Sim Sung-Chur, Robbins Matthew D, Wijeratne Saranga, Wang Hui, Yang Wencai, Francis David M
First, second, and sixth authors: Department of Horticulture and Crop Science, The Ohio State University, Ohio Agricultural Research and Development Center, Wooster 44691; first author: Department of Bioresources Engineering, Sejong University, 98 Gunja-dong Gwangjin-gu Seoul, 143-747 Korea; second author: USDA Forage & Range Research Laboratory, Logan, UT 84322; third author: Molecular and Cellular Imaging Center, The Ohio State University, Ohio Agricultural Research and Development Center, Wooster 44691; fourth and fifth authors: Department of Vegetable Science, China Agricultural University, Beijing 100193, China; and fourth author: Dupont Pioneer, Woodstock, ON, N4S 7V6, Canada.
Phytopathology. 2015 Nov;105(11):1437-45. doi: 10.1094/PHYTO-02-15-0051-R. Epub 2015 Oct 28.
Bacterial spot of tomato is caused by at least four species of Xanthomonas with multiple physiological races. We developed a complex breeding population for simultaneous discovery of marker-trait linkage, validation of existing quantitative trait loci (QTL), and pyramiding of resistance. Six advanced accessions with resistance from distinct sources were crossed in all combinations and their F1 hybrids were intercrossed. Over 1,100 segregating progeny were evaluated in the field following inoculation with X. euvesicatoria race T1 strains. We selected 5% of the most resistant and 5% of the most susceptible progeny for evaluation as plots in two subsequent replicated field trials inoculated with T1 and T3 (X. perforans) strains. The estimated heritability of T1 resistance was 0.32. In order to detect previously reported resistance genes, as well as novel QTL, we explored methods to correct for population structure and analysis based on single markers or haplotypes. Both single-point and haplotype analyses identified strong associations in the genomic regions known to carry Rx-3 (chromosome 5) and Rx-4/Xv3 (chromosome 11). Accounting for kinship and structure generally improved the fit of statistical models. Detection of known loci was improved by adding kinship or a combination of kinship and structure using a Q matrix from model-based clustering. Additional QTL were detected on chromosomes 1, 4, 6, and 7 for T1 resistance and chromosomes 2, 4, and 6 for T3 resistance (P < 0.01). Haplotype analysis improved our ability to trace the origin of positive alleles. These results demonstrate that both known and novel associations can be identified using complex breeding populations that have experienced directional selection.
番茄细菌性斑点病由至少四种具有多个生理小种的黄单胞菌引起。我们构建了一个复合育种群体，用于同时发现标记-性状连锁关系、验证现有数量性状位点（QTL）以及聚合抗性。将六个来自不同来源的抗性先进种质进行所有组合的杂交，并使它们的F1杂种相互杂交。在接种丁香假单胞菌番茄致病变种T1菌株后，在田间对1100多个分离后代进行了评估。我们选择了5%抗性最强和5%最感病的后代作为小区，在随后两次接种T1和T3（穿孔假单胞菌）菌株的重复田间试验中进行评估。T1抗性的估计遗传力为0.32。为了检测先前报道的抗性基因以及新的QTL，我们探索了校正群体结构的方法以及基于单标记或单倍型的分析方法。单点分析和单倍型分析均在已知携带Rx-3（5号染色体）和Rx-4/Xv3（11号染色体）的基因组区域中发现了强关联。考虑亲缘关系和群体结构通常会改善统计模型的拟合度。通过添加亲缘关系或使用基于模型聚类的Q矩阵将亲缘关系和群体结构相结合，已知位点的检测得到了改善。在1号、4号、6号和7号染色体上检测到了T1抗性的额外QTL，在2号、4号和6号染色体上检测到了T3抗性的额外QTL（P<0.01）。单倍型分析提高了我们追踪正向等位基因起源的能力。这些结果表明，使用经过定向选择的复合育种群体可以识别已知和新的关联。
