scholarly journals Identification of QTL regions and candidate genes for growth and feed efficiency in broilers

2021 ◽  
Vol 53 (1) ◽  
Author(s):  
Wei Li ◽  
Maiqing Zheng ◽  
Guiping Zhao ◽  
Jie Wang ◽  
Jie Liu ◽  
...  
Keyword(s):  
Body Weight ◽  
Candidate Genes ◽  
Feed Intake ◽  
Feed Efficiency ◽  
Genetic Variance ◽  
Significant Snps ◽  
Abdominal Fat ◽  
Chromosome 1 ◽  
Thigh Muscle ◽  
Genome Wide

Abstract Background Feed accounts for about 70% of the total cost of poultry meat production. Residual feed intake (RFI) has become the preferred measure of feed efficiency because it is phenotypically independent of growth rate and body weight. In this study, our aim was to estimate genetic parameters and identify quantitative trait loci (QTL) for feed efficiency in 3314 purebred broilers using a genome-wide association study. Broilers were genotyped using a custom 55 K single nucleotide polymorphism (SNP) array. Results Estimates of genomic heritability for seven growth and feed efficiency traits, including body weight at 28 days of age (BW28), BW42, average daily feed intake (ADFI), RFI, and RFI adjusted for weight of abdominal fat (RFIa), ranged from 0.12 to 0.26. Eleven genome-wide significant SNPs and 15 suggestively significant SNPs were detected, of which 19 clustered around two genomic regions. A region on chromosome 16 (2.34–2.66 Mb) was associated with both BW28 and BW42, and the most significant SNP in this region, AX_101003762, accounted for 7.6% of the genetic variance of BW28. The other region, on chromosome 1 (91.27–92.43 Mb) was associated with RFI and ADFI, and contains the NSUN3 and EPHA6 as candidate genes. The most significant SNP in this region, AX_172588157, accounted for 4.4% of the genetic variance of RFI. In addition, a genomic region containing the gene AGK on chromosome 1 was found to be associated with RFIa. The NSUN3 and AGK genes were found to be differentially expressed in breast muscle, thigh muscle, and abdominal fat between male broilers with high and low RFI. Conclusions We identified QTL regions for BW28 and BW42 (spanning 0.32 Mb) and RFI (spanning 1.16 Mb). The NSUN3, EPHA6, and AGK were identified as the most likely candidate genes for these QTL. These genes are involved in mitochondrial function and behavioral regulation. These results contribute to the identification of candidate genes and variants for growth and feed efficiency in poultry.

scholarly journals New insights from genome-wide association analysis using imputed whole-genome sequence: the genetic mechanisms underlying residual feed intake in chickens

2019 ◽  
Author(s):  
Shaopan Ye ◽  
Zitao Chen ◽  
Rongrong Zheng ◽  
Shuqi Diao ◽  
Jinyan Teng ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Feed Intake ◽  
Feed Efficiency ◽  
Significant Snps ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Environmental Footprint ◽  
Genome Wide ◽  
Component Traits ◽  
Genetic Mechanisms

Abstract Background: Poultry feed occupies the largest cost of poultry production, which is estimated up to 70%. Moreover, it is pressure on the agricultural industry to reduce emissions and improve its environmental footprint, simultaneously increasing output to meet the growing demand for protein worldwide. Therefore, improving feed efficiency (FE) play an important role to improve profits and their environmental footprint in broiler production. In this study, using imputed whole genome sequencing (WGS) data, genome-wide association analysis (GWAS) was performed to identify SNPs and genes associated with residual feed intake (RFI) and its component traits. Furthermore, transcriptomic analysis between high- and low-RFI groups was performed to validate candidate genes from GWAS. Results: Results showed that heritability estimates of average daily gain (ADG), average daily feed intake (ADFI) , and RFI were 0.29 (0.004), 0.37 (0.005), and 0.38 (0.004), respectively. Using imputed sequence-based GWAS, we identified seven significant SNPs and five candidate genes ( MTSS I-BAR domain containing 1, MTSS1; folliculin, FLCN; COP9 signalosome subunit 3, COPS3; 5',3'-nucleotidase, mitochondrial, NT5M; and gametocyte specific factor 1, GTSF1) associated with RFI, twenty significant SNPs and one candidate gene ( inositol polyphosphate multikinase, IPMK ) associated with ADG, and one significant SNP and one candidate gene ( coatomer protein complex subunit alpha, COPA ) associated with ADFI. After performing transcriptomic analysis between high- and low-RFI groups, both 38 up-regulated and 26 down-regulated genes were identified in high-RFI group. Furthermore, integrating regional conditional GWAS and transcriptome analysis, ras related dexamethasone induced 1 (RASD1) was the only one overlapped gene associated with RFI, which also suggested that the region (GGA14: 4767015 -4882318) is a new quantitative trait locus (QTL) associated with RFI. Conclusions: In conclusions, using imputed sequence-based GWAS is an efficient method to identify significant SNPs and candidate genes in chicken. Our results provide valuable insights into the genetic mechanisms of RFI and component traits, which would further improve the genetic gain of feed efficiency rapidly and cost-effectively in the context of marker-assisted breeding selection. Keywords: Whole genome sequence, GWAS, transcriptome analysis, feed efficiency, chickens.

scholarly journals PSIII-16 Genome-wide association mapping and functional analysis of body weight, feed intake and walking ability in turkeys

2020 ◽  
Vol 98 (Supplement_4) ◽  
pp. 234-235
Author(s):  
Emhimad Abdalla ◽  
Bayode Makanjuola ◽  
Benjamin Wood ◽  
Christine F Baes ◽  
Ryley J Vanderhout
Keyword(s):  
Gene Ontology ◽  
Body Weight ◽  
Feed Intake ◽  
Growth Traits ◽  
Gene Set Enrichment Analysis ◽  
Genome Wide Association ◽  
Chromosome 1 ◽  
Walking Ability ◽  
Genome Wide ◽  
The Impact

Abstract The underlying genetic mechanisms affecting turkey growth traits have not been widely investigated. Over the last few years, genome-wide association studies (GWAS) became the de facto approach to identify candidate regions associated with complex phenotypes and diseases in livestock. In the present study, we performed GWAS to identify regions associated with growth traits, feed intake and walking ability in a breeding turkey line. This was followed by studying the functional evidence that may support the impact of those regions on the economic traits in turkeys. A total of 31,950 phenotypic records for body weight, feed intake and walking ability with genomic (56,393 SNP) data were provided by Hybrid Turkeys, Kitchener, Canada. The analysis was carried out using a mixed linear model with hatch-week-year and sex fitted as fixed effects and the accumulated effect of all markers captured by the genomic relationship matrix fitted as random polygenic effects. Significant markers were observed on several chromosomes across the turkey genome. For example, COL8A1 and RBPMS2 genes were identified on chromosome 1 and 12, respectively, and associated with body weight. Furthermore, a gene-set enrichment analysis was performed for each trait. These functional and positional analyses uncovered a number of gene ontology functional terms, Reactome pathways and Medical Subject Headings that showed significant enrichment of genes associated with the studied traits. Many of the observed gene ontology functional terms (e.g., skeletal muscle tissue growth, regulation of digestive system process, and adult walking behavior) are known to be related to body growth, feed intake and walking ability. The results of this study revealed novel candidate genomic regions and candidate genes that could be managed within a turkey breeding program.

scholarly journals Association of residual feed intake with growth performance, carcass traits, meat quality, and blood variables in native chickens

2020 ◽  
Vol 98 (7) ◽  
Author(s):  
Lei Yang ◽  
Xiaolong Wang ◽  
Tingting He ◽  
Fengliang Xiong ◽  
Xianzhen Chen ◽  
...  
Keyword(s):  
Body Weight ◽  
Growth Performance ◽  
Meat Quality ◽  
Feed Intake ◽  
Feed Efficiency ◽  
Carcass Traits ◽  
Plasma Concentrations ◽  
Abdominal Fat ◽  
Native Chickens ◽  
Blood Variables

Abstract Improving feed efficiency is a primary goal in poultry breeding strategies. Residual feed intake (RFI) in chickens typically calculated during the growing period is a measure of feed efficiency that is independent of the level of production. The objective of this study was to evaluate phenotypic correlations of growth performance, carcass traits, meat quality, and blood variables with RFI in growing native chickens. A total of 1,008 chickens were selected for the experiment to derive RFI. After the RFI measurement period of 42 d, 25 chickens with low RFI values, 25 chickens with medium RFI values, and 25 chickens with high RFI values were selected. The RFI was significantly positively correlated with feed conversion ratio and average daily feed intake, while it was not significantly correlated with initial body weight (BW), final BW, average daily body weight gain, and metabolic BW0.75. The abdominal fat weight and yield of high RFI group were significantly greater than those of medium and low RFI groups, and the abdominal fat yield was significantly positively correlated with RFI. Moreover, the plasma insulin-like growth factor 1 (IGF-1) content of low RFI group was significantly greater than those of high and medium RFI groups. The plasma concentrations of adrenocorticotropic hormone, triiodothyronine (T3), and cortisol of high RFI birds were significantly greater than that of low RFI birds. RFI was significantly positively correlated with plasma concentrations of T3 and cortisol, while it was significantly negatively correlated with plasma concentration of IGF-1. In addition, the serum levels of glucose and triglyceride of high RFI birds were significantly lower than that of low RFI birds. The serum low-density lipoprotein cholesterol (LDL-C) content of high RFI group was significantly greater than that of medium and low RFI groups, and it was significantly positively correlated with RFI. Our data suggested that selection of chickens with low RFI values may be beneficial to reduce fat deposition in native chickens without affecting the meat quality. Circulating IGF-1, T3, cortisol, and LDL-C concentrations can be used as indirect selection indicators of feed efficiency in native chickens. The effect of IGF-1, T3, cortisol, and LDL-C on feed efficiency of native chickens should be carefully examined and validated in future breeding programs.

scholarly journals Identification of Major Loci and Candidate Genes for Meat Production-Related Traits in Broilers

2021 ◽  
Vol 12 ◽  
Author(s):  
Xinting Yang ◽  
Jiahong Sun ◽  
Guiping Zhao ◽  
Wei Li ◽  
Xiaodong Tan ◽  
...  
Keyword(s):  
Candidate Gene ◽  
Genetic Variance ◽  
Carcass Traits ◽  
Significant Snps ◽  
Major Effect ◽  
Carcass Composition ◽  
Thigh Muscle ◽  
Meat Production ◽  
Muscle Weight ◽  
Genome Wide

BackgroundCarcass traits are crucial characteristics of broilers. However, the underlying genetic mechanisms are not well understood. In the current study, significant loci and major-effect candidate genes affecting nine carcass traits related to meat production were analyzed in 873 purebred broilers using an imputation-based genome-wide association study.ResultsThe heritability estimates of nine carcass traits, including carcass weight, thigh muscle weight, and thigh muscle percentage, were moderate to high and ranged from 0.21 to 0.39. Twelve genome-wide significant SNPs and 118 suggestively significant SNPs of 546,656 autosomal variants were associated with carcass traits. All SNPs for six weight traits (body weight at 42 days of age, carcass weight, eviscerated weight, whole thigh weight, thigh weight, and thigh muscle weight) were clustered around the 24.08 Kb region (GGA24: 5.73–5.75 Mb) and contained only one candidate gene (DRD2). The most significant SNP, rs15226023, accounted for 4.85–7.71% of the estimated genetic variance of the six weight traits. The remaining SNPs for carcass composition traits (whole thigh percentage and thigh percentage) were clustered around the 42.52 Kb region (GGA3: 53.03–53.08 Mb) and contained only one candidate gene (ADGRG6). The most significant SNP in this region, rs13571431, accounted for 11.89–13.56% of the estimated genetic variance of two carcass composition traits. Some degree of genetic differentiation in ADGRG6 between large and small breeds was observed.ConclusionWe identified one 24.08 Kb region for weight traits and one 42.52 Kb region for thigh-related carcass traits. DRD2 was the major-effect candidate gene for weight traits, and ADGRG6 was the major-effect candidate gene for carcass composition traits. Our results supply essential information for causative mutation identification of carcass traits in broilers.

scholarly journals PSVIII-38 Late-Breaking Abstract: Estimating genetic parameters of feed efficiency traits in American mink

2020 ◽  
Vol 98 (Supplement_4) ◽  
pp. 347-347
Author(s):  
Pourya Davoudi ◽  
Duy Ngoc Do ◽  
Guoyu Hu ◽  
Siavash Salek Ardestani ◽  
Younes Miar
Keyword(s):  
Body Weight ◽  
Genetic Correlation ◽  
Feed Intake ◽  
Feed Efficiency ◽  
Fixed Effects ◽  
Genetic Parameters ◽  
American Mink ◽  
Genetic Correlations ◽  
Final Body Weight ◽  
Selection For

Abstract Feed cost is the major input cost in the mink industry and thus improvement of feed efficiency through selection for high feed efficient mink is necessary for the mink farmers. The objective of this study was to estimate the heritability, phenotypic and genetic correlations for different feed efficiency measures, including final body weight (FBW), daily feed intake (DFI), average daily gain (ADG), feed conversion ratio (FCR) and residual feed intake (RFI). For this purpose, 1,088 American mink from the Canadian Center for Fur Animal Research at Dalhousie Faculty of Agriculture were recorded for daily feed intake and body weight from August 1 to November 14 in 2018 and 2019. The univariate models were used to test the significance of sex, birth year and color as fixed effects, and dam as a random effect. Genetic parameters were estimated via bivariate models using ASReml-R version 4. Estimates of heritabilities (±SE) were 0.41±0.10, 0.37±0.11, 0.33±0.14, 0.24±0.09 and 0.22±0.09 for FBW, DFI, ADG, FCR and RFI, respectively. The genetic correlation (±SE) was moderate to high between FCR and RFI (0.68±0.15) and between FCR and ADG (-0.86±0.06). In addition, RFI had low non-significant (P > 0.05) genetic correlations with ADG (0.04 ± 0.26) and BW (0.16 ± 0.24) but significant (P < 0.05) high genetic correlation with DFI (0.74 ± 0.11) indicating that selection for lower RFI will reduce feed intake without adverse effects on the animal size and growth rate. The results suggested that RFI can be implemented in genetic/genomic selection programs to reduce feed intake in the mink production system.

Genetic and phenotypic parameter estimates between production, feed intake, feed efficiency, body weight and linear type traits in first lactation Holsteins

1999 ◽  
Vol 79 (4) ◽  
pp. 425-431 ◽  
Author(s):  
B. W. Kennedy ◽  
J. C. M. Dekkers ◽  
R. K. Moore ◽  
L. Jairath
Keyword(s):  
Body Weight ◽  
Body Size ◽  
Total Energy ◽  
Energy Intake ◽  
Milk Yield ◽  
Feed Intake ◽  
Feed Efficiency ◽  
Genetic Correlations ◽  
Total Energy Intake ◽  
Type Traits

Production and feed intake data on 36 115 first lactation Holstein cows obtained from Quebec Dairy Herd Analysis Service were combined with conformation data from the Holstein Association of Canada to estimate genetic correlations among production, energy intake, and conformation traits. Traits considered were 305-d milk yield, 305-d grain energy and total energy intake, feed efficiency (fat corrected milk yield/total energy intake), body weight at calving, capacity, size, stature, rump width and final score. Genetic and phenotypic parameters were estimated using Restricted Maximum Likelihood based on two-trait animal mixed model analyses. The model contained fixed effects of herd-year, season of calving, age of calving, sire group and a random animal genetic effect. Estimates of heritability were within the published range for all traits. Of the conformation traits examined, capacity, size and stature had the highest correlations with body weight, with phenotypic correlations between 0.36 and 0.43, and genetic correlations between 0.61 and 0.79. Feed efficiency was negatively correlated to all body size measures, both phenotypically (−0.01 to −0.29) and genetically (−0.31 to −0.53), but most significantly with body weight, capacity, size, and stature. Fat-corrected milk yield showed negligible phenotypic and low to moderately negative genetic (−0.07 to −0.29) correlations with body weight and related type traits. Total energy intake was positively related to all measures of body size, most notably body weight, while grain energy intake had moderately negative genetic correlations (−0.20 to −0.40) with the same body size traits. Because of their detrimental relationships with feed efficiency, negative selection emphasis should be placed on body weight and the related type traits capacity, size and stature. Capacity, size and stature are of moderate utility when selecting indirectly for body weight, total energy intake and feed efficiency. Key words: Dairy cattle, genetics, production, conformation, feed efficiency

scholarly journals 434 Late-Breaking: Expression of Growth hormone Gene (GH) and Insulin-like growth factor (IGF-2) in metabolic tissues of pigs are affected by unconventional dietary feed sources

2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 42-43
Author(s):  
Ufuoma G Sorhue ◽  
Ikenna Omeje ◽  
Ifeanyichukwu udeh ◽  
Adimabua M Moemeka ◽  
Raphael E Onainor
Keyword(s):  
Growth Hormone ◽  
Body Weight ◽  
Weight Gain ◽  
Growth Factor ◽  
Feed Intake ◽  
Feed Efficiency ◽  
Conversion Ratio ◽  
Feed Conversion Ratio ◽  
Growth Hormone Gene ◽  
Feed Conversion

Abstract This study was conducted to examine the growth performance and expression patterns of growth hormone gene and insulin-like growth factor in metabolic tissues of pigs fed different unconventional feed sources. A total of 45 growing pigs were randomly assigned to 5 dietary treatments at 9 animals per treatment and 3 animals per replicate. Treatment one (T1) comprise of whole maize (WM) which served as the control, T2: brewers dried grain (BDG), T3: cassava peel meal (CPM), T4: plantain peel meal (PPM) and T5: corn husk meal (CHM) at 35% inclusion in the diet. Data collected and analyzed includes; initial body weight (IBW), final body weight (FBW), average daily feed intake (ADFI), average daily weight gain (ADG), feed conversion ratio (FCR) and feed efficiency (FE). At the end of the feeding trial, three animals per treatment (one animal per replicate) were slaughtered; the duodenum and liver were collected and stored using RNALater prior to RNA extraction. Real-time qPCR was performed in 40cycles using the PowerUp SYBR Green reagent and analysed using the Delta-Delta Ct method. All data were subjected to analysis of variance in a completely randomized design. The results showed that the treatment diets had effect on growth performance with significant differences (P < 0.05) observed for average final weight, average total weight gain, average daily feed intake, feed conversion ratio and feed efficiency while the initial weight were not significantly different (P > 0.05). IGF-2 was differentially expressed in the liver and duodenum across treatments while significant differences were not observed in the expression pattern of the growth hormone gene in both tissues. This study showed promise for the use of unconventional feeding stuffs in pig feeding and reveals that genes influencing performance characters are differentially expressed in relation to the source of unconventional feeds used in compounding pig diet.

scholarly journals A multi-breed GWAS for morphometric traits in four Beninese indigenous cattle breeds reveals loci associated with conformation, carcass and adaptive traits

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Sèyi Fridaïus Ulrich Vanvanhossou ◽  
Carsten Scheper ◽  
Luc Hippolyte Dossa ◽  
Tong Yin ◽  
Kerstin Brügemann ◽  
...  
Keyword(s):  
Immune Response ◽  
Candidate Genes ◽  
Feed Efficiency ◽  
Morphological Traits ◽  
Carcass Traits ◽  
Potential Candidate ◽  
Adaptive Traits ◽  
Morphometric Traits ◽  
Indigenous Cattle ◽  
Genome Wide

Abstract Background Specific adaptive features including disease resistance and growth abilities in harsh environments are attributed to indigenous cattle breeds of Benin, but these breeds are endangered due to crossbreeding. So far, there is a lack of systematic trait recording, being the basis for breed characterizations, and for structured breeding program designs aiming on conservation. Bridging this gap, own phenotyping for morphological traits considered measurements for height at withers (HAW), sacrum height (SH), heart girth (HG), hip width (HW), body length (BL) and ear length (EL), including 449 cattle from the four indigenous Benin breeds Lagune, Somba, Borgou and Pabli. In order to utilize recent genomic tools for breed characterizations and genetic evaluations, phenotypes for novel traits were merged with high-density SNP marker data. Multi-breed genetic parameter estimations and genome-wide association studies (GWAS) for the six morphometric traits were carried out. Continuatively, we aimed on inferring genomic regions and functional loci potentially associated with conformation, carcass and adaptive traits. Results SNP-based heritability estimates for the morphometric traits ranged between 0.46 ± 0.14 (HG) and 0.74 ± 0.13 (HW). Phenotypic and genetic correlations ranged from 0.25 ± 0.05 (HW-BL) to 0.89 ± 0.01 (HAW-SH), and from 0.14 ± 0.10 (HW-BL) to 0.85 ± 0.02 (HAW-SH), respectively. Three genome-wide and 25 chromosome-wide significant SNP positioned on different chromosomes were detected, located in very close chromosomal distance (±25 kb) to 15 genes (or located within the genes). The genes PIK3R6 and PIK3R1 showed direct functional associations with height and body size. We inferred the potential candidate genes VEPH1, CNTNAP5, GYPC for conformation, growth and carcass traits including body weight and body fat deposition. According to their functional annotations, detected potential candidate genes were associated with stress or immune response (genes PTAFR, PBRM1, ADAMTS12) and with feed efficiency (genes MEGF11 SLC16A4, CCDC117). Conclusions Accurate measurements contributed to large SNP heritabilities for some morphological traits, even for a small mixed-breed sample size. Multi-breed GWAS detected different loci associated with conformation or carcass traits. The identified potential candidate genes for immune response or feed efficiency indicators reflect the evolutionary development and adaptability features of the breeds.

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