High-throughput genotyping of the spelt gene pool reveals patterns of agricultural history in Europe

Abstract

Spelt, a close relative of hexaploid bread wheat and a dominant wheat subspecies cultivated in Europe before the 20 th century, still plays an important role as a high-value niche product today.Compared to most other cereals, spelt has not been subjected to intensive breeding in the 20 th century. Even today, mostly traditional landraces are cultivated on a regional scale. The traditional way of spelt cultivation has limited the extensive exchange of germ plasm and intermixing of genetic material, which makes spelt an ideal crop to study the early agricultural history of cereals in Europe. Here, we unraveled the population structure and agricultural history of spelt based on 22,999 high-quality SNPs obtained by genotyping-by-sequencing on 267 spelt accessions covering the entire cultivation range. SNP markers were aligned to the high-quality bread wheat reference genome, which allowed us to analyze individual subgenomes. Our analyses of genetic variation revealed that bread wheat and spelt are most likely of monophyletic origin, but that European spelt diverged from bread wheat by hybridization with tetraploid emmer wheats. Interestingly, spelt accessions from the Iberian Peninsula formed a separate clade that was distinct from the Central European accessions for all three subgenomes. Demographic modelling indicated that Iberian spelt was introduced into Europe independently from Central European spelt. Our analysis provides a comprehensive assessment of spelt diversity and history. The separate introduction of Iberian spelt is supported by recent molecular evidence of two independent prehistoric migrations of ancient farmers from the Near East into Europe.

Genotyping-by-Sequencing Derived Single Nucleotide Polymorphisms Provide the First Well-Resolved Phylogeny for the Genus Triticum (Poaceae)

“…The discrepancy of the archaeological record where bread wheat was ahead of spelt wheat (Nesbitt and Samuel, 1996) would also be explained by this concept. Recently, Abrouk et al (2018) reported the European spelt markedly differed from Asian spelt/bread wheat and various reports suggested the European spelt wheat diverged from bread wheat by hybridization with tetraploid emmer wheat (Blatter et al, 2002(Blatter et al, , 2004. Several morphological and molecular studies also suggested the polyphyletic nature of European and Asian spelt wheat (Dvorak et al, 2012).…”

Recent Progress in Germplasm Evaluation and Gene Mapping to Enable Breeding of Drought-Tolerant Wheat

“…Recent advancements in genomics (e.g., genotype by sequencing, see below) have enabled exploration of this genetic diversity, leading to the discovery of markers and associated quantitative trait loci (QTLs) that can be utilized in marker assisted selection and genomic selection to accelerate variety development (Huang and Han, 2014). Wheat has a large and complex genome (Marcussen et al, 2014;Shi and Ling, 2017;Uauy, 2017;Abrouk et al, 2018). Very recently, however, an annotated reference whole genome sequence for bread wheat was released, which described 107,891 high-confidence level genes (IWGSC, 2018).…”