A comparison of Chinese wild and cultivar soybean with European soybean collections on genetic diversity by Genome-Wide Scan

Abstract

Although soybeans (Glycine max [L.] Merr.) originated in China and have spread worldwide, artificial selection for different breeding targets and methods in various regions can alter the genetic makeup of soybeans, enabling them to adapt to different environments. China has established a soybean germplasm gene bank that stores over 30,000 soybean germplasms from all over the world, but it contains few modern European varieties. The selective sweep analysis is an effective method for evaluating genetic diversity among populations and subpopulations. To compare the genetic diversity between Chinese and European germplasms, we genotyped 797 European varieties, 804 Chinese elite cultivars and landraces, and 54 Chinese wild varieties using the ZDX1 array, respectively. An analysis of 158,315 SNPs demonstrated a higher genetic diversity in Chinese wild soybeans and cultivars. Moreover, population structure findings indicated that European varieties possess partial Chinese ancestry. The joint analysis of pi, FST and XP-CLR identified 140 selected regions between Chinese and European germplasms in total. Specifically, the Chinese collection had 124 regions distributed across 15 chromosomes, while the European collection had 16 regions spread over 10 chromosomes. The QTLs identified within these selected regions highlight the significant differences in breeding targets across regions, providing a scientific basis for both Chinese and European breeders to utilize these germplasm resources.