Sequence polymorphism of the waxy gene in waxy maize accessions and characterization of a new waxy allele

Meijie Luo,Shengli Xi,Jiuran Zhao,Yanxin Zhao,Mengsi Kong,Yaxing Shi,Li Xu,Baishan Lu,Yang Yang,Yanli Fan,Chunhui Li,Zhen Feng,Yunxia Zhang,Yamin Shi

doi:10.1038/s41598-020-72764-3

Meijie Luo, Shengli Xi + Show 12 more

Open Access

https://doi.org/10.1038/s41598-020-72764-3

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Abstract

Waxy maize has many excellent characteristics in terms of its nutritional and economic value. In recent decades, the waxy maize germplasm has increased dramatically as a result of different selection methods. We collected 200 waxy maize inbred accessions from different origins to study their genetic diversity and phylogenetic relationships, and to identify new waxy mutations. A simple sequence repeat (SSR) analysis revealed wide genetic diversity among the 200 waxy maize accessions. The maize accessions were clustered into three groups. We sequenced the waxy gene from the first to the 14th exon. Nucleotide variation analysis of 167 waxy maize and 14 flint maize lines revealed some nucleotide differences in the waxy gene among different waxy maize groups, and much narrower nucleotide diversity in waxy maize than in flint maize. In a phylogenetic analysis, waxy maize carrying the same mutation allele clustered together, and waxy maize carrying different mutation alleles distributed in different groups; waxy maize was intermixed with flint maize in each branch, and wx-D7 waxy maize separated significantly from waxy maize lines carrying wx-D10, wx-124 and wx-hAT mutant alleles. The wx-hAT was a new waxy mutation identified in this study. It consisted of a 2286-bp transposon inserted into the middle of exon three of the waxy gene. A PCR marker specific for the wx-hAT allele was developed. These results will be useful for the utilization and preservation of the waxy maize germplasm, and the PCR marker has potential uses in waxy maize breeding programs.

Highlights

Waxy maize has many excellent characteristics in terms of its nutritional and economic value
An association analysis between allelic variations of waxy and starch physicochemical properties showed that waxy allelic variation affects the gel consistency, gelatinization temperature, and pasting viscosity properties of rice starch, implying that certain waxy alleles have been favored for grain quality improvement[15,16]
The cluster analysis grouped the 200 waxy inbred lines into three main groups: group A included 63 accessions, group B included 59 accessions, and group C included 78 accessions (Fig. 1b). These results show that there was wide genetic diversity among the tested waxy maize accessions

Summary

Introduction

Waxy maize has many excellent characteristics in terms of its nutritional and economic value. We collected 200 waxy maize inbred accessions from different origins to study their genetic diversity and phylogenetic relationships, and to identify new waxy mutations. The wx-hAT was a new waxy mutation identified in this study It consisted of a 2286bp transposon inserted into the middle of exon three of the waxy gene. Among the known mutant alleles of the waxy gene in maize, wx-stonor, wx-B5, wx-G, wx-M, wx-I, wx-K, wx-Cin[4] and wx-Rina are RNA transposon insertion m utations[3,8]. Comparison of waxy sequence variation among maize germplasm accessions provides insights into selection at the maize waxy locus during domestication, and can highlight mutations in the waxy gene that will be useful for the germplasm utilization and quality breeding of waxy maize[16,17]

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