1
|
Du T, Hu Y, Sun Y, Ye C, Shen E. The complete chloroplast genome of weedy rye Secale cereale subsp. segetale. Mitochondrial DNA B Resour 2022; 7:959-960. [PMID: 35692639 PMCID: PMC9176342 DOI: 10.1080/23802359.2022.2080600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Weedy rye (Secale cereale subsp. segetale Zhukov 1928) is a problematic weed species in wheat field. However, it can potentially provide valuable genetics resources to increase the genetic variations and introduce desirable genes for rye and wheat breeding. Here, we assembled the complete chloroplast genome of S. cereale subsp. segetale. The chloroplast genome is 137,051 bp in length, containing a large single copy region (81,090 bp), a small single copy region (12,795 bp) and two separated inverted repeat regions (21,583 bp). A total of 131 unique genes were annotated, consisting of 82 protein-coding genes, 41 tRNA genes, and 8 rRNA genes. The phylogenetic analysis showed that Secale cereale subsp. segetale (weedy rye) and S. cereale subsp. cereale (rye) clustered together as sisters to other Secale species.
Collapse
Affiliation(s)
- Tianyu Du
- Shandong (Linyi) Institute of Modern Agriculture of Zhejiang University, Linyi, China
- Institute of Crop Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yiyu Hu
- Institute of Crop Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yanqing Sun
- Institute of Crop Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Chuyu Ye
- Institute of Crop Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Enhui Shen
- Shandong (Linyi) Institute of Modern Agriculture of Zhejiang University, Linyi, China
- Institute of Crop Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- The Rural Development Academy, Zhejiang University, Hangzhou, China
| |
Collapse
|
2
|
Abd El-Moneim D, Contreras R, Silva-Navas J, Gallego FJ, Figueiras AM, Benito C. Repression of Mitochondrial Citrate Synthase Genes by Aluminum Stress in Roots of Secale cereale and Brachypodium distachyon. FRONTIERS IN PLANT SCIENCE 2022; 13:832981. [PMID: 35463451 PMCID: PMC9021840 DOI: 10.3389/fpls.2022.832981] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 03/02/2022] [Indexed: 06/14/2023]
Abstract
Aluminum (Al) toxicity in acid soils influences plant development and yield. Almost 50% of arable land is acidic. Plants have evolved a variety of tolerance mechanisms for Al. In response to the presence of Al, various species exudate citrate from their roots. Rye (Secale cereale L.) secretes both citrate and malate, making it one of the most Al-tolerant cereal crops. However, no research has been done on the role of the mitochondrial citrate synthase (mCS) gene in Al-induced stress in the rye. We have isolated an mCS gene, encoding a mitochondrial CS isozyme, in two S. cereale cultivars (Al-tolerant cv. Ailés and Al-sensitive inbred rye line Riodeva; ScCS4 gene) and in two Brachypodium distachyon lines (Al-tolerant ABR8 line and Al-sensitive ABR1 line; BdCS4 gene). Both mCS4 genes have 19 exons and 18 introns. The ScCS4 gene was located on the 6RL rye chromosome arm. Phylogenetic studies using cDNA and protein sequences have shown that the ScCS4 gene and their ScCS protein are orthologous to mCS genes and CS proteins of different Poaceae plants. Expression studies of the ScCS4 and BdSC4 genes show that the amount of their corresponding mRNAs in the roots is higher than that in the leaves and that the amounts of mRNAs in plants treated and not treated with Al were higher in the Al-tolerant lines than that in the Al-sensitive lines of both species. In addition, the levels of ScCS4 and BdCS4 mRNAs were reduced in response to Al (repressive behavior) in the roots of the tolerant and sensitive lines of S. cereale and B. distachyon.
Collapse
|
3
|
Skuza L, Filip E, Szućko I, Bocianowski J. SPInDel Analysis of the Non-Coding Regions of cpDNA as a More Useful Tool for the Identification of Rye (Poaceae: Secale) Species. Int J Mol Sci 2020; 21:ijms21249421. [PMID: 33321948 PMCID: PMC7762986 DOI: 10.3390/ijms21249421] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 12/07/2020] [Accepted: 12/08/2020] [Indexed: 01/09/2023] Open
Abstract
Secale is a small but very diverse genus from the tribe Triticeae (family Poaceae), which includes annual, perennial, self-pollinating and open-pollinating, cultivated, weedy and wild species of various phenotypes. Despite its high economic importance, classification of this genus, comprising 3–8 species, is inconsistent. This has resulted in significantly reduced progress in the breeding of rye which could be enriched with functional traits derived from wild rye species. Our previous research has suggested the utility of non-coding sequences of chloroplast and mitochondrial DNA in studies on closely related species of the genus Secale. Here we applied the SPInDel (Species Identification by Insertions/Deletions) approach, which targets hypervariable genomic regions containing multiple insertions/deletions (indels) and exhibiting extensive length variability. We analysed a total of 140 and 210 non-coding sequences from cpDNA and mtDNA, respectively. The resulting data highlight regions which may represent useful molecular markers with respect to closely related species of the genus Secale, however, we found the chloroplast genome to be more informative. These molecular markers include non-coding regions of chloroplast DNA: atpB-rbcL and trnT-trnL and non-coding regions of mitochondrial DNA: nad1B-nad1C and rrn5/rrn18. Our results demonstrate the utility of the SPInDel concept for the characterisation of Secale species.
Collapse
Affiliation(s)
- Lidia Skuza
- Institute of Biology, University of Szczecin, 13 Wąska, 71-415 Szczecin, Poland; (E.F.); (I.S.)
- The Centre for Molecular Biology and Biotechnology, University of Szczecin, 13 Wąska, 71-415 Szczecin, Poland
- Correspondence:
| | - Ewa Filip
- Institute of Biology, University of Szczecin, 13 Wąska, 71-415 Szczecin, Poland; (E.F.); (I.S.)
- The Centre for Molecular Biology and Biotechnology, University of Szczecin, 13 Wąska, 71-415 Szczecin, Poland
| | - Izabela Szućko
- Institute of Biology, University of Szczecin, 13 Wąska, 71-415 Szczecin, Poland; (E.F.); (I.S.)
- The Centre for Molecular Biology and Biotechnology, University of Szczecin, 13 Wąska, 71-415 Szczecin, Poland
| | - Jan Bocianowski
- Department of Mathematical and Statistical Methods, Faculty of Agronomy and Bioengineering, Poznań University of Life Sciences, 28 Wojska Polskiego, 60-637 Poznań, Poland;
| |
Collapse
|
4
|
Daskalova N, Spetsov P. Taxonomic Relationships and Genetic Variability of Wild Secale L. Species as a Source for Valued Traits in Rye, Wheat and Triticale Breeding. CYTOL GENET+ 2020. [DOI: 10.3103/s0095452720010041] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
5
|
Skuza L, Szućko I, Filip E, Strzała T. Genetic diversity and relationship between cultivated, weedy and wild rye species as revealed by chloroplast and mitochondrial DNA non-coding regions analysis. PLoS One 2019; 14:e0213023. [PMID: 30811487 PMCID: PMC6392296 DOI: 10.1371/journal.pone.0213023] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 02/13/2019] [Indexed: 11/18/2022] Open
Abstract
The genus Secale is small but very diverse. Despite the high economic importance, phylogenetic relationships of rye species have not been fully determined, and they are extremely important for the process of breeding of new cultivars that can be enriched with functional traits derived from wild rye species. The study analyzed the degree of relationship of 35 accessions of the genus Secale, representing 13 most often distinguished species and subspecies, originating from various seed collections in the world, based on the analysis of non-coding regions of the chloroplast (cpDNA) and mitochondrial genome (mtDNA), widely used in phylogenetic and population plant studies, because of a higher rate of evolution than the coding regions. There was no clear genetic structure between different species and subspecies, which may indicated the introgression between these taxa. The obtained data confirmed that S. vavilovii was very similar to S. cereale, which confirmed the assumption that they might share a common ancestor. The results also confirmed the divergence of S. sylvestre from other species and subspecies of rye. Areas that may be useful molecular markers in studies on closely related species of the genus Secale were also indicated.
Collapse
Affiliation(s)
- Lidia Skuza
- Department of Molecular Biology and Cytology, The Institute for Research on Biodiversity, Faculty of Biology, University of Szczecin, Szczecin, Poland
- The Centre for Molecular Biology and Biotechnology, Faculty of Biology, University of Szczecin, Szczecin, Poland
- * E-mail:
| | - Izabela Szućko
- Department of Molecular Biology and Cytology, The Institute for Research on Biodiversity, Faculty of Biology, University of Szczecin, Szczecin, Poland
- The Centre for Molecular Biology and Biotechnology, Faculty of Biology, University of Szczecin, Szczecin, Poland
| | - Ewa Filip
- Department of Molecular Biology and Cytology, The Institute for Research on Biodiversity, Faculty of Biology, University of Szczecin, Szczecin, Poland
- The Centre for Molecular Biology and Biotechnology, Faculty of Biology, University of Szczecin, Szczecin, Poland
| | - Tomasz Strzała
- Department of Genetics, Faculty of Biology and Animal Science, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| |
Collapse
|
6
|
Maraci Ö, Özkan H, Bilgin R. Phylogeny and genetic structure in the genus Secale. PLoS One 2018; 13:e0200825. [PMID: 30024916 PMCID: PMC6053196 DOI: 10.1371/journal.pone.0200825] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 06/29/2018] [Indexed: 11/18/2022] Open
Abstract
Secale L. is a small but important genus that includes cultivated rye. Although genetic diversity of cultivated rye is high, patterns of genetic diversity in the whole genus, and potential factors affecting the distribution of genetic diversity remain elusive. The population structure and distribution of genetic variation within Secale, and its correlation with taxonomic delimitation, cultivation status or spatial distribution in relation to geography and climate zones were analyzed in this study. A collection of 726 individual plants derived from 139 different accessions representing Secale cereale, S. vavilovii, S. strictum, and S. sylvestre were investigated using SSR analysis and sequence diversity analysis of a nuclear EST region. Our results indicated that perennial S. strictum subspecies are genetically divergent from annual forms of the genus. Existence of two distinct clusters within the annual taxa was observed, one corresponding to samples from Asia, and a second to those outside of Asia. No clear genetic structure was observed between different annual species/subspecies, indicating introgression between these taxa. The analysis of cultivated rye revealed that landrace populations from the Middle East have the highest genetic diversity, supporting the idea of the area being the center of origin for cultivated rye. Considering high adaptive potential of those populations, Middle Eastern landraces should be regarded as genetic resources reservoirs for new niches and future breeding programs.
Collapse
Affiliation(s)
- Öncü Maraci
- Department of Animal Behaviour, Bielefeld University, Bielefeld, Germany
- Evolutionary Biology, Bielefeld University, Bielefeld, Germany
- Institute of Environmental Sciences, Boğaziçi University, Istanbul, Turkey
| | - Hakan Özkan
- Department of Field Crops, Faculty of Agriculture, University of Çukurova, Adana,Turkey
| | - Raşit Bilgin
- Institute of Environmental Sciences, Boğaziçi University, Istanbul, Turkey
| |
Collapse
|
7
|
Monteiro F, Vidigal P, Barros AB, Monteiro A, Oliveira HR, Viegas W. Genetic Distinctiveness of Rye In situ Accessions from Portugal Unveils a New Hotspot of Unexplored Genetic Resources. FRONTIERS IN PLANT SCIENCE 2016; 7:1334. [PMID: 27630658 PMCID: PMC5006150 DOI: 10.3389/fpls.2016.01334] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 08/18/2016] [Indexed: 05/21/2023]
Abstract
Rye (Secale cereale L.) is a cereal crop of major importance in many parts of Europe and rye breeders are presently very concerned with the restrict pool of rye genetic resources available. Such narrowing of rye genetic diversity results from the presence of "Petkus" pool in most modern rye varieties as well as "Petkus" × "Carsten" heterotic pool in hybrid rye breeding programs. Previous studies on rye's genetic diversity revealed moreover a common genetic background on landraces (ex situ) and cultivars, regardless of breeding level or geographical origin. Thus evaluation of in situ populations is of utmost importance to unveil "on farm" diversity, which is largely undervalued. Here, we perform the first comprehensive assessment of rye's genetic diversity and population structuring using cultivars, ex situ landraces along a comprehensive sampling of in situ accessions from Portugal, through a molecular-directed analysis using SSRs markers. Rye genetic diversity and population structure analysis does not present any geographical trend but disclosed marked differences between genetic backgrounds of in situ accessions and those of cultivars/ex situ collections. Such genetic distinctiveness of in situ accessions highlights their unexplored potential as new genetic resources, which can be used to boost rye breeding strategies and the production of new varieties. Overall, our study successfully demonstrates the high prospective impact of comparing genetic diversity and structure of cultivars, ex situ, and in situ samples in ascertaining the status of plant genetic resources (PGR).
Collapse
Affiliation(s)
- Filipa Monteiro
- Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de LisboaLisboa, Portugal
- *Correspondence: Filipa Monteiro
| | - Patrícia Vidigal
- Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de LisboaLisboa, Portugal
| | - André B. Barros
- Colégio F3 Food, Farming and Forestry, Universidade de LisboaLisboa, Portugal
| | - Ana Monteiro
- Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de LisboaLisboa, Portugal
| | - Hugo R. Oliveira
- Plant Biology/Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do PortoPorto, Portugal
- Faculty of Life Sciences, Manchester Institute of Biotechnology, University of ManchesterManchester, UK
| | - Wanda Viegas
- Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de LisboaLisboa, Portugal
| |
Collapse
|