Evaluation of genetic diversity and population structure of wheat core collection using SNP and KASP markers for major agronomic traits

Abstract Background Wheat is one of the most important food crops worldwide. Numerous studies have shown that genetic diversity lost the process of wheat breeding because of the pursuit of earlier heading date and higher yield. Reduced genetic diversity leads to decreased adaptability to the environment and resistance to pests and diseases posing a serious threat to wheat production safety. Results This study investigated the genetic diversity of a global wheat collection stored at the National Agrobiodiversity Center of South Korea. A total of 397 global wheat core collections were selected from 19,698 accessions, with associated traits accumulated from 1984 to 2017. The genetic diversity of the core collections was analyzed using 198 neutral SNPs and KASP markers to explore the population structure and genetic diversity within the global wheat collection. The results indicate that cultivars developed in the past decade exhibit higher genetic diversity than both the cultivars deposited before 2015 and the landraces. This suggests that the genetic diversity observed in the newly developed cultivars may originate from the introduction of novel wild germplasms or artificially induced mutant breeding materials. In addition, the traits prediction system established using the KASP marker genotyping results can explain 52.7% of the heading date variation and 42.9% of the 1000-grain weight variation. Conclusions Overall, this study monitored the genetic diversity of wheat cultivars bred in the past decade and concluded that modern wheat breeding model have reversed the trend of continuous reduction in genetic diversity of cultivars. The trait prediction system established using KASP markers could provide a platform for the selection of new wheat materials for future breeding.