Identifying Wild Versus Cultivated Gene-Alleles Conferring Seed Coat Color and Days to Flowering in Soybean.

Cheng Liu,Xianlian Chen,Shihua Xiang,Qingyuan He,Wubin Wang,Hongyan Yang,Wei Han,Junyi Gai,Xinyang Hu

doi:10.3390/ijms22041559

Cheng Liu, Xianlian Chen + Show 7 more

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https://doi.org/10.3390/ijms22041559

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Abstract

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)×N24852(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.

Highlights

Annual wild soybeans (G. soja Sieb. and Zucc.) are recognized as the wild progenitor of the cultivated soybeans (G. max (L.) Merr.) [1]
Markers, in comparison to the previous SojaCSSLP1-4 populations, the ratio of heterozygous segment was significantly reduced, accounting for only 0.02%, which may improve the accuracy of quantitative trait locus (QTL) mapping (Table S1)
H2I2K2L2 and H2I2J2L2 genetic background caused significantly days to flowering (DTF) 4.6 and 3.6 days shorter comparing to the 38 accessions with NN1138-2 haplotype H2I2J2K2L2, respectively (Table 5). These results further demonstrated that the gene-alleles/haplotypes of Seed Coat Color (SCC) and DTF detected in SojaCSSLP5, as well as in their parents N24852 and NN1138-2, have the same functions in the Chinese soybean germplasm population, these genealleles/haplotypes are correct and universal

Summary

Introduction

Annual wild soybeans (G. soja Sieb. and Zucc.) are recognized as the wild progenitor of the cultivated soybeans (G. max (L.) Merr.) [1]. Zucc.) are recognized as the wild progenitor of the cultivated soybeans (G. max (L.) Merr.) [1]. The overall economic characters of wild soybean are inferior to those of the cultivated soybean, the potential of utilizing G. soja as a source of genetic diversity to improve the cultivated soybean, especially in coping with abiotic and biotic stresses, has been emphasized and demonstrated case by case [2,3]. It is expected to explore and transfer useful wild gene-alleles into soybeans through breeding programs. In order to map the useful qualitative gene and quantitative trait locus (QTL) along with their corresponding alleles in wild soybeans, researchers have developed different kinds of genetic population, such as recombinant inbred line populations, doubled-haploid populations, natural populations, etc.

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