Identification of domestication-related loci associated with flowering time and seed size in soybean with the RAD-seq genotyping method

Authors: LING, ZHOU - Nanjing Agricultural University; SHI-B0, WANG - Nanjing Agricultural University; RONGJUN, HE - Nanjing Agricultural University; QING-CHUN, GENG - Nanjing Agricultural University; JIA, WEN - Nanjing Agricultural University; Song, Qijian; ZHENZHEN, WU - Beijing Genome Institute; GUANG-JUN, LI - Nanjing Agricultural University; YU-QIN, LIU - Nanjing Agricultural University; JIANBO, JIAN - Nanjing Agricultural University; YUAN, NIU - Nanjing Agricultural University; LI, ZHANG - Nanjing Agricultural University; WEN-LONG, REN - Nanjing Agricultural University; YUAN-MING, ZHANG - Nanjing Agricultural University

Submitted to: Scientific Reports
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/2/2015
Publication Date: 3/23/2015
Citation: Ling, Z., Shi-B0, W., Rongjun, H., Qing-Chun, G., Jia, W., Song, Q., Zhenzhen, W., Guang-Jun, L., Yu-Qin, L., Jianbo, J., Yuan, N., Li, Z., Wen-Long, R., Yuan-Ming, Z. 2015. Identification of domestication-related loci associated with flowering time and seed size in soybean with the RAD-seq genotyping method. Scientific Reports. 5:9350.

Interpretive Summary: The transitions from vegetative to reproductive growth (days to flowering) and from generation to generation through seeds are important stages of the plant life cycle. Flowering time reflects the adaptation of a plant to its environment. Seeds are important in the reproduction and spread of flowering plants, and seed size partly reflects the efficiency of plant production. The cultivated soybean (G. max) differs from the wild soybean (G. soja) for flowering time and seed size. Previous research has resulted in the discovery of many Quantitative Trait Loci (QTL) associated with seed size and genes associated with flowering time. However, the molecular mechanisms underlying these two traits in the soybean remain to be addressed. In this study, restriction-site-associated DNA (RAD) tags from 14 wild, 153 landrace, and 119 bred soybean accessions were sequenced, and the DNA sequence variations were analyzed to detect domestication related (DR) loci by testing the independence between the SNPs and soybean populations (wild, landrace, and bred) and comparing the genetic diversity between the wild and cultivated soybeans. Genome-wide associations of the detected DR loci vs. flowering time and seed size were studied. Candidate genes predicted to be involved in these two traits were identified based on the transcriptome expression level of the genes in soybean and the gene functions annotated in other species. The molecular mechanisms of the domestication of the flowering time and seed size in soybean were discussed. The results of this research are of interest to scientists who are attempting to discover new genes from the wild soybean that are of use in the genetic improvement of cultivated soybean.

Technical Abstract: Flowering time and seed size are related to domestication. In this study, we explored the molecular mechanisms underlying these two domestication-related (DR) traits based on the restriction site associated DNA re-sequencing of 14 wild, 153 landrace, and 119 bred accessions. A total of 48 DR loci were identified and these loci were non-uniformly distributed in the soybean genome. Among these loci, a total of 6 DR loci on chromosomes 11, 12 and 15 was associated with flowering time, and four DR loci on chromosomes 11 and 16 were associated with seed size. A total of five and three genes were associated with flowering time and seed size, respectively. The genes Glyma11g18720 and Glyma05g28130 may regulate flowering time through the light-signalling pathway OTLD1 that regulates FLC expression in Arabidopsis, and Glyma11g15480 and its 24 co-expressed genes may regulate seed size as NOT2A regulates seed development in Arabidopsis.