Association Analysis for Bacterial Spot Resistance in a Directionally Selected Complex Breeding Population of Tomato.
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.
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.
Sung-Chur
SC
Sim
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.
Matthew D
MD
Robbins
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.
Saranga
S
Wijeratne
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.
Hui
H
Wang
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.
Wencai
W
Yang
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.
David M
DM
Francis
D060467:Disease Resistance / Q000235:genetics*; D054884:Host-Pathogen Interactions; D018551:Solanum lycopersicum / Q000235:genetics* / Q000276:immunology / Q000382:microbiology; D015233:Models, Statistical; D010641:Phenotype; D000069600:Plant Breeding / Q000379:methods*; D010935:Plant Diseases; D011110:Polymorphism, Genetic; D040641:Quantitative Trait Loci; D012641:Selection, Genetic; D000068618:Selective Breeding; D014974:Xanthomonas / Q000502:physiology*
population structure; selective genotyping