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

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.

Genetic diversity and association mapping in the Colombian Central Collection of Solanum tuberosum L. Andigenum group using SNPs markers

“…Based on its LD value, potato behaves as a self-pollinated crop even if it is an outcrossing species. The clonal propagation of potato limits the number of meiotic generations and in consequence the recombination events [ 33 – 35 , 118 ]. The LD in Andigena and Phureja decayed slowly, previous works also reported a slow LD decay for potato populations: 1 cM [ 33 ], 10 cM [ 35 ] and 5 cM [ 34 ].…”

Molecular analysis of mutant granule-bound starch synthase-I (waxy1) gene in diverse waxy maize inbreds

“…The mean PIC of markers present within wx1 locus is lower than PIC of genome-based SSRs observed in waxy germplasm. For example, Hung et al (2012) and Hao et al (2015) reported PIC of 0.46 and 0.31 in waxy germplasm, respectively. The higher PIC values, 0.70 and 0.62 among waxy maize germplasm were observed by Zheng et al (2013) and Sa et al (2015), respectively.…”

Microsatellite marker-based characterization of waxy maize inbreds for their utilization in hybrid breeding

“…In contrast, Sa et al (2015) reported higher number of alleles [1268 alleles, 6.34 average alleles/locus and 2-14 alleles/locus] among 40 waxy inbreds of South Korea using 200 SSRs. Further, Hao et al (2015) analysed 110 waxy maize accessions using 2751 single nucleotide polymorphisms (SNPs) and detected two alleles/locus. In the present study, allele size ranged from 60 bp (phi028) to 300 bp (bnlg1635 and phi113) across markers, which revealed the presence of high genetic diversity of the loci analysed.…”

“…The germplasm base of waxy corn is narrow compared to normal maize, as few countries have active waxy corn breeding programme. Only few reports from China (Yu et al 2012;Zheng et al 2013;Hao et al 2015), Vietnam (Liet and Tinh 2009;Hung et al 2012) and Korea (Park et al 2008;Sa et al 2015) are available on molecular characterization of waxy inbreds. In India, so far waxy trait has not been utilized in the breeding programme, despite the fact that people in north-eastern states of the country prefers waxy maize as a food over traditional maize.…”