Microsatellite-based QTL mapping for yield and horticultural traits in cacao (Theobroma cacao L.)

In cacao, a perennial crop, SSR could ease/facilitate and speed up/accelerate selection for yield, vigour and their components. This investigation was conducted to identify Quantitative Trait Loci (QTL) underlying these traits in three hybrid progenies created, at CNRA in Côte d'Ivoire, from crosses (SCA6 x H) x C1, (P7 x ICS100) x C1 and (P7 x ICS95 x) x C1 and, encompassing, respectively, 179, 173 and 183 plants. Yield related-traits were recorded during three full campains years. In each progeny, Kruskal-Wallis test and interval mapping were applied on a SSR based-linkage map. QTLs detected are: 18 for yield components (healthy ripe pods number, pods weight, dried beans weight, one-hundred dried beans weight) on chromosomes 1, 2, 4, 6, 10, with a major for PW (R² = 34.3 %) borded by markers mTcCIR168 and mTcCIR18 on chromosome 4 of the parent derived from “P7 x ICS95”, two for trunk girth on chromosome 4, three for yield efficiency. Some clusters of QTLs of yield components were observed on chromosomes 1, 4 and 6, 6 suggesting pleiotropic and/or polysgenic effects. The chromosome 4 carried most of QTLs. Some QTLs of the healthy ripe pods number, pods weight, dried beans weight, stable across progenies, genetic backgrounds and years, and moreover linked to markers mTcCIR168 and smTcCIR18, are useful in breeding programs.