Strategies to develop polymorphic markers for Coffea arabica L

• Published in: Euphytica 2010-05, Vol.173 (2), p.243-253
• Main Authors: Zarate, L.-A, Cristancho, M.-A, Moncada, P
• Format: Article
• Language: English
• Subjects: Agronomy. Soil science and plant productions; Analysis; bacterial artificial chromosomes; Biological and medical sciences; Biomarkers; Biomedical and Life Sciences; Biotechnology; chromosome mapping; cleaved amplified polymorphism sequences; Coffea arabica; Coffee; Development strategies; expressed sequence tags; Fundamental and applied biological sciences. Psychology; Genetic markers; genetic polymorphism; genetic techniques and protocols; genetic variation; Genetics; Genetics and breeding of economic plants; genotype; Genotypes; Life Sciences; methodology; molecular sequence data; nucleotide sequences; Plant Genetics and Genomics; Plant Pathology; Plant Physiology; Plant Sciences; Polymorphism; sequence analysis; single nucleotide polymorphism; Single nucleotide polymorphisms; single strand conformational polymorphism
• ISSN: 0014-2336; 1573-5060
• DOI: 10.1007/s10681-009-0102-6

This study reports the implementation of three strategies for the development of genetic markers and their evaluation in both progenitors of an F2 population used for the construction of a genetic map of Coffea arabica. The strategies were Cleaved Amplified Polymorphic Sequences (CAPS), Single Strand Conformational Polymorphism (SSCP), and sequence analysis predicted Single Nucleotide Polymorphism (SNP). The methodologies were developed from different sequence sources: For CAPS, we used 25 COS sequences derived from Hedyotis spp. and 29 COSII sequences derived from Solanaceae and Rubiaceae species; for SSCP, we used 111 coffee EST sequences, 50 COSII sequences, and 10 C. arabica BAC end sequences. A low polymorphism was identified with the CAPS and SSCP methodologies. A total of 61 SNPs were identified in silico from 5,371 ESTs of coffee and from amplified, cloned, and sequenced COSII markers. Sixteen of these SNPs were validated with Luminex technology and 2 of them were polymorphic in C. arabica genotypes. This study highlights the difficulties of finding polymorphism in the species C. arabica where SNP identification seems to be the best strategy to search for polymorphic markers for this low diversity plant.