Multi-Locus Genome-Wide Association Study and Genomic Selection of Kernel Moisture Content at the Harvest Stage in Maize.

Guangfei Zhou,Qiuli Zhu,Huhua Lu,Lin Xue,Zhenliang Zhang,Derong Hao,Mingliang Shi,Guoqing Chen,Xudong Song,Yuxiang Mao,Huimin Zhang

doi:10.3389/fpls.2021.697688

Abstract

Kernel moisture content at the harvest stage (KMC) is an important trait that affects the mechanical harvesting of maize grain, and the identification of genetic loci for KMC is beneficial for maize molecular breeding. In this study, we performed a multi-locus genome-wide association study (ML-GWAS) to identify quantitative trait nucleotides (QTNs) for KMC using an association mapping panel of 251 maize inbred lines that were genotyped with an Affymetrix CGMB56K SNP Array and phenotypically evaluated in three environments. Ninety-eight QTNs for KMC were detected using six ML-GWAS models (mrMLM, FASTmrMLM, FASTmrEMMA, PLARmEB, PKWmEB, and ISIS EM-BLASSO). Eleven of these QTNs were considered to be stable, as they were detected by at least four ML-GWAS models under a uniformed environment or in at least two environments and BLUP using the same ML-GWAS model. With qKMC5.6 removed, the remaining 10 stable QTNs explained <10% of the phenotypic variation, suggesting that KMC is mainly controlled by multiple minor-effect genetic loci. A total of 63 candidate genes were predicted from the 11 stable QTNs, and 10 candidate genes were highly expressed in the kernel at different time points after pollination. High prediction accuracy was achieved when the KMC-associated QTNs were included as fixed effects in genomic selection, and the best strategy was to integrate all KMC QTNs identified by all six ML-GWAS models. These results further our understanding of the genetic architecture of KMC and highlight the potential of genomic selection for KMC in maize breeding.

Highlights

Kernel moisture content at the harvest stage (KMC) is one of the important traits that influence maize mechanical harvesting, especially in high latitude areas (Sala et al, 2012; Li et al, 2017)
The change in kernel moisture is primarily caused by moisture evaporation into the air and is readily influenced by environmental factors and other agronomic traits; this is known as the field dehydration stage (Brooking, 1990; Reid et al, 2010)
The LnP(D) values increased as K increased from 1 to 10 without an obvious inflection point, and K reached its peak at K = 6 (Figure 1A), suggesting that this association mapping panel could be divided into six subgroups (Figure 1B)

Summary

Introduction

Kernel moisture content at the harvest stage (KMC) is one of the important traits that influence maize mechanical harvesting, especially in high latitude areas (Sala et al, 2012; Li et al, 2017). The high KMC of currently used maize varieties restricts mechanical harvesting and represents the major barrier to maize development in China (Zhou et al, 2016, 2020; Li et al, 2017). The second phase lasts from physiological maturity to harvest During this phase, the change in kernel moisture is primarily caused by moisture evaporation into the air and is readily influenced by environmental factors and other agronomic traits; this is known as the field dehydration stage (Brooking, 1990; Reid et al, 2010). Moisture from the kernels can be transported to other plant parts through the cob and stem in response to water potential differences (Zhou et al, 2018)

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