Identification of domestication-related loci associated with flowering time and seed size in soybean with the RAD-seq genotyping method
نویسندگان
چکیده
Flowering time and seed size are traits related to domestication. However, identification of domestication-related loci/genes of controlling the traits in soybean is rarely reported. In this study, we identified a total of 48 domestication-related loci based on RAD-seq genotyping of a natural population comprising 286 accessions. Among these, four on chromosome 12 and additional two on chromosomes 11 and 15 were associated with flowering time, and four on chromosomes 11 and 16 were associated with seed size. Of the five genes associated with flowering time and the three genes associated with seed size, three genes Glyma11g18720, Glyma11g15480 and Glyma15g35080 were homologous to Arabidopsis genes, additional five genes were found for the first time to be associated with these two traits. Glyma11g18720 and Glyma05g28130 were co-expressed with five genes homologous to flowering time genes in Arabidopsis, and Glyma11g15480 was co-expressed with 24 genes homologous to seed development genes in Arabidopsis. This study indicates that integration of population divergence analysis, genome-wide association study and expression analysis is an efficient approach to identify candidate domestication-related genes.
منابع مشابه
Identification of quantitative trait loci for flowering time by a combination of restriction site–associated DNA sequencing and bulked segregant analysis in soybean
Soybean (Glycine max) has a paleopolyploid genome, and many re-sequencing experiments to characterize soybean genotypes have been conducted using next-generation sequencing platforms. The accumulation of information about single nucleotide polymorphisms (SNPs) throughout the soybean genome has accelerated identification of genomic regions related to agronomically important traits through associ...
متن کاملIdentification and Validation of Candidate Genes Associated with Domesticated and Improved Traits in Soybean.
Soybean, an important source of vegetable oils and proteins for humans, has undergone significant phenotypic changes during domestication and improvement. However, there is limited knowledge about genes related to these domesticated and improved traits, such as flowering time, seed development, alkaline-salt tolerance, and seed oil content (SOC). In this study, more than 106,000 single nucleoti...
متن کاملSpecial features of RAD Sequencing data: implications for genotyping
Restriction site-associated DNA Sequencing (RAD-Seq) is an economical and efficient method for SNP discovery and genotyping. As with other sequencing-by-synthesis methods, RAD-Seq produces stochastic count data and requires sensitive analysis to develop or genotype markers accurately. We show that there are several sources of bias specific to RAD-Seq that are not explicitly addressed by current...
متن کاملA Multiple QTL-Seq Strategy Delineates Potential Genomic Loci Governing Flowering Time in Chickpea
Identification of functionally relevant potential genomic loci using an economical, simpler and user-friendly genomics-assisted breeding strategy is vital for rapid genetic dissection of complex flowering time quantitative trait in chickpea. A high-throughput multiple QTL-seq strategy was employed in two inter (Cicer arietinum desi accession ICC 4958 × C reticulatum wild accession ICC 17160)- a...
متن کاملPCR-based markers for identification of some allelic variation at Glu-1 and Glu-3 loci in common wheat
Marker assisted selection (MAS) is a tool for breeding, screening, and genetic characterization of germplasm. Allelic variation of both high and low molecular weight glutenin subunits (HMW/LMW-GS) is associated with the rheological properties of wheat flour. In this study, we investigated glutenin pattern using SDS-PAGE and their PCR based on DNA markers in 60 advanced wheat lines and cultivars...
متن کامل