QTL detection for grain size and shape traits using an improved genetic map in einkorn wheat (Triticum monococcum L.)

Einkorn wheat is a diploid (A m A m genome) and is the first cultivated crop that initiated agriculture. It is related to durum and bread wheat, and it harbours unique genes that can be used for wheat improvement. Grain size and shape are the main breeding targets due to their direct relation to yield and milling quality. To understand the genetic control of the grain size and shape-related traits in Einkorn wheat, a biparental population of 150 F 8 recombinant inbred lines (RILs) derived from a cross between an advanced einkorn line (ID1623) and a cultivar (MONLIS) was used. The RIL population was genotyped with SNP, Silico-DArT, and SSR markers and a genetic map comprising seven linkage groups (representing n = 7) was constructed. The map contained 3716 markers distributed across 760 loci with a total length of 1216.09 cM and an average density of one locus every 1.60 cM. Composite Interval Mapping was used to detect the quantitative trait loci (QTLs) controlling seven grain size and shape-related traits using genetic map and the phenotypic data collected from five different environments and the BLUP (Best Linear Unbiased Prediction) values. A total of 33 QTLs (25 novel QTLs) were detected, which were distributed on all the seven einkorn chromosomes. Of these, 14 QTLs distributed on four chromosomes (2A m , 3A m , 5A m , and 6A m ) were stable across environments. Three QTL hot spots were observed on chromosomes 2A m , 5A m and 6A m . Seven QTLs, one each for the seven traits with highest PVE% (up to 14–26% PVE in individual environments) were recommended for marker-assisted recurrent selection for improvement of grain traits in einkorn wheat. The study thus provides novel and important genetic information to help understand the genetic control of grain size and shape-related traits and also the genomic resources for use in cultivated einkorn wheat breeding.