Selective sweeps identification in distinct groups of cultivated rye (Secale cereale L.) germplasm provides potential candidate genes for crop improvement
Abstract Background During 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.)...
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| Format: | Article |
| Language: | English |
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BMC
2023-06-01
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| Series: | BMC Plant Biology |
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| Online Access: | https://doi.org/10.1186/s12870-023-04337-1 |
| _version_ | 1797801507677011968 |
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| author | Anna Hawliczek Ewa Borzęcka Katarzyna Tofil Nikolaos Alachiotis Leszek Bolibok Piotr Gawroński Dörthe Siekmann Bernd Hackauf Roman Dušinský Miroslav Švec Hanna Bolibok-Brągoszewska |
| author_facet | Anna Hawliczek Ewa Borzęcka Katarzyna Tofil Nikolaos Alachiotis Leszek Bolibok Piotr Gawroński Dörthe Siekmann Bernd Hackauf Roman Dušinský Miroslav Švec Hanna Bolibok-Brągoszewska |
| author_sort | Anna Hawliczek |
| collection | DOAJ |
| description | Abstract Background During 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. Results Population 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. Conclusions Our 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. |
| first_indexed | 2024-03-13T04:51:31Z |
| format | Article |
| id | doaj.art-71c2409dee5b4d93a95d8bec4bbd1466 |
| institution | Directory Open Access Journal |
| issn | 1471-2229 |
| language | English |
| last_indexed | 2024-03-13T04:51:31Z |
| publishDate | 2023-06-01 |
| publisher | BMC |
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| series | BMC Plant Biology |
| spelling | doaj.art-71c2409dee5b4d93a95d8bec4bbd14662023-06-18T11:10:55ZengBMCBMC Plant Biology1471-22292023-06-0123111710.1186/s12870-023-04337-1Selective sweeps identification in distinct groups of cultivated rye (Secale cereale L.) germplasm provides potential candidate genes for crop improvementAnna Hawliczek0Ewa Borzęcka1Katarzyna Tofil2Nikolaos Alachiotis3Leszek Bolibok4Piotr Gawroński5Dörthe Siekmann6Bernd Hackauf7Roman Dušinský8Miroslav Švec9Hanna Bolibok-Brągoszewska10Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw, University of Life Sciences-SGGWDepartment of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw, University of Life Sciences-SGGWDepartment of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw, University of Life Sciences-SGGWFaculty of Electrical Engineering, Mathematics and Computer Science, University of TwenteDepartment of Silviculture, Institute of Forest Sciences, Warsaw University of Life Sciences-SGGWDepartment of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw, University of Life Sciences-SGGWHYBRO Saatzucht GmbH & Co. KGJulius Kühn-InstitutDepartment of Botany, Faculty of Natural Sciences, Comenius University in BratislavaDepartment of Botany, Faculty of Natural Sciences, Comenius University in BratislavaDepartment of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw, University of Life Sciences-SGGWAbstract Background During 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. Results Population 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. Conclusions Our 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.https://doi.org/10.1186/s12870-023-04337-1RyeSecale cereale LSelective sweepsGenetic diversityPopulation structureGBS |
| spellingShingle | Anna Hawliczek Ewa Borzęcka Katarzyna Tofil Nikolaos Alachiotis Leszek Bolibok Piotr Gawroński Dörthe Siekmann Bernd Hackauf Roman Dušinský Miroslav Švec Hanna Bolibok-Brągoszewska Selective sweeps identification in distinct groups of cultivated rye (Secale cereale L.) germplasm provides potential candidate genes for crop improvement BMC Plant Biology Rye Secale cereale L Selective sweeps Genetic diversity Population structure GBS |
| title | Selective sweeps identification in distinct groups of cultivated rye (Secale cereale L.) germplasm provides potential candidate genes for crop improvement |
| title_full | Selective sweeps identification in distinct groups of cultivated rye (Secale cereale L.) germplasm provides potential candidate genes for crop improvement |
| title_fullStr | Selective sweeps identification in distinct groups of cultivated rye (Secale cereale L.) germplasm provides potential candidate genes for crop improvement |
| title_full_unstemmed | Selective sweeps identification in distinct groups of cultivated rye (Secale cereale L.) germplasm provides potential candidate genes for crop improvement |
| title_short | Selective sweeps identification in distinct groups of cultivated rye (Secale cereale L.) germplasm provides potential candidate genes for crop improvement |
| title_sort | selective sweeps identification in distinct groups of cultivated rye secale cereale l germplasm provides potential candidate genes for crop improvement |
| topic | Rye Secale cereale L Selective sweeps Genetic diversity Population structure GBS |
| url | https://doi.org/10.1186/s12870-023-04337-1 |
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