Genome-Wide Association Study and Genomic Prediction on Plant Architecture Traits in Sweet Corn and Waxy Corn

Dongdong Dang; Yuan Guan; Hongjian Zheng; Xuecai Zhang; Ao Zhang; Hui Wang; Yanye Ruan; Li Qin

doi:10.3390/plants12020303

Plants (Jan 2023)

Genome-Wide Association Study and Genomic Prediction on Plant Architecture Traits in Sweet Corn and Waxy Corn

Dongdong Dang,
Yuan Guan,
Hongjian Zheng,
Xuecai Zhang,
Ao Zhang,
Hui Wang,
Yanye Ruan,
Li Qin

Affiliations

Dongdong Dang: Shenyang City Key Laboratory of Maize Genomic Selection Breeding, College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
Yuan Guan: CIMMYT-China Specialty Maize Research Center, Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
Hongjian Zheng: CIMMYT-China Specialty Maize Research Center, Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
Xuecai Zhang: International Maize and Wheat Improvement Center (CIMMYT), El Batan, Texcoco 56237, Mexico
Ao Zhang: Shenyang City Key Laboratory of Maize Genomic Selection Breeding, College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
Hui Wang: CIMMYT-China Specialty Maize Research Center, Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
Yanye Ruan: Shenyang City Key Laboratory of Maize Genomic Selection Breeding, College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
Li Qin: Shenyang City Key Laboratory of Maize Genomic Selection Breeding, College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China

DOI: https://doi.org/10.3390/plants12020303
Journal volume & issue: Vol. 12, no. 2
p. 303

Abstract

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Sweet corn and waxy corn has a better taste and higher accumulated nutritional value than regular maize, and is widely planted and popularly consumed throughout the world. Plant height (PH), ear height (EH), and tassel branch number (TBN) are key plant architecture traits, which play an important role in improving grain yield in maize. In this study, a genome-wide association study (GWAS) and genomic prediction analysis were conducted on plant architecture traits of PH, EH, and TBN in a fresh edible maize population consisting of 190 sweet corn inbred lines and 287 waxy corn inbred lines. Phenotypic data from two locations showed high heritability for all three traits, with significant differences observed between sweet corn and waxy corn for both PH and EH. The differences between the three subgroups of sweet corn were not obvious for all three traits. Population structure and PCA analysis results divided the whole population into three subgroups, i.e., sweet corn, waxy corn, and the subgroup mixed with sweet and waxy corn. Analysis of GWAS was conducted with 278,592 SNPs obtained from resequencing data; 184, 45, and 68 significantly associated SNPs were detected for PH, EH, and TBN, respectively. The phenotypic variance explained (PVE) values of these significant SNPs ranged from 3.50% to 7.0%. The results of this study lay the foundation for further understanding the genetic basis of plant architecture traits in sweet corn and waxy corn. Genomic selection (GS) is a new approach for improving quantitative traits in large plant breeding populations that uses whole-genome molecular markers. The marker number and marker quality are essential for the application of GS in maize breeding. GWAS can choose the most related markers with the traits, so it can be used to improve the predictive accuracy of GS.

Published in Plants

ISSN: 2223-7747 (Online)
Publisher: MDPI AG
Country of publisher: Switzerland
LCC subjects: Science: Botany
Website: http://www.mdpi.com/journal/plants

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