Abstract
Waxy maize (Zea mays L. var. ceratina) is an important vegetable and economic crop that is thought to have originated from cultivated flint maize and most recently underwent divergence from common maize. In this study, a total of 110 waxy and 110 common maize inbred lines were genotyped with 3072 SNPs to evaluate the genetic diversity, population structure, and linkage disequilibrium decay as well as identify putative loci that are under positive selection. The results revealed abundant genetic diversity in the studied panel and that genetic diversity was much higher in common than in waxy maize germplasms. Principal coordinate analysis and neighbor-joining cluster analysis consistently classified the 220 accessions into two major groups and a mixed group with mixed ancestry. Subpopulation structure in both waxy and common maize sets were associated with the germplasm origin and corresponding heterotic groups. The LD decay distance (1500–2000 kb) in waxy maize was lower than that in common maize. Fourteen candidate loci were identified as under positive selection between waxy and common maize at the 99% confidence level. The information from this study can assist waxy maize breeders by enhancing parental line selection and breeding program design.
Highlights
Waxy maize (Zea mays L. var. ceratina) is a type of maize with nearly 100% amylopectin in endosperm, which is mainly consumed as fresh vegetable in Asian countries such as in China, Japan, Korea, and the Philippines, and it is used as raw material for food industries, textiles, adhesive, and paper industries [1,2,3,4,5]
These accessions included 110 Chinese waxy maize accessions selected from a wide range of geographical locations in China to try to encompass genetic diversity within landraces and inbred lines and 110 common maize accessions composed of the traditional landraces and improved maize inbred lines
A total of 220 germplasm accessions in the studied panel that contained 110 waxy maize and 110 common maize germplasms were genotyped with 3072 Single nucleotide polymorphism (SNP)
Summary
Waxy maize (Zea mays L. var. ceratina) is a type of maize with nearly 100% amylopectin in endosperm, which is mainly consumed as fresh vegetable in Asian countries such as in China, Japan, Korea, and the Philippines, and it is used as raw material for food industries, textiles, adhesive, and paper industries [1,2,3,4,5]. Waxy maize was first discovered in China in 1908 [6] and was later found in other places in Asia [7, 8]. Waxy maize landraces are abundant in China, most of which are distributed in Southwestern China [2]. Chinese waxy maize is thought to have evolved from the non-glutinous domesticated American maize, which was introduced into China about 500 years ago [9]. Karyotype, isozyme, and DNA markers, waxy maize was suggested to have originated from the Yunnan-Guangxi region in China [10,11,12,13].
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