Genomic insights into the origin and evolution of spelt (Triticum spelta L.) as a valuable gene pool for modern wheat breeding

Spelt (T. aestivum ssp. spelta) is an important wheat subspecies mainly cultivated in Europe before the 20th century, which has contributed to modern wheat breeding as a valuable genetic resource. However, the origin and maintenance of spelt populations remain elusive. Here, based on a resequencing dataset of 416 worldwide wheat accessions, including representative spelt wheat, we demonstrated that European spelt emerged when primitive hexaploid wheat spread to the west and hybridized with pre-settled domesticated emmer, the putative maternal donor. Genomic introgression regions from domesticated emmer confer spelt’s primitive morphological characters used for species taxonomy, such as tenacious glumes and later flowering. We further propose the haplotype-based ‘spelt index’ to identify spelt-type wheat varieties and to quantify the utilization of the spelt gene pool in modern wheat cultivars. This study deciphered the genetic basis underlying the establishment of spelt wheat subspecies in a specific ecological niche and revealed the vital role of spelt gene pool as a unique germplasm resource in contributing to modern wheat breeding.