BackgroundDespite many success stories of genome wide association studies (GWAS), challenges exist in QTL detection especially in datasets with many levels of relatedness. In this study we compared four methods of GWA on a dataset simulated for the 15th QTL-MAS workshop. The four methods were 1) Mixed model analysis (MMA), 2) Random haplotype model (RHM), 3) Genealogy-based mixed model (GENMIX), and 4) Bayesian variable selection (BVS). The data consisted of phenotypes of 2000 animals from 20 sire families and were genotyped with 9990 SNPs on five chromosomes.ResultsOut of the eight simulated QTL, these four methods MMA, RHM, GENMIX and BVS identified 6, 6, 8 and 7 QTL respectively and 4 QTL were common across the methods. GENMIX had the highest power to detect QTL however it also produced 4 false positives. BVS was the second best method in terms of power, detecting all QTL except the one on chromosome 5 with epistatic interaction. Two spurious associations were obtained across methods. Though all the methods considered the full pedigree in the analyses, it was not sufficient to avoid all the spurious associations arising due to family structure.ConclusionsUsing several methods with divergent approaches for GWAS can be useful in gaining confidence on the QTL identified. In our comparison, GENMIX was found to be the best method in terms of power but it needs appropriate correction for multiple testing to avoid the false positives. This study shows that the issues of multiple testing and the relatedness among study samples need special attention in GWAS.
A major part of the growth performance in birds is the result of the combined effects of genes, including the general and specific combining ability that requires the design of an optimal mating system. The aim of this study was to fit the best model for each body weight trait from hatch to 45 days and the estimation of the variance components and the genetic parameters for the body weight traits of a crossbred population. This crossbred population was created by 4 strains of Japanese quail, including the Italian Speckled (A), Tuxedo (B), Pharaoh (C), A&M Texas (D), and the body weights of the different combinations were analyzed by 24 models including the direct genetic effect, the non-additive genetic effects including dominance and epistatic effects, the maternal permanent environmental and maternal genetic effects. The selection of the best fit model of each trait was performed based on the deviance information criteria. The variance components were estimated using a single-trait animal model analyzed with Gibbs sampling. At the early stage of bird growth, maternal genetic and maternal permanent environmental effects had a considerable contribution to the best model, but the contribution of these effects reduced with an increase in the bird's age and the additive variance contribution increased. Adding non-additive genetic effects (dominance and epistasis) to the models significantly reduced the variance of the error and the additive genetic variance estimated with high accuracy. The estimated heritability of body weight traits for the body weights of hatch, 5, 10, 15, 20, 25, 30, 35, 40, and 45 d were 0.316, 0.170, 0.251, 0.153, 0.132, 0.164, 0.290, 0.425, 0.476, and 0.362, respectively. The ratio of maternal genetic and maternal permanent environmental was considerable especially on early age body weight but the ratio of dominance and epistatic variances on each of the body weight traits was less than 4.5% of the total variance, but led to a more accurate estimates of the direct additive genetic.
In order to evaluate some physical and qualitative characteristics of Naeini sheep wool for using in textile industry, herds from 6 different regions of Isfahan province were chosen. Staple length from 3 different body parts (shoulder, side and britch) was measured prior to shearing. Wool samples were taken from a 100 cm2 surface on the mid-side of the Animals. Then the samples were transferred to the Laboratory of Animal Sciences for evaluations of some quality characteristics and to the Fiber Physics Laboratory for measuring tenacity, breaking strength and elongation at break of fibers. The means and standard deviations of staple length were estimated (10.8 +/- 2.36), (9.71 +/- 3.14) and (10.99 +/- 2.49) cm for shoulder, side and britch parts, respectively. The total average staple length of Naeini sheep (10.5 cm) is suitable for using in textile industry. Wool fibers of Naeini sheep have desirable tenacity and breaking strength (1.22 cN/dtex and 13.76 centi-Newton) to resist against mechanical tensions of the spinning step. However, Naeini sheep wool fibers have an adequate, but not a desirable % elongation at break (28.6%). Based on the fiber diameter mean of Naeini sheep and its variation (28.51 +/- 4.33 microm) the fleece grade of Naeini sheep was predicted 54's, which is an intermediate grade. However, by conducting breeding programs toward enhancing fleece grade, Naeini sheep wool will be simply applicable in textile industry.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
hi@scite.ai
10624 S. Eastern Ave., Ste. A-614
Henderson, NV 89052, USA
Copyright © 2024 scite LLC. All rights reserved.
Made with 💙 for researchers
Part of the Research Solutions Family.