Study of Genetic Diversity of Coffea canephora Pierre ex A. Froehner Accessions by RAPD Markers

Achar, A. M. D.; Danial, George; Awati, Mallikarjuna; Udayakumar, M.; Prasad, T. G.

doi:10.3923/ijpbg.2015.95.105

Cited by 4 publications

(3 citation statements)

References 23 publications

(24 reference statements)

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“…ISSR markers generated a mean similarity coefficient of 0.68 in Coffea canephora which is close with Coffea arabica (0.70), while Coffea liberica had moderate variation (mean similarity coefficient = 0.61). The low level of polymorphism in Coffea canephora supports the finding of Achar et al (2015). Coffea liberica is naturally cross-pollinated and it is grown in the Philippines using seeds.…”

Section: Genetic Relationship and Clustering Analysissupporting

confidence: 68%

Short Communication: Genetic polymorphism of registered and popularly cultivated coffee (Coffea spp.) in the Philippines using inter-simple sequence repeats markers

2020

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Abstract. Panaligan AC, Baltazar MD, Alejandro GJD. 2020. Short Communication: Genetic polymorphism of registered and popularly cultivated coffee (Coffea spp.) in the Philippines using inter-simple sequence repeats markers. Biodiversitas 21: 4228-4233. Three Coffea species, namely Coffea arabica, Coffea canephora and Coffea liberica have been commercially cultivated in the Philippines. Genetic variability analysis of these species is important for the conservation of genetic resources and breeding programs. Hence, this study was carried out to identify polymorphic inter-simple sequence repeats (ISSR) markers and determine the genetic variation of these three commercially cultivated coffee species. Twenty-nine DNA samples from young coffee leaves were extracted and PCR amplified. Of the 29 primers used, seven produced clear and reproducible bands. In the 54 bands produced, 51 were polymorphic. The number of bands amplified by each primer varied from 5 to 12 with an average of 7.71 bands. Polymorphism percentage ranged from 80 to 100. This is the first time that ISSR markers were used to determine the genetic variation of coffee in the Philippines. The study demonstrated the efficiency of ISSR markers to assess genetic variation in cultivated coffee species. The ISSR markers were able to differentiate the coffee germplasm at the interspecific and intraspecific levels. These results suggest the potential of ISSR markers for genetic diversity analysis of commercial coffee and varietal identification of elite varieties using DNA fingerprinting.

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Section: Genetic Relationship and Clustering Analysissupporting

confidence: 68%

Short Communication: Genetic polymorphism of registered and popularly cultivated coffee (Coffea spp.) in the Philippines using inter-simple sequence repeats markers

2020

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“…The amplified products were electrophoresed at 60 volt, 400 watt, for 2 hours in 1.2% (w/w) agarose gel, stained in ethidium bromide solution, and then visualized in a UV transilluminator. Initially, a set of 40 primers selected from the studies of Achar et al (2015), Gimase et al (2014), and Kathurima et al (2012) were prescreened for PCR optimization of genomic DNA of 24 clones of Robusta coffee (Coffea canephora Pierre ex A. Froehner). Eleven out of the 40 primers produced sharp, clear, and reproduceable bands and were used in this study (Table 2).…”

Section: Genomic Dna Extraction and Pcr Conditionmentioning

confidence: 99%

“…Studies on genetic diversity of Robusta coffee based on RAPD markers have also been reported (Awati et al 2018;Achar et al 2015: Tshilenge et al 2009Diniz et al 2005;Cabral et al 2002). Still, such a study is needed on Robusta coffee grown in a particular agroclimatic condition, such as that of Lampung.…”

Section: Introductionmentioning

confidence: 99%

Genetic diversity among 24 clones of robusta coffee in Lampung based on RAPD markers

et al. 2021

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Abstract. Ramadiana S, Hapsoro D, Evizal R, Setiawan K, Karyanto A, Yusnita. 2021. Genetic diversity among 24 clones of robusta coffee in Lampung based on RAPD markers. Biodiversitas 22: 3122-3129. This study aimed to estimate the genetic diversity among 24 clones of Robusta coffee from Lampung, Indonesia, by use of RAPD markers. The clones consisted of 18 local and 6 BP clones. These BP clones were developed from a breeding program of The Indonesian Coffee and Cocoa Research Institute. Genomic DNAs extracted from these clones were subjected to polymerase chain reaction and the amplified products were run using gel electrophoresis. Eleven random primers produced clear, reproducible, scorable bands. Fifty-four of 86 bands showed polymorphism and were used to construct a dendrogram based on UPGMA Jaccard's Similarity Coefficients. The genetic base of the population was narrow (average genetic similarity 68.4%), ranging from 26-93%. The genetic similarity of the local clones was higher than that of BP clones. The clones were clustered into five groups. Group 1 contained one clone (BP 534), while each of Group II-V contained more than one clone. The average genetic similarity of BP 534 to each clone of Group II-V was 41%. The genetic similarity of clones in Group II, III, IV, and V were 55.5%, 43.0%, 81.1%, and 80.1%, respectively. This research should be very useful for selecting parents in a breeding program to produce better clones of Robusta coffee.

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Inheritance of RAPD and ISSR markers in hybrid derivatives of inter-specific coffee hybrid (Coffea congensis Froehner x Coffea canephora Pierre): Implications on genetic improvement and plant variety protection

Kumar,

Nanthini,

Rao

et al. 2023

Preprint

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An inter-specific hybrid involving Coffea congensis x Coffea canephora is popularly known as C x R coffee hybrid in India. This hybrid was developed with the primary objective of reducing the plant size for high density cultivation and also to improve the coffee beverage quality. Though this hybrid is popularly cultivated in India, segregation of this hybrid due to cross pollination either within the hybrid or with other diploid species of Coffea is one of the major problems to achieve seed purity and higher yield. To utilize DNA marker assisted selection (MAS), two dominant DNA markers (RAPD and ISSR) were analyzed for their utility. About 24 RAPD and 15 ISSR primers were tested for screening the effective primers and only three RAPD and five ISSR primers were found suitable for discriminating the parent. These selective RAPD and ISSR primers produced nine and 23 polymorphic bands respectively with size range of 400 bp – 1200 bp in RAPD and 100 bp – 2000 bp in ISSR. Species specific RAPD and ISSR markers were found in female (Coffea congensis) and male (Coffea canephora) parent of the hybrid and certain of these RAPD and ISSR markers and they are found to inherit into F1 and backcross progenies. The primers for suitability for marker assisted selection were evaluated with parameters such as Polymorphic information content (PIC), effective multiplex ratio (EMR), marker index (MI) and resolving power (RP). Importance of these markers in genetic improvement of this hybrid is discussed.

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Study of Genetic Diversity of Coffea canephora Pierre ex A. Froehner Accessions by RAPD Markers

Cited by 4 publications

References 23 publications

Short Communication: Genetic polymorphism of registered and popularly cultivated coffee (Coffea spp.) in the Philippines using inter-simple sequence repeats markers

Short Communication: Genetic polymorphism of registered and popularly cultivated coffee (Coffea spp.) in the Philippines using inter-simple sequence repeats markers

Genetic diversity among 24 clones of robusta coffee in Lampung based on RAPD markers

Inheritance of RAPD and ISSR markers in hybrid derivatives of inter-specific coffee hybrid (Coffea congensis Froehner x Coffea canephora Pierre): Implications on genetic improvement and plant variety protection

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