Identification of candidate genes involved in Witches’ broom disease resistance in a segregating mapping population of Theobroma cacao L. in Brazil

Abstract

BackgroundWitches’ broom disease (WBD) caused by the fungus Moniliophthora perniciosa is responsible for considerable economic losses for cacao producers. One of the ways to combat WBD is to plant resistant cultivars. Resistance may be governed by a few genetic factors, mainly found in wild germplasm.ResultsWe developed a dense genetic linkage map with a length of 852.8 cM that contains 3,526 SNPs and is based on the MP01 mapping population, which counts 459 trees from a cross between the resistant ‘TSH 1188’ and the tolerant ‘CCN 51’ at the Mars Center for Cocoa Science in Barro Preto, Bahia, Brazil. Seven quantitative trait loci (QTL) that are associated with WBD were identified on five different chromosomes using a multi-trait QTL analysis for outbreeders. Phasing of the haplotypes at the major QTL region on chromosome IX on a diversity panel of genotypes clearly indicates that the major resistance locus comes from a well-known source of WBD resistance, the clone ‘SCAVINA 6’. Various potential candidate genes identified within all QTL may be involved in different steps leading to disease resistance. Preliminary expression data indicate that at least three of these candidate genes may play a role during the first 12 h after infection, with clear differences between ‘CCN 51’ and ‘TSH 1188’.ConclusionsWe combined the information from a large mapping population with very distinct parents that segregate for WBD, a dense set of mapped markers, rigorous phenotyping capabilities and the availability of a sequenced genome to identify several genomic regions that are involved in WBD resistance. We also identified a novel source of resistance that most likely comes from the ‘CCN 51’ parent. Thanks to the large population size of the MP01 population, we were able to pick up QTL and markers with relatively small effects that can contribute to the creation and selection of more tolerant/resistant plant material.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2415-x) contains supplementary material, which is available to authorized users.

QTL mapping and identification of SNP-haplotypes affecting yield components of Theobroma cacao L.

“…The QTL intervals flanked by SNP markers with LOD scores higher than 3.1 were considered as significant. We used the genetic linkage map from the MP01 population ('TSH 1188' × 'CCN 51'), published in 2016 11 . Figure 3 provides the genomic positions and Table 2 the percentage of phenotypic variation explained by each region flanked by the SNP markers with significant LOD scores.…”

“…4-7). So far in the MP01 population, the maternal alleles have been reported as the ones more affecting the economically important traits, such as disease resistance 11,29 , and fat content and fatty acid composition 25 . Likewise, our study showed that the alleles from 'TSH 1188' are the ones controlling the QTL regions with a higher LOD scores, such as the one found on chromosome IV.…”

“…The female parent is related to Iquitos and Nanay genetic groups 13,24 , and the male parent has predominant ancestries from Iquitos, Criollo, and Amelonado 13,14,24 . Those parents contrast for many important traits, and the MP01 progenies segregate for disease resistance 11,29,51 , pod color 5 , fat content and fat composition 25 . The MP01 population also segregates for yield.…”

Cacao biotechnology: current status and future prospects

“…() provide a valuable genomic resource for cacao breeding. The latest genetic linkage map of cacao includes SNP data obtained from a large mapping population (459 trees) of a cross between WBD resistant, TSH 1,188 and WBD tolerant (moderately resistant to WBD) CCN (Royaert et al ., ). It contains 3526 SNP markers and has a length of 852.8 cM.…”

“…This rapid discovery of molecular markers also permits the efficient identification and study, in cacao, of the genetic basis of QTL for many agronomic traits such as bean traits and the number of ovules per ovary (Clement et al ., ), butter content and its hardness in cocoa beans (Araújo et al ., ), diseases resistance for Ceratocystis wilt (Santos et al ., ), resistance for Phytophthora species (Akaza et al ., ; Clement et al ., ; Efombagn et al ., ; Flament et al ., ; Lanaud et al ., ; Legavre et al ., ; Motilal et al ., ; Risterucci et al ., ), resistance for WBD (Brown et al ., ; Faleiro et al ., ; Motilal et al ., ; Queiroz et al ., ; Royaert et al ., ), number of filled seeds (Motilal et al ., ), yield (Clement et al ., ; Crouzillat et al ., ) and self‐compatibility/incompatibility (Royaert et al ., ; da Silva et al ., ). Furthermore, meta‐analysis on QTL related to disease resistance in cacao has been performed by Lanaud et al .…”