Marker assisted selection and breeding for leaf rust resistance in coffee (Coffea arabica L.) - some recent leads

Coffee leaf rust (CLR) caused by the obligate parasitic fungus Hemileia vastatrix Berk. et Br is the major disease of concern for arabica coffee (Coffee arabica L). Resistance to CLR is conditioned by at least nine genes, S(H)1 to S(H)9, either singly or In combination; the corresponding virulence factors in pathogen are v1 to v9. Two sequence-characterized DNA markers (Sat244 and BA-124-12K-f) closely linked to S(H)3 gene, one of the highly effective genes for rust resistance were validated and used for maintenance breeding of the country's most popular arabica strain S.795 and marker assisted gene pyramiding. Analysis of randomly identified plants of S.795 with both SCAR markers gave clear amplification profiles that could distinguish the presence or absence of S(H)3 gene. The marker Sat 244 is more efficient for distinguishing the homozygous and heterozygous status of S(H)3 gene. Linkage of marker to the gene and trait of interest was confirmed through bioassays by screening S(H)3-positive and S(H)3-negative plants against specific rust races (race I & VIII). The marker data strongly corresponded with the result of bioassays and SCAR analysis has been used for selection of desirable plants in random populations of S.795. Clonal seed plots of the selected plants have been established for supply of quality seed of S.795 variety to the industry. Further, two F(2) progenies derived from crosses between S(H)3 donor parents and other pure as well as introgressed arabica lines were screened with SCAR markers and plants homozygous to S(H)3 were identified. Crosses were effected for marker assisted gene pyramiding of S(H)3 with other rust resistance genes of diploid origin in C. arabica background. This initial lead in successful application of marker-assisted selection in coffee has potential implications in strategic deployment of coffee varieties to achieve durable rust resistance.