Abstract
The Chinese soybean germplasm pool (CSGP) comprises annual wild (WA), farmers’ landrace (LR) and released cultivar (RC) populations, and ecoregion subpopulations in WA/LR/RC (ecoregion IV/III/II/I). A representative sample consisted of 1,024 accessions was studied for pubescence color (PC) and flower color (FC). In the evolution from WA (brown PC and mainly purple FC) to LR then to RC, with above wild characteristic changed, while gray PC, and white FC emerged and their frequency increased. Using 36,952 genomic SNPLDB markers with 100,092 haplotypes, the association between markers and bi-phenotypic traits was detected using χ2 association analysis under single locus model and RTM-GWAS procedure under multi-locus model, respectively. Multiple markers co-associated with individual bi-phenotypic trait with the most significant markers containing multiple rather than two haplotypes even for a bi-phenotypic trait. On a marker/locus, each haplotype corresponds to two colors, except one (FC-1-5) out of 11 haplotypes for single color. The major candidate gene was annotated with its alleles identified from the population sequencing data. Similarly, multiple alleles identified and each corresponds to two colors except three (a8/a9/b3) out of 12 alleles for single color. The major haplotypes/alleles in LR and RC were traced to WA ecoregion subpopulations, the WAIV and WAIII genotypes showed genetically more close to the cultivated subpopulations, therefore, WA from Ecoregion IV and III were inferred as the common ancestor for cultivated soybeans. The marker-haplotypes/gene-alleles not exactly coincided with the bi-phenotypic trait has challenged to the traditional Mendelian genetics, which was discussed and to be further studied.
Highlights
Mendelian inheritance started the modern genetics using a pair of pea parents with a pair of relative characteristics
It is known that cultivated soybean [G. max (L.) Merr.] was domesticated from annual wild soybean (G. soja Sieb. and Zucc.) about 5,000 years ago (Zhou et al, 2015), originally annual wild soybean was with brown pubescence color (PC) and purple flower color (FC) (Zhuang et al, 1996), while in the cultivated soybeans, gray PC and white FC emerged, and with their frequencies increased gradually (Chang, 1990)
All wild population (WA) subpopulations are brown PC; in LR, 1http://www.soybase.org from LRIV northward to LRI, the brown PC frequency showed a reduced tendency and vice versa for gray PC; in released cultivar (RC), the brown PC frequency was less than gray PC frequency in all subpopulations; brown PC as the primitive phenotype has the highest frequency in LRIV of LR and RCIV in RC, gray PC as a new phenotype increased gradually during the evolution (Table 1)
Summary
Mendelian inheritance started the modern genetics using a pair of pea parents with a pair of relative characteristics (white vs. purple flower). Since the previous genetic studies on pigmentation traits mainly used bi-parental populations, there were only two types of alleles. Simple Mendelian inheritance was found for the two traits as indicated above. It is known that cultivated soybean [G. max (L.) Merr.] was domesticated from annual wild soybean Zucc.) about 5,000 years ago (Zhou et al, 2015), originally annual wild soybean was with brown PC and purple FC (Zhuang et al, 1996), while in the cultivated soybeans, gray PC and white FC emerged, and with their frequencies increased gradually (Chang, 1990). PC and FC were a bi-phenotypic trait in natural populations as indicated above. It is generally understood that anthocyanin accumulation determines PC and FC, flavonoid 3 5 -hydroxylase (F3 5 H), dihydroflavonol4-reductase (DFR), and flavonoid 3 hydroxylase (F3 H) play a crucial role in producing anthocyanin (Yang et al, 2010; Sundaramoorthy et al, 2017)
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
