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Sabana AA, Antony G, Rajesh MK, Gangaraj KP, Niral V, Sudha R, Jerard BA. Development and characterization of non-coding RNA-derived simple sequence repeat markers in coconut (Cocos nucifera L.). Funct Integr Genomics 2022; 22:1243-1251. [DOI: 10.1007/s10142-022-00911-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 10/17/2022] [Accepted: 10/18/2022] [Indexed: 11/29/2022]
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Rajesh MK, Gangurde SS, Pandey MK, Niral V, Sudha R, Jerard BA, Kadke GN, Sabana AA, Muralikrishna KS, Samsudeen K, Karun A, Prasad TSK. Insights on Genetic Diversity, Population Structure, and Linkage Disequilibrium in Globally Diverse Coconut Accessions Using Genotyping-by-Sequencing. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2021; 25:796-809. [PMID: 34757849 DOI: 10.1089/omi.2021.0159] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Genotyping-by-sequencing (GBS) has emerged as a cost-effective approach for genome-wide discovery of single-nucleotide polymorphism (SNP) markers and high-throughput genotyping. In this study, 96 coconut palms, representing 16 accessions from globally diverse origins, were genotyped using the GBS strategy. A total of 10,835 high-quality SNPs, which were identified after stringent filtering, were utilized to assess genetic diversity, population structure, and linkage disequilibrium (LD) analyses. The polymorphism information content (PIC) values of SNPs ranged from 0.1 to 0.4, with a large proportion of SNPs (8633 nos.; 79.7%) having a higher PIC in the range of 0.3-0.4. The genetic diversity analysis revealed the existence of a high level of variation in coconut accessions, with an average expected heterozygosity (He) value of 0.43. Unweighted neighbor-joining phylogenetic tree and Bayesian-based model population structure grouped coconut genotypes into four main clusters. The accessions are generally clustered based on their height (tall or dwarf), with a few accession clusterings based on geographical origins. Investigation of LD pattern in coconut indicated a relatively rapid LD decay with a short range (9 kb). The results obtained in this study will contribute to enhancing the capacity of coconut researchers to utilize genetic diversity for further genetic improvement. In addition, it would open up possibilities for performing genomic studies such as genome-wide association studies and genomic selection to accelerate the efficiency and speed of coconut genetic improvement.
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Affiliation(s)
- Muliyar Krishna Rajesh
- Division of Crop Improvement, ICAR-Central Plantation Crops Research Institute (ICAR-CPCRI), Kasaragod, Kerala, India
| | - Sunil Shivaji Gangurde
- Centre of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Telangana, India
| | - Manish Kumar Pandey
- Centre of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Telangana, India
| | - Vittal Niral
- Division of Crop Improvement, ICAR-Central Plantation Crops Research Institute (ICAR-CPCRI), Kasaragod, Kerala, India
| | - Raju Sudha
- Division of Crop Improvement, ICAR-Central Plantation Crops Research Institute (ICAR-CPCRI), Kasaragod, Kerala, India
| | - Bosco Augustine Jerard
- ICAR-Central Island Agricultural Research Institute (ICAR-CIARI), Port Blair, Andaman and Nicobar Islands, India
| | | | - Abdulla Abdulla Sabana
- Division of Crop Improvement, ICAR-Central Plantation Crops Research Institute (ICAR-CPCRI), Kasaragod, Kerala, India
| | | | - Kukkamgai Samsudeen
- Division of Crop Improvement, ICAR-Central Plantation Crops Research Institute (ICAR-CPCRI), Kasaragod, Kerala, India
| | - Anitha Karun
- Division of Crop Improvement, ICAR-Central Plantation Crops Research Institute (ICAR-CPCRI), Kasaragod, Kerala, India
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Preethi P, Rahman S, Naganeeswaran S, Sabana AA, Gangaraj KP, Jerard BA, Niral V, Rajesh MK. Development of EST-SSR markers for genetic diversity analysis in coconut (Cocos nucifera L.). Mol Biol Rep 2020; 47:9385-9397. [PMID: 33215363 DOI: 10.1007/s11033-020-05981-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 11/05/2020] [Indexed: 01/08/2023]
Abstract
Genetic improvement in coconut relies on exploiting the vast existing diversity among coconut accessions. Robust molecular markers are a pre-requisite for efficient characterization of genetic diversity. Microsatellites or simple sequence repeats (SSRs), mined from expressed sequence tags (ESTs), constitute an important resource for analysis of genetic diversity as they are abundant, polymorphic and represent function regions of the genome. We have identified a total of 318,528 putative EST-SSRs from 130,942 unigenes utilizing a leaf transcriptome dataset of coconut. Among the EST-SSRs, dinucleotide repeats were abundant (219,912; 69.04%) followed by trinucleotide (70,722; 22.2%) and tetra-nucleotide repeats (6281; 1.9%). Among the dinucleotide repeat motifs, the dominant repeat was AG/CT (35.87%), followed by AT/AT (18.59%), while the dominant trinucleotide repeat was AAG/CTT (4.59%). One hundred and twenty EST-SSR primer pairs were designed and utilized to amplify six DNA samples of coconut accessions. Fifty primers (41.7%) produced reproducible polymorphic fragments of expected sizes, from which a total of 10 primers were selected for the diversity assessment in 186 palms of 50 coconut accessions, comprising of 25 each of tall and dwarf accessions. A total of 137 alleles were detected with an average of 13.7 alleles per SSR locus. The number of alleles observed at each locus in the data set ranged from 7 to 22. All the loci showed 100% polymorphism with respect to the samples screened. The average observed heterozygosity was 0.46. The PIC values ranged from 0.79 (CnKGDEST129 and CnKGDEST100) to 0.91 (CnKGDEST117 and CnKGDEST122) with a mean value of 0.85, indicating the capacity of the EST-SSR markers to detect high levels of polymorphism. The cluster analysis revealed that accessions were generally clustered based on their relative similarity and irrespective of their geographic origins. The present study demonstrates the usefulness of transcriptome sequencing as a rapid and cost-effective methodology for the development of molecular markers. The EST-SSR markers generated through this study constitute useful and reliable tools for assessment of genetic diversity and marker-assisted selection in coconut.
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Affiliation(s)
- P Preethi
- ICAR-Central Plantation Crops Research Institute, Kasaragod, Kerala, India
| | - Shafeeq Rahman
- ICAR-Central Plantation Crops Research Institute, Kasaragod, Kerala, India
| | - S Naganeeswaran
- ICAR-Central Plantation Crops Research Institute, Kasaragod, Kerala, India.,Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - A A Sabana
- ICAR-Central Plantation Crops Research Institute, Kasaragod, Kerala, India
| | - K P Gangaraj
- ICAR-Central Plantation Crops Research Institute, Kasaragod, Kerala, India
| | - B A Jerard
- ICAR-Central Plantation Crops Research Institute, Kasaragod, Kerala, India.,ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, India
| | - V Niral
- ICAR-Central Plantation Crops Research Institute, Kasaragod, Kerala, India
| | - M K Rajesh
- ICAR-Central Plantation Crops Research Institute, Kasaragod, Kerala, India.
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Osorio-Montalvo P, De-la-Peña C, Oropeza C, Nic-Can G, Córdova-Lara I, Castillo-Castro E, Sáenz-Carbonell L. A peak in global DNA methylation is a key step to initiate the somatic embryogenesis of coconut palm (Cocos nucifera L). PLANT CELL REPORTS 2020; 39:1345-1357. [PMID: 32789543 DOI: 10.1007/s00299-020-02568-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 06/25/2020] [Accepted: 07/10/2020] [Indexed: 05/08/2023]
Abstract
DNA methylation, morphogenesis and gene expression during the somatic embryogenesis of Coconut are affected by 5-Azacytidine pretreatments, indicating that DNA methylation is an important factor throughout this process. Somatic embryogenesis (SE) is a process that can aid in the production of elite Cocos nucifera palms. It has been well established that epigenetic mechanisms are regulators of cell differentiation programs; however, their role in the coconut somatic embryogenesis has not yet been addressed. To this end, the morphogenetic changes, the global DNA methylation and the expression profiles of the SE-related genes and DNA methyltransferases genes were evaluated during the SE process, with and without the presence of 5-Azacytidine (AzaC). The results show that three days of pretreatments with 15 µM and 20 µM of AzaC significantly increased early somatic embryo formation (four- and tenfold, respectively). A clear peak of the global percentage of DNA methylation (approximately 13%) was determined at the beginning of the culture, followed by a re-establishing stage and a steady increase thereafter; in all cases, the levels of DNA methylation were lower after the pretreatments with AzaC. Additionally, the expression profiles of the SERK, WUS, BBM and LEC genes are modulated during the SE process and the pretreatments with AzaC affect the expression profiles of these genes, even at early stages. Furthermore, increased levels of expression were observed for the genes encoding for DNA methyltransferases (MET, CMT and DRM) at early and late stages of SE, indicating that DNA methylation is an important factor throughout the SE.
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Affiliation(s)
- Pedro Osorio-Montalvo
- Centro de Investigación Científica de Yucatán, Unidad de Biotecnología, Calle 43 No. 130, entre 32 y 34, Col. Chuburná de Hidalgo, 97205, Mérida, Yucatán, México
| | - Clelia De-la-Peña
- Centro de Investigación Científica de Yucatán, Unidad de Biotecnología, Calle 43 No. 130, entre 32 y 34, Col. Chuburná de Hidalgo, 97205, Mérida, Yucatán, México
| | - Carlos Oropeza
- Centro de Investigación Científica de Yucatán, Unidad de Biotecnología, Calle 43 No. 130, entre 32 y 34, Col. Chuburná de Hidalgo, 97205, Mérida, Yucatán, México
| | - Geovanny Nic-Can
- CONACYT-Campus de Ciencias Exactas e Ingeniería, Universidad Autónoma de Yucatán, Mérida, Yucatán, México
| | - Iván Córdova-Lara
- Centro de Investigación Científica de Yucatán, Unidad de Biotecnología, Calle 43 No. 130, entre 32 y 34, Col. Chuburná de Hidalgo, 97205, Mérida, Yucatán, México
| | - Eduardo Castillo-Castro
- Centro de Investigación Científica de Yucatán, Unidad de Biotecnología, Calle 43 No. 130, entre 32 y 34, Col. Chuburná de Hidalgo, 97205, Mérida, Yucatán, México
| | - Luis Sáenz-Carbonell
- Centro de Investigación Científica de Yucatán, Unidad de Biotecnología, Calle 43 No. 130, entre 32 y 34, Col. Chuburná de Hidalgo, 97205, Mérida, Yucatán, México.
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