，并鉴定出与炭疽病和BCMV抗性相关的抗病基因的扩展本地库。有了泛基因组背景下的变异数据，现在对普通菜豆农艺性状进行高分辨率定位是可行的。
