Genetic Diversity Analysis of Coconut (<i>Cocos nucifera</i> L.) Genotypes and Hybrids Using Molecular Marker

Uk, Kandoliya; Joshi, A.; Mori, Disha S; Marviya, GV; Golakiya, B. A.

doi:10.5958/0974-4479.2018.00004.7

Cited by 3 publications

(3 citation statements)

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“…IMA hybrids' female parents were either MYD or MRD, which also belonged to cluster II. This result is in line with Kandoliya et al (2018), which show that the female parent and its hybrid progenies belonged to the same cluster. 2018), the tall coconut accessions mostly belonged to the same cluster in phylogenetic analysis.…”

Section: Phylogenetic Analysissupporting

confidence: 82%

Mining and validating novel SSR markers based on coconut (Cocos nucifera L.) whole genome and their use for phylogenetic analysis

et al. 2022

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Abstract. Hatta ANNL, Sukma D, Maskromo I, Sudarsono. 2022. Mining and validating novel SSR markers based on coconut (Cocos nucifera L.) whole genome and their use for phylogenetic analysis. Biodiversitas 23: 5122-5131. The coconut (Cocos nucifera L.) genome sequences were available at the chromosome level in 2019, and they can be used to develop the whole genome SSR markers. This study aimed to conduct in silico analysis of the whole coconut genome to mine SSR sequences, design SSR markers distributed across coconut chromosomes, validate the designed primers to generate SSR markers, and use them for the phylogenetic analysis of coconuts. The SSR loci were mined from publicly available coconut genomes. Targeted primers for amplifying 20 dinucleotide SSR loci were selected and used for phylogenetic analysis of coconuts. The SSR mining identified 543,774 dinucleotide repeat motifs across the coconut genome, and most of the dinucleotide SSRs are AG (46.18%) and AT (40.03%) repeats. Primer pairs targeted to amplify 876 SSR loci and distributed in 16 coconut chromosomes were successfully designed and deposited in a public data repository for public access. The 237 SSR primer loci were novel and could generate new SSR markers. Among 20 selected and tested primers, 18 produced SSR markers, and 15 pairs yielded polymorphic markers when used to evaluate 25 coconut accessions. The analysis showed that the designed SSR primers were informative for evaluating coconut genetic diversity and phylogenetic analysis.

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Section: Phylogenetic Analysissupporting

confidence: 82%

Mining and validating novel SSR markers based on coconut (Cocos nucifera L.) whole genome and their use for phylogenetic analysis

et al. 2022

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“…In addition, the cluster similarity coefficient values for the different marker systems also ranged from 22% for RAPD to 83% for ISSR and from 50% to 97% for SSR. Based on these results, it was determined that all three molecular marker methods provided similarly accurate assessments of the genetic diversity of coconut genotypes [71].…”

Section: Genetic Diversity Studies Using Molecular Markersmentioning

confidence: 99%

“…Thus, the application of SSR has been very successfully employed for diversity studies within and between populations and accessions. Its utilization has been successfully extended in marker-trait association studies [70][71][72][73][74].…”

Section: Genetic Diversity Studies Using Molecular Markersmentioning

confidence: 99%

Genomics and Transcriptomics Reveal Genetic Contribution to Population Diversity and Specific Traits in Coconut

Yousefi

Abdullah

Hatta

et al. 2023

Plants

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Coconut is an economically important palm species with a long history of human use. It has applications in various food, nutraceuticals, and cosmetic products, and there has been renewed interest in coconut in recent years due to its unique nutritional and medicinal properties. Unfortunately, the sustainable growth of the coconut industry has been hampered due to a shortage of good quality seedlings. Genetic improvement through the traditional breeding approach faced considerable obstacles due to its perennial nature, protracted juvenile period, and high heterozygosity. Molecular biotechnological tools, including molecular markers and next-generation sequencing (NGS), could expedite genetic improvement efforts in coconut. Researchers have employed various molecular markers to reveal genetic diversity among coconut populations and for the construction of a genetic map for exploitation in coconut breeding programs worldwide. Whole genome sequencing and transcriptomics on the different varieties have generated a massive amount of publicly accessible sequence data, substantially improving the ability to analyze and understand molecular mechanisms affecting crop performance. The production of high-yielding and disease-resilient coconuts and the deciphering of the complex coconut genome’s structure can profit tremendously from these technologies. This paper aims to provide a comprehensive review of the progress of coconut research, using genomics, transcriptomics, and molecular markers initiatives.

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Diversity Studies Using Molecular Markers

Perera

Bandupriya

Thomas

et al. 2020

Coconut Biotechnology: Towards the Sustainability of the ‘Tree of Life’

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Genetic Diversity Analysis of Coconut (Cocos nucifera L.) Genotypes and Hybrids Using Molecular Marker

Cited by 3 publications

References 0 publications

Mining and validating novel SSR markers based on coconut (Cocos nucifera L.) whole genome and their use for phylogenetic analysis

Mining and validating novel SSR markers based on coconut (Cocos nucifera L.) whole genome and their use for phylogenetic analysis

Genomics and Transcriptomics Reveal Genetic Contribution to Population Diversity and Specific Traits in Coconut

Diversity Studies Using Molecular Markers

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