Genetic architecture of maize yield traits dissected by QTL mapping and GWAS in maize
Xiao Zhang,
Zhiyong Ren,
Bowen Luo,
Haixu Zhong,
Peng Ma,
Hongkai Zhang,
Hongmei Hu,
Yikai Wang,
Haiying Zhang,
Dan Liu,
Ling Wu,
Zhi Nie,
Yonghui Zhu,
Wenzhu He,
Suzhi Zhang,
Shunzong Su,
Yaou Shen,
Shibin Gao
Affiliations
Xiao Zhang
Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, Sichuan, China; Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, Sichuan, China
Zhiyong Ren
Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, Sichuan, China; Guangxi QingQing Agricultural Technology CO. LTD., Nanning 530000, Guangxi, China
Bowen Luo
Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, Sichuan, China; Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, Sichuan, China
Haixu Zhong
Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, Sichuan, China; Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, Sichuan, China
Peng Ma
Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, Sichuan, China; Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, Sichuan, China
Hongkai Zhang
Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, Sichuan, China; Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, Sichuan, China
Hongmei Hu
Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, Sichuan, China; Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, Sichuan, China
Yikai Wang
Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, Sichuan, China; Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, Sichuan, China
Haiying Zhang
Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, Sichuan, China; Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, Sichuan, China
Dan Liu
Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, Sichuan, China; Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, Sichuan, China
Ling Wu
Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, Sichuan, China; Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, Sichuan, China
Zhi Nie
Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, Sichuan, China
Yonghui Zhu
Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, Sichuan, China
Wenzhu He
Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, Sichuan, China
Suzhi Zhang
Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, Sichuan, China; Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, Sichuan, China; State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu 611130, Sichuan, China
Shunzong Su
College of Agronomy, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
Yaou Shen
Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, Sichuan, China; Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, Sichuan, China; State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu 611130, Sichuan, China
Shibin Gao
Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, Sichuan, China; Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, Sichuan, China; State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu 611130, Sichuan, China; Corresponding author.
The study of yield traits can reveal the genetic architecture of grain yield for improving maize production. In this study, an association panel comprising 362 inbred lines and a recombinant inbred line population derived from X178 × 9782 were used to identify candidate genes for nine yield traits. High-priority overlap (HPO) genes, which are genes prioritized in a genome-wide association study (GWAS), were investigated using coexpression networks. The GWAS identified 51 environmentally stable SNPs in two environments and 36 pleiotropic SNPs, including three SNPs with both attributes. Seven hotspots containing 41 trait-associated SNPs were identified on six chromosomes by permutation. Pyramiding of superior alleles showed a highly positive effect on all traits, and the phenotypic values of ear diameter and ear weight consistently corresponded with the number of superior alleles in tropical and temperate germplasm. A total of 61 HPO genes were detected after trait-associated SNPs were combined with the coexpression networks. Linkage mapping identified 16 environmentally stable and 16 pleiotropic QTL. Seven SNPs that were located in QTL intervals were assigned as consensus SNPs for the yield traits. Among the candidate genes predicted by our study, some genes were confirmed to function in seed development. The gene Zm00001d016656 encoding a serine/threonine protein kinase was associated with five different traits across multiple environments. Some genes were uniquely expressed in specific tissues and at certain stages of seed development. These findings will provide genetic information and resources for molecular breeding of maize grain yield.
