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Allele

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Ildiko Karsai – One of the best experts on this subject based on the ideXlab platform.

  • Allele frequencies in the vrn a1 vrn b1 and vrn d1 vernalization response and ppd b1 and ppd d1 photoperiod sensitivity genes and their effects on heading in a diverse set of wheat cultivars triticum aestivum l
    Molecular Breeding, 2014
    Co-Authors: Tibor Kiss, Krisztina Balla, Otto Veisz, Laszlo Lang, Zoltan Bedő, Simon Griffiths, Peter Isaac, Ildiko Karsai

    Abstract:

    Heading of cereals is determined by complex genetic and environmental factors in which genes responsible for vernalization and photoperiod sensitivity play a decisive role. Our aim was to use diagnostic molecular markers to determine the main Allele types in VRN-A1, VRN-B1, VRN-D1, PPD-B1 and PPD-D1 in a worldwide wheat collection of 683 genotypes and to investigate the effect of these Alleles on heading in the field. The dominant VRN-A1, VRN-B1 and VRN-D1 Alleles were present at a low frequency. The PPD-D1a photoperiod-insensitive Allele was carried by 57 % of the cultivars and was most frequent in Asian and European cultivars. The PPD-B1 photoperiod-insensitive Allele was carried by 22 % of the genotypes from Asia, America and Europe. Nine versions of the PPD-B1-insensitive Allele were identified based on gene copy number and intercopy structure. The Allele compositions in PPD-D1, PPD-B1 and VRN-D1 significantly influenced heading and together explained 37.5 % of the phenotypic variance. The role of gene model increased to 39.1 % when PPD-B1 intercopy structure was taken into account instead of overall PPD-B1 type (sensitive vs. insensitive). As a single component, PPD-D1 had the most important role (28.0 % of the phenotypic variance), followed by PPD-B1 (12.3 % for PPD-B1_overall, and 15.1 % for PPD-B1_intercopy) and VRN-D1 (2.2 %). Significant gene interactions were identified between the marker Alleles within PPD-B1 and between VRN-D1 and the two PPD1 genes. The earliest heading genotypes were those with the photoperiod-insensitive Allele in PPD-D1 and PPD-B1, and with the spring Allele for VRN-D1 and the winter Alleles for VRN-A1 and VRN-B1. This combination could only be detected in genotypes from Southern Europe and Asia. Late-heading genotypes had the sensitivity Alleles for both PPD1 genes, regardless of the allelic composition of the VRN1 genes. There was a 10-day difference in heading between the earliest and latest groups under field conditions.

Tibor Kiss – One of the best experts on this subject based on the ideXlab platform.

  • Allele frequencies in the vrn a1 vrn b1 and vrn d1 vernalization response and ppd b1 and ppd d1 photoperiod sensitivity genes and their effects on heading in a diverse set of wheat cultivars triticum aestivum l
    Molecular Breeding, 2014
    Co-Authors: Tibor Kiss, Krisztina Balla, Otto Veisz, Laszlo Lang, Zoltan Bedő, Simon Griffiths, Peter Isaac, Ildiko Karsai

    Abstract:

    Heading of cereals is determined by complex genetic and environmental factors in which genes responsible for vernalization and photoperiod sensitivity play a decisive role. Our aim was to use diagnostic molecular markers to determine the main Allele types in VRN-A1, VRN-B1, VRN-D1, PPD-B1 and PPD-D1 in a worldwide wheat collection of 683 genotypes and to investigate the effect of these Alleles on heading in the field. The dominant VRN-A1, VRN-B1 and VRN-D1 Alleles were present at a low frequency. The PPD-D1a photoperiod-insensitive Allele was carried by 57 % of the cultivars and was most frequent in Asian and European cultivars. The PPD-B1 photoperiod-insensitive Allele was carried by 22 % of the genotypes from Asia, America and Europe. Nine versions of the PPD-B1-insensitive Allele were identified based on gene copy number and intercopy structure. The Allele compositions in PPD-D1, PPD-B1 and VRN-D1 significantly influenced heading and together explained 37.5 % of the phenotypic variance. The role of gene model increased to 39.1 % when PPD-B1 intercopy structure was taken into account instead of overall PPD-B1 type (sensitive vs. insensitive). As a single component, PPD-D1 had the most important role (28.0 % of the phenotypic variance), followed by PPD-B1 (12.3 % for PPD-B1_overall, and 15.1 % for PPD-B1_intercopy) and VRN-D1 (2.2 %). Significant gene interactions were identified between the marker Alleles within PPD-B1 and between VRN-D1 and the two PPD1 genes. The earliest heading genotypes were those with the photoperiod-insensitive Allele in PPD-D1 and PPD-B1, and with the spring Allele for VRN-D1 and the winter Alleles for VRN-A1 and VRN-B1. This combination could only be detected in genotypes from Southern Europe and Asia. Late-heading genotypes had the sensitivity Alleles for both PPD1 genes, regardless of the allelic composition of the VRN1 genes. There was a 10-day difference in heading between the earliest and latest groups under field conditions.

Joshua R Kohn – One of the best experts on this subject based on the ideXlab platform.

  • population structure at the s locus of sorbus aucuparia l rosaceae maloideae
    Molecular Ecology, 2007
    Co-Authors: Olivier Raspé, Joshua R Kohn

    Abstract:

    Low sequence divergence within functional Alleles is predicted for the self-incompatibility locus because of strong negative frequency-dependent selection. Nevertheless, sequence variation within functional Alleles is essential for current models of the evolution of new mating types. We genotyped the stylar self-incompatibility RNase of 20 Sorbus aucuparia from a population in the Pyrenees mountains of France in order to compare Alleles found there to those previously sampled in a Belgian population. Both populations returned 20 different Alleles from samples of 20 individuals, providing maximum-likelihood estimates of 24.4 (95% CI 20–34) Alleles in each. Ten Alleles occurred in both samples. The maximum likelihood (ML) estimate of the overlap in the Alleles present in both populations was 16, meaning that an estimated eight Alleles are private to each population, and a total of 32 Alleles occur across the two populations examined. We used Fisher’s (1961) missing plot method to estimate that 40 Alleles occur in the species. In accord with population genetics theory, we observed at most one synonymous sequence difference between copies of Alleles sampled from the different populations and no variation within populations. Phylogenetic analysis shows that nearly every Allele in S. aucuparia arose prior to divergence of this species from members of three different genera of the Rosaceae subfamily, Maloideae. Lack of observable sequence variation within Alleles, coupled with the slow pace of allelic relative to taxonomic diversification, implies that finding intermediate stages in the process of new Allele creation will be difficult in this group.

  • s Allele diversity in sorbus aucuparia and crataegus monogyna rosaceae maloideae
    Heredity, 2002
    Co-Authors: Olivier Raspé, Joshua R Kohn

    Abstract:

    RT-PCR was used to obtain the first estimates from natural populations of allelic diversity at the RNase-based gametophytic self-incompatibility locus in the Rosaceae. A total of 20 Alleles were retrieved from 20 Sorbus aucuparia individuals, whereas 17 Alleles were found in 13 Crataegus monogyna samples. Estimates of population-level Allele numbers fall within the range observed in the Solanaceae, the only other family with RNase-based incompatibility for which estimates are available. The nucleotide diversity of S-Allele sequences was found to be much lower in the two Rosaceae species as compared with the Solanaceae. This was not due to a lower sequence divergence among most closely related Alleles. Rather, it is the depth of the entire genealogy that differs markedly in the two families, with Rosaceae S-Alleles exhibiting more recent apparent coalescence. We also investigated patterns of selection at the molecular level by comparing nucleotide diversity at synonymous and nonsynonymous sites. Stabilizing selection was inferred for the 5′ region of the molecule, while evidence of diversifying selection was present elsewhere.