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Dong Y, Li G, Zhang X, Feng Z, Li T, Li Z, Xu S, Xu S, Liu W, Xue J. Genome-Wide Association Study for Maize Hybrid Performance in a Typical Breeder Population. Int J Mol Sci 2024; 25:1190. [PMID: 38256265 PMCID: PMC10816832 DOI: 10.3390/ijms25021190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/14/2024] [Accepted: 01/16/2024] [Indexed: 01/24/2024] Open
Abstract
Maize is one of the major crops that has demonstrated success in the utilization of heterosis. Developing high-yield hybrids is a crucial part of plant breeding to secure global food demand. In this study, we conducted a genome-wide association study (GWAS) for 10 agronomic traits using a typical breeder population comprised 442 single-cross hybrids by evaluating additive, dominance, and epistatic effects. A total of 49 significant single nucleotide polymorphisms (SNPs) and 69 significant pairs of epistasis were identified, explaining 26.2% to 64.3% of the phenotypic variation across the 10 traits. The enrichment of favorable genotypes is significantly correlated to the corresponding phenotype. In the confident region of the associated site, 532 protein-coding genes were discovered. Among these genes, the Zm00001d044211 candidate gene was found to negatively regulate starch synthesis and potentially impact yield. This typical breeding population provided a valuable resource for dissecting the genetic architecture of yield-related traits. We proposed a novel mating strategy to increase the GWAS efficiency without utilizing more resources. Finally, we analyzed the enrichment of favorable alleles in the Shaan A and Shaan B groups, as well as in each inbred line. Our breeding practice led to consistent results. Not only does this study demonstrate the feasibility of GWAS in F1 hybrid populations, it also provides a valuable basis for further molecular biology and breeding research.
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Affiliation(s)
- Yuan Dong
- Key Laboratory of Biology and Genetic Breeding of Maize in Arid Area of Northwest Region, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Guoliang Li
- National Maize Improvement Center of China, Key Laboratory of Crop Heterosis and Utilization (MOE), China Agricultural University, Beijing 100193, China
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany
| | - Xinghua Zhang
- Key Laboratory of Biology and Genetic Breeding of Maize in Arid Area of Northwest Region, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Zhiqian Feng
- Key Laboratory of Biology and Genetic Breeding of Maize in Arid Area of Northwest Region, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Ting Li
- Key Laboratory of Biology and Genetic Breeding of Maize in Arid Area of Northwest Region, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Zhoushuai Li
- Key Laboratory of Biology and Genetic Breeding of Maize in Arid Area of Northwest Region, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Shizhong Xu
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Shutu Xu
- Key Laboratory of Biology and Genetic Breeding of Maize in Arid Area of Northwest Region, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Wenxin Liu
- National Maize Improvement Center of China, Key Laboratory of Crop Heterosis and Utilization (MOE), China Agricultural University, Beijing 100193, China
| | - Jiquan Xue
- Key Laboratory of Biology and Genetic Breeding of Maize in Arid Area of Northwest Region, College of Agronomy, Northwest A&F University, Yangling 712100, China
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