Range Of Linkage Disequilibrium Research Articles

Mining candidate genes for grape seed traits based on a genome-wide association study

Seedlessness has always been a valuable quality characteristic of edible grape varieties. Although the production of seedless grapes has been ongoing for decades, the genetic complexity of seedless grapes is not yet fully understood. Therefore, determining the genetic mechanisms and key regulatory genes of seedless grapes is of great significance for seedless grape breeding and meeting market demands. The emergence of high-throughput analysis software offers greater possibilities for mining genes related to plant organ development. Specifically, to mine a greater number of candidate genes related to grape seed traits, this study used the seed trait parameters analyzed by Tomato Analyzer as the target trait and then used a genome-wide association study (GWAS) to mine candidate genes. In the two-year analysis using principal component analysis (PCA), we extracted five principal components with a cumulative contribution rate of 96.586 %. The cumulative contribution rate for component 1 reached 87.352 %. Correlation analysis revealed correlation coefficients ranging from 0.54 to 0.98 among the seven basic traits. The GWAS results indicated that 370 SNP loci were significantly correlated with seed traits. These SNP loci were distributed on 18 chromosomes, except for chromosome 4, with most SNP loci distributed on chromosome 18. Based on the physical location of single nucleotide polymorphism (SNP) markers significantly associated with seed-related traits in the grape reference genome, candidate genes are screened within the range of linkage disequilibrium (LD) attenuation distance, both upstream and downstream of the significant SNP loci. These candidate genes were mainly transcription factor-related genes (VvMADS4 and VvMADS5), ubiquitin ligase-related genes (E3 ubiquitin ligase BIG BROTHER), serine/threonine protein kinase-related genes, and carbohydrate metabolism-related genes (Sucrose Synthase 2) and simultaneously controlled multiple (at least two or more) seed traits. These results indicate that seed traits are jointly regulated by some genes involved in seed morphology regulation. In this work, we identified new gene loci related to grape seed traits. Identifying molecular markers closely related to these seed traits is of great significance for breeding seedless grape varieties.

Genome-wide epistatic expression quantitative trait loci discovery in four human tissues reveals the importance of local chromosomal interactions governing gene expression.

BackgroundEpistasis (synergistic interaction) among SNPs governing gene expression is likely to arise within transcriptional networks. However, the power to detect it is limited by the large number of combinations to be tested and the modest sample sizes of most datasets. By limiting the interaction search space firstly to cis-trans and then cis-cis SNP pairs where both SNPs had an independent effect on the expression of the most variable transcripts in the liver and brain, we greatly reduced the size of the search space.ResultsWithin the cis-trans search space we discovered three transcripts with significant epistasis. Surprisingly, all interacting SNP pairs were located nearby each other on the chromosome (within 290 kb-2.16 Mb). Despite their proximity, the interacting SNPs were outside the range of linkage disequilibrium (LD), which was absent between the pairs (r2 < 0.01). Accordingly, we redefined the search space to detect cis-cis interactions, where a cis-SNP was located within 10 Mb of the target transcript. The results of this show evidence for the epistatic regulation of 50 transcripts across the tissues studied. Three transcripts, namely, HLA-G, PSORS1C1 and HLA-DRB5 share common regulatory SNPs in the pre-frontal cortex and their expression is significantly correlated. This pattern of epistasis is consistent with mediation via long-range chromatin structures rather than the binding of transcription factors in trans. Accordingly, some of the interactions map to regions of the genome known to physically interact in lymphoblastoid cell lines while others map to known promoter and enhancer elements. SNPs involved in interactions appear to be enriched for promoter markers.ConclusionsIn the context of gene expression and its regulation, our analysis indicates that the study of cis-cis or local epistatic interactions may have a more important role than interchromosomal interactions.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1300-3) contains supplementary material, which is available to authorized users.

Estimation of linkage disequilibrium in the Nero Siciliano Italian autochtonous breed using the Illumina 60K SNP array

Local breeds represent an important component of the overall farm animal diversity to be maintained and exploited. The new high-throughput molecular technologies allow a wide range of massive, simultaneous genomic analysis. Commercial SNP genotyping platforms are a suitable tool for the genetic characterization and the study of inter-breeds diversity. Linkage disequilibrium, the nonrandom association of alleles at different loci, has received increasing attention in recent years as a result of the availability of genome sequences and large numbers of identified SNP. This study aims to assess the genomic structure of the Nero Siciliano pig, an Italian population reared in eastern Sicily, through the analysis of the extent and range of linkage disequilibrium using the SNP analyzed through the PorcineSNP60 Genotyping BeadChip. Moreover molecular data from other four Italian breeds/populations were also included in the linkage analysis. Linkage disequilibrium may reveal much about breed history, genetic relationships and represent an extremely valuable tool in planning the marker density required to be efficient in marker assisted selection. The Nero Siciliano breed showed the lowest value of average linkage disequilibrium probably due to the lack of systematic selection strategies and variable linkage disequilibrium rates were found in different genomic regions among the analyzed populations.

Characterizing linkage disequilibrium in pig populations.

Knowledge of the extent and range of linkage disequilibrium (LD), defined as non-random association of alleles at two or more loci, in animal populations is extremely valuable in localizing genes affecting quantitative traits, identifying chromosomal regions under selection, studying population history, and characterizing/managing genetic resources and diversity. Two commonly used LD measures, r(2) and D', and their permutation based adjustments, were evaluated using genotypes of more than 6,000 pigs from six commercial lines (two terminal sire lines and four maternal lines) at ~4,500 autosomal SNPs (single nucleotide polymorphisms). The results indicated that permutation only partially removed the dependency of D' on allele frequency and that r(2) is a considerably more robust LD measure. The maximum r(2) was derived as a function of allele frequency. Using the same genotype dataset, the extent of LD in these pig populations was estimated for all possible syntenic SNP pairs using r(2) and the ratio of r(2) over its theoretical maximum. As expected, the extent of LD highest for SNP pairs was found in tightest linkage and decreased as their map distance increased. The level of LD found in these pig populations appears to be lower than previously implied in several other studies using microsatellite genotype data. For all pairs of SNPs approximately 3 centiMorgan (cM) apart, the average r(2) was equal to 0.1. Based on the average population-wise LD found in these six commercial pig lines, we recommend a spacing of 0.1 to 1 cM for a whole genome association study in pig populations.