Combined linkage and association mapping of flowering time in Sunflower (Helianthus annuus L.)

Cadic, Eléna; Coque, Marie; Vear, Félicity; Grezes-Besset, Bruno; Pauquet, Jérôme; Piquemal, Joël; Lippi, Yannick; Blanchard, Philippe; Romestant, Michel; Pouilly, Nicolas; Rodrı́guez-Lázaro, David; Gouzy, Jérôme; Langlade, Nicolas B.; Mangin, Brigitte; Vincourt, Patrick

doi:10.1007/s00122-013-2056-2

Cited by 53 publications

(66 citation statements)

References 73 publications

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“…Rogers & Bernatchez ; Cadic et al . ; Berner et al . ), and we have previously referred to this methodology as ‘selection signature QTL’ (ssQTL), as each QTL is explicitly linked to a set of divergent loci between species/populations (Parsons & Albertson ).…”

Section: Resultsmentioning

confidence: 99%

Genetic basis of continuous variation in the levels and modular inheritance of pigmentation in cichlid fishes

et al. 2014

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Variation in pigmentation type and levels is a hallmark of myriad evolutionary radiations, and biologists have long been fascinated by the factors that promote and maintain variation in coloration across populations. Here, we provide insights into the genetic basis of complex and continuous patterns of colour variation in cichlid fishes, which offer a vast diversity of pigmentation patterns that have evolved in response to both natural and sexual selection. Specifically, we crossed two divergent cichlid species to generate an F2 mapping population that exhibited extensive variation in pigmentation levels and patterns. Our experimental design is robust in that it combines traditional quantitative trait locus (QTL) analysis with population genomics, which has allowed us to move efficiently from QTL interval to candidate gene. In total, we detected 41 QTL and 13 epistatic interactions that underlie melanocyte- and xanthophore-based coloration across the fins and flanks of these fishes. We also identified 2 QTL and 1 interaction for variation in the magnitude of integration among these colour traits. This finding in particular is notable as there are marked differences both within and between species with respect to the complexity of pigmentation patterns. While certain individuals are characterized by more uniform ‘integrated’ colour patterns, others exhibit many more degrees of freedom with respect to the distribution of colour ‘modules’ across the fins and flank. Our data reveal, for the first time, a genetic basis for this difference. Finally, we implicate pax3a as a mediator of continuous variation in the levels of xanthophore-based colour along the cichlid flank.

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Section: Resultsmentioning

confidence: 99%

Genetic basis of continuous variation in the levels and modular inheritance of pigmentation in cichlid fishes

et al. 2014

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“…Association mapping was based on a set of 65 534 SNP with MAF > 0.05. Similarly to our previous work (Cadic et al ), two association models were performed using EMMA (Kang et al ) based on the Yu et al model (2006). Both models included a correction for the genomic relatedness using the alike‐in‐state (AIS) kinship estimated with EMMA version v1.1.2 R package (Villanova et al ) using all the previously mentioned SNPs.…”

Section: Methodsmentioning

confidence: 99%

Genetic control of plasticity of oil yield for combined abiotic stresses using a joint approach of crop modelling and genome‐wide association

Mangin

Casadebaig

Cadic

et al. 2017

Plant Cell & Environment

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Understanding the genetic basis of phenotypic plasticity is crucial for predicting and managing climate change effects on wild plants and crops. Here, we combined crop modelling and quantitative genetics to study the genetic control of oil yield plasticity for multiple abiotic stresses in sunflower. First, we developed stress indicators to characterize 14 environments for three abiotic stresses (cold, drought and nitrogen) using the SUNFLO crop model and phenotypic variations of three commercial varieties. The computed plant stress indicators better explain yield variation than descriptors at the climatic or crop levels. In those environments, we observed oil yield of 317 sunflower hybrids and regressed it with three selected stress indicators. The slopes of cold stress norm reaction were used as plasticity phenotypes in the following genome-wide association study. Among the 65 534 tested Single Nucleotide Polymorphisms (SNPs), we identified nine quantitative trait loci controlling oil yield plasticity to cold stress. Associated single nucleotide polymorphisms are localized in genes previously shown to be involved in cold stress responses: oligopeptide transporters, lipid transfer protein, cystatin, alternative oxidase or root development. This novel approach opens new perspectives to identify genomic regions involved in genotype-by-environment interaction of a complex traits to multiple stresses in realistic natural or agronomical conditions.

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“…We used CarthaGène v1.3 [34] to build the genetic maps. We added the genotypic data of markers from a consensus map [35] to the set of the 2164 SNPs to assign them to the appropriate LG to the group 0.3 8 in CarthaGène. They were ordered using the lkh 1 -1 function in CarthaGène for each group.…”

Section: Methodsmentioning

confidence: 99%

Genetic Control of Water Use Efficiency and Leaf Carbon Isotope Discrimination in Sunflower (Helianthus annuus L.) Subjected to Two Drought Scenarios

et al. 2014

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High water use efficiency (WUE) can be achieved by coordination of biomass accumulation and water consumption. WUE is physiologically and genetically linked to carbon isotope discrimination (CID) in leaves of plants. A population of 148 recombinant inbred lines (RILs) of sunflower derived from a cross between XRQ and PSC8 lines was studied to identify quantitative trait loci (QTL) controlling WUE and CID, and to compare QTL associated with these traits in different drought scenarios. We conducted greenhouse experiments in 2011 and 2012 by using 100 balances which provided a daily measurement of water transpired, and we determined WUE, CID, biomass and cumulative water transpired by plants. Wide phenotypic variability, significant genotypic effects, and significant negative correlations between WUE and CID were observed in both experiments. A total of nine QTL controlling WUE and eight controlling CID were identified across the two experiments. A QTL for phenotypic response controlling WUE and CID was also significantly identified. The QTL for WUE were specific to the drought scenarios, whereas the QTL for CID were independent of the drought scenarios and could be found in all the experiments. Our results showed that the stable genomic regions controlling CID were located on the linkage groups 06 and 13 (LG06 and LG13). Three QTL for CID were co-localized with the QTL for WUE, biomass and cumulative water transpired. We found that CID and WUE are highly correlated and have common genetic control. Interestingly, the genetic control of these traits showed an interaction with the environment (between the two drought scenarios and control conditions). Our results open a way for breeding higher WUE by using CID and marker-assisted approaches and therefore help to maintain the stability of sunflower crop production.

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Combined linkage and association mapping of flowering time in Sunflower (Helianthus annuus L.)

Cited by 53 publications

References 73 publications

Genetic basis of continuous variation in the levels and modular inheritance of pigmentation in cichlid fishes

Genetic basis of continuous variation in the levels and modular inheritance of pigmentation in cichlid fishes

Genetic control of plasticity of oil yield for combined abiotic stresses using a joint approach of crop modelling and genome‐wide association

Genetic Control of Water Use Efficiency and Leaf Carbon Isotope Discrimination in Sunflower (Helianthus annuus L.) Subjected to Two Drought Scenarios

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