Genome-Wide Association Study of Ear Related Traits in Maize Hybrids

Abstract

【Objective】Ear traits are important components of grain yield in maize. Dissecting their genetic basis and mining significant SNPs using genome-wide association study (GWAS) can provide references for cloning functional genes and breeding high-yield maize varieties. 【Method】A total of 115 superior inbred lines from Shaan A group and Shaan B group, as well as four domestic backbone lines were selected as parents. Based on NCⅡ genetic design, an association population consisting of 442 hybrids was constructed, which was planted in two different environments to collect phenotype data of ear traits. Meanwhile, all parental lines were sequenced by the tunable genotyping by sequencing (tGBS) protocols. According to the genotype of inbred lines, altogether 19 461 high-quality SNPs were inferred in the association population. Then, GWAS was performed using 19 461 SNPs and phenotype data by three models including additive, dominance and epistasis, respectively. Combining with the transcriptome data of maize ear related tissues in the public database and the annotation information of genes, candidate genes were predicted. 【Result】Phenotypic data analysis showed that eight ear traits followed a continuous distribution, and there were 3.78%-45.25% of phenotypic variation. Analysis of variance indicated that environment and genotype effects reached an extremely significant level (P＜0.001), and the range of broad-sense heritability was from 54.15% to 68.89%. And there were significantly positive or negative correlations among ear traits of hybrids. In total, 16, 3, 79 significant SNPs/pairs were identified under additive, dominant, and epistatic models, respectively. The significant loci detected by the three models cumulatively explained 38.21%-60.69% of the phenotypic variation of each trait. The cumulative phenotypic variation of significant SNP detected by additive model and epistatic model was 0.00-41.26% and 15.18%-45.36%, respectively. Effect analysis of significant SNPs identified by additive and dominant models showed most SNPs with additive or partial dominance effects, and only two with over-dominance effects. Further, only seven single-SNPs and five interaction pairs explained more than 5% of the phenotypic variation, and 17 candidate genes were predicted based on the SNP locations and gene expression information. 【Conclusion】Ear traits of maize hybrids were mainly affected by additive and epistasis effects, but less by dominance effects. Multiple SNPs identified by additive and dominant models showed additive and partially dominance effects, and aggregating favorable alleles of these SNPs could improve the target traits.