Exploring Selective Sweeps Controlling Various Traits in Archaeological Soybean

The history of soybean (Glycine max) domestication was explored using genome sequence data obtained from archaeological soybeans dated at 1208 AD. The frequencies of the ancient soybean alleles were calculated in 302 modern soybean accessions comprising wild, landrace, and cultivated soybeans in chromosomal regions that underwent selective sweep for domestication and improvement traits. Most of the favored alleles for domestication traits are present in the ancient soybean chromosomes, although in some segments the frequency of ancient soybean alleles is low in cultivated soybean but common in landraces and wild soybean. This suggests that most of the domestication traits had been selected at 1208 AD, but some modern cultivars had accumulated new alleles in the last 800 years. In selective sweep regions associated with improvement traits, there are several segments where the ancient soybean shows more resemblance to modern cultivars than landraces, suggesting that selection for those segments had been completed 800 years ago. Nevertheless, there are also segments where the ancient soybean is more similar to landraces than modern cultivars, which indicate that the ancient soybean was not selected for the associated improvement trait. Since the selective sweep regions associated with improvement traits often coincide with traits that are important for modern application like oil content, it is understandable that such trait was absent 800 years ago since there was possibly no selection for such trait in that period. Overall, the results indicate a surprisingly advanced selection progress being achieved 800 years ago in a soybean sample obtained in Korea.