Selective sweeps identification in distinct groups of cultivated rye (Secale cereale L.) germplasm provides potential candidate genes for crop improvement

BMC Plant Biology

Research

Roman Dušinský¹  Miroslav Švec¹  Hanna Bolibok-Brągoszewska²  Ewa Borzęcka²  Anna Hawliczek²  Piotr Gawroński²  Katarzyna Tofil²  Leszek Bolibok³  Nikolaos Alachiotis⁴  Dörthe Siekmann⁵  Bernd Hackauf⁶ 

[1] Department of Botany, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia;Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw, University of Life Sciences-SGGW, Warsaw, Poland;Department of Silviculture, Institute of Forest Sciences, Warsaw University of Life Sciences-SGGW, Warsaw, Poland;Faculty of Electrical Engineering, Mathematics and Computer Science, University of Twente, Enschede, The Netherlands;HYBRO Saatzucht GmbH & Co. KG, Schenkenberg, Germany;Julius Kühn-Institut, Groß Lüsewitz, Germany;

关键词: Rye;    Secale cereale;    Selective sweeps;    Genetic diversity;    Population structure;    GBS;    DArTseq;   

DOI  :  10.1186/s12870-023-04337-1

 received in 2023-01-22, accepted in 2023-06-07,  发布年份 2023

来源: Springer

【 摘 要 】

BackgroundDuring domestication and subsequent improvement plants were subjected to intensive positive selection for desirable traits. Identification of selection targets is important with respect to the future targeted broadening of diversity in breeding programmes. Rye (Secale cereale L.) is a cereal that is closely related to wheat, and it is an important crop in Central, Eastern and Northern Europe. The aim of the study was (i) to identify diverse groups of rye accessions based on high-density, genome-wide analysis of genetic diversity within a set of 478 rye accessions, covering a full spectrum of diversity within the genus, from wild accessions to inbred lines used in hybrid breeding, and (ii) to identify selective sweeps in the established groups of cultivated rye germplasm and putative candidate genes targeted by selection.ResultsPopulation structure and genetic diversity analyses based on high-quality SNP (DArTseq) markers revealed the presence of three complexes in the Secale genus: S. sylvestre, S. strictum and S. cereale/vavilovii, a relatively narrow diversity of S. sylvestre, very high diversity of S. strictum, and signatures of strong positive selection in S. vavilovii. Within cultivated ryes we detected the presence of genetic clusters and the influence of improvement status on the clustering. Rye landraces represent a reservoir of variation for breeding, and especially a distinct group of landraces from Turkey should be of special interest as a source of untapped variation. Selective sweep detection in cultivated accessions identified 133 outlier positions within 13 sweep regions and 170 putative candidate genes related, among others, to response to various environmental stimuli (such as pathogens, drought, cold), plant fertility and reproduction (pollen sperm cell differentiation, pollen maturation, pollen tube growth), and plant growth and biomass production.ConclusionsOur study provides valuable information for efficient management of rye germplasm collections, which can help to ensure proper safeguarding of their genetic potential and provides numerous novel candidate genes targeted by selection in cultivated rye for further functional characterisation and allelic diversity studies.

【 授权许可】

CC BY   
© The Author(s) 2023

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