A meta–QTL analysis of disease resistance traits of Theobroma cacao L.

Lanaud, Claire; Fouet, Olivier; Clément, Didier; Boccara, Michel; Risterucci, Ange-Marie; Surujdeo-Maharaj, Surendra; Legavre, Thierry; Argout, Xavier

doi:10.1007/s11032-009-9297-4

Cited by 93 publications

(81 citation statements)

References 45 publications

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“…This method can identify major, common QTLs out of large numbers of QTLs, and provide consensus positions for these meta-QTLs. Meta-QTL analyses for flowering time in maize (Chardon et al 2004), disease resistance traits of Theobroma cacao L. (Lanaud et al 2009), earliness traits in bread wheat (Hanocq et al 2007), rice root genetic architecture (Courtois et al 2009), and plant height in wheat (Griffiths et al 2012), have demonstrated the usefulness of this approach in predicting the number of "real" QTLs from the observed QTLs and in accurately locating consensus…”

Section: Discussionmentioning

confidence: 99%

In silico integration of quantitative trait loci for seed yield and yield-related traits in Brassica napus

Zhou

Mason

et al. 2013

Mol Breeding

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Section: Discussionmentioning

confidence: 99%

In silico integration of quantitative trait loci for seed yield and yield-related traits in Brassica napus

Zhou

Mason

et al. 2013

Mol Breeding

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“…The linkage mapping studies that have been carried out in cacao have concentrated on mapping QTL within F1 or F2 mapping populations. While this work has been valuable in identifying some QTL in the cacao genome (see Lanaud et al 2009;Motamayor et al 2013;Royaert et al 2011;Schnell et al 2007), its effect on cacao breeding and research has been limited by a number of factors. These include small mapping populations derived from relatively heterozygous parents, funding inconsistencies, and the pervasive mislabeling of elite cacao varieties.…”

Section: Communicated By D Grattapagliamentioning

confidence: 99%

Assessing microsatellite linkage disequilibrium in wild, cultivated, and mapping populations of Theobroma cacao L. and its impact on association mapping

Stack

Royaert²,

Gutiérrez³

et al. 2015

Tree Genetics & Genomes

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Linkage disequilibrium (LD) measured over the genomes of a species can provide important indications for how future association analyses should proceed. This information can be advantageous especially for slow-growing, perennial crops such as Theobroma cacao, where experimental crosses are inherently time-consuming and logistically expensive. While LD has been evaluated in cacao, previous work has been focused on relatively narrow genetic bases. We use microsatellite marker data collected from a uniquely diverse sample of individuals broadly covering both wild and cultivated varieties to gauge the LD present in the different cacao diversity groups and populations. We find that genome-wide LD decays far more rapidly in the wild and primitive diversity groups of cacao as compared to those representing cultivated varieties. The impact that such differences can have on association analyses is demonstrated using phenotypic data on pod color and genotypic data from two cacao populations with contrasting patterns of LD decay. Our results indicate that the more rapid LD decay in wild and primitive germplasm can lead to higher-resolution mapping intervals when compared to results from cultivated germplasm. Through simulations, we demonstrate how future association mapping analyses, comprising of cacao samples with a wild or primitive background, will likely exhibit lower LD and would be more suitable for fine-scale association mapping analyses. As many traits targeted by cacao breeders are found exclusively in wild and primitive germplasm, association mapping in wild cacao populations holds significant promise for cacao improvement through marker-assisted breeding and emphasize the need to further explore the natural diversity of Amazonian cacao.

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“…Meta-QTL analysis has also been successfully conducted in several other crops like maize Truntzler et al, 2010;Hao et al, 2010;Li et al, 2011;Wang et al, 2006;Coque et al, 2008), cotton (Rong et al, 2007), rice (Ballini et al, 2008;Norton et al, 2008;Khowaja et al, 2009), rapeseed (Shi et al, 2009), potato (Danan et al, 2011), cocoa (Lanaud et al, 2009), soybean (Guo et al, 2006;Sun et al, 2012) and apricot (Marandel et al, 2009). …”

Section: Introductionmentioning

confidence: 99%

Meta-analysis of QTLs Involved in Pre-harvest Sprouting Tolerance and Dormancy in Bread Wheat

Tyagi¹,

Gupta²

2012

tgg

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In common wheat, meta-analysis of quantitative trait loci (QTL) associated with pre-harvest sprouting tolerance (PHST) and dormancy was carried out using results of 15 studies involving 15 different mapping populations. The study was restricted to only four chromosomes including three chromosomes of homoeologous group 3 (3A, 3B and 3D) and the chromosome 4A, since QTLs for PHST and dormancy on these four chromosomes were reported in several earlier studies, thus making these chromosomes suitable for meta-QTL analysis. The software BioMercator 2.1 was used to build a consensus map, and QTLs were projected on to this map for conducting meta-analysis. Using 36 of the 50 original QTLs, 8 meta-QTLs (MQTLs) were identified: 7 MQTLs were located on chromosomes of homoeologous group 3 including 3A (2 MQTL), 3B (3 MQTL) and 3D (2 MQTL), 1 MQTL was located on chromosome 4A. Confidence intervals (C.I.) for each of these 8 MQTLs were particularly narrow. The mapping information for 50 QTLs was also used for "overview" analysis to visualize important genomic regions carrying the MQTLs for PHST and dormancy. Co-localizations between candidate genes for dormancy/PHST (taVP1 and TaGA20-ox1) and MQTL positions appeared globally significant, although these candidate genes deserve further investigation. Markers associated with 8 MQTLs identified during the present study should prove helpful for introgression of tolerance against pre-harvest sprouting (PHS) into high yielding wheat varieties through marker-assisted selection (MAS).

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A meta–QTL analysis of disease resistance traits of Theobroma cacao L.

Cited by 93 publications

References 45 publications

In silico integration of quantitative trait loci for seed yield and yield-related traits in Brassica napus

In silico integration of quantitative trait loci for seed yield and yield-related traits in Brassica napus

Assessing microsatellite linkage disequilibrium in wild, cultivated, and mapping populations of Theobroma cacao L. and its impact on association mapping

Meta-analysis of QTLs Involved in Pre-harvest Sprouting Tolerance and Dormancy in Bread Wheat

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