Study of simple sequence repeat markers from coffee expressed sequences associated to leaf miner resistance

Abstract

The objective of this work was to identify expressed simple sequence repeats (SSR) markers associated to leaf miner resistance in coffee progenies. Identification of SSR markers was accomplished by directed searches on the Brazilian Coffee Expressed Sequence Tags (EST) database. Sequence analysis of 32 selected SSR loci showed that 65% repeats are of tetra-, 21% of tri- and 14% of dinucleotides. Also, expressed SSR are localized frequently in the 5'-UTR of gene transcript. Moreover, most of the genes containing SSR are associated with defense mechanisms. Polymorphisms were analyzed in progenies segregating for resistance to the leaf miner and corresponding to advanced generations of a Coffea arabica x Coffea racemosa hybrid. Frequency of SSR alleles was 2.1 per locus. However, no polymorphism associated with leaf miner resistance was identified. These results suggest that marker-assisted selection in coffee breeding should be performed on the initial cross, in which genetic variability is still significant.

Large-scale analysis of differential gene expression in coffee genotypes resistant and susceptible to leaf miner–toward the identification of candidate genes for marker assisted-selection

“…The lack of knowledge of molecular aspects controlling the resistance response, and the restricted genetic variability of breeding populations [34] limit the development of genomic-based selection tools. In this context, we aimed to provide information on molecular aspects of leaf-miner defense mechanisms and identification of reliable candidate-marker genes for assisted-selection.…”

“…At the Agronomic Institute (Campinas, Brazil) leaf-miner resistance genes have been transferred from C. racemosa to C. arabica through traditional breeding strategies, and although the program is currently at advanced generations, no resistant commercial cultivar is available yet. The lack of knowledge of molecular aspects controlling the resistance response, and the restricted genetic variability of breeding populations [ 34 ] limit the development of genomic-based selection tools. In this context, we aimed to provide information on molecular aspects of leaf-miner defense mechanisms and identification of reliable candidate-marker genes for assisted-selection.…”

Microsatellite markers in analysis of resistance to coffee leaf miner in Arabica coffee

“…In addition, 28 EST-SSR primers (Pinto et al, 2007) and three more SSR loci, already characterized for coffee biotic stress (Herrera et al, 2009) (1) CA1, non embryogenic callus; LV5, pointer leaf -orthotropic branch without Bion -short; LV9, pointer leaf -plagiotropic branches without Bion -short; RT3, root without Bion; RT5, root with Bion; CL2, hypocotyl callus with and without Bion; FR1, flower bud no. 6, lead no.…”

“…However, the difficulty in stabilizing this trait in the genotypes indicates the need for more studies. So far, molecular studies of leaf miner resistance did not help to determine the nature of this resistance in Arabica coffee plants (Mondego et al, 2005;Pinto et al, 2007).…”