Fine genetic characterization of elite maize germplasm using high-throughput SNP genotyping
- 1.2k Downloads
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.
KeywordsInbred Line Association Mapping Polymorphism Information Content Maize Inbred Line Heterotic Group
This work was partly supported by the Ministry of Science and Technology of China (2011CB100100, 2011DFA30450), National Natural Science Foundation (U1138304), CAAS (Innovation Program) and the Ministry of Agriculture of China (2011-G15, Baozhong Project). We are grateful to Dr. Alain Charcosset for language correcting and suggestions on data analyses. We also thank anonymous reviewers for suggestions to improve the quality of this manuscript.
- Bernardo R (1990) Methods used in developing maize inbreds. Maydica 35:1–16Google Scholar
- Ganal MW, Durstewitz G, Polley A, Be’rard A, Buckler ES, Charcosset A, Clarke JD, Graner E, Hansen M, Joets J, Paslier ML, McMullen M, Montalent P, Rose M, Schön CC, Sun Q, Walter H, Martin O, Falque M (2011) A large Maize (Zea mays L.) SNP genotyping array: development and germplasm genotyping, and genetic mapping to compare with the B73 reference genome. PLoS ONE 6(12):e28334PubMedCentralPubMedCrossRefGoogle Scholar
- Lai J, Li R, Xu X, Jin W, Xu M, Zhao H, Xiang Z, Song W, Ying K, Zhang M, Jiao Y, Ni P, Zhang J, Li D, Guo X, Ye K, Jian M, Wang B, Zheng H, Liang H, Zhang X, Wang S, Chen S, Li J, Fu Y, Springer Nathan M, Yang H, Wang J, Dai J, Schnable Patrick S, Wang J (2010) Genome-wide patterns of genetic variation among elite maize inbred lines. Nat Genet 42:1027–1030PubMedCrossRefGoogle Scholar
- Li S (1997) The development and application of maize inbred line “Huangzaosi”. Beijing Agric Sci 15:19–21 (in Chinese)Google Scholar
- Li Y, Wang T (2010) Germplasm base of maize breeding in China and formation of foundation parents. J Maize Sci 18:1–8 (in Chinese)Google Scholar
- Liu Z, Wu X, Liu H, Li Y, Li Q, Wang F, Shi Y, Song Y, Song W, Zhao J, Lai J, Li Y, Wang T (2012) Genetic diversity and population structure of important Chinese maize inbred lines revealed by 40 core simple sequence repeats (SSRs). Scientia Agricultura Sinica 45:2107–2138 (in Chinese)Google Scholar
- Lu Y, Yan J, Guimaraes CT, Taba S, Hao Z, Gao S, Chen S, Li J, Zhang S, Vivek BS, Magorokosho C, Mugo S, Makumbi D, Parentoni SN, Shah T, Rong T, Crouch JH, Xu Y (2009) Molecular characterization of global maize breeding germplasm based on genome-wide single nucleotide polymorphisms. Theor Appl Genet 120:93–115PubMedCrossRefGoogle Scholar
- Troyer AF (1990) A retrospective view of corn genetic resources. J Hered 81:17–24Google Scholar
- Wang Y, Wang Z, Wang Y (1997) Studies on the heterosis utilizing models of main maize germplasms in China. Scientia Agricutural Sinica 30:16–24 (in Chinese)Google Scholar
- Yu Y, Wang R, Zhao J, Shi Y, Song Y, Wang T, Li Y (2007) Genetic diversity and structure of the core collection for maize inbred lines in China. Maydica 52:181–194Google Scholar
- Zeng S (1990) The maize germplasm base of hybrid in China. Scientia Agricultura Sinica 23:1–9 (in Chinese)Google Scholar