Genome-wide association mapping and genomic prediction of stalk rot in two mid-altitude tropical maize populations
Junqiao Song,
Angela Pacheco,
Amos Alakonya,
Andrea S. Cruz-Morales,
Carlos Muñoz-Zavala,
Jingtao Qu,
Chunping Wang,
Xuecai Zhang,
Felix San Vicente,
Thanda Dhliwayo
Affiliations
Junqiao Song
College of Agronomy, Henan University of Science and Technology, Luoyang 471000, Henan, China; International Maize and Wheat Improvement Center (CIMMYT), El Batan, Mexico; Anyang Academy of Agricultural Sciences, Anyang 455000, Henan, China
Angela Pacheco
International Maize and Wheat Improvement Center (CIMMYT), El Batan, Mexico
Amos Alakonya
International Maize and Wheat Improvement Center (CIMMYT), El Batan, Mexico
Andrea S. Cruz-Morales
International Maize and Wheat Improvement Center (CIMMYT), El Batan, Mexico
Carlos Muñoz-Zavala
International Maize and Wheat Improvement Center (CIMMYT), El Batan, Mexico
Jingtao Qu
CIMMYT-China Specialty Maize Research Center, Crop Breeding, and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
Chunping Wang
College of Agronomy, Henan University of Science and Technology, Luoyang 471000, Henan, China; Corresponding authors.
Xuecai Zhang
International Maize and Wheat Improvement Center (CIMMYT), El Batan, Mexico
Felix San Vicente
International Maize and Wheat Improvement Center (CIMMYT), El Batan, Mexico
Thanda Dhliwayo
International Maize and Wheat Improvement Center (CIMMYT), El Batan, Mexico; Corresponding authors.
Maize stalk rot reduces grain yield and quality. Information about the genetics of resistance to maize stalk rot could help breeders design effective breeding strategies for the trait. Genomic prediction may be a more effective breeding strategy for stalk-rot resistance than marker-assisted selection. We performed a genome-wide association study (GWAS) and genomic prediction of resistance in testcross hybrids of 677 inbred lines from the Tuxpeño and non-Tuxpeño heterotic pools grown in three environments and genotyped with 200,681 single-nucleotide polymorphisms (SNPs). Eighteen SNPs associated with stalk rot shared genomic regions with gene families previously associated with plant biotic and abiotic responses. More favorable SNP haplotypes traced to tropical than to temperate progenitors of the inbred lines. Incorporating genotype-by-environment (G × E) interaction increased genomic prediction accuracy.
