Integration of GWAS models and GS reveals the genetic architecture of ear shank in maize.

IF 2.6 3区 生物学 Q2 GENETICS & HEREDITY
Gene Pub Date : 2024-12-05 DOI:10.1016/j.gene.2024.149140
Jiale Jiang, Jiaojiao Ren, Yukang Zeng, Xiaoming Xu, Shaohang Lin, Zehui Fan, Yao Meng, Yirui Ma, Xin Li, Penghao Wu
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引用次数: 0

Abstract

Maize is one of the most important crops for human food, animal feed, and industrial raw materials. Ear shank length (ESL) and ear shank node number (ESNN) are crucial selection criteria in maize breeding, impacting grain yield and dehydration rate during mechanical harvesting. To unravel the genetic basis of ESL and ESNN in maize, an association panel consisting of 379 multi-parent doubled-haploid (DH) lines was developed for genome-wide association studies (GWAS) and genomic selection (GS). The heritabilities of ESL and ESNN were 0.68 and 0.55, respectively, which were controlled by genetic factors and genotype-environment interaction factors. Using five different models for GWAS, 11 significant single nucleotide polymorphisms (SNPs) located on chromosomes 1, 2, and 4 were identified for ESL, with the phenotypic variation explained (PVE) value of each single SNP ranging from 4.91% to 21.35%, and 11 significant SNPs located on chromosomes 1, 2, 4, and 5 were identified for ESNN, with the PVE value of each SNP ranging from 1.22% to 18.42%. Genetic regions in bins 1.06, 2.06, and 2.08 were significantly enriched in SNPs associated with ear shank-related traits. The GS prediction accuracy using all markers by the five-fold cross-validation method for ESL and ESNN was 0.39 and 0.37, respectively, which was significantly improved by using only 500-1000 significant SNPs with the lowest P-values. The optimal training population size (TPS) and marker density (MD) for ear shank-related traits were 50%-60% and 3000, respectively. Our results provide new insights into the GS of ear shank-related traits.

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来源期刊
Gene
Gene 生物-遗传学
CiteScore
6.10
自引率
2.90%
发文量
718
审稿时长
42 days
期刊介绍: Gene publishes papers that focus on the regulation, expression, function and evolution of genes in all biological contexts, including all prokaryotic and eukaryotic organisms, as well as viruses.
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