title: Characterizing the population structure and genetic diversity of maize breeding germplasm in Southwest China using genome-wide SNP markers.
abstract: Maize breeding germplasm used in Southwest China has high complexity because of the diverse ecological features of this area. In this study, the population structure, genetic diversity, and linkage disequilibrium decay distance of 362 important inbred lines collected from the breeding program of Southwest China were characterized using the MaizeSNP50 BeadChip with 56,110 single nucleotide polymorphisms (SNPs).
  
  
  
  With respect to population structure, two (Tropical and Temperate), three (Tropical, Stiff Stalk and non-Stiff Stalk), four [Tropical, group A germplasm derived from modern U.S. hybrids (PA), group B germplasm derived from modern U.S. hybrids (PB) and Reid] and six (Tropical, PB, Reid, Iowa Stiff Stalk Synthetic, PA and North) subgroups were identified. With increasing K value, the Temperate group showed pronounced hierarchical structure with division into further subgroups. The Genetic Diversity of each group was also estimated, and the Tropical group was more diverse than the Temperate group. Seven low-genetic-diversity and one high-genetic-diversity regions were collectively identified in the Temperate, Tropical groups, and the entire panel. SNPs with significant variation in allele frequency between the Tropical and Temperate groups were also evaluated. Among them, a region located at 130 Mb on Chromosome 2 showed the highest genetic diversity, including both number of SNPs with significant variation and the ratio of significant SNPs to total SNPs. Linkage disequilibrium decay distance in the Temperate group was greater (2.5-3 Mb) than that in the entire panel (0.5-0.75 Mb) and the Tropical group (0.25-0.5 Mb). A large region at 30-120 Mb of Chromosome 7 was concluded to be a region conserved during the breeding process by comparison between S37, which was considered a representative tropical line in Southwest China, and its 30 most similar derived lines.
  
  
  
  For the panel covered most of widely used inbred lines in Southwest China, this work representatively not only illustrates the foundation and evolution trend of maize breeding resource as a theoretical reference for the improvement of heterosis, but also provides plenty of information for genetic researches such as genome-wide association study and marker-assisted selection in the future.
authors: Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, People's Republic of China.|Key laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, People's Republic of China.
authors: Xiao
authors: X
authors: Zhang
authors: Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, People's Republic of China.|Mianyang Academy of Agricultural Sciences, Mianyang, 621023, Sichuan, China.
authors: Hua
authors: H
authors: Zhang
authors: Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, People's Republic of China.|Key laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, People's Republic of China.
authors: Lujiang
authors: L
authors: Li
authors: Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, People's Republic of China.|Key laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, People's Republic of China.
authors: Hai
authors: H
authors: Lan
authors: Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, People's Republic of China.|Key laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, People's Republic of China.
authors: Zhiyong
authors: Z
authors: Ren
authors: Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, People's Republic of China.|Key laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, People's Republic of China.
authors: Dan
authors: D
authors: Liu
authors: Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, People's Republic of China.|Key laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, People's Republic of China.
authors: Ling
authors: L
authors: Wu
authors: Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, People's Republic of China.|Key laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, People's Republic of China.
authors: Hailan
authors: H
authors: Liu
authors: DuPont Crop Genetics Research, Route 141 and Henry Clay Road, Wilmington, DE, 19880-0353, USA.
authors: Jennifer
authors: J
authors: Jaqueth
authors: DuPont Crop Genetics Research, Route 141 and Henry Clay Road, Wilmington, DE, 19880-0353, USA.
authors: Bailin
authors: B
authors: Li
authors: Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, People's Republic of China.|Key laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, People's Republic of China.
authors: Guangtang
authors: G
authors: Pan
authors: Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, People's Republic of China. shibingao@163.com.|Key laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, People's Republic of China. shibingao@163.com.
authors: Shibin
authors: S
authors: Gao
mesh_terms: D002681:China; D032461:Chromosomes, Plant / Q000235:genetics; D005787:Gene Frequency; D055106:Genome-Wide Association Study / Q000379:methods*; D015810:Linkage Disequilibrium; D000069600:Plant Breeding; D020641:Polymorphism, Single Nucleotide; D012639:Seeds / Q000235:genetics; D003313:Zea mays / Q000145:classification* / Q000235:genetics
keywords: Breeding; Diversity; Maize; Population structure; SNP array; Southwest China; Temperate group; Tropical group