title: Geography and end use drive the diversification of worldwide winter rye populations.
abstract: To meet the current challenges in human food production, improved understanding of the genetic diversity of crop species that maximizes the selection efficacy in breeding programs is needed. The present study offers new insights into the diversity, genetic structure and demographic history of cultivated rye (Secale cereale L.). We genotyped 620 individuals from 14 global rye populations with a different end use (grain or forage) at 32 genome-wide simple sequence repeat markers. We reveal the relationships among these populations, their sizes and the timing of domestication events using population genetics and model-based inference with approximate Bayesian computation. Our main results demonstrate (i) a high within-population variation and genetic diversity, (ii) an unexpected absence of reduction in diversity with an increasing improvement level and (iii) patterns suggestive of multiple domestication events. We suggest that the main drivers of diversification of winter rye are the end use of rye in two early regions of cultivation: rye forage in the Mediterranean area and grain in northeast Europe. The lower diversity and stronger differentiation of eastern European populations were most likely due to more intensive cultivation and breeding of rye in this region, in contrast to the Mediterranean region where it was considered a secondary crop or even a weed. We discuss the relevance of our results for the management of gene bank resources and the pitfalls of inference methods applied to crop domestication due to violation of model assumptions and model complexity.
authors.affiliation: Population Genetics, TUM School of Life Sciences Weihenstephan, Technische Universität München, Liesel-Beckmann-Str. 2, 85354, Freising, Germany.
authors.forename: Florence
authors.initials: F
authors.lastname: Parat
authors.affiliation: Plant Breeding, TUM School of Life Sciences Weihenstephan, Technische Universität München, Liesel-Beckmann-Str. 2, 85354, Freising, Germany.
authors.forename: Grit
authors.initials: G
authors.lastname: Schwertfirm
authors.affiliation: Plant Breeding, TUM School of Life Sciences Weihenstephan, Technische Universität München, Liesel-Beckmann-Str. 2, 85354, Freising, Germany.
authors.forename: Ulrike
authors.initials: U
authors.lastname: Rudolph
authors.affiliation: State Plant Breeding Institute, Universität Hohenheim, Fruwirthstr. 21, 70599, Stuttgart, Germany.
authors.forename: Thomas
authors.initials: T
authors.lastname: Miedaner
authors.affiliation: KWS LOCHOW GMBH, 29296, Bergen, Germany.
authors.forename: Viktor
authors.initials: V
authors.lastname: Korzun
authors.affiliation: Plant Breeding, TUM School of Life Sciences Weihenstephan, Technische Universität München, Liesel-Beckmann-Str. 2, 85354, Freising, Germany.
authors.forename: Eva
authors.initials: E
authors.lastname: Bauer
authors.affiliation: Plant Breeding, TUM School of Life Sciences Weihenstephan, Technische Universität München, Liesel-Beckmann-Str. 2, 85354, Freising, Germany.
authors.forename: Chris-Carolin
authors.initials: CC
authors.lastname: Schön
authors.affiliation: Population Genetics, TUM School of Life Sciences Weihenstephan, Technische Universität München, Liesel-Beckmann-Str. 2, 85354, Freising, Germany.
authors.forename: Aurélien
authors.initials: A
authors.lastname: Tellier
mesh_terms: D001499:Bayes Theorem; D005060:Europe; D014644:Genetic Variation; D005828:Genetics, Population; D005838:Genotype; D005843:Geography; D019083:Mediterranean Region; D018895:Microsatellite Repeats; D008957:Models, Genetic; D000069600:Plant Breeding; D057685:Plant Weeds / Q000235:genetics; D012434:Secale / Q000235:genetics*
keywords: ABC model; SSR marker; domestication; genetic diversity; population structure