Evaluation of soybean germplasm conserved in NIAS genebank and development of mini core collections

Abstract

Genetic variation and population structure among 1603 soybean accessions, consisted of 832 Japanese landraces, 109 old and 57 recent Japanese varieties, 341 landrace from 16 Asian countries and 264 wild soybean accessions, were characterized using 191 SNP markers. Although gene diversity of Japanese soybean germplasm was slight lower than that of exotic soybean germplasm, population differentiation and clustering analyses indicated clear genetic differentiation among Japanese cultivated soybeans, exotic cultivated soybeans and wild soybeans. Nine hundred ninety eight Japanese accessions were separated to a certain extent into groups corresponding to their agro-morphologic characteristics such as photosensitivity and seed characteristics rather than their geographical origin. Based on the assessment of the SNP markers and several agro-morphologic traits, accessions that retain gene diversity of the whole collection were selected to develop several soybean sets of different sizes using an heuristic approach; a minimum of 12 accessions can represent the observed gene diversity; a mini-core collection of 96 accession can represent a major proportion of both geographic origin and agro-morphologic trait variation. These selected sets of germplasm will provide an effective platform for enhancing soybean diversity studies and assist in finding novel traits for crop improvement.

Keywords: Genebank; Glycine max; Glycine soja; LD; SNP; mini core collection.

Fig. 1

Geographical distribution of cultivated soybean accessions analyzed in the present study. Japan was subdivided into 11 historic regions.

Fig. 2

Distribution of 936 SNPs on the chromosome-scale assembly of soybean genome, Glyma 1.0, and their gene diversity values among 69 Japanese accessions (black dot) and 26 exotic accessions (horizontal line). Arrows indicate that the location of SNPs which were used to evaluate a large set of soybean germplasm. Dark bars below each graph indicate presumed pericentromeric regions.

Fig. 3

Decay of the squared correlation of allele frequencies (r²) with physical distance in bp in Japanese crossbred (A), landrace (B) and exotic germplasm (C).

Fig. 4

The differences in the frequency of gene diversity for individual SNP locus classified by each germplasm groups.

Fig. 5

Genetic admixture between Japanese and exotic cultivated soybeans, and wild soybeans. Estimated individual membership to three major groups (K = 3); white (Japanese cultivated soybeans), gray (Exotic cultivated soybeans) and black (wild soybeans).

Fig. 6

A neighbor-joining phylogenetic tree of 1,603 accessions, Japanese (n = 998) and exotic cultivated soybeans (n = 341), Japanese (n = 74) and exotic wild soybeans (n = 190), based on the allele sharing distance. The letters in square bracket for Japanese clusters are phenotype information such as the representative ecological types followed by DF, days to flowering, FH, period from first flowering to start harvest, PH, plant height, SW, 100 seed weight, and seed coat color. Numeric characters after DF, FH, PH and SW and in a round bracket indicate that average and standard deviation among accessions in the cluster, respectively.

Fig. 7

Comparison of phenotypic variation of selected 96 mini-core collection (black) with all accessions (white). A) 100 seed weight; B) days to flowering time; C) plant height; D) days to beginning of maturity (R7); Japanese (upper) and exotic (lower) germplasm comparison.

Fig. 8

Variation of flowering time among Japanese soybeans evaluated at the experimental field in A3 region.

Fig. 9

Morphological variation in the seeds among ‘Japanese soybean mini-core collection ver. 1’ (left) and ‘Exotic mini-core collection ver. 1’ (right). The picture order reflects the genetic relatedness.