Genetic Diversity Among Ethiopian Coffee (Coffea Arabica L.) Collections Available In Indian Gene Bank Using Sequence Related Amplified Polymorphism Markers

Abstract

The South-Western highlands of Ethiopia are considered to be the centre of origin and diversity of the arabica coffee, Coffea arabica. More than 80 accessions of arabica coffee collected from Ethiopia are available in Indian gene bank. However, the genetic diversity of these accessions is not studied in detail. In the present study, genetic diversity analysis of 48 accessions collected from eight provinces of Ethiopia was carried out using Sequence-related amplified Polymorphism (SRAP) marker. Among the thirty two SRAP primer combinations tested, 14 primer pairs were polymorphic and generated 203 distinct fragments. The number of fragments ranged from 7 to 21 with a mean of 14.5 fragments per primer combination. Of the total 203 amplified fragments, 182 (89.65%) were polymorphic and the percent of polymorphism ranged from 53.84% to a maximum of 100% using different primers. The average resolving power (Rp) and average polymorphism information content (PIC) of the 14 SRAP primer combinations was 14.31 and 0.648 respectively. A total of 13 rare alleles were obtained from SRAP assays, of which six rare alleles were obtained from the accessions collected from Shoa province. The UPGMA clustering algorithm from SRAP analysis grouped the 48 coffee accessions into two major clusters. The accessions collected from particular province clustered together which could be attributed to the substantial gene flow between adjacent population and the influence of geographical origin on genetic diversity. The study demonstrated the existence of substantial genetic variation in Ethiopian germplasm which could be utilized in coffee germplasm conservation and improvement program.

Genetic diversity and population structure of a Peruvian Coffea arabica L. collection

“…The PCR amplification was obtained with 14 combinations of 12 primers (5 forward and 7 reverse) (Table 3) which were selected from Mishra et al (2014) to show the highest percentages of polymorphism. The PCR amplification was carried out in 10 μL containing 60 ng DNA, 3 mM each primer, 2.5 mM MgCl2, 0.2 mM dNTPs, 1 U Taq DNA polymerase and 1X buffer solution.…”

“…The PCR amplification was carried out in 10 μL containing 60 ng DNA, 3 mM each primer, 2.5 mM MgCl2, 0.2 mM dNTPs, 1 U Taq DNA polymerase and 1X buffer solution. The amplification profile was set according to Mishra et al (2014). The amplification products were separated by electrophoresis on 2.5% agarose gels and visualized under UV light.…”

“…In C. arabica crop the genetic analysis has been performed with molecular markers such as random amplified polymorphic DNA (RAPD), inter-simple sequence repeats (ISSR) (Yan et al, 2019), amplified fragment length polymorphism (AFLP), restriction fragment length polymorphisms (RFLP), simple sequence repeat (SSR or microsatellites) and expressed sequence tag-derived simple sequence repeats (EST-SSRs). Microsatellites, despite showing some limits in their use in tetraploid species such as coffee, have been considered very efficient to determine the genetic diversity, population structure and germplasm characterization in coffee collections (Vieira et al, 2010;Teressa et al, 2010;Geleta et al, 2012;Al-Murish et al, 2013;Mishra et al, 2014;Motta et al, 2014;Ferrao et al, 2015;Alemayehu, 2017;Vieira et al, 2017). Microsatellites have also been shown to be useful in linkage mapping (Pestana et al, 2015).…”

“…Microsatellites have also been shown to be useful in linkage mapping (Pestana et al, 2015). Sequence-related amplified polymorphism (SRAP) markers have recently been used efficiently in studies of genetic diversity and population structure in germplasm collections of coffee (Al-Murish et al, 2013;Mishra et al, 2014;Jingade et al, 2019;Yan et al, 2019). These are characterized by a forward primer containing a GGCC sequence close to the 3' terminus, which preferably aligns with GC-rich sequences in coding regions.…”

Genetic diversity using random amplified polymorphic DNA (RAPD) and inter-simple sequence repeats (ISSR) markers in Tinospora cordifolia from the Rayalseema region in Andhra Pradesh

“…The DNA profiling technique using Random amplified polymorphic DNA (RAPD) and inter-simple sequence repeats (ISSR), is extensively used in plants for the study of biodiversity, gene identification, and identifying markers linked with traits of interest. Plant genetic stability study using molecular markers in medicinal plants like Withania somnifera and Capparis deciduas (Tyagi et al, 2010) and other plants like coffee species (Mishra et al, 2014), artichoke (Sharaf-Eldin et al, 2015), bamboo (Desai et al, 2015), rye grass (Ghariani et al, 2015), and lemongrass (Bishoyi et al, 2016) has been reported.…”