Fine genetic characterization of elite maize germplasm using high-throughput SNP genotyping
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- 作者：Xun Wu (1) (2) (3)
Yongxiang Li (2)
Yunsu Shi (2)
Yanchun Song (2)
Tianyu Wang (2)
Yubi Huang (1)
Yu Li (2) - 刊名：Theoretical and Applied Genetics
- 出版年：2014
- 出版时间：March 2014
- 年：2014
- 卷：127
- 期：3
- 页码：621-631
- 全文大小：1,130 KB
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Yongxiang Li (2)
Yunsu Shi (2)
Yanchun Song (2)
Tianyu Wang (2)
Yubi Huang (1)
Yu Li (2)
1. Maize Institute, Sichuan Agricultural Unversity, Ya’an, 625014, Sichuan, China
2. Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
3. Nanchong Academy of Agricultural Sciences, Nanchong, 637000, Sichuan, China - ISSN：1432-2242
文摘
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.