Genetic Diversity and Molecular Evolution of Chinese Waxy Maize Germplasm

Abstract

Waxy maize (Zea mays L. var. certaina Kulesh), with many excellent characters in terms of starch composition and economic value, has grown in China for a long history and its production has increased dramatically in recent decades. However, the evolution and origin of waxy maize still remains unclear. We studied the genetic diversity of Chinese waxy maize including typical landraces and inbred lines by SSR analysis and the results showed a wide genetic diversity in the Chinese waxy maize germplasm. We analyzed the origin and evolution of waxy maize by sequencing 108 samples, and downloading 52 sequences from GenBank for the waxy locus in a number of accessions from genus Zea. A sharp reduction of nucleotide diversity and significant neutrality tests (Tajima’s D and Fu and Li’s F*) were observed at the waxy locus in Chinese waxy maize but not in nonglutinous maize. Phylogenetic analysis indicated that Chinese waxy maize originated from the cultivated flint maize and most of the modern waxy maize inbred lines showed a distinct independent origin and evolution process compared with the germplasm from Southwest China. The results indicated that an agronomic trait can be quickly improved to meet production demand by selection.

Identification of Genetic Differentiation between Waxy and Common Maize by SNP Genotyping

“…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 ].…”

“…Understanding how genetic variation is distributed within and among different germplasm collections is vital to germplasm management by monitoring genetic shifts that occur during domestication, germplasm conservation, and breeding [ 16 , 17 ]. Recently, application of RAPD and SSR markers has enabled identification of genetic diversity in waxy maize landraces and inbred lines; there is abundant genetic diversity in waxy maize, and waxy and common maize genetically differed [ 2 , 18 – 22 ]. With the development of molecular systematics, comparison of DNA sequence variation between closely related species has provided insight into the amount of divergence between sibling species [ 1 ].…”

“…With the development of molecular systematics, comparison of DNA sequence variation between closely related species has provided insight into the amount of divergence between sibling species [ 1 ]. Sequence comparison and phylogenetic analysis for genes of waxy and Globulin-1 indicated that Chinese waxy maize originated from cultivated flint maize and most recently diverged from common maize [ 1 , 2 ].…”

“…Genomic regions or genes affected by natural and artificial selection have been detected by studies in some plants [ 24 , 25 ]. To date, genetic diversity and evolution analysis of waxy maize has primarily relied on analysis of small panels of accessions characterized by a limited number of markers or only some particular gene regions (e.g., waxy and Globulin-1 gene) [ 1 , 2 , 11 , 18 , 26 ]. Single nucleotide polymorphism (SNP) genotyping is cost-effective, accurate, and fast; it has been frequently used for high-throughput analysis of plants, which facilitates genome-wide analysis of sequence variation, genetic diversity, and detection of outlier loci with selective signatures that affected genetic differentiation in germplasm collections [ 15 , 27 ].…”

Genome-wide distribution comparative and composition analysis of the SSRs in Poaceae

“…Currently, SSR markers are being used to integratee genetic maps and physical maps in plants and represent an efficient tool for breeders and geneticists to link phenotypic variations with genotypic variations [ 4 ]. Moreover, as tools for studying molecular evolution, SSR markers are used in investigating the origin, genetic diversity and dynamics of population evolution [ 8 , 14 ]. Furthermore, SSR markers are the commonly used markers for molecular marker assisted selection (MAS), which in turn directs molecular breeding [ 15 , 16 ].…”