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

Abstract

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.

The re-emergence of Liberica coffee as a major crop plant

“…dewevrei 17,46 . Morphological and molecular data 37,42,[47][48][49] support the recognition of two varieties for C. liberica: var. liberica and var.…”

“…The apt epithet 'excelsa' has persisted and is still the most widely used common name for var. dewevrei 17,36,37,[47][48][49] . Excelsa is used in the remaining narrative for var.…”

Screening of yield and growth-related SSR markers in Philippine coffee

“…However, it was noteworthy to discover bands which were specific to either Liberica and Excelsa. Morphological differences in the leaf have been found between these two types (Cao et al 2014;Baltazar and Buot 2019), however genetic differences have been limited except for markers such as AFLPs (N'diaye et al 2005) and ISSRs (Panaligan et al 2020). It was also interesting to find a band specific to the Yellow Bourbon variety of Arabica.…”

Decoding Evolution of Rubioideae: Plastomes Reveal Sweet Secrets of Codon Usage, Diagnostides, and Superbarcoding

“…The organellar genomes of Rubiaceae species have never been used as superbarcodes, and scientists have mainly worked with nuclear DNA fragments such as internal transcribed spacers (ITS) and single genes or regions of plastome: matK, trnH-psbA, rbcL, rps16, ndhF, petD, and trnT-trnF [60][61][62][63]. Normally, superbarcodes should be diverse enough to distinguish interspecies differences, so the mitochondrial genome is very rarely used in plant species delimitation.…”