QTL Analysis of Kernel-Related Traits in Maize Using an Immortalized F2 Population

Zhanhui Zhang,Dong Ding,Zonghua Liu,Jihua Tang,Haochuan Li,Yanmin Hu,Mengmeng Qiao,Zhiyuan Fu,Weihua Li,James C. Nelson

doi:10.1371/journal.pone.0089645

Zhanhui Zhang, Dong Ding + Show 8 more

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https://doi.org/10.1371/journal.pone.0089645

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Abstract

Kernel size and weight are important determinants of grain yield in maize. In this study, multivariate conditional and unconditional quantitative trait loci (QTL), and digenic epistatic analyses were utilized in order to elucidate the genetic basis for these kernel-related traits. Five kernel-related traits, including kernel weight (KW), volume (KV), length (KL), thickness (KT), and width (KWI), were collected from an immortalized F2 (IF2) maize population comprising of 243 crosses performed at two separate locations over a span of two years. A total of 54 unconditional main QTL for these five kernel-related traits were identified, many of which were clustered in chromosomal bins 6.04–6.06, 7.02–7.03, and 10.06–10.07. In addition, qKL3, qKWI6, qKV10a, qKV10b, qKW10a, and qKW7a were detected across multiple environments. Sixteen main QTL were identified for KW conditioned on the other four kernel traits (KL, KWI, KT, and KV). Thirteen main QTL were identified for KV conditioned on three kernel-shape traits. Conditional mapping analysis revealed that KWI and KV had the strongest influence on KW at the individual QTL level, followed by KT, and then KL; KV was mostly strongly influenced by KT, followed by KWI, and was least impacted by KL. Digenic epistatic analysis identified 18 digenic interactions involving 34 loci over the entire genome. However, only a small proportion of them were identical to the main QTL we detected. Additionally, conditional digenic epistatic analysis revealed that the digenic epistasis for KW and KV were entirely determined by their constituent traits. The main QTL identified in this study for determining kernel-related traits with high broad-sense heritability may play important roles during kernel development. Furthermore, digenic interactions were shown to exert relatively large effects on KL (the highest AA and DD effects were 4.6% and 6.7%, respectively) and KT (the highest AA effects were 4.3%).

Highlights

Many biologically and agriculturally important traits are defined by complex genetic mechanisms
Of the 54 unconditional main quantitative trait loci (QTL) identified for five kernelrelated traits, many of which clustered in chromosomal bins 10.06–10.07, 6.04–6.06, and 7.02–7.03
Within the 10.06–10.07 genomic region, Peng et al (2011) identified QTL for kernel weight (KW), KV, KL, and KWI in two F2:3 populations [8]; and within this region, a QTL for grain yield was found by Tuberosa et al (2002) [36]

Summary

Introduction

Many biologically and agriculturally important traits are defined by complex genetic mechanisms. They are controlled by interacting networks comprised of multiple genes with relatively small genetic effects, and determined by their constituent traits [1,2]. Maize kernel weight is affected by multiple biological processes. These processes can be studied at different organizational levels, with respects to two very important maize yieldrelated traits: kernel size and kernel growth rate [9,10,11]. During the kernel development process, kernel growth rate is dynamic and determines the final kernel weight [4]. Numerous studies have focused on kernel development at the cellular and tissue level [4,13,14], as well as kernel growth at the whole-plant level during the grain-filling period [9,15,16]

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