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

Date
2019-01-01
Authors
Liu, Min
Tan, Xiaolong
Lubberstedt, Thomas
Yang, Yan
Liu, Peng
Zhang, Xiaoxiang
Zhang, Yinchao
Wang, Lei
Hu, Yu
Ma, Langlang
Li, Zhaoling
Zhang, Yanling
Zou, Chaoying
Lin, Haijian
Gao, Shibin
Lee, Michael
Lubberstedt, Thomas
Pan, Guangtang
Shen, Yaou
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Agronomy
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Kernel 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.

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This article is published as Liu, Min, Xiaolong Tan, Yan Yang, Peng Liu, Xiaoxiang Zhang, Yinchao Zhang, Lei Wang et al. "Analysis of the genetic architecture of maize kernel size traits by combined linkage and association mapping." Plant biotechnology journal (2019). doi: 10.1111/pbi.13188.

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