Genetic Diversity and Population Structure Analysis of Coffee (Coffea canephora) Germplasm Collections in Indian Gene Bank Employing SRAP and SCoT Markers

Abstract

Coffea canephora Pierre ex Frohener is popularly known as robusta coffee contributes to about 39% of the total world coffee production. Coffea canephora a native to West Africa was introduced to India as early as 1900 AD. However adequate information regarding the diversity and genetic structure of C. canephora germplasm available in India is not yet available. In the present study, sequence related amplified polymorphism (SRAP) and start codon targeted (SCoT) molecular markers were employed to access the genetic diversity and relationships of 58 C. canephora germplasm accessions available in the Indian gene bank. Forty-nine SRAP and thirty-one SCoT primers amplified 632 and 331 fragments respectively, of which 507 (80.22%) and 225 (67.97%) were polymorphic. The average polymorphism information content (SRAP, 0.48; SCoT, 0.37) and resolving power (SRAP, 15.60; SCoT,14.84) revealed high genetic diversity among the accessions The SRAP markers were found more informative with regards to the amount of diversity detected which is evident from effective multiplex ratio (SRAP = 8.59, SCoT = 5.61) and marker index (SRAP = 4.60, SCoT = 2.58). The neighbor-joining clustering revealed that 58 accessions were grouped into four major clusters which were also supported by Principal coordinate analysis. An admixture model-based clustering method in STRUCTURE grouped all the accessions in four subpopulations (K = 4) as similar to NJ clustering. Our study demonstrated the suitability of SRAP and SCoT markers for coffee genetic diversity and discovered thirty-one diverse genotypes in the germplasm that could be integrated into the C. canephora genetic improvement program.