title: Identification and Validation of Loci Governing Seed Coat Color by Combining Association Mapping and Bulk Segregation Analysis in Soybean.
abstract: Soybean seed coat exists in a range of colors from yellow, green, brown, black, to bicolor. Classical genetic analysis suggested that soybean seed color was a moderately complex trait controlled by multi-loci. However, only a couple of loci could be detected using a single biparental segregating population. In this study, a combination of association mapping and bulk segregation analysis was employed to identify genes/loci governing this trait in soybean. A total of 14 loci, including nine novel and five previously reported ones, were identified using 176,065 coding SNPs selected from entire SNP dataset among 56 soybean accessions. Four of these loci were confirmed and further mapped using a biparental population developed from the cross between ZP95-5383 (yellow seed color) and NY279 (brown seed color), in which different seed coat colors were further dissected into simple trait pairs (green/yellow, green/black, green/brown, yellow/black, yellow/brown, and black/brown) by continuously developing residual heterozygous lines. By genotyping entire F2 population using flanking markers located in fine-mapping regions, the genetic basis of seed coat color was fully dissected and these four loci could explain all variations of seed colors in this population. These findings will be useful for map-based cloning of genes as well as marker-assisted breeding in soybean. This work also provides an alternative strategy for systematically isolating genes controlling relative complex trait by association analysis followed by biparental mapping.
authors.affiliation: The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) and MOA Key Lab of Soybean Biology (Beijing), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P. R. China.
authors.forename: Jian
authors.initials: J
authors.lastname: Song
authors.affiliation: The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) and MOA Key Lab of Soybean Biology (Beijing), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P. R. China.
authors.forename: Zhangxiong
authors.initials: Z
authors.lastname: Liu
authors.affiliation: The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) and MOA Key Lab of Soybean Biology (Beijing), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P. R. China.
authors.forename: Huilong
authors.initials: H
authors.lastname: Hong
authors.affiliation: The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) and MOA Key Lab of Soybean Biology (Beijing), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P. R. China.
authors.forename: Yansong
authors.initials: Y
authors.lastname: Ma
authors.affiliation: The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) and MOA Key Lab of Soybean Biology (Beijing), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P. R. China.
authors.forename: Long
authors.initials: L
authors.lastname: Tian
authors.affiliation: The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) and MOA Key Lab of Soybean Biology (Beijing), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P. R. China.
authors.forename: Xinxiu
authors.initials: X
authors.lastname: Li
authors.affiliation: The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) and MOA Key Lab of Soybean Biology (Beijing), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P. R. China.
authors.forename: Ying-Hui
authors.initials: YH
authors.lastname: Li
authors.affiliation: The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) and MOA Key Lab of Soybean Biology (Beijing), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P. R. China.
authors.forename: Rongxia
authors.initials: R
authors.lastname: Guan
authors.affiliation: The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) and MOA Key Lab of Soybean Biology (Beijing), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P. R. China.
authors.forename: Yong
authors.initials: Y
authors.lastname: Guo
authors.affiliation: The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) and MOA Key Lab of Soybean Biology (Beijing), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P. R. China.
authors.forename: Li-Juan
authors.initials: LJ
authors.lastname: Qiu
mesh_terms: D001947:Breeding; D002874:Chromosome Mapping; D056426:Genetic Loci / Q000235:genetics*; D005819:Genetic Markers / Q000235:genetics; D005838:Genotype; D010858:Pigmentation; D020641:Polymorphism, Single Nucleotide; D012639:Seeds / Q000378:metabolism*; D013025:Glycine max / Q000235:genetics* / Q000378:metabolism
chemical_list: D005819:Genetic Markers