Genetic diversity and relationship between domesticated rye and its wild relatives as revealed through genotyping‐by‐sequencing

Abstract

Rye ( Secale cereale L.) is a cereal grass that is an important food crop in Central and Eastern Europe. In contrast to its close relatives wheat and barley, it was not a founder crop of Neolithic agriculture, but is considered a secondary domesticate that may have become a crop plant only after a transitory phase as a weed. As a minor crop of only local importance, genomic resources in rye are underdeveloped, and few population genetic studies using genomewide markers have been published to date. We collected genotyping‐by‐sequencing data for 603 individuals from 101 genebank accessions of domesticated rye and its wild progenitor S. cereale subsp. vavilovii and related species in the genus Secale . Variant detection in the context of a recently published draft sequence assembly of cultivated rye yielded 55,744 single nucleotide polymorphisms with present genotype calls in 90% of samples. Analysis of population structure recapitulated the taxonomy of the genus Secale . We found only weak genetic differentiation between wild and domesticated rye with likely gene flow between the two groups. Moreover, incomplete lineage sorting was frequent between Secale species because of either ongoing gene flow or recent speciation. Our study highlights the necessity of gauging the representativeness of ex situ germplasm collections for domestication studies and motivates a more in‐depth analysis of the interplay between sequence divergence and reproductive isolation in the genus Secale .

Chromosome-scale genome assembly provides insights into rye biology, evolution, and agronomic potential

“…We included a second S. cereale genotype, ‘Lo225’, an inbred line from which the mapping population used for assembly was derived. To provide phylogenetic context, we extended the Secale phylogeny of Schreiber et al (2019) 33 , adding 347 genotypes, and calling variants against the new genome assembly (Methods; fig. M-PHYLO).…”

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

“…It is conceivable that these two ancient human populations also brought along and cultivated cereals of slightly different origin. Interestingly, a difference between Iberian and Eastern European germplasm was also observed for rye, another cereal crop that has its origin in the Fertile Crescent (Parat et al, 2016;Schreiber, Himmelbach, Borner, & Mascher, 2018). Parat et al (2016) explained this difference with different usage of rye (forage vs. human consumption).…”

The genomics of domestication special issue editorial

“…The third section concerns introgression between wild and domestic populations (Owens, Baute, Hubner, & Rieseberg, ; Schreiber, Himmelbach, Börner, & Mascher, ; Taitano et al., ; Vigueira et al., ). The first of these studies authored by Vigueira et al.…”

“…Lastly, Schreiber et al. () examine the secondary domesticated species rye, while not part of the original Neolithic package it nevertheless has become an important staple in much of Eurasia. They find that there is little genetic differentiation between domestic and wild rye, likely indicating large‐scale gene flow within the native range.…”

“…The third section concerns introgression between wild and domestic populations (Owens, Baute, Hubner, & Rieseberg, 2018;Schreiber, Himmelbach, Börner, & Mascher, 2018;Taitano et al, 2018;Vigueira et al, 2017). The first of these studies authored by Vigueira et al (2017) explores weedy rice inside and outside the rice native range, to understand diverse mechanisms for de-domestication.…”