Genome-Wide Variation Analysis of Four Vegetable Soybean Cultivars Based on Re-Sequencing

Abstract

Vegetable soybean is a type of value-added specialty soybean, served as a fresh vegetable or snack in China. Due to the difference from other types, it is important to understand the genetic structure and diversity of vegetable soybean for further utilization in breeding programs. The four vegetable cultivars, Taiwan-75, Zhexiandou No. 8, Zhexian No. 9 and Zhexian No. 10 are popular soybean varieties planted in Zhejiang province, and have large pods and intermediate maturity. The clustering showed a close relationship of these four cultivars in simple sequence repeat analysis. To reveal the genome variation of vegetable soybean, these four improved lines were analyzed by whole-genome re-sequencing. The average sequencing depth was 7X and the coverage ratio of each cultivar was at least more than 94%. Compared with the reference genome, a large number of single-nucleotide polymorphisms, insertion/deletions and structure variations were identified with different chromosome distributions. The average heterozygosity rate of the single-nucleotide polymorphisms was 11.99% of these four cultivars. According to the enrichment analysis, there were 23,371 genes identified with putative modifications, and a total of 282 genes were related to carbohydrate metabolic processes. These results provide useful information for genetic research and future breeding, which can facilitate the selection procedures in vegetable soybean breeding.

Global Status of Vegetable Soybean

“…Yu et al [ 94 ] re-sequenced the four vegetable soybean varieties (Taiwan-75, Zhexiandou No. 8, Zhexian No.…”

Genetic and Phenotypic Characterization of Soybean Landraces Collected from the Zhejiang Province in China

“…The soybean (Glycine max) is a legume species that is native to China and known all over the world due to its history of more than 5000 years [1][2][3]. Because of its protein, oil, isoflavones, unsaturated fatty acids, vitamins, and other nutrients, soybean has become an important crop as a food, oil, and forage [2][3][4].…”

“…The soybean (Glycine max) is a legume species that is native to China and known all over the world due to its history of more than 5000 years [1][2][3]. Because of its protein, oil, isoflavones, unsaturated fatty acids, vitamins, and other nutrients, soybean has become an important crop as a food, oil, and forage [2][3][4]. There have been more than 43,000 soybean germplasm resources preserved in the National Crop Germplasm Resource Bank of China (Beijing), including 8518 wild soybean (Glycine soja) germplasm resources and 3265 imported germplasm resources from abroad [2,5,6].…”

“…Summer soybeans are sown from late June to early July and harvested in late October. Autumn soybeans are sown from late July to early August and harvested in early November [3,11]. Zhejiang is one of the provinces with a large number of the autumn soybean resources collected and preserved in China [2,3,11].…”

“…Autumn soybeans are sown from late July to early August and harvested in early November [3,11]. Zhejiang is one of the provinces with a large number of the autumn soybean resources collected and preserved in China [2,3,11]. These landraces contain rich genetic resources, which are the foundation for the promotion and development of the characteristic soybean industry in this locality.…”