Mapping QTL for yield components, vigor, and resistance to<i>Phytophthora palmivora</i>in<i>Theobroma cacao</i>L.

Clément, Didier; Risterucci, Ange-Marie; Motamayor, Juan Carlos; N'Goran, Jeanne A.K.; Lanaud, Claire

doi:10.1139/g02-125

Cited by 46 publications

(38 citation statements)

References 23 publications

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“…These SSRs were already useful tools for the identification of QTLs related to morphological or disease resistance traits (Crouzillat et al 2000;Flament et al 2001;Risterucci et al 2003;Clement et al 2003;Queiroz et al 2003;Brown et al 2007;Brown et al 2005). The high level of polymorphism for these SSR markers also helped to create a composite map by mapping SSRs (bridge markers) common to three different maps , and led to the establishment of a consensus map derived from ten different progenies, which has enabled a meta-analysis of QTLs related to resistance traits in cocoa (Lanaud et al 2009).…”

Section: Introductionmentioning

confidence: 99%

Structural characterization and mapping of functional EST-SSR markers in Theobroma cacao

Fouet

Allègre

Argout

et al. 2011

Tree Genetics & Genomes

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Theobroma cacao L. is a major cash crop for tropical countries, providing incomes for 14 million small farmers. Establishing sustainable disease resistance and maintaining cocoa qualities are among the major objectives of breeding programs. To enrich the high-density genetic map, useful for all cocoa genetic studies, with gene-based markers, a recently produced large EST resource was mined to develop expressed sequence tag-based simple sequence repeat markers (EST-SSRs) defined in genes with a putative known function. A set of 174 polymorphic EST-SSRs was identified from a selection of 314 non-redundant EST-SSRs with a putative known function. Of them, 115 loci were mapped on the cocoa reference map. This new map contains 582 codominant markers arranged in ten linkage groups corresponding to the haploid number of chromosomes. An average interval between markers of 1.3 cM was found, with approximately one SSR every 2 cM. This new set of EST-SSRs includes 14 candidate genes for plant resistance or cocoa qualities. The percentage of polymorphic SSRs varied depending on the different gene regions from which they originated, with respectively 54%, 69%, and 82% of polymorphic EST-SSRs originating from coding sequences, and from the non-coding untranslated 5′ UTR and 3′UTR regions. This new map contains a set of 384 SSR markers that are easily transferable across different mapping populations and useful for all genetic analyses in T. cacao. The new set of EST-SSRs will be a useful tool for studying the functional diversity of populations and for carrying out association mapping studies.

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Section: Introductionmentioning

confidence: 99%

Structural characterization and mapping of functional EST-SSR markers in Theobroma cacao

Fouet

Allègre

Argout

et al. 2011

Tree Genetics & Genomes

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“…Several regions of the genome involved in yield components and Phytophthora spp. resistance were identified (Crouzillat et al 2000;Flament et al 2001;Lanaud et al 2002;ClØment et al 2003aClØment et al , 2003bRisterucci et al 2003) and confirmed the polygenic nature of this quantitative resistance in cocoa. A region of chromosome 6 appears particularly interesting and gave QTL for yield components and resistance to Phytophthora.…”

Section: Introductionmentioning

confidence: 83%

“…Recently, both RGAs and defence gene analogues (DGA) were isolated from cocoa genomic DNA using degenerate primers designed from conserved domains of several plant resistance and defence genes including the NBS motif (Kuhn et al 2003, present in a number of resistance genes such as the tobacco N; the STK (serine/threonine kinases) subdomains of plants such as the Pto tomato gene; and conserved domains of two defence gene families, the pathogenesis-related proteins (PR) of classes 2 and 5 ). Most of the RGA and PR2-DGA clones, isolated by Lanaud et al (2004), were mapped in a segregating population and co-localizations were observed between some RGA and DGA, and QTL for resistance to Phytophthora previously identified in several progenies (Crouzillat et al 2000, Lanaud et al 2002, ClØment et al 2003bRisterucci et al 2003).…”

Section: Introductionmentioning

confidence: 99%

Creation of BAC genomic resources for cocoa (Theobroma cacao L.) for physical mapping of RGA containing BAC clones

et al. 2004

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We have constructed and validated the first cocoa ( Theobroma cacao L.) BAC library, with the aim of developing molecular resources to study the structure and evolution of the genome of this perennial crop. This library contains 36,864 clones with an average insert size of 120 kb, representing approximately ten haploid genome equivalents. It was constructed from the genotype Scavina-6 (Sca-6), a Forastero clone highly resistant to cocoa pathogens and a parent of existing mapping populations. Validation of the BAC library was carried out with a set of 13 genetically-anchored single copy and one duplicated markers. An average of nine BAC clones per probe was identified, giving an initial experimental estimation of the genome coverage represented in the library. Screening of the library with a set of resistance gene analogues (RGAs), previously mapped in cocoa and co-localizing with QTL for resistance to Phytophthora traits, confirmed at the physical level the tight clustering of RGAs in the cocoa genome and provided the first insights into the relationships between genetic and physical distances in the cocoa genome. This library represents an available BAC resource for structural genomic studies or map-based cloning of genes corresponding to important QTLs for agronomic traits such as resistance genes to major cocoa pathogens like Phytophthora spp ( palmivora and megakarya), Crinipellis perniciosa and Moniliophthora roreri.

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“…For this reason, we used co-dominant markers (SSRs) to facilitate both the map construction and QTL detection (Van Ooijen 2006;Van Ooijen 2009;Jourjon et al 2005). This type of approach was proved to be successful in other plant species (Clement et al 2003;Souza et al 2013). In our study, the two bi-parental maps were similar for both genetic map sizes and number of loci mapped.…”

Section: Genetic Map Constructionmentioning

confidence: 99%

Comparison of three QTL detection models on biochemical, sensory, and yield characters in Coffea canephora

Mangin¹,

Lefebvre-Pautigny

Jasson³

et al. 2014

Tree Genetics & Genomes

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Coffea canephora is subject to enormous competitive challenges from other crops, especially for farmer sustainability and consumer requirements. Coffee breeding programs have to focus on specific traits linked to these two key targets, such as quality character, largely depending on the bean's biochemical composition and field yield. Two segregating populations A and B, from crosses between a hybrid (Congolese×Guinean) FRT58 parental clone and a Congolese FRT51 genotype and between two Congolese parents FRT67 and FRT51, respectively, were used to characterize the quantitative trait loci (QTL) involved in agronomic and biochemical traits. A consensus genetic map was established using 249 SSRs covering 1,201 cM. Three QTL detection models per population with MapQTL (model I) and MCQTL (model II) followed by a connected population approach with MCQTL (model III) were compared based on their efficiency, precision for QTL detection, and their genetic effect assessment (additive, dominance, and parental-favorable allele). The analysis detected a total of 143 QTLs, 60 of which were shared between the three models; 28 found with two models; and two, 13, and 40 specific from models I, II, and III, respectively. The last model III based on connected populations is much more efficient in detecting QTLs with low variance explained and led to the genetic characterization of favorable allele. Thanks to this comparison of three QTL detection models on our quantitative genetic study, we will give a new insight for coffee breeding programs dedicated to managing complex agronomic or qualitative traits.

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Mapping QTL for yield components, vigor, and resistance toPhytophthora palmivorainTheobroma cacaoL.

Cited by 46 publications

References 23 publications

Structural characterization and mapping of functional EST-SSR markers in Theobroma cacao

Structural characterization and mapping of functional EST-SSR markers in Theobroma cacao

Creation of BAC genomic resources for cocoa (Theobroma cacao L.) for physical mapping of RGA containing BAC clones

Comparison of three QTL detection models on biochemical, sensory, and yield characters in Coffea canephora

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