Unraveling the genetic architecture of grain size in einkorn wheat through linkage and homology mapping, and transcriptomic profiling

Understanding the genetic architecture of grain size is a prerequisite to manipulate the grain development and improve the yield potential in crops. Here, we conducted a whole genome-wide QTL mapping of grain size related traits in einkorn wheat using a high-density genetic map and explored the candidate genes underlying QTL through homologous analysis and RNA sequencing. The genetic map spanned 1873 cM and contained 9937 SNP markers assigned to 1551 bins in seven chromosomes, which revealed strong collinearity and high genome coverage by comparing with the physical maps of wheat and barley. Six grain size related traits were surveyed with >80% heritability. In total, 42 QTL were identified and assigned to 17 genomic regions, and explained 52.3-66.7% phenotypic variations. Thirty genes involved in grain development were mapped to 12 regions. RNA sequencing provided 4959 genes differentially expressed between the two parents, from which twenty genes involved in grain development and starch biosynthesis were mapped to nine regions with 26 QTL. This study unravels the genetic architectures of einkorn wheat grain size and the underlying genes using high-density genetic map, which will facilitate genetic mapping, genome assembling and comparative genomics in wheat taxa.