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 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 The Ghrelin Receptor (Ghsr) Gene Polymorphism in Indonesian Local Chicken and Crossbreed Is Associated With Carcass Traits

2018 ◽  
Vol 19 (2) ◽  
pp. 71
Author(s):  
Isyana Khaerunnisa ◽  
Jakaria Jakaria ◽  
Irma Isnafia Arief ◽  
Cahyo Budiman ◽  
Cece Sumantri
Keyword(s):  
Growth Hormone ◽  
Gene Polymorphism ◽  
Candidate Gene ◽  
Carcass Traits ◽  
Carcass Composition ◽  
Growth Hormone Secretagogue ◽  
Ghrelin Receptor ◽  
Chicken Carcass ◽  
Parent Stock ◽  
Local Chicken

Ghrelin receptor (GHSR) gene is candidate gene for growth performance in chicken by modulating growth hormone release from the pituitary by binding to its ligand of ghrelin. Ghrelin gene, or growth hormone secretagogue (GHS) gene, is well known as feed intake and energy homeostasis regulator in mammals and birds. The objectives of this study were to identify the polymorphism of the T1857C GHSR locus in Indonesian local chicken and to evaluate its effects on carcass traits. The gene polymorphism was identified using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) using Hin6I restriction enzyme. Effect of genotype on carcass composition was analyzed using SAS General Linear Model (GLM) procedure. The genotyping was performed on 343 individuals including Merawang, Pelung, Sentul, Kampung, broiler (strain Cobb, parent stock), F1 crossbred of Kampung x broiler (strain Cobb, parent stock), and F2 crossbred of Kampung x broiler (strain Cobb, parent stock). All individuals were successfully amplified and were resulted in a 470 bp PCR product. This locus was polymorphic with two alleles (T and C) and three genotypes (TT, CT, and CC). The T allele and TT genotype were predominant in all populations. Individuals with CT genotype were significantly had higher live weight at 26w, carcass weight, commercial cuts weights, and muscles weights than TT genotype in F2 crossbred of Kampung x broiler population. Association of the T1857C GHSR locus-polymorphism with chicken carcass composition has been described in Indonesian chicken, providing evidence that GHSR might be an important candidate gene for chicken carcass traits.

scholarly journals Genome-wide association study reveals the genetic determinism of growth traits in a Gushi-Anka F2 chicken population

Heredity ◽  
2020 ◽  
Author(s):  
Yanhua Zhang ◽  
Yuzhe Wang ◽  
Yiyi Li ◽  
Junfeng Wu ◽  
Xinlei Wang ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Growth Traits ◽  
Carcass Traits ◽  
Significant Snps ◽  
Genome Wide Association ◽  
Pathway Enrichment Analysis ◽  
Genome Wide ◽  
A Genome ◽  
Genetic Mechanisms

Abstract Chicken growth traits are economically important, but the relevant genetic mechanisms have not yet been elucidated. Herein, we performed a genome-wide association study to identify the variants associated with growth traits. In total, 860 chickens from a Gushi-Anka F2 resource population were phenotyped for 68 growth and carcass traits, and 768 samples were genotyped based on the genotyping-by-sequencing (GBS) method. Finally, 734 chickens and 321,314 SNPs remained after quality control and removal of the sex chromosomes, and these data were used to carry out a GWAS analysis. A total of 470 significant single-nucleotide polymorphisms (SNPs) for 43 of the 68 traits were detected and mapped on chromosomes (Chr) 1–6, -9, -10, -16, -18, -23, and -27. Of these, the significant SNPs in Chr1, -4, and -27 were found to be associated with more than 10 traits. Multiple traits shared significant SNPs, indicating that the same mutation in the region might have a large effect on multiple growth or carcass traits. Haplotype analysis revealed that SNPs within the candidate region of Chr1 presented a mosaic pattern. The significant SNPs and pathway enrichment analysis revealed that the MLNR, MED4, CAB39L, LDB2, and IGF2BP1 genes could be putative candidate genes for growth and carcass traits. The findings of this study improve our understanding of the genetic mechanisms regulating chicken growth and carcass traits and provide a theoretical basis for chicken breeding programs.

scholarly journals QTL mapping for growth and carcass traits in an Iberian by Landrace pig intercross: additive, dominant and epistatic effects

2002 ◽  
Vol 80 (2) ◽  
pp. 145-154 ◽  
Author(s):  
L. VARONA ◽  
C. OVILO ◽  
A. CLOP ◽  
J. L. NOGUERA ◽  
M. PÉREZ-ENCISO ◽  
...  
Keyword(s):  
Carcass Traits ◽  
Live Weight ◽  
Carcass Composition ◽  
Backfat Thickness ◽  
Longissimus Muscle ◽  
Muscle Area ◽  
Phenotypic Data ◽  
Genome Wide ◽  
A Genome ◽  
Set Up

Results from a QTL experiment on growth and carcass traits in an experimental F2 cross between Iberian and Landrace pigs are reported. Phenotypic data for growth, length of carcass and muscle mass, fat deposition and carcass composition traits from 321 individuals corresponding to 58 families were recorded. Animals were genotyped for 92 markers covering the 18 porcine autosomes (SSC). The results from the genomic scan show genomewide significant QTL in SSC2 (longissimus muscle area and backfat thickness), SSC4 (length of carcass, backfat thickness, loin, shoulder and belly bacon weights) and SSC6 (longissimus muscle area, backfat thickness, loin, shoulder and belly bacon weights). Suggestive QTL were also found on SSC1, SSC5, SSC7, SSC8, SSC9, SSC13, SCC14, SSC16 and SSC17. A bidimensional genomic scan every 10 cM was performed to detect interaction between QTL. The joint action of two suggestive QTL in SSC2 and SSC17 led to a genome-wide significant effect in live weight. The results of the bidimensional genomic scan showed that the genetic architecture was mainly additive or the experimental set-up did not have enough power to detect epistatic interactions.

scholarly journals Identification of genomic regions affecting grain peroxidase activity in bread wheat using genome-wide association study

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Zhengfu Zhou ◽  
Huiyue Guan ◽  
Congcong Liu ◽  
Ziwei Zhang ◽  
Shenghui Geng ◽  
...  
Keyword(s):  
Association Study ◽  
Candidate Gene ◽  
Genome Wide Association Study ◽  
Significant Snps ◽  
Regulatory Elements ◽  
Genome Wide Association ◽  
Genetic Loci ◽  
Genome Wide ◽  
A Genome ◽  
Genomic Regions

Abstract Background Peroxidase (POD) activity plays an important role in flour-based product quality, which is mainly associated with browning and bleaching effects of flour. Here, we performed a genome-wide association study (GWAS) on POD activity using an association population consisted with 207 wheat world-wide collected varieties. Our study also provide basis for the genetic improvement of flour color-based quality in wheat. Results Twenty quantitative trait loci (QTLs) were detected associated with POD activity, explaining 5.59–12.67% of phenotypic variation. Superior alleles were positively correlated with POD activity. In addition, two SNPs were successfully developed to KASP (Kompetitive Allele-Specific PCR) markers. Two POD genes, TraesCS2B02G615700 and TraesCS2D02G583000, were aligned near the QTLs flanking genomic regions, but only TraesCS2D02G583000 displayed significant divergent expression levels (P < 0.001) between high and low POD activity varieties in the investigated association population. Therefore, it was deduced to be a candidate gene. The expression level of TraesCS2D02G583000 was assigned as a phenotype for expression GWAS (eGWAS) to screen regulatory elements. In total, 505 significant SNPs on 20 chromosomes (excluding 4D) were detected, and 9 of them located within 1 Mb interval of TraesCS2D02G583000. Conclusions To identify genetic loci affecting POD activity in wheat grain, we conducted GWAS on POD activity and the candidate gene TraesCS2D02G583000 expression. Finally, 20 QTLs were detected for POD activity, whereas two QTLs associated SNPs were converted to KASP markers that could be used for marker-assisted breeding. Both cis- and trans-acting elements were revealed by eGWAS of TraesCS2D02G583000 expression. The present study provides genetic loci for improving POD activity across wide genetic backgrounds and largely improved the selection efficiency for breeding in wheat.

scholarly journals Prediction of carcass composition of lambs by joint dissection and carcass traits

2020 ◽  
Vol 44 (5) ◽  
pp. 1125-1135
Author(s):  
Pembe Dilara KEÇİCİ ◽  
Nurşen ÖZTÜRK ◽  
Hülya YALÇINTAN ◽  
Ömür KOÇAK ◽  
Alper YILMAZ ◽  
...  
Keyword(s):  
Hind Limb ◽  
Carcass Traits ◽  
Carcass Characteristics ◽  
Cost Effective ◽  
Carcass Composition ◽  
Tissue Composition ◽  
Prediction Equations ◽  
Muscle Weight ◽  
Joint Tissue ◽  
Total Fat

The aim of the study was to test the possibility of using carcass measurements and joint tissue composition to predict the half-carcass tissue composition of lambs more accurately. With this purpose in mind, 6 different carcass joints (neck, flank, shoulder, ribs, hind limb, and tail) from 42 Kıvırcık male lambs were dissected. In addition, various carcass characteristics were recorded. When carcass characteristics and measurements were used alone in the prediction equations, accuracy (between 37%–68%) was similar to the equations that included only joint dissections (36%–75%). However, when joint dissection and various carcass traits were combined, half-carcass tissue composition was predicted more accurately (65%–90%) than in measures using either joint dissection or various carcass traits alone. Flank was the most successful predictive joint for prediction of muscle weight, when combined with some carcass traits, while the equation built with hind limb and various carcass traits was most successful for predicting total fat weight. Carcass traits yielded accuracy that was similar to joint dissection results, especially for muscle and total fat weights. Therefore, for these parameters, carcass traits are preferred as this measure is cost-effective, noninvasive, and practical. However, for greater accuracy, joint dissection and various carcass characteristics and measurements should be combined

scholarly journals A genome-wide association analysis for body weight at 35 days measured on 137,343 broiler chickens

2021 ◽  
Vol 53 (1) ◽  
Author(s):  
Christos Dadousis ◽  
Adriana Somavilla ◽  
Joanna J. Ilska ◽  
Martin Johnsson ◽  
Lorena Batista ◽  
...  
Keyword(s):  
Sample Size ◽  
Genetic Variance ◽  
Leptin Receptor ◽  
Significant Snps ◽  
Genome Wide Association ◽  
Large Sample Size ◽  
Total Genetic Variance ◽  
Large Sample ◽  
Genome Wide ◽  
Genomic Regions

Abstract Background Body weight (BW) is an economically important trait in the broiler (meat-type chickens) industry. Under the assumption of polygenicity, a “large” number of genes with “small” effects is expected to control BW. To detect such effects, a large sample size is required in genome-wide association studies (GWAS). Our objective was to conduct a GWAS for BW measured at 35 days of age with a large sample size. Methods The GWAS included 137,343 broilers spanning 15 pedigree generations and 392,295 imputed single nucleotide polymorphisms (SNPs). A false discovery rate of 1% was adopted to account for multiple testing when declaring significant SNPs. A Bayesian ridge regression model was implemented, using AlphaBayes, to estimate the contribution to the total genetic variance of each region harbouring significant SNPs (1 Mb up/downstream) and the combined regions harbouring non-significant SNPs. Results GWAS revealed 25 genomic regions harbouring 96 significant SNPs on 13 Gallus gallus autosomes (GGA1 to 4, 8, 10 to 15, 19 and 27), with the strongest associations on GGA4 at 65.67–66.31 Mb (Galgal4 assembly). The association of these regions points to several strong candidate genes including: (i) growth factors (GGA1, 4, 8, 13 and 14); (ii) leptin receptor overlapping transcript (LEPROT)/leptin receptor (LEPR) locus (GGA8), and the STAT3/STAT5B locus (GGA27), in connection with the JAK/STAT signalling pathway; (iii) T-box gene (TBX3/TBX5) on GGA15 and CHST11 (GGA1), which are both related to heart/skeleton development); and (iv) PLAG1 (GGA2). Combined together, these 25 genomic regions explained ~ 30% of the total genetic variance. The region harbouring significant SNPs that explained the largest portion of the total genetic variance (4.37%) was on GGA4 (~ 65.67–66.31 Mb). Conclusions To the best of our knowledge, this is the largest GWAS that has been conducted for BW in chicken to date. In spite of the identified regions, which showed a strong association with BW, the high proportion of genetic variance attributed to regions harbouring non-significant SNPs supports the hypothesis that the genetic architecture of BW35 is polygenic and complex. Our results also suggest that a large sample size will be required for future GWAS of BW35.

scholarly journals Genomic basis of striking fin shapes and colours in the fighting fish

2021 ◽  
Author(s):  
Le Wang ◽  
Fei Sun ◽  
Zi Yi Wan ◽  
Baoqing Ye ◽  
Yanfei Wen ◽  
...  
Keyword(s):  
Evolutionary Biology ◽  
Association Studies ◽  
Regulatory Element ◽  
Regulatory Elements ◽  
Major Effect ◽  
Betta Splendens ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Phenotypic Variations ◽  
Genomic Basis

Abstract Resolving the genomic basis underlying phenotypic variations is a question of great importance in evolutionary biology. However, understanding how genotypes determine the phenotypes is still challenging. Centuries of artificial selective breeding for beauty and aggression resulted in a plethora of colors, long fin varieties, and hyper-aggressive behavior in the air-breathing Siamese fighting fish (Betta splendens), supplying an excellent system for studying the genomic basis of phenotypic variations. Combining whole genome sequencing, QTL mapping, genome-wide association studies and genome editing, we investigated the genomic basis of huge morphological variation in fins and striking differences in coloration in the fighting fish. Results revealed that the double tail, elephant ear, albino and fin spot mutants each were determined by single major-effect loci. The elephant ear phenotype was likely related to differential expression of a potassium ion channel gene, kcnh8. The albinotic phenotype was likely linked to a cis-regulatory element acting on the mitfa gene and the double tail mutant was suggested to be caused by a deletion in a zic1/zic4 co-enhancer. Our data highlight that major loci and cis-regulatory elements play important roles in bringing about phenotypic innovations and establish Bettas as new powerful model to study the genomic basis of evolved changes.

Sign in / Sign up

Export Citation Format

Share Document