Haplotype variations in QTL for salt tolerance in Chinese wheat accessions identified by marker-based and pedigree-based kinship analyses

Abstract Most modern wheat cultivars were selected on the basis of yield-related indices measured under optimal fertilizer and irrigation inputs. With climate change, land degradation and salinity caused by sea water encroachment, wheat is increasingly subjected to environmental stress. Moreover, expanding urbanization increasingly encroaches upon prime agricultural land in countries like China, and alternative cropping areas must be found. Some of these areas have moderate constraining factors, such as salinity. Therefore, it is important to investigate whether current genetic materials and breeding procedures are maintaining adequate variability to address future problems caused by abiotic stress. In this study, a panel of 307 wheat accessions, including local landraces, exotic cultivars used in Chinese breeding programs and Chinese cultivars released during different periods since 1940, were subjected to a genome-wide association study to dissect the genetic basis of salinity tolerance. Both marker-based and pedigree-based kinship analyses revealed that favorable haplotypes were introduced in some exotic cultivars as well as a limited number of Chinese landraces from the 1940s. However, improvements in salinity tolerance during modern breeding are not as obvious as that of yield. To broaden genetic diversity for increasing salt tolerance, there is a need to refocus attention on local landraces that have high degrees of salinity tolerance and carry rare favorable alleles that have not been exploited in breeding.