Nucleotide Diversity of the Maize ZmCNR13 Gene and Association With Ear Traits

Zhihao Zuo; Yue Lu; Minyan Zhu; Rujia Chen; Enying Zhang; Derong Hao; Qianfeng Huang; Hanyao Wang; Yanze Su; Zhichao Wang; Yang Xu; Pengcheng Li; Chenwu Xu; Zefeng Yang

doi:10.3389/fgene.2021.773597

Nucleotide Diversity of the Maize ZmCNR13 Gene and Association With Ear Traits

Front Genet. 2021 Oct 26:12:773597. doi: 10.3389/fgene.2021.773597. eCollection 2021.

Authors

Zhihao Zuo^{1

2

3}, Yue Lu^{1

2

3}, Minyan Zhu^{1

2

3}, Rujia Chen^{1

2

3}, Enying Zhang⁴, Derong Hao⁵, Qianfeng Huang^{1

2}, Hanyao Wang¹, Yanze Su¹, Zhichao Wang¹, Yang Xu^{1

2

3}, Pengcheng Li^{1

2

3}, Chenwu Xu^{1

2

3}, Zefeng Yang^{1

2

3}

Affiliations

¹ Jiangsu Key Laboratory of Crop Genetics and Physiology Key Laboratory of Plant Functional Genomics of the Ministry of Education Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China.
² Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China.
³ Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China.
⁴ College of Agronomy, Qingdao Agricultural University, Qingdao, China.
⁵ Jiangsu Yanjiang Institute of Agricultural Sciences, Nantong, China.

Abstract

The maize (Zea mays L.) ZmCNR13 gene, encoding a protein of fw2.2-like (FWL) family, has been demonstrated to be involved in cell division, expansion, and differentiation. In the present study, the genomic sequences of the ZmCNR13 locus were re-sequenced in 224 inbred lines, 56 landraces and 30 teosintes, and the nucleotide polymorphism and selection signature were estimated. A total of 501 variants, including 415 SNPs and 86 Indels, were detected. Among them, 51 SNPs and 4 Indels were located in the coding regions. Although neutrality tests revealed that this locus had escaped from artificial selection during the process of maize domestication, the population of inbred lines possesses lower nucleotide diversity and decay of linkage disequilibrium. To estimate the association between sequence variants of ZmCNR13 and maize ear characteristics, a total of ten ear-related traits were obtained from the selected inbred lines. Four variants were found to be significantly associated with six ear-related traits. Among them, SNP2305, a non-synonymous mutation in exon 2, was found to be associated with ear weight, ear grain weight, ear diameter and ear row number, and explained 4.59, 4.61, 4.31, and 8.42% of the phenotypic variations, respectively. These results revealed that natural variations of ZmCNR13 might be involved in ear development and can be used in genetic improvement of maize ear-related traits.

Keywords: ZmCNR13; association analysis; ear-related traits; maize; nucleotide polymorphism.