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Kumar K, Gupta P, Singh KN, Nirgude MS, Srivastava H, Sharma S, Sevanthi AM, Durgesh K, Jain PK, Gaikwad K. Whole chloroplast genome-specific non-synonymous SNPs reveal the presence of substantial diversity in the pigeonpea mini-core collection. 3 Biotech 2023; 13:365. [PMID: 37840876 PMCID: PMC10575842 DOI: 10.1007/s13205-023-03785-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 09/13/2023] [Indexed: 10/17/2023] Open
Abstract
To unravel the plastid genome diversity among the cultivated groups of the pigeonpea germplasm, we characterized the SNP occurrence and distribution of 142 pigeonpea mini-core collections based on their reference-based assembly of the chloroplast genome. A total of 8921 SNPs were found, which were again filtered and finally 3871 non-synonymous SNPs were detected and used for diversity estimates. These 3871 SNPs were classified into 12 groups and were present in only 44 of the 125 genes, demonstrating the presence of a precise mechanism for maintaining the whole chloroplast genome throughout evolution. The Acetyl-CoA carboxylase D gene possesses the maximum number of SNPs (12.29%), but the Adenosine Tri-Phosphate synthatase cluster genes (atpA, atpB, atpE, atpF, atpH, and atpI) altogether bear 43.34% of the SNPs making them most diverse. Various diversity estimates, such as the number of effective alleles (1.013), Watterson's estimate (0.19), Tajima's D ( - 3.15), Shannon's information index (0.036), suggest the presence of less diversity in the cultivated gene pool of chloroplast genomes. The genetic relatedness estimates based on pairwise correlations were also in congruence with these diversity descriptors and indicate the prevalence of rare alleles in the accessions. Interestingly, no stratification was observed either through STRUCTURE, PCoA, or phylogenetic analysis, indicating the common origin of the chloroplast in all the accessions used, irrespective of their geographical distribution. Further 6194 Cleaved Amplified Polymorphic Sequences (CAPS) markers for 531 SNPs were developed and validated in a selected set of germplasm. Based on these results, we inferred that all of the cultivated gene pools of pigeonpea have a common origin for the chloroplast genome and they possess less diversity in protein-coding regions, indicating a stable and evolved plastid genome. At the same time, all diversity analysis indicates the occurrence of rare alleles, suggesting the suitability of the mini-core collection in future pigeonpea improvement programs. In addition, the development of chloroplast genome-based CAPS markers would have utility in pigeonpea breeding programs. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03785-8.
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Affiliation(s)
- Kuldeep Kumar
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
- ICAR-Indian Institute of Pulses Research, Kanpur, Uttar Pradesh India
| | - Palak Gupta
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | | | | | | | - Sandhya Sharma
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | | | - Kumar Durgesh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | - Kishor Gaikwad
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
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2
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Che Y, Yang Y, Yang Y, Wei L, Guo J, Yang X, Li X, Liu W, Li L. Construction of a high-density genetic map and mapping of a spike length locus for rye. PLoS One 2023; 18:e0293604. [PMID: 37903124 PMCID: PMC10615298 DOI: 10.1371/journal.pone.0293604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 10/16/2023] [Indexed: 11/01/2023] Open
Abstract
Genetic maps provide the foundation for QTL mapping of important traits of crops. As a valuable food and forage crop, rye (Secale cereale L., RR) is also one of the tertiary gene sources of wheat, especially wild rye, Secale cereale subsp. segetale, possessing remarkable stress tolerance, tillering capacity and numerous valuable traits. In this study, based on the technique of specific-locus amplified fragment sequencing (SLAF-seq), a high-density single nucleotide polymorphism (SNP) linkage map of the cross-pollinated (CP) hybrid population crossed by S. cereale L (female parent) and S. cereale subsp. segetale (male parent) was successfully constructed. Following preprocessing, the number of 1035.11 M reads were collected and 2425800 SNP were obtained, of which 409134 SNP were polymorphic. According to the screening process, 9811 SNP markers suitable for constructing linkage groups (LGs) were selected. Subsequently, all of the markers with MLOD values lower than 3 were filtered out. Finally, an integrated map was constructed with 4443 markers, including 1931 female mapping markers and 3006 male mapping markers. A major quantitative trait locus (QTL) linked with spike length (SL) was discovered at 73.882 cM on LG4, which explained 25.29% of phenotypic variation. Meanwhile two candidate genes for SL, ScWN4R01G329300 and ScWN4R01G329600, were detected. This research presents the first high-quality genetic map of rye, providing a substantial number of SNP marker loci that can be applied to marker-assisted breeding. Additionally, the finding could help to use SLAF marker mapping to identify certain QTL contributing to important agronomic traits. The QTL and the candidate genes identified through the high-density genetic map above may provide diverse potential gene resources for the genetic improvement of rye.
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Affiliation(s)
- Yonghe Che
- Hebei Key Laboratory of Crop Stress Biology, Qinhuangdao, Hebei, China
- College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei, China
| | - Yunjie Yang
- Hebei Key Laboratory of Crop Stress Biology, Qinhuangdao, Hebei, China
- College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei, China
| | - Yanping Yang
- Hebei Key Laboratory of Crop Stress Biology, Qinhuangdao, Hebei, China
- College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei, China
| | - Lai Wei
- Hebei Key Laboratory of Crop Stress Biology, Qinhuangdao, Hebei, China
- College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei, China
| | - Juan Guo
- Hebei Key Laboratory of Crop Stress Biology, Qinhuangdao, Hebei, China
- College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei, China
| | - Xinming Yang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiuquan Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Weihua Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lihui Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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3
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Ibrahim AA, Alwutayd KM, Safhi FA, Alshegaihi RM, Alqurashi M, Alyamani A, Aloufi S, Alharthi B, Fayad E, Abd El-Moneim D. Characterization and comparative genomic analyses of complete chloroplast genome on Trema orientalis L. GENETIC RESOURCES AND CROP EVOLUTION 2023. [DOI: 10.1007/s10722-023-01678-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 07/06/2023] [Indexed: 09/02/2023]
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4
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Skuza L, Androsiuk P, Gastineau R, Paukszto Ł, Jastrzębski JP, Cembrowska-Lech D. Molecular structure, comparative and phylogenetic analysis of the complete chloroplast genome sequences of weedy rye Secale cereale ssp. segetale. Sci Rep 2023; 13:5412. [PMID: 37012409 PMCID: PMC10070434 DOI: 10.1038/s41598-023-32587-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 03/29/2023] [Indexed: 04/05/2023] Open
Abstract
The complete chloroplast genome of Secale cereale ssp. segetale (Zhuk.) Roshev. (Poaceae: Triticeae) was sequenced and analyzed to better use its genetic resources to enrich rye and wheat breeding. The study was carried out using the following methods: DNA extraction, sequencing, assembly and annotation, comparison with other complete chloroplast genomes of the five Secale species, and multigene phylogeny. As a result of the study, it was determined that the chloroplast genome is 137,042 base pair (bp) long and contains 137 genes, including 113 unique genes and 24 genes which are duplicated in the IRs. Moreover, a total of 29 SSRs were detected in the Secale cereale ssp. segetale chloroplast genome. The phylogenetic analysis showed that Secale cereale ssp. segetale appeared to share the highest degree of similarity with S. cereale and S. strictum. Intraspecific diversity has been observed between the published chloroplast genome sequences of S. cereale ssp. segetale. The genome can be accessed on GenBank with the accession number (OL688773).
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Affiliation(s)
- Lidia Skuza
- Institute of Biology, University of Szczecin, 71415, Szczecin, Poland.
- Centre for Molecular Biology and Biotechnology, Institute of Biology, University of Szczecin, 71415, Szczecin, Poland.
| | - Piotr Androsiuk
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury, 10719, Olsztyn, Poland
| | - Romain Gastineau
- Institute of Marine and Environmental Sciences, University of Szczecin, 70383, Szczecin, Poland
| | - Łukasz Paukszto
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury, 10719, Olsztyn, Poland
| | - Jan Paweł Jastrzębski
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury, 10719, Olsztyn, Poland
| | - Danuta Cembrowska-Lech
- Department of Physiology and Biochemistry, Institute of Biology, University of Szczecin, Felczaka 3c St., 71412, Szczecin, Poland
- Sanprobi Sp. z o. o. Sp. k., Kurza Stopka 5c St., 70535, Szczecin, Poland
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5
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Sun Y, Shen E, Hu Y, Wu D, Feng Y, Lao S, Dong C, Du T, Hua W, Ye CY, Zhu J, Zhu QH, Cai D, Skuza L, Qiu J, Fan L. Population genomic analysis reveals domestication of cultivated rye from weedy rye. MOLECULAR PLANT 2022; 15:552-561. [PMID: 34971791 DOI: 10.1016/j.molp.2021.12.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 12/17/2021] [Accepted: 12/24/2021] [Indexed: 06/14/2023]
Abstract
Rye (Secale cereale) is an important crop with multiple uses and a valuable genetic resource for wheat breeding. However, due to its complex genome and outcrossing nature, the origin of cultivated rye remains elusive. The geneticist N.I. Vavilov proposed that cultivated rye had been domesticated from weedy rye, rather than directly from wild species like other crops. Unraveling the domestication history of rye will extend our understanding of crop evolution and upend our inherent understanding of agricultural weeds. To this end, in this study we generated the 8.5 Tb of whole-genome resequencing data from 116 worldwide accessions of wild, weedy, and cultivated rye, and demonstrated that cultivated rye was domesticated directly from weedy relatives with a similar but enhanced genomic selection by humans. We found that a repertoire of genes that experienced artificial selection is associated with important agronomic traits, including shattering, grain yield, and disease resistance. Furthermore, we identified a composite introgression in cultivated rye from the wild perennial Secale strictum and detected a 2-Mb introgressed fragment containing a candidate ammonium transporter gene with potential effect on the grain yield and plant growth of rye. Taken together, our findings unravel the domestication history of cultivated rye, suggest that interspecific introgression serves as one of the likely causes of obscure species taxonomy of the genus Secale, and provide an important resource for future rye and wheat breeding.
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Affiliation(s)
- Yanqing Sun
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China; Zhejiang University Zhongyuan Institute, Zhengzhou 450000, China; Shandong (Linyi) Institute of Modern Agriculture of Zhejiang University, Linyi 310014, China
| | - Enhui Shen
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China; Zhejiang University Zhongyuan Institute, Zhengzhou 450000, China; Shandong (Linyi) Institute of Modern Agriculture of Zhejiang University, Linyi 310014, China
| | - Yiyu Hu
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Dongya Wu
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Yu Feng
- Institute of Ecology, Zhejiang University, Hangzhou 310058, China
| | - Sangting Lao
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Chenfeng Dong
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Tianyu Du
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Wei Hua
- Institute of Crops, Zhejiang Academy of Agricultural Sciences, Hangzhou 322105, China
| | - Chu-Yu Ye
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Jinhuan Zhu
- Institute of Crops, Zhejiang Academy of Agricultural Sciences, Hangzhou 322105, China
| | - Qian-Hao Zhu
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT 2601, Australia
| | - Daguang Cai
- Department of Molecular Phytopathology and Biotechnology, Christian-Albrechts-University of Kiel, 24118 Kiel, Germany
| | - Lidia Skuza
- Institute of Biology, University of Szczecin, 71-415 Szczecin, Poland
| | - Jie Qiu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200235, China
| | - Longjiang Fan
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China; Zhejiang University Zhongyuan Institute, Zhengzhou 450000, China; Shandong (Linyi) Institute of Modern Agriculture of Zhejiang University, Linyi 310014, China.
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6
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Skuza L. Primer Design for the Analysis of Closely Related Species: Application of Noncoding mtDNA and cpDNA Sequences. Methods Mol Biol 2022; 2392:83-91. [PMID: 34773616 DOI: 10.1007/978-1-0716-1799-1_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Noncoding regions of the chloroplast (cpDNA) and mitochondrial (mtDNA) genomes are commonly used in plant phylogenetic and population studies. Consensus primers, which are homologous to most coding regions, but amplify variable noncoding regions, are very useful for this purpose. However, high genetic diversity of plants poses a problem in developing molecular methods that require conserved DNA sequences between species.This chapter describes the protocol for designing PCR primers suitable for analysis of closely related plant species. As an example, we used PCR primer design for cpDNA noncoding regions of the rye (Secale).
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Affiliation(s)
- Lidia Skuza
- Institute of Biology, University of Szczecin, Szczecin, Poland.
- The Centre for Molecular Biology and Biotechnology, University of Szczecin, Szczecin, Poland.
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7
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A ddRADseq Survey of the Genetic Diversity of Rye (Secale cereale L.) Landraces from the Western Alps Reveals the Progressive Reduction of the Local Gene Pool. PLANTS 2021; 10:plants10112415. [PMID: 34834778 PMCID: PMC8624659 DOI: 10.3390/plants10112415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/29/2021] [Accepted: 11/04/2021] [Indexed: 11/29/2022]
Abstract
Rye (Secale cereale L.) has been at the basis of agriculture for centuries in most mountainous and northern areas of Eurasia, because it is more resistant than other cereals to low temperatures and poor soils. Rye deserves to be re-evaluated as a source of “environmentally resilient” genes in the future as well, and particularly in a perspective to grow cereals able to withstand global warming. According to recent studies, modern rye varieties have a relatively narrow genetic pool, a condition that is worsening in the most recent breeding processes. The preservation of local landraces as unique sources of genetic diversity has therefore become important, in order to preserve the genetic heritage of rye. In this study, genetic diversity of rye landraces collected in a sector of the Italian Alps particularly suited to traditional agriculture was investigated using the ddRADseq technique. A few landraces still managed with family farming turned out to be genetically distant from the commercial varieties currently in use, highlighting that the phenomenon of homogenization of the local genetic pool can be still circumvented. Ex situ conservation of genetically divergent landraces is a valid tool to avoid the dissipation of an as yet unexplored genetic potential.
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8
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The complete chloroplast genome of Secale sylvestre (Poaceae: Triticeae). J Appl Genet 2021; 63:115-117. [PMID: 34392474 PMCID: PMC8755654 DOI: 10.1007/s13353-021-00656-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 07/19/2021] [Accepted: 07/27/2021] [Indexed: 11/17/2022]
Abstract
Secale sylvestre is a wild species of rye, morphologically distinct from domestic species. To draw comparisons between species based on molecular features, it is important to have high-quality sequences, especially in the case of organellar genomes. For such reason, the complete chloroplast genome of Secale sylvestre Host introd. no. 6047 will provide useful data for ecological, agricultural, and phylogenetic purposes. Here we present the complete, annotated chloroplast genome sequence of Secale sylvestre Host introd. no. 6047. The genome is 137116 base pair (bp) long. It is the first complete chloroplast genome that can be used as a reference genome for further analysis. The genome can be accessed on GenBank with the accession number (MW557517).
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Wen F, Wu X, Li T, Jia M, Liu X, Liao L. The complete chloroplast genome of Stauntonia chinensis and compared analysis revealed adaptive evolution of subfamily Lardizabaloideae species in China. BMC Genomics 2021; 22:161. [PMID: 33676415 PMCID: PMC7937279 DOI: 10.1186/s12864-021-07484-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 02/25/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Stauntonia chinensis DC. belongs to subfamily Lardizabaloideae, which is widely grown throughout southern China. It has been used as a traditional herbal medicinal plant, which could synthesize a number of triterpenoid saponins with anticancer and anti-inflammatory activities. However, the wild resources of this species and its relatives were threatened by over-exploitation before the genetic diversity and evolutionary analysis were uncovered. Thus, the complete chloroplast genome sequences of Stauntonia chinensis and comparative analysis of chloroplast genomes of Lardizabaloideae species are necessary and crucial to understand the plastome evolution of this subfamily. RESULTS A series of analyses including genome structure, GC content, repeat structure, SSR component, nucleotide diversity and codon usage were performed by comparing chloroplast genomes of Stauntonia chinensis and its relatives. Although the chloroplast genomes of eight Lardizabaloideae plants were evolutionary conserved, the comparative analysis also showed several variation hotspots, which were considered as highly variable regions. Additionally, pairwise Ka/Ks analysis showed that most of the chloroplast genes of Lardizabaloideae species underwent purifying selection, whereas 25 chloroplast protein coding genes were identified with positive selection in this subfamily species by using branch-site model. Bayesian and ML phylogeny on CCG (complete chloroplast genome) and CDs (coding DNA sequences) produced a well-resolved phylogeny of Lardizabaloideae plastid lineages. CONCLUSIONS This study enhanced the understanding of the evolution of Lardizabaloideae and its relatives. All the obtained genetic resources will facilitate future studies in DNA barcode, species discrimination, the intraspecific and interspecific variability and the phylogenetic relationships of subfamily Lardizabaloideae.
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Affiliation(s)
- Feng Wen
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China.
| | - Xiaozhu Wu
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China.,State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Tongjian Li
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Mingliang Jia
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Xinsheng Liu
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Liang Liao
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
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10
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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.
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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;
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11
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Teshome GE, Mekbib Y, Hu G, Li ZZ, Chen J. Comparative analyses of 32 complete plastomes of Tef ( Eragrostis tef ) accessions from Ethiopia: phylogenetic relationships and mutational hotspots. PeerJ 2020; 8:e9314. [PMID: 32596045 PMCID: PMC7307559 DOI: 10.7717/peerj.9314] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 05/17/2020] [Indexed: 12/31/2022] Open
Abstract
Eragrostis tef is an important cereal crop in Ethiopia with excellent storage properties, high–quality food, and the unique ability to thrive in extreme environmental conditions. However, the application of advanced molecular tools for breeding and conservation of these species is extremely limited. Therefore, developing chloroplast genome resources and high-resolution molecular markers are valuable to E. tef population and biogeographic studies. In the current study, we assembled and compared the complete plastomes of 32 E. tef accessions. The size of the plastomes ranged from 134,349 to 134,437 bp with similar GC content (∼38.3%). Genomes annotations revealed 112 individual genes, including 77 protein-coding, 31 tRNA, and 4 rRNA genes. Comparison of E. tef plastomes revealed a low degree of intraspecific sequence variations and no structural differentiations. Furthermore, we found 34 polymorphic sites (13 cpSSRs, 12 InDels, and 9 SNPs) that can be used as valuable DNA barcodes. Among them, the majority (88%) of the polymorphic sites were identified in the noncoding genomic regions. Nonsynonymous (ka) and synonymous (ks) substitution analysis showed that all PCGs were under purifying selection (ka/ks <1). The phylogenetic analyses of the whole plastomes and polymorphic region sequences were able to distinguish the accession from the southern population, indicating its potential to be used as a super-barcode. In conclusion, the newly generated plastomes and polymorphic markers developed here could be a useful genomic resource in molecular breeding, population genetics and the biogeographical study of E. tef.
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Affiliation(s)
- Girma Eshetu Teshome
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, Hubei, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yeshitila Mekbib
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, Hubei, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Guangwan Hu
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Zhi-Zhong Li
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jinming Chen
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei, China
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12
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Liu D, Cui Y, He J, Li S, Li Q, Liang D, Wang J, Shi X, Wang C, Dong K, Liu T, Zhang L, Ren R, Yang T, Feng G, Liu Z. Genetic Diversity and Classification of the Cytoplasm of Chinese Elite Foxtail Millet [ Setaria italica (L.) P. Beauv.] Parental Lines Revealed by Chloroplast Deoxyribonucleic Acid Variation. Front Genet 2019; 10:1198. [PMID: 31824578 PMCID: PMC6882946 DOI: 10.3389/fgene.2019.01198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 10/29/2019] [Indexed: 12/03/2022] Open
Abstract
Due to the maternal inheritance of cytoplasm, using foxtail millet [Setaria italica (L.) P. Beauv.] male sterile lines with a single cytoplasmic source as the female parent will inevitably lead to a narrow source of cytoplasm in hybrids, which may make them vulnerable to infection by cytoplasm-specific pathogens, ultimately leading to destructive yield losses. To assess cytoplasmic genetic diversity in plants, molecular markers derived from chloroplast DNA (cpDNA) have been used. However, such markers have not yet been applied to foxtail millet. In this study, we designed and screened nine pairs of polymorphic foxtail millet-specific primers based on its completely sequenced cpDNA. Using these primers, we analyzed the genetic diversity and cytoplasmic types of 130 elite foxtail millet parental lines collected in China. Our results revealed that the cytoplasmic genetic diversity of these accessions was low and needs to be increased. The parental lines were divided into four cytoplasmic types according to population structure analysis and a female parent-derivative evolutionary graph, indicating that the cytoplasmic types of elite foxtail millet lines were rather limited. A principal component analysis (PCA) plot was linked with the geographic and ecological distribution of accessions for each cytoplasmic type, as well as their basal maternal parents. Collectively, our results suggest that enriching cytoplasmic sources through the use of accessions from diverse ecological regions and other countries as the female parent may improve foxtail millet breeding programs, and prevent infection by cytoplasm-specific pathogens.
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Affiliation(s)
- Dan Liu
- Tianjin Crop Research Institute, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Yanjiao Cui
- Department of Life Sciences, Tangshan Normal University, Tangshan, China
| | - Jihong He
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, China
| | - Suying Li
- Department of Life Sciences, Tangshan Normal University, Tangshan, China
| | - Qiang Li
- Department of Life Sciences, Tangshan Normal University, Tangshan, China
| | - Dan Liang
- Tianjin Crop Research Institute, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Jianhe Wang
- Tianjin Crop Research Institute, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Xiaowei Shi
- Tianjin Crop Research Institute, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Conglei Wang
- Tianjin Crop Research Institute, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Kongjun Dong
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, China
| | - Tianpeng Liu
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, China
| | - Lei Zhang
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, China
| | - Ruiyu Ren
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, China
| | - Tianyu Yang
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, China
| | - Gang Feng
- Tianjin Crop Research Institute, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Zhengli Liu
- Department of Life Sciences, Tangshan Normal University, Tangshan, China
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