Analysis of the genetic architecture of maize kernel size traits by combined linkage and association mapping.

Min Liu,Xiaolong Tan,Yanling Zhang,Zhaoling Li,Langlang Ma,Guangtang Pan,Thomas Lübberstedt,Chaoying Zou,Peng Liu,Yu Hu,Yinchao Zhang,Yaou Shen,Michael Lee,Haijian Lin,Shibin Gao,Yan Yang,Xiaoxiang Zhang,Lei Wang

doi:10.1111/pbi.13188

Min Liu, Xiaolong Tan + Show 16 more

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https://doi.org/10.1111/pbi.13188

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Abstract

SummaryKernel size‐related traits are the most direct traits correlating with grain yield. The genetic basis of three kernel traits of maize, kernel length (KL), kernel width (KW) and kernel thickness (KT), was investigated in an association panel and a biparental population. A total of 21 single nucleotide polymorphisms (SNPs) were detected to be most significantly (P < 2.25 × 10−6) associated with these three traits in the association panel under four environments. Furthermore, 50 quantitative trait loci (QTL) controlling these traits were detected in seven environments in the intermated B73 × Mo17 (IBM) Syn10 doubled haploid (DH) population, of which eight were repetitively identified in at least three environments. Combining the two mapping populations revealed that 56 SNPs (P < 1 × 10−3) fell within 18 of the QTL confidence intervals. According to the top significant SNPs, stable‐effect SNPs and the co‐localized SNPs by association analysis and linkage mapping, a total of 73 candidate genes were identified, regulating seed development. Additionally, seven miRNAs were found to situate within the linkage disequilibrium (LD) regions of the co‐localized SNPs, of which zma‐miR164e was demonstrated to cleave the mRNAs of Arabidopsis CUC1,CUC2 and NAC6 in vitro. Overexpression of zma‐miR164e resulted in the down‐regulation of these genes above and the failure of seed formation in Arabidopsis pods, with the increased branch number. These findings provide insights into the mechanism of seed development and the improvement of molecular marker‐assisted selection (MAS) for high‐yield breeding in maize.

Highlights

Maize (Zea mays) is one of the most important staple crops, which serves as a resource for human nutrition, animal feed and bioenergy (Godfray et al, 2010)
Seven miRNAs were found to situate within the linkage disequilibrium (LD) regions of the co-localized single nucleotide polymorphisms (SNPs), of which zma-miR164e was demonstrated to cleave the mRNAs of Arabidopsis CUC1, CUC2 and NAC6 in vitro
kernel width (KW) was consistently significantly positively correlated with kernel thickness (KT) [r = 0.293 (E1a), 0.217 (E2a), 0.309 (E3a); P < 0.01] across the three environments, and kernel length (KL) was significantly negatively correlated with KT [r = À0.252 (E2a), À0.127 (E3a); P < 0.05] across two of the environments (Table S3)

Summary

Introduction

Maize (Zea mays) is one of the most important staple crops, which serves as a resource for human nutrition, animal feed and bioenergy (Godfray et al, 2010). Zhang et al (2017a) detected 108 QTL for eight ear and grain traits by combined linkage and association mapping (Zhang et al, 2017a) These researches in maize are relatively fewer compared to those involving rice. Numerous genes involved in rice kernel traits have been isolated and functionally characterized using map-based cloning and GWAS strategies, such as LONG KERNEL 3 (GS3), GRAIN SIZE 5 (GS5), GRAIN WEIGHT 2 (GW2), GRAIN WIDTH 5 (GW5), Grain Width/Length QTL on chromosome 7 (GW7/GL7) and GRAIN WIDTH 8 (GW8; Fan et al, 2006; Li et al, 2011; Mao et al, 2010; Si et al, 2015; Song et al, 2007; Wang et al, 2012b, 2015a,b; Weng et al, 2008).

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