Record Details

Comparison of sequencing-based and array-based genotyping platforms for genomic prediction of maize hybrid performance

CGSpace

View Archive Info
 
 
Field Value
 
Title Comparison of sequencing-based and array-based genotyping platforms for genomic prediction of maize hybrid performance
 
Creator Yu, Guangning
Cui, Yanru
Jiao, Yuxin
Zhou, Kai
Xin Wang
Yang, Wenyan
Xu, Yiyi
Yang, Kun
Zhang, Xuecai
Pengcheng Li
Zefeng Yang
Yang Xu
Chenwu Xu
 
Subject marker-assisted selection
maize
single nucleotide polymorphism
hybrids
 
Description Genomic selection (GS) is a powerful tool for improving genetic gain in maize breeding. However, its routine application in large-scale breeding pipelines is limited by the high cost of genotyping platforms. Although sequencing-based and array-based genotyping platforms have been used for GS, few studies have compared prediction performance among platforms. In this study, we evaluated the predictabilities of four agronomic traits in 305 maize hybrids derived from 149 parental lines subjected to genotyping by sequencing (GBS), a 40K SNP array, and target sequence capture (TSC) using eight GS models. The GBS marker dataset yielded the highest predictabilities for all traits, followed by TSC and SNP array datasets. We investigated the effect of marker density and statistical models on predictability among genotyping platforms and found that 1K SNPs were sufficient to achieve comparable predictabilities to 10K and all SNPs, and BayesB, GBLUP, and RKHS performed well, while XGBoost performed poorly in most cases. We also selected significant SNP subsets using genome-wide association study (GWAS) analyses in three panels to predict hybrid performance. GWAS facilitated selecting effective SNP subsets for GS and thus reduced genotyping cost, but depended heavily on the GWAS panel. We conclude that there is still room for optimization of the existing SNP array, and using genotyping by target sequencing (GBTS) techniques to integrate a few functional markers identified by GWAS into the 1K SNP array holds great promise of being an effective strategy for developing desirable GS breeding arrays.
 
Date 2022
2023-01-04T13:06:32Z
2023-01-04T13:06:32Z
 
Type Journal Article
 
Identifier Yu, G., Cui, Y., Jiao, Y., Zhou, K., Wang, X., Yang, W., Xu, Y., Yang, K., Zhang, X., Li, P., Yang, Z., Xu, Y., & Xu, C. (2022). Comparison of sequencing-based and array-based genotyping platforms for genomic prediction of maize hybrid performance. The Crop Journal, S2214514122002173. https://hdl.handle.net/10883/22283
2214-5141
https://hdl.handle.net/10568/126559
https://hdl.handle.net/10883/22283
https://doi.org/10.1016/j.cj.2022.09.004
 
Language en
 
Rights CC-BY-NC-ND-4.0
Open Access
 
Format application/pdf
 
Publisher Elsevier
 
Source The Crop Journal