Fine genetic characterization of elite maize germplasm using high-throughput SNP genotyping

Abstract

To investigate the genetic structure of Chinese maize germplasm, the MaizeSNP50 BeadChip with 56,110 single nucleotide polymorphisms (SNPs) was used to genotype a collection of 367 inbred lines widely used in maize breeding of China. A total of 41,819 informative SNPs with minor allele number of more than 0.05 were used to estimate the genetic diversity, relatedness, and linkage disequilibrium (LD) decay. Totally 1,015 SNPs evenly distributed in the genome were selected randomly to evaluate the population structure of these accessions. Results showed that two main groups could be determined i.e., the introduced germplasm and the local germplasm. Further, five subgroups corresponding to different heterotic groups, that is, Reid Yellow Dent (Reid), Lancaster Sure Crop (Lancaster), P group (P), Tang Sipingtou (TSPT), and Tem-tropic I group (Tem-tropic I), were determined. The genetic diversity of within subgroups was highest in the Tem-Tropic I and lowest in the P. Most lines in this panel showed limited relatedness with each other. Comparisons of gene diversity showed that there existed some conservative genetic regions in specific subgroups across the ten chromosomes, i.e., seven in the Lancaster, seven in the Reid, six in the TSPT, five in the P, and two in the Tem-Tropical I. In addition, the results also revealed that there existed fifteen conservative regions transmitted from Huangzaosi, an important foundation parent, to its descendants. These are important for further studies since the outcomes may provide clues to understand why Huangzaosi could become a foundation parent in Chinese maize breeding. For the panel of 367 elite lines, average LD distance was 391 kb and varied among different chromosomes as well as in different genomic regions of one chromosome. This analysis uncovered a high natural genetic diversity in the elite maize inbred set, suggesting that the panel can be used in association study, esp. for temperate regions.

Genetic properties of 240 maize inbred lines and identity-by-descent segments revealed by high-density SNP markers

“…These values are very close to those determined by Wu et al (2014) using 41,819 SNPs across 367 inbred lines and finding values of 0.364 and 0.291, respectively. However, the values for average gene diversity and PIC in the present study are much smaller than those obtained in the three previous studies (Xie et al 2007;Yang et al 2010;Yu et al 2007), all of which found average gene diversity and PIC values of[0.500.…”

“…In the present study, the five subgroups Lan, LRC, PB, Reid, and SPT were defined in a manner largely consistent with the subgroups defined by previous studies (Wu et al 2014;Xie et al 2007;Yu et al 2007). Differences in the numbers of inferred subgroups can be attributed to the difference in the numbers and kinds of markers and inbred lines used in population structure studies Xie et al 2007;Yang et al 2010;Yu et al 2007).…”

“…Population structure in Chinese maize germplasm A number of studies have inferred that maize inbred lines used commonly in China belong to four to six subgroups (Wu et al 2014;Xie et al 2007;Yu et al 2007). The stratification of Chinese maize inbred lines is mainly due to their genetic isolation by distance and the introduction of foreign germplasm, which has also occurred in Arabidopsis thaliana (Sharbel et al 2000).…”

“…According to the genetic components analysis conducted by Wu et al (2014), each derivative was compared with its foundation parent using SNPs without missing genotypes in the foundation parent and with a missing rate\0.200 among its derivatives.…”

“…Meanwhile, four subgroups have recently been determined in a set of 95 Chinese maize inbred lines using 145 SSR markers, which defined Reid as including PA and BSSS, and attributed LRC to Lan . Although the genetic properties of some inbred lines in China have been analyzed (Sun 2007;Wang et al 2008;Wu et al 2014;Xie et al 2007), a phenotypically diverse panel including different inbred lines should be characterized in fine detail using highdensity markers to provide higher quality data for germplasm improvement, development of new inbred lines, and association mapping.…”