Chromosomal features revealed by comparison of genetic maps of Glycine max and Glycine soja

Genome Assembly of the Popular Korean Soybean Cultivar Hwangkeum

“…Our recent genetic map study showed multiple mega-scale discordant regions between the Williams reference genome and our genetic maps (Lee et al 2020). However, comparison between the Williams 82 and Lee genome sequences resulted in no mega-scale structural variant (Valliyodan et al 2019).…”

“…The scaffolding and gap-filling were then repeated with paired-end reads. Finally, ALLMAPS (Tang et al 2015) was used to construct the 20 pseudo-chromosomes by anchoring the assembled contigs/scaffolds to two genetic maps (WH and HI maps) that had been constructed using Hwangkeum as a parental line (Lee et al 2020). In our previous study, we constructed four high-density genetic maps from Williams 82K (G. max) by Hwangkeum (G. max) (referred to as WH), Hwangkem by IT182932 (Glycine soja) (HI), Williams 82K by IT182932 (WI), and IT182932 by IT182819 (G. soja) (II) populations.…”

Purging of deleterious mutations during domestication in the predominant selfing crop soybean

“…This pattern of recombination frequency distribution have been well supported experimentally by studies of multi-parental maize mapping populations 16,18 , although recombination rates were detected to be almost entirely suppressed in pericentromeric regions in those mapping populations. With available estimates of the recombination rate (R) from four soybean inter-crossed bi-parental populations, which captured ~38,000 meiotic crossovers 19 , we compared our estimates of historical recombination rates with empirical estimates of the recombination rate. Overall, R and ρ were weakly, significantly correlated, indicating that our historical recombination rate estimates inferred on the basis of the SNP distribution likely reflected naturally occurring recombination patterns (Spearman correlation coefficient = 0.256, P = 7.945e-16).…”

“…Beagle (v5.0) was used for imputing genotypes at sites not on the 36,647 SoySNP50K data using 10.5 million SNP data from 781 soybean genomes. A genetic map constructed from a population of 233 recombinant inbred individuals derived from a cross between Williams 82K and IT182932 19 was used as the fine-scale recombination map input for imputation.…”

“…Evidence for selection of domestication across the genome was evaluated by comparing domesticated versus wild soybean genomes. Individual SNPs were assigned at positions along with a recombinant inbred genetic map derived from a cross between G. max "Williams 82 K" and G. soja "IT182932"19 . Markers located on the insertion of unanchored scaffolds or different chromosome segments as well as on chromosome segments whose physical or genetic orders were not collinear between the reference genome and our genetic maps were excluded from the genetic map.…”