Browsing by Author "Alcalde, J. A."

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    Analysis of genome-wide structure, diversity and fine mapping of Mendelian traits in traditional and village chickens
    (2012) Wragg, D.; Mwacharo, J. M.; Alcalde, J. A.; Hocking, P. M.; Hanotte, O.
    Extensive phenotypic variation is a common feature among village chickens found throughout much of the developing world, and in traditional chicken breeds that have been artificially selected for traits such as plumage variety. We present here an assessment of traditional and village chicken populations, for fine mapping of Mendelian traits using genome-wide single-nucleotide polymorphism (SNP) genotyping while providing information on their genetic structure and diversity. Bayesian clustering analysis reveals two main genetic backgrounds in traditional breeds, Kenyan, Ethiopian and Chilean village chickens. Analysis of linkage disequilibrium (LD) reveals useful LD (r(2)>= 0.3) in both traditional and village chickens at pairwise marker distances of similar to 10 Kb; while haplotype block analysis indicates a median block size of 11-12 Kb. Association mapping yielded refined mapping intervals for duplex comb (Gga 2:38.55-38.89 Mb) and rose comb (Gga 7:18.41-22.09 Mb) phenotypes in traditional breeds. Combined mapping information from traditional breeds and Chilean village chicken allows the oocyan phenotype to be fine mapped to two small regions (Gga 1:67.25-67.28 Mb, Gga 1:67.28-67.32 Mb) totalling similar to 75 Kb. Mapping the unmapped earlobe pigmentation phenotype supports previous findings that the trait is sex-linked and polygenic. A critical assessment of the number of SNPs required to map simple traits indicate that between 90 and 110 K SNPs are required for full genome-wide analysis of haplotype block structure/ancestry, and for association mapping in both traditional and village chickens. Our results demonstrate the importance and uniqueness of phenotypic diversity and genetic structure of traditional chicken breeds for fine-scale mapping of Mendelian traits in the species, with village chicken populations providing further opportunities to enhance mapping resolutions. Heredity (2012) 109, 6-18; doi:10.1038/hdy.2012.9; published online 7 March 2012
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    Isolation of WDR and bHLH genes related to flavonoid synthesis in grapevine (Vitis vinifera L.)
    (2010) Matus, J. T.; Poupin, M. J.; Canon, P.; Bordeu, E.; Alcalde, J. A.; Arce-Johnson, P.
    Anthocyanins and tannins are two of the most abundant flavonoids found in grapevine, and their synthesis is derived from the phenylpropanoid pathway. As described for model species such as Arabidopsis thaliana, maize and petunia, the end-point branches of this pathway are tightly regulated by the combinatorial interaction of three families of regulatory factors; MYB, bHLH (also known as MYC) and WDR proteins. Among these, only MYB genes have been previously identified in grapes. Here, we report the isolation of the first members from the WDR and bHLH families found in Vitis vinifera, named WDR1, WDR2 and MYCA1. WDR1 contributed positively to the accumulation of anthocyanins when it was overexpressed in A. thaliana, although it was not possible to determine the function of WDR2 by ectopic expression. The sub-cellular localizations of WDR1 and MYCA1 were observed by means of GFP-fusion proteins, indicating both cytoplasm and nuclear localization, in contrast to the localization of a MYB factor exclusively in the nucleus. The expression patterns of these genes were quantified in coloured reproductive organs throughout development, and correlated with anthocyanin accumulation and the expression profiles of the flavonoid-related MYBA1-2, UFGT, and ANR genes. In vitro grapevine plantlets grown under high salt concentrations showed a cultivar-dependent response for anthocyanin accumulation, which correlated with the expression of MYBA1-2, MYCA1 and WDR1 genes. These results suggest that MYCA1 may regulate ANR and UFGT and that this last control is easier to distinguish whenever MYBA genes are absent or in low abundance. Future studies should address the specific interactions of these proteins and their quantitative contribution to flavonoid synthesis in grape berries.
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    S-Abscisic acid, 2-chloroethylphosphonic acid and indole-3-acetic acid treatments modify grape (Vitis vinifera L. 'Cabernet Sauvignon') hormonal balance and wine quality
    (JKI-INSTITUT REBENZUCHTUNG, 2012) Gonzalez, A. S.; Olea, P.; Bordeu, E.; Alcalde, J. A.; Geny, L.
    The phenolic composition of red wine strongly determines its quality. Even when the applications of plant growth regulator (PGR) affect grape quality, there is almost no information on the effect of these treatments on the grape's internal hormonal balance and the wine composition and quality. In the present study, changes in the internal hormonal content following the application of (+)-S-abscisic acid (S-ABA), 2-chloroethylphosphonic acid (CEPA) and indole-3-acetic acid (IAA) at veraison were examined to determine their effects on 'Cabernet Sauvignon' grapes and wine composition in a plants in containers experiment and in a commercial vineyard experiment. Applied PGRs had a significant effect on the hormonal balance and phenolic composition of grape skins. The S-ABA-treated grapes showed a significantly higher skin internal free abscisic acid concentration in the plants in container experiment and the CEPA-treated grapes showed a reduction in skin internal IAA concentration in the commercial vineyard experiment. Winemaking was performed in the commercial vineyard experiment. Wine's chemical composition was affected by these treatments and an up-to 63 % increase in malvidin-3-glucoside concentration and an up-to 70 A increase in total tannin concentration were found in wines made from the CEPA-treated grapes. The alcohol content was 10.3 % higher (from 12.6 to 13.9 % v v(-1)) in wines made from the CEPA-treated grapes. No significant differences in the wine sensory attributes (aroma and mouth-feel) between the control and the PGR-treated wines were identified by a sensory panel.