Dataset Information

Genomic dissection of maternal, additive and non-additive genetic effects for growth and carcass traits in Nile tilapia.

ABSTRACT: BACKGROUND:The availability of both pedigree and genomic sources of information for animal breeding and genetics has created new challenges in understanding how they can be best used and interpreted. This study estimated genetic variance components based on genomic information and compared these to the variance components estimated from pedigree alone in a population generated to estimate non-additive genetic variance. Furthermore, the study examined the impact of the assumptions of Hardy-Weinberg equilibrium (HWE) on estimates of genetic variance components. For the first time, the magnitude of inbreeding depression for important commercial traits in Nile tilapia was estimated by using genomic data. RESULTS:The study estimated the non-additive genetic variance in a Nile tilapia population of full-sib families and, when present, it was almost entirely represented by additive-by-additive epistatic variance, although in pedigree studies this non-additive variance is commonly assumed to arise from dominance. For body depth (BD) and body weight at harvest (BWH), the proportion of additive-by-additive epistatic to phenotypic variance was estimated to be 0.15 and 0.17 using genomic data (P?

SUBMITTER: Joshi R

PROVIDER: S-EPMC6964056 | biostudies-literature | 2020 Jan

REPOSITORIES: biostudies-literature

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Genomic dissection of maternal, additive and non-additive genetic effects for growth and carcass traits in Nile tilapia.

Joshi Rajesh R Meuwissen Theo H E THE Woolliams John A JA Gjøen Hans M HM

Genetics, selection, evolution : GSE 20200115 1

<h4>Background</h4>The availability of both pedigree and genomic sources of information for animal breeding and genetics has created new challenges in understanding how they can be best used and interpreted. This study estimated genetic variance components based on genomic information and compared these to the variance components estimated from pedigree alone in a population generated to estimate non-additive genetic variance. Furthermore, the study examined the impact of the assumptions of Hard ...[more]

PMID: 31941436

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Project description:BackgroundAs pre-cut and pre-packaged chilled meat becomes increasingly popular, integrating the carcass-cutting process into the pig industry chain has become a trend. Identifying quantitative trait loci (QTLs) of pork cuts would facilitate the selection of pigs with a higher overall value. However, previous studies solely focused on evaluating the phenotypic and genetic parameters of pork cuts, neglecting the investigation of QTLs influencing these traits. This study involved 17 pork cuts and 12 morphology traits from 2,012 pigs across four populations genotyped using CC1 PorcineSNP50 BeadChips. Our aim was to identify QTLs and evaluate the accuracy of genomic estimated breed values (GEBVs) for pork cuts.ResultsWe identified 14 QTLs and 112 QTLs for 17 pork cuts by GWAS using haplotype and imputation genotypes, respectively. Specifically, we found that HMGA1, VRTN and BMP2 were associated with body length and weight. Subsequent analysis revealed that HMGA1 primarily affects the size of fore leg bones, VRTN primarily affects the number of vertebrates, and BMP2 primarily affects the length of vertebrae and the size of hind leg bones. The prediction accuracy was defined as the correlation between the adjusted phenotype and GEBVs in the validation population, divided by the square root of the trait's heritability. The prediction accuracy of GEBVs for pork cuts varied from 0.342 to 0.693. Notably, ribs, boneless picnic shoulder, tenderloin, hind leg bones, and scapula bones exhibited prediction accuracies exceeding 0.600. Employing better models, increasing marker density through genotype imputation, and pre-selecting markers significantly improved the prediction accuracy of GEBVs.ConclusionsWe performed the first study to dissect the genetic mechanism of pork cuts and identified a large number of significant QTLs and potential candidate genes. These findings carry significant implications for the breeding of pork cuts through marker-assisted and genomic selection. Additionally, we have constructed the first reference populations for genomic selection of pork cuts in pigs.

Project description:BackgroundCurrently, meat cut traits are integrated in pig breeding objectives to gain extra profit. However, little is known about the heritability of meat cut proportions (MCP) and their correlations with other traits. The aims of this study were to assess the heritability and genetic correlation of MCP with carcass and meat quality traits using single nucleotide polymorphism chips and conduct a genome-wide association study (GWAS) to identify candidate genes for MCP.ResultsSeventeen MCP, 12 carcass, and seven meat quality traits were measured in 2012 pigs from four populations (Landrace; Yorkshire; Landrace and Yorkshire hybrid pigs; Duroc, and Landrace and Yorkshire hybrid pigs). Estimates of the heritability for MCP ranged from 0.10 to 0.55, with most estimates being moderate to high and highly consistent across populations. In the combined population, the heritability estimates for the proportions of scapula bone, loin, back fat, leg bones, and boneless picnic shoulder were 0.44 ± 0.04, 0.36 ± 0.04, 0.44 ± 0.04, 0.38 ± 0.04, and 0.39 ± 0.04, respectively. Proportion of middle cuts was genetically significantly positively correlated with intramuscular fat content and backfat depth. Proportion of ribs was genetically positively correlated with carcass oblique length and straight length (0.35 ± 0.08 to 0.45 ± 0.07) and negatively correlated with backfat depth (- 0.26 ± 0.10 to - 0.45 ± 0.10). However, weak or nonsignificant genetic correlations were observed between most MCP, indicating their independence. Twenty-eight quantitative trait loci (QTL) for MCP were detected by GWAS, and 24 new candidate genes related to MCP were identified, which are involved with growth, height, and skeletal development. Most importantly, we found that the development of the bones in different parts of the body may be regulated by different genes, among which HMGA1 may be the strongest candidate gene affecting forelimb bone development. Moreover, as previously shown, VRTN is a causal gene affecting vertebra number, and BMP2 may be the strongest candidate gene affecting hindlimb bone development.ConclusionsOur results indicate that breeding programs for MCP have the potential to enhance carcass composition by increasing the proportion of expensive cuts and decreasing the proportion of inexpensive cuts. Since MCP are post-slaughter traits, the QTL and candidate genes related to these traits can be used for marker-assisted and genomic selection.

Project description:Swine industry breeding goals are mostly directed towards meat quality and carcass traits due to their high economic value. Yet, studies on meat quality and carcass traits including both phenotypic and genotypic information remain limited, particularly in commercial crossbred swine. The objectives of this study were to estimate the heritabilities for different carcass composition traits and meat quality traits and to estimate the genetic and phenotypic correlations between meat quality, carcass composition, and growth traits in 2 large commercial swine populations: The Maschhoffs LLC (TML) and Smithfield Premium Genetics (SPG), using genotypes and phenotypes data. The TML data set consists of 1,254 crossbred pigs genotyped with 60K SNP chip and phenotyped for meat quality, carcass composition, and growth traits. The SPG population included over 35,000 crossbred pigs phenotyped for meat quality, carcass composition, and growth traits. For TML data sets, the model included fixed effects of dam line, contemporary group (CG), gender, as well as random additive genetic effect and pen nested within CG. For the SPG data set, fixed effects included parity, gender, and CG, as well as random additive genetic effect and harvest group. Analyses were conducted using BLUPF90 suite of programs. Univariate and bivariate analyses were implemented to estimate heritabilities and correlations among traits. Primal yield traits were uniquely created in this study. Heritabilities [high posterior density interval] of meat quality traits ranged from 0.08 [0.03, 0.16] for pH and 0.08 [0.03, 0.1] for Minolta b* to 0.27 [0.22, 0.32] for marbling score, except intramuscular fat with the highest estimate of 0.52 [0.40, 0.62]. Heritabilities of primal yield traits were higher than that of primal weight traits and ranged from 0.17 [0.13, 0.25] for butt yield to 0.45 [0.36, 0.55] for ham yield. The genetic correlations of meat quality and carcass composition traits with growth traits ranged from moderate to high in both directions. High genetic correlations were observed for male and female for all traits except pH. The genetic parameter estimates of this study indicate that a multitrait approach should be considered for selection programs aimed at meat quality and carcass composition in commercial swine populations.

Project description:Nile tilapia (Oreochromis niloticus) is a globally significant aquaculture species rapidly gaining status as a farmed commodity. In West Africa, wild Nile tilapia genetic resources are abundant yet knowledge of fine-scale population structure and patterns of natural genetic variation are limited. Coinciding with this is a burgeoning growth in tilapia aquaculture in Ghana and other countries within the region underpinned by locally available genetic resources. Using 192 single nucleotide polymorphism (SNP) markers this study conducted a genetic survey of Nile tilapia throughout West Africa, sampling 23 wild populations across eight countries (Benin, Burkina Faso, Côte d'Ivoire, Ghana, Togo, Mali, Gambia and Senegal), representing the major catchments of the Volta, Niger, Senegal and Gambia River basins. A pattern of isolation-by-distance and significant spatial genetic structure was identified throughout West Africa (Global FST = 0.144), which largely corresponds to major river basins and, to a lesser extent, sub-basins. Two populations from the Gambia River (Kudang and Walekounda), one from the western Niger River (Lake Sélingué) and one from the upper Red Volta River (Kongoussi) showed markedly lower levels of diversity and high genetic differentiation compared to all other populations, suggesting genetically isolated populations occurring across the region. Genetic structure within the Volta Basin did not always follow the pattern expected for sub-river basins. This study identifies clear genetic structuring and differentiation amongst West African Nile tilapia populations, which concur with broad patterns found in previous studies. In addition, we provide new evidence for fine-scale genetic structuring within the Volta Basin and previously unidentified genetic differences of populations in Gambia. The 192 SNP marker suite used in this study is a useful tool for differentiating tilapia populations and we recommend incorporating this marker suite into future population screening of O. niloticus. Our results form the basis of a solid platform for future research on wild tilapia genetic resources in West Africa, and the identification of potentially valuable germplasm for use in ongoing breeding programs for aquaculture.

Dataset Information

Genomic dissection of maternal, additive and non-additive genetic effects for growth and carcass traits in Nile tilapia.

Publications

Genomic dissection of maternal, additive and non-additive genetic effects for growth and carcass traits in Nile tilapia.

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