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

Abstract

HighlightGenome-wide linkage and homology mapping revealed 17 genomic regions through a high-density einkorn wheat genetic map constructed using RAD-seq, and transcription levels of 20 candidate genes were explored using RNA-seq.\n\nAbstractUnderstanding the genetic architecture of grain size is a prerequisite to manipulate the grain development and improve the yield potential in crops. In this study, we conducted a whole genome-wide QTL mapping of grain size related traits in einkorn wheat by constructing a high-density genetic map, and explored the candidate genes underlying QTL through homologous analysis and RNA sequencing. The high-density genetic map spanned 1873 cM and contained 9937 SNP markers assigned to 1551 bins in seven chromosomes. Strong collinearity and high genome coverage of this map were revealed with the physical maps of wheat and barley. Six grain size related traits were surveyed in five agro-climatic environments with 80% or more broad-sense heritability. In total, 42 QTL were identified and assigned to 17 genomic regions on six chromosomes and accounted for 52.3-66.7% of the phenotypic variations. Thirty homologous genes involved in grain development were located in 12 regions. RNA sequencing provided 4959 genes differentially expressed between the two parents. Twenty differentially expressed genes involved in grain size development and starch biosynthesis were mapped to nine regions that contained 26 QTL, indicating that the starch biosynthesis pathway played a vital role on grain development in einkorn wheat. This study provides new insights into the genetic architecture of grain size in einkorn wheat, the underlying genes enables the understanding of grain development and wheat genetic improvement, and the map facilitates the mapping of quantitative traits, map-based cloning, genome assembling and comparative genomics in wheat taxa.