Abstract
BackgroundMaize 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).ResultsWith 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.ConclusionsFor 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3041-3) contains supplementary material, which is available to authorized users.
Highlights
Maize breeding germplasm used in Southwest China has high complexity because of the diverse ecological features of this area
When K = 2, the whole panel could be grouped into Tropical and Temperate groups which the representative inbred lines were S37 and 18–599; When K = 3, the Temperate group was further divided into Stiff Stalk (SS) and non-Stiff Stalk (NSS) groups, including representative inbred lines Qi319 and Ye478, respectively; When K = 4, PA and PB were further separated which the representative inbred lines were 698–3 and 18–599; When K = 6, besides the Tropical subgroup, other inbred lines could be clustered into Iowa Stiff Stalk Synthetic (BSSS), Reid, PA, PB and North group, the representative inbred lines were B73, Ye478, 698–3, 18– 599, and Dan340, respectively
Using the MaizeSNP50 BeadChip, we performed the population structure, genetic diversity (GD), and linkage disequilibrium (LD) decay distance analysis of 362 important inbred lines collected from the breeding program of Southwest China for the first time
Summary
Maize breeding germplasm used in Southwest China has high complexity because of the diverse ecological features of this area. 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). From the 1930s to the present, three stages in maize hybrid breeding history have been defined according to the source of parents: (1) Inbred lines directly derived from landraces during the 1930s–1950s; (2) Inbred lines derived from crosses among artificial selected inbred lines during the 1950s–1980s and (3) Inbred lines developed from cultivating elite inbred lines for commercial use [4]. Owing to the number of valuable loci targeted during artificial selection, the GD of maize has gradually narrowed during the breeding process [6]
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