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Anderson, J.R., Zein, I., Wenzel, G., Krützfeldt, B., Eder, J., Ouzunova, M., Lübberstedt, T. 2007. High levels of linkage disequilibrium and associations with forage quality at a Phenylalanine Ammonia-Lyase locus in European maize ( Zea mays L.) inbreds

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1053 Bulmer, M. G. (1974): Linkage disequilibrium and genetic variability. Genet. Res. Camb. 23 : 281-289. Linkage disequilibrium and genetic variability

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Genetic structure of 142 parent lines of sorghum [Sorghum bicolor (L.) Moench] was analyzed using model-based approach based on SSR markers. Forty-one selected from 103 SSR markers were used to analyze the parent lines, which generated 189 alleles revealed by each marker ranging from 2 to 11 with an average of 4.6 per marker. The polymorphic information content (PIC) value was 0.543 with a range of 0.089 to 0.850. All the parent lines were assigned to 7 subgroups, named Kafir, Kaoliang, Feterita, Shallu, Hegari, Milo and Durra. Parent lines without clear pedigree record were clustered into their corresponding groups, and genetic components of each line were estimated by Q-values. Information of this study would be useful for breeders to conclude their genetic background and select appropriate parents for germplasm improvement and hybrid breeding, and thus improve the efficiency of breeding programs.

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Genetics underpins many ways in which individuals differ. The purpose of this paper is to advance a model with testable hypotheses regarding the cause of the genetic basis of personality. We proceed by developing the suggestion that diversity in personality genes evolved to constrain parasitic elements of culture and discuss its implications. In particular, a critical test of this hypothesis is whether personality genes show fluctuating linkage disequilibrium and a dispersed distribution throughout the genome. It is further suggested that this Red Queen process has facilitated the evolution of intelligence and allowed a higher mutation rate in relevant genes. The model’s empirical predictions are discussed in the context of alternative explanations, including those regarding intragenomic conflict, economics, and heterozygote advantage.

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Sympatric speciation is a composite phenomenon requiring both ecological differentiation and the evolution of a mating structure that induces reproductive isolation. Ecological and sexual selection models have addressed these two aspects of sympatric speciation separately. We briefly discuss the recent results of these models and argue that the evolution of ecological and mating strategies are mutually dependent processes rather than independent phenomena corresponding to incompatible views of sympatric speciation. Then, we consider a combined model incorporating ecological interactions and sexual selection. In this model, sympatric speciation is initiated by simultaneous evolutionary branching of ecological strategy, leading to ecological differentiation, and mating strategies, resulting in assortative mating. Both types of evolutionary branching can be understood as the outcome of a competition process in which individuals compete for a spectrum of either ecological resources or mating opportunities. Speciation is completed when a linkage disequilibrium between ecological and mating types splits the population into two ecologically differentiated and reproductively isolated groups. Using a combined analytical and individual-based simulation approach, we illustrate the different dynamical regimes and characterize the necessary conditions for sympatric speciation in the model.

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Wheat kernel morphology is a very important trait for wheat yield improvement. This is the first report of association analysis of kernel morphology traits in wheat breeding lines. In Qinghai, China, the research described here involved genome-wide association analysis in breeding lines derived from synthetic hexaploid wheat with a mixed linear model to identify the quantitative trait loci (QTLs) related to kernel morphology. The 8033 effective Diversity Array Technology (DArT) markers produced a genetic map of 5901.84 cM with an average density of 1.36 markers/cM. Population structure analysis classified 507 breeding lines into three groups by Bayesian structure analysis using unlinked markers. Linkage disequilibrium decay was observed with a map coverage of 2.78 cM. Marker-trait association analysis showed that 15 DArT markers for kernel morphology were detected, located on nine chromosomes, and explained 2.6%–4.0% of the phenotypic variation of kernel area (KA), kernel width (KW), kernel length (KL) and thousand-kernel weight (TKW). The marker 1139297 was related to both the KL and KA traits. Only six DArT markers were close to known QTLs. The parent SHW-L1 carried eight favored alleles, while other seven favored alleles were derived from elite common wheat cultivars. These QTLs, identified in elite breeding lines, should help us understand the kernel morphology trait better, and to provide germplasm for breeding new wheat cultivars for Qinghai Province or other regions.

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Acta Physiologica Hungarica
Authors: S. Flores-Martínez, J. Martínez, M. Machorro-Lazo, A. García-Zapién, L. Salgado-Goytia, E. Cruz-Quevedo, M. Morán-Moguel and J. Sánchez-Corona

344 Beaudet AL, Feldman GL, Fernbach SD, Buffone GJ, O’Brien WE: Linkage disequilibrium, cystic fibrosis, and genetic counseling. Am. J. Hum. Genet. 44, 319–326 (1989

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Cereal Research Communications
Authors: L. Brbaklić, D. Trkulja, A. Kondić-Špika, S. Mikić, M. Tomičić and B. Kobiljski

Chen, X., Min, D., Yasir, T.A., Hu, Y.G. 2012. Genetic diversity, population structure and linkage disequilibrium in elite Chinese winter wheat investigated with SSR markers. PLoS one 7 (9):e44510. doi: 10.1371/journal.pone 0044510

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Prion protein is encoded by the prion protein gene (PRNP). Polymorphisms of several members of the prion gene family have shown association with prion diseases in several species. Recent studies on a novel member of the prion gene family in rams have shown that prion-related protein gene (PRNT) has a linkage with codon 26 of prion-like protein (PRND). In a previous study, codon 26 polymorphism of PRND has shown connection with PRNP haplotype which is strongly associated with scrapie vulnerability. In addition, the genotype of a single nucleotide polymorphism (SNP) at codon 26 of PRND is related to fertilisation capacity. These findings necessitate studies on the SNP of PRNT gene which is connected with PRND. In goat, several polymorphism studies have been performed for PRNP, PRND, and shadow of prion protein gene (SPRN). However, polymorphism on PRNT has not been reported. Hence, the objective of this study was to determine the genotype and allelic distribution of SNPs of PRNT in 238 Korean native goats and compare PRNT DNA sequences between Korean native goats and several ruminant species. A total of five SNPs, including PRNT c.-114G > T, PRNT c.-58A > G in the upstream of PRNT gene, PRNT c.71C > T (p.Ala24Val) and PRNT c.102G > A in the open reading frame (ORF) and c.321C > T in the downstream of PRNT gene, were found in this study. All five SNPs of caprine PRNT gene in Korean native goat are in complete linkage disequilibrium (LD) with a D’ value of 1.0. Interestingly, comparative sequence analysis of the PRNT gene revealed five mismatches between DNA sequences of Korean native goats and those of goats deposited in the GenBank. Korean native black goats also showed 5 mismatches in PRNT ORF with cattle. To the best of our knowledge, this is the first genetic research of the PRNT gene in goat.

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, Bertorelle G, Verlingue C, Raguénès O, Mercier B, Férec C: Linkage disequilibrium between the four most commun cystic fibrosis mutations and microsatellite haplotypes in the Celtic population of Brittany. Hum. Genet. 98, 223–227 (1996) Férec C

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