期刊
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
卷 22, 期 4, 页码 -出版社
MDPI
DOI: 10.3390/ijms22041559
关键词
annual wild soybean (G; soja Sieb; and Zucc; ); chromosome segment substitution line (CSSL); cultivated soybean (G; max (L; ) Merr; ); days to flowering; seed coat color; SNP linkage disequilibrium block (SNPLDB); whole-genome re-sequencing
资金
- Natural Science Foundation of China [31601325]
- National Key RAMP
- D Program of China [2016YFD0100304]
- Natural Science Foundation of Jiangsu Province [BK20160713]
- MOE 111 Project [B08025]
- MOE Program for Changjiang Scholars and Innovative Research Team in University [PCSIRT_17R55]
- MOA CARS-04 program [CARS-04]
- Jiangsu Higher Education PAPD Program
- Fundamental Research Funds for the Central Universities
- Jiangsu JCIC-MCP
In this study, an improved wild soybean chromosome segment substitution line (CSSL) population, SojaCSSLP5, was developed, which was genotyped through whole-genome resequencing to identify genetic changes from wild soybean to cultivated soybean. Using the SNPLDB-map, several candidate genes related to seed-coat color and days to flowering were identified and verified, demonstrating the efficiency of the CSSL population in identifying candidate wild vs. cultivated gene-alleles. The integration of parental DNA and RNA sequencing data provided a reliable platform for further research on genetic changes between wild and cultivated soybean.
Annual wild soybean (G. soja) is the ancestor of the cultivated soybean (G. max). To reveal the genetic changes from soja to max, an improved wild soybean chromosome segment substitution line (CSSL) population, SojaCSSLP5, composed of 177 CSSLs with 182 SSR markers (SSR-map), was developed based on SojaCSSLP1 generated from NN1138-2(max)xN24852(soja). The SojaCSSLP5 was genotyped further through whole-genome resequencing, resulting in a physical map with 1366 SNPLDBs (SNP linkage-disequilibrium blocks), which are composed of more markers/segments, shorter marker length and more recombination breakpoints than the SSR-map and caused 721 new wild substituted segments. Using the SNPLDB-map, two loci co-segregating with seed-coat color (SCC) and six loci for days to flowering (DTF) with 88.02% phenotypic contribution were identified. Integrated with parental RNA-seq and DNA-resequencing, two SCC and six DTF candidate genes, including three previously cloned (G, E2 and GmPRR3B) and five newly detected ones, were predicted and verified at nucleotide mutant level, and then demonstrated with the consistency between gene-alleles and their phenotypes in SojaCSSLP5. In total, six of the eight genes were identified with the parental allele-pairs coincided to those in 303 germplasm accessions, then were further demonstrated by the consistency between gene-alleles and germplasm phenotypes. Accordingly, the CSSL population integrated with parental DNA and RNA sequencing data was demonstrated to be an efficient platform in identifying candidate wild vs. cultivated gene-alleles.
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