Single-locus Trait Research Articles

Food/Feed and Environmental Risk Assessment of Insect-resistant and Herbicide-tolerant Genetically Modified Maize GA21 from Syngenta Seeds for Food and Feed Uses, Import and Processing under Regulation (EC) No 1829/2003 (EFSA/GMO/UK/2005/19)

Food/Feed and Environmental Risk Assessment of Insect-resistant and Herbicide-tolerant Genetically Modified Maize GA21 from Syngenta Seeds for Food and Feed Uses, Import and Processing under Regulation (EC) No 1829/2003 (EFSA/GMO/UK/2005/19)

Food/Feed and Environmental Risk Assessment of Insect-Resistant and Herbicide-Tolerant Genetically Modified Maize Bt11 from Syngenta Seeds for Food and Feed Uses, Import and Processing under Regulation (EC) No 1829/2003 (EFSA/GMO/RX/Bt11)

Food/Feed and Environmental Risk Assessment of Insect-Resistant and Herbicide-Tolerant Genetically Modified Maize Bt11 from Syngenta Seeds for Food and Feed Uses, Import and Processing under Regulation (EC) No 1829/2003 (EFSA/GMO/RX/Bt11)

Food and Environmental Risk Assessment of Herbicide-tolerant Genetically Modified Maize NK603 for Food Uses, Import and Processing under Directive 2001/18/EC (Notification C/ES/00/01)

Food and Environmental Risk Assessment of Herbicide-tolerant Genetically Modified Maize NK603 for Food Uses, Import and Processing under Directive 2001/18/EC (Notification C/ES/00/01)

Food, Feed and Environmental Risk Assessment of Glufosinatetolerant Genetically Modified Oilseed Rape T45 for Food and Feed Uses, Import and Processing Under Regulation (EC) No 1829/2003 (Application EFSA/GMO/UK/2005/25)

Food, Feed and Environmental Risk Assessment of Glufosinatetolerant Genetically Modified Oilseed Rape T45 for Food and Feed Uses, Import and Processing Under Regulation (EC) No 1829/2003 (Application EFSA/GMO/UK/2005/25)

Environmental Risk Assessment of Glufosinate-Tolerant Genetically Modified Oilseed Rape T45 for Food and Feed Uses, Import and Processing under Regulation (EC) No 1829/2003 (Application EFSA/GMO/UK/2005/25)

Environmental Risk Assessment of Glufosinate-Tolerant Genetically Modified Oilseed Rape T45 for Food and Feed Uses, Import and Processing under Regulation (EC) No 1829/2003 (Application EFSA/GMO/UK/2005/25)

TCR Vbeta usage differences are associated with Marek’s disease resistance in the chicken.

Abstract Marek’s disease (MD) is a herpesvirus-induced lymphoma in chickens which is of prime importance to the poultry industry, costing over $1 billion annually. Although vaccination controls the disease, virulence shifts have prompted efforts to improve genetic resistance in the host. We studied T cell responses in two models of MD resistance in inbred layer chicken lines. The first model is MHC-matched lines which have been selected for resistance (Line 6) or susceptibility (Line 7). The second model involves MHC-congenic lines which differ in MHC alleles known to be associated with higher (Line B21) or lower (Line B19) MD resistance. We characterized the usage of Vbeta-1+ and Vbeta-2+ TCRs in the T cell populations of birds infected and uninfected with Marek’s disease virus (MDV). Vbeta-1 and Vbeta-2 are the only two Vbeta gene families present in the chicken TCR loci, and are highly homologous within family. We found that resistant lines had a higher proportion of spleen T cells expressing Vbeta-1+ TCRs than susceptible lines, and that responses to infection were visible as shifts toward increased usage of Vbeta-1+ TCRs in CD8+, but not CD4+, T cell populations. While differences between MHC-congenic lines were small, resistant Line 6 showed a significant Vbeta-1+ CD8+ response as early as 8 days post infection, while susceptible Line 7 did not. We then characterized a panel of 6C.7 recombinant congenic lines, finding that TCR usage is most likely a single-locus trait, but interacts with other loci to produce a larger Vbeta-1+ T cell pool in more MD-resistant lines. We hypothesize that the reduced receptor diversity in the chicken may have led to strong selection effects on TCR-antigen-MHC fit which impact resistance to MDV infection or tumorigenesis.

Inheritance of Glyphosate Resistance in Hairy Fleabane (Conyza bonariensis) from California

Inheritance of glyphosate resistance was investigated in hairy fleabane populations from California as part of providing the information needed to predict and manage resistance and to gain insight into resistance mechanism (or mechanisms) present in the populations. Three glyphosate-resistant individuals grown from seed collected from distinct sites near Fresno, CA, were crossed to individuals from the same susceptible population to create reciprocal F1populations. A single individual from each of the F1populations was used to create a backcross population with a susceptible maternal parent, and an F2population. Based on dose response analyses, reciprocal F1populations were not statistically different from each other, more similar to the resistant parent, and statistically different from the susceptible parent, consistent with nuclear control of the trait and dominance to incomplete dominance of resistance over susceptibility in all three crosses. Glyphosate resistance in two of the three crosses segregated in the backcross and the F2populations as a single-locus trait. In the remaining cross, the resistant parent had approximately half the resistance level as the other two resistant parents, and the segregation of glyphosate resistance in backcross and F2populations conformed to a two-locus model with resistance alleles acting additively and at least two copies of the allele required for expression of resistance. This two-locus model of the segregation of glyphosate resistance has not been reported previously. Variation in the pattern of inheritance and the level of resistance indicate that multiple resistance mechanisms may be present in hairy fleabane populations in California.

Latitudinal clines in body size, but not in thermal tolerance or heat-shock cognate 70 (HSC70), in the highly-dispersing intertidal gastropod Littorina keenae (Gastropoda: Littorinidae)

Natural populations of widely-distributed animals often exhibit clinal variation in phenotypic traits or in allele frequencies of a particular gene over their geographical range. A planktotrophic intertidal snail, Littorina keenae is broadly distributed along the north-eastern Pacific coast through a large latitudinal range (24°50′N–43°18′N). We tested for latitudinal clines in two complex phenotypic traits – thermal tolerance and body size – and one single locus trait – heat shock cognate 70 (HSC70 )–i nL. keenae along almost its entire geographical range. We found only weak evidence for a latitudinal cline in the thermal tolerance and no evidence for a cline in allele frequencies at HSC70. However, as predicted by Bergmann’s rule, we detected a strong latitudinal cline that accounted for 60% of the variance in body size (R 2 = 0.598; P < 0.001). In contrast, body size did not significantly affect thermal tolerance. HSC70 showed no genetic differentiation among the populations, supporting our previous mitochondrial gene-based estimate of high gene flow during this snail’s free-swimming larval stage. Given that L. keenae experiences panmixia along its species range, the observed size cline may be partially or entirely caused by a phenotypically plastic response to local thermal environments rather than by genetic divergence in body size among populations in response to locally optimizing natural selection. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 100, 494–505.

Global haplotype partitioning for maximal associated SNP pairs.

BackgroundGlobal partitioning based on pairwise associations of SNPs has not previously been used to define haplotype blocks within genomes. Here, we define an association index based on LD between SNP pairs. We use the Fisher's exact test to assess the statistical significance of the LD estimator. By this test, each SNP pair is characterized as associated, independent, or not-statistically-significant. We set limits on the maximum acceptable proportion of independent pairs within all blocks and search for the partitioning with maximal proportion of associated SNP pairs. Essentially, this model is reduced to a constrained optimization problem, the solution of which is obtained by iterating a dynamic programming algorithm.ResultsIn comparison with other methods, our algorithm reports blocks of larger average size. Nevertheless, the haplotype diversity within the blocks is captured by a small number of tagSNPs. Resampling HapMap haplotypes under a block-based model of recombination showed that our algorithm is robust in reproducing the same partitioning for recombinant samples. Our algorithm performed better than previously reported models in a case-control association study aimed at mapping a single locus trait, based on simulation results that were evaluated by a block-based statistical test. Compared to methods of haplotype block partitioning, we performed best on detection of recombination hotspots.ConclusionOur proposed method divides chromosomes into the regions within which allelic associations of SNP pairs are maximized. This approach presents a native design for dimension reduction in genome-wide association studies. Our results show that the pairwise allelic association of SNPs can describe various features of genomic variation, in particular recombination hotspots.

Pollinator preferences and the persistence of crop genes in wild radish populations (Raphanus raphanistrum, Brassicaceae)

Crop-weed hybridization can potentially influence the evolutionary ecology of wild populations. Many crops are known to hybridize with wild relatives, but few studies have looked at the long-term persistence of crop genes in the wild. This study investigated one factor in the hybridization process in radish: differential pollinator visitation to wild radish (Raphanus raphanistrum) vs. crop-wild F1 hybrids (R. sativus x R. raphanistrum). Wild genotypes had yellow flowers, a recessive single-locus trait, whereas hybrids always had white or pale pink flowers. In experimental arrays in northern Michigan, total pollinator visitation was significantly biased toward wild plants when the frequencies of wild and hybrid plants were equal. Syrphid flies, the most frequent visitors, preferred wild plants while bumble bees showed no preference. This pattern was also observed when hybrid plants were overrepresented in the array (12 hybrid:2 wild). In contrast, when hybrid plants were rare (2 hybrid:12 wild), neither morph was preferred by any pollinator group. Later in the summer, pollinators were also observed in a large experimental garden with nearly equal frequencies of wild and hybrid plants. Cabbage butterflies (Pieris rapae) strongly overvisited wild plants, while bumble bees showed a slight preference for hybrids. Taken together, these studies suggest that F1 hybrids may not be at a disadvantage with regard to pollinator visits when they occur at low frequencies or when bumble bees are frequent flower visitors. Thus, variation in the proportion of white-flowered morphs among wild radish populations could be influenced by different histories of crop-to-wild hybridization, as well as by variation in the composition of local pollinator taxa.

Identification of susceptibility loci contributing to a complex disease using conventional segregation, linkage, and association methods.

We set out to apply conventional analytic methods to a GAW data set of nuclear families with an oligogenic disease that has a population prevalence of 0.023. We chose methods generally applied to disorders with at least one major gene. Our approaches included: 1) complex segregation analysis under two models of ascertainment, 2) linkage analysis assuming either a single-locus trait with possible genetic heterogeneity or a two-locus trait, and 3) allelic association studies using both a case/control approach and the haplotype relative risk (HRR) test. The association study was the only analysis of the three that provided evidence for genes playing a role in the etiology of this disorder.