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- Title
Dynamic genetic features of chromosomes revealed by comparison of soybean genetic and sequence-based physical maps.
- Authors
Lee, Woo; Kim, Namshin; Kim, Jiwoong; Moon, Jung-Kyung; Jeong, Namhee; Choi, Ik-Young; Kim, Sang; Chung, Won-Hyong; Kim, Hong; Lee, Suk-Ha; Jeong, Soon-Chun
- Abstract
Despite the intensive soybean [ Glycine max (L.) Merrill] genome studies, the high chromosome number (20) of the soybean plant relative to many other major crops has hindered the development of a high-resolution genomewide genetic map derived from a single population. Here, we report such a map, which was constructed in an F population derived from a cross between G. max and G. soja lines using indel polymorphisms detected via a G. soja genome resequencing. By targeting novel indel markers to marker-poor regions, all marker intervals were reduced to under 6 cM on a genome scale. Comparison of the Williams 82 soybean reference genome sequence and our genetic map indicated that marker orders of 26 regions were discrepant with each other. In addition, our comparison showed seven misplaced and two absent markers in the current Williams 82 assembly and six markers placed on the scaffolds that were not incorporated into the pseudomolecules. Then, we showed that, by determining the missing sequences located at the presumed beginning points of the five major discordant segments, these observed discordant regions are mostly errors in the Williams 82 assembly. Distributions of the recombination rates along the chromosomes were similar to those of other organisms. Genotyping of indel markers and genome resequencing of the two parental lines suggested that some marker-poor chromosomal regions may represent introgression regions, which appear to be prevalent in soybean. Given the even and dense distribution of markers, our genetic map can serve as a bridge between genomics research and breeding programs.
- Subjects
PLANT chromosomes; SOYBEAN; CROP genetics; NUCLEOTIDE sequence; PLANT gene mapping; PLANT chromosome numbers; COMPARATIVE studies; GENETIC polymorphisms in plants
- Publication
Theoretical & Applied Genetics, 2013, Vol 126, Issue 4, p1103
- ISSN
0040-5752
- Publication type
Article
- DOI
10.1007/s00122-012-2039-8