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

Spelt(Triticum aestivum ssp.spelta)is an important wheat subspecies mainly cultivated in Europe before the 20th century that has contributed to modern wheat breeding as a valuable genetic resource.However,relatively little is known about the origins and maintenance of spelt populations.Here,using resequencing data from 416 worldwide wheat accessions,including representative spelt wheat,we demonstrate that Eu-ropean 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 laterflowering.We propose a haplotype-based"spelt index"to identify spelt-type wheat vari-eties and to quantify utilization of the spelt gene pool in modern wheat cultivars.This study reveals the ge-netic basis for the establishment of the spelt wheat subspecies in a specific ecological niche and the vital role of the spelt gene pool as a unique germplasm resource in modern wheat breeding.