Single nucleotide polymorphisms in chicken lmbr1 gene were associated with chicken growth and carcass traits

Lmbr1 is the key candidate gene controlling vertebrate limb development, but its effects on animal growth and carcass traits have never been reported. In this experiment, lmbr1 was taken as the candi-date gene affecting chicken growth and carcass traits. T/C and G/A mutations located in exon 16 and one A/C mutation located in intron 5 of chicken lmbr1 were detected from Silky, White Plymouth Rock broilers and their F2 crossing chickens by PCR-SSCP and sequencing methods. The analysis of vari-ance (ANOVA) results suggests that T/C polymorphism of exon 16 had significant association with eviscerated yield rate (EYR), gizzard rate (GR), shank and claw rate (SCR) and shank girth (SG); A/C polymorphism of intron 5 was significantly associated with SCR, liver rate and head-neck weight (HNW), while both sites had no significant association with other growth and carcass traits. These results demonstrate that lmbr1 gene could be a genetic locus or linked to a major gene significantly affecting these growth and carcass traits in chicken.     

Associations of growth hormone secretagogue receptor (GHSR) genes polymorphisms and protein structure changes with carcass traits in sheep

Growth hormone secretagogue receptor (GHSR), a G protein-coupled receptor that binds ghrelin, plays an important role in the central regulation of pituitary growth hormone secretion, food intake, and energy homeostasis. Ghrelin receptor (GHSR) modulates many physiological effects and therefore is a candidate gene for sheep production performance. Polymorphism of the GHSR gene was detected by PCR-SSCP and DNA sequencing methods in 463 individuals. Two different structures in protein and nine single nucleotide polymorphisms (SNPs) were identified. The evaluation of the associations between these SSCP patterns with carcass traits suggests a positive effect of genotype TT and B structure on carcass weight, and body length (P<0.05). In addition, the animal with TC had greater abdominal fat than those with TT and CC (P<0.05) while CC genotype contributed to low blood cholesterol (P=0.04). The results confirm the hints suggesting that GHSR is a preferential target for further investigation on mutations that influence carcass trait variations.     

Single nucleotide polymorphisms in the insulin‐like growth factor 1 (IGF1) gene are associated with growth‐related traits in farmed Atlantic salmon

Understanding the genetic basis of variation in traits related to growth and fillet quality in Atlantic salmon is of importance to the aquaculture industry. Several growth‐related QTL have been identified via the application of genetic markers. The IGF1 gene is considered a highly conserved and crucial growth‐regulating gene in salmonid species. However, the association between polymorphisms in the IGF1 gene and growth‐related traits in Atlantic salmon is unknown. Therefore, in this study, regions of the Atlantic salmon IGF1 gene were sequenced, aligned and compared across individuals. Three SNPs were identified in the putative promoter (SNP1, g.5763G>T; GenBank no. AGKD01012745 ), intron 1 (SNP2, g.7292C>T; GenBank no. AGKD01012745 ) and intron 3 (SNP3, g.4671A>C; GenBank no. AGKD01133398 ) regions respectively. These SNPs were genotyped in a population of 4800 commercial Atlantic salmon with data on several weight and fillet traits measured at harvest (at approximately 3 years of age). In a mixed model, association analysis of individual SNPs, SNP1 and SNP3 were both significantly associated with several weight traits (P < 0.05). The estimated additive effect on overall harvest weight was approximately 35 and 110 g for SNPs 1 and 3 respectively. A haplotype analysis confirmed the association between genetic variation in the IGF1 gene with overall body weight (P < 0.05) and fillet component traits (P < 0.05). Our findings suggest the identified nucleotide polymorphisms of the IGF1 gene may either affect farmed Atlantic salmon growth directly or be in population‐wide linkage disequilibrium with causal variation, highlighting their possible utility as candidates for marker‐assisted selection in the aquaculture industry.     

Single nucleotide polymorphisms in the corticotrophin-releasing hormone and pro-opiomelancortin genes are associated with growth and carcass yield in beef cattle

A single nucleotide polymorphism (SNP) in the corticotrophin-releasing hormone gene (CRH C22G) alters the fourth amino acid in the signal sequence from proline to arginine. Two other SNPs (CRH A145G and C240G) occur in the propeptide region at residue positions 45 and 77, respectively, that result in serine/asparagine and histidine/aspartic acid substitutions respectively. These SNPs, as well as SNPs in pro-opiomelancortin (POMC), leptin (LEP) and melanocortin-4 receptor (MC4R), were evaluated for associations with average daily gain, end-of-test rib-eye area, shipping weight and hot carcass weight in a group of 256 steers using a general linear model. The CRH C22G SNP was associated with end-of-test rib-eye area (P < 0.034) and hot carcass weight (P < 0.0015). The SNP in POMC was associated with shipping weight (P < 0.0078) and hot carcass weight (P = 0.006) while it approached significance for average daily gain (P < 0.07). The SNP in MC4R approached significance for hot carcass weight (P < 0.085) while no significance was observed between the leptin SNP and the above listed traits. Because both CRH and POMC regulate appetite, potential interaction effects between these two genes were assessed. The absence of an interaction effect between CRH and POMC with hot carcass weight suggests that these genes act independently to increase carcass yield. These gene effects used singularly or together could result in an economic benefit to the beef industry.     

Single nucleotide polymorphisms in chicken lmbr1 gene were associated with chicken growth and carcass traits

Lmbr1 is the key candidate gene controlling vertebrate limb development, but its effects on animal growth and carcass traits have never been reported. In this experiment, lmbr1 was taken as the candidate gene affecting chicken growth and carcass traits. T/C and G/A mutations located in exon 16 and one A/C mutation located in intron 5 of chicken lmbr1 were detected from Silky, White Plymouth Rock broilers and their F₂ crossing chickens by PCR-SSCP and sequencing methods. The analysis of variance (ANOVA) results suggests that T/C polymorphism of exon 16 had significant association with eviscerated yield rate (EYR), gizzard rate (GR), shank and claw rate (SCR) and shank girth (SG); A/C polymorphism of intron 5 was significantly associated with SCR, liver rate and head-neck weight (HNW), while both sites had no significant association with other growth and carcass traits. These results demonstrate that lmbr1 gene could be a genetic locus or linked to a major gene significantly affecting these growth and carcass traits in chicken. Supported by the State Major Basic Research Development Program (Grant No. G20000161) and Beijing Natural Science Foundation (Grant No. 5011002)     

Single nucleotide polymorphisms in the growth hormone and insulin-like growth factor-1 genes are associated with milk production, body condition score and fertility traits in dairy cows

The somatotrophic axis (GH-IGF) is a key regulator of animal growth and development, affecting performance traits that include milk production, growth rate, body composition, and fertility. The aim of this study was to quantify the association of previously identified SNPs in bovine growth hormone (GH1) and insulin-like growth factor 1 (IGF-1) genes with direct performance trait measurements of lactation and fertility in Holstein-Friesian lactating dairy cows. Sixteen SNPs in both IGF-1 and GH1 were genotyped across 610 cows and association analyses were carried out with traits of economic importance including calving interval, pregnancy rate to first service and 305-day milk production, using animal linear mixed models accounting for additive genetic effects. Two IGF-1 SNPs, IGF1i1 and IGF1i2, were significantly associated with body condition score at calving, while a single IGF-1 SNP, IGF1i3, was significantly associated with milk production, including milk yield (means ± SEM; 751.3 ± 262.0 kg), fat yield (21.3 ± 10.2 kg) and protein yield (16.5 ± 8.0 kg) per lactation. Only one GH1 SNP, GH33, was significantly associated with milk protein yield in the second lactation (allele substitution effect of 9.8 ± 5.0 kg). Several GH1 SNPs were significantly associated with fertility, including GH32, GH35 and GH38 with calving to third parity (22.4 ± 11.3 days) (GH32 and GH38 only), pregnancy rate to first service (0.1%) and overall pregnancy rate (0.05%). The results of this study demonstrate the effects of variants of the somatotrophic axis on milk production and fertility traits in commercial dairy cattle.     

Single nucleotide polymorphisms in the imprinted bovine insulin-like growth factor 2 receptor gene (IGF2R) are associated with body size traits in Irish Holstein-Friesian cattle

The regulation of the bioavailability of insulin‐like growth factors (IGFs) is critical for normal mammalian growth and development. The imprinted insulin‐like growth factor 2 receptor gene (IGF2R) encodes a transmembrane protein receptor that acts to sequester and degrade excess circulating insulin‐like growth factor 2 (IGF‐II) – a potent foetal mitogen – and is considered an important inhibitor of growth. Consequently, IGF2R may serve as a candidate gene underlying important growth‐ and body‐related quantitative traits in domestic mammalian livestock. In this study, we have quantified genotype–phenotype associations between three previously validated intronic bovine IGF2R single nucleotide polymorphisms (SNPs) (IGF2R:g.64614T>C, IGF2R:g.65037T>C and IGF2R:g.86262C>T) and a range of performance traits in 848 progeny‐tested Irish Holstein‐Friesian artificial insemination sires. Notably, all three polymorphisms analysed were associated (P ≤ 0.05) with at least one of a number of performance traits related to animal body size: angularity, body depth, chest width, rump width, and animal stature. In addition, the C‐to‐T transition at the IGF2R:g.65037T>C polymorphism was positively associated with cow carcass weight and angularity. Correction for multiple testing resulted in the retention of two genotype–phenotype associations (animal stature and rump width). None of the SNPs analysed were associated with any of the milk traits examined. Analysis of pairwise r² measures of linkage disequilibrium between all three assayed SNPs ranged between 0.41 and 0.79, suggesting that some of the observed SNP associations with performance may be independent. To our knowledge, this is one of the first studies demonstrating associations between IGF2R polymorphisms and growth‐ and body‐related traits in cattle. These results also support the increasing body of evidence that imprinted genes harbour polymorphisms that contribute to heritable variation in phenotypic traits in domestic livestock species.     

Association between polymorphisms of Myf5 and POU1F1 genes with growth and carcass traits in Hanwoo (Korean cattle)

Myogenic factor 5 (Myf5) and POU class 1 homeobox 1 (POU1F1) genes play important roles in growth and development of mammals. Bovine Myf5 and POU1F1 were characterized to detect genetic variation at these loci and to replace them to economic traits in 367 cattle representing Hanwoo (325) and Angus (37). Two single nucleotide polymorphisms (SNPs) were identified in intron 2 (A1948G SNP) of Myf5 and exon 6 (A15635G SNP) of POU1F1 by sequence analyses of genomic DNA. Statistical analysis indicated that the Myf5 polymorphisms significantly (0.05) associated backfat thickness and live weight at 6-months-of-age and that POU1F1 polymorphisms significantly influenced carcass weight and live weight at 24-month of age, and backfat thickness. The interaction between Myf5 and POU1F1 was significant on carcass weight, M. longissimus dorsi area, backfat thickness and marbling score. The results implicate Myf5 and POU1F1 as candidate genes of growth and carcass traits, and suggest that the interaction between Myf5 and POU1F1 strongly affect growth and carcass traits in cattle.     

Single nucleotide polymorphisms in exon 10 of the chinchilla growth hormone receptor (GHR) gene

The aim of this study was to detect SNPs in exon 10 of the chinchilla growth hormone receptor gene (GHR) by comparative sequencing. Sixty females of the same breed (Standard) were analysed. Four new SNPs were identified, which cause 3 amino acid substitutions in the intracellular domain of the receptor: G/C at position 135 bp (in relation to the total sequence of exon 10) (gln/his), CAG/AAA at 352 bp and 354 bp (gln/lys), and C/A at 641 bp (thr/asn).     

Single nucleotide polymorphisms in chicken <Emphasis Type="Italic">lmbr1</Emphasis> gene were associated with chicken growth and carcass traits

Lmbr1 is the key candidate gene controlling vertebrate limb development, but its effects on animal growth and carcass traits have never been reported. In this experiment, lmbr1 was taken as the candidate gene affecting chicken growth and carcass traits. T/C and G/A mutations located in exon 16 and one A/C mutation located in intron 5 of chicken lmbr1 were detected from Silky, White Plymouth Rock broilers and their F₂ crossing chickens by PCR-SSCP and sequencing methods. The analysis of variance (ANOVA) results suggests that T/C polymorphism of exon 16 had significant association with eviscerated yield rate (EYR), gizzard rate (GR), shank and claw rate (SCR) and shank girth (SG); A/C polymorphism of intron 5 was significantly associated with SCR, liver rate and head-neck weight (HNW), while both sites had no significant association with other growth and carcass traits. These results demonstrate that lmbr1 gene could be a genetic locus or linked to a major gene significantly affecting these growth and carcass traits in chicken.     

Single nucleotide polymorphisms of the prolactin receptor (PRLR) gene and its association with growth traits in chinese cattle

Genetic polymorphism of the prolactin receptor (PRLR) gene was detected by PCR-SSCP and DNA sequencing methods in 665 individuals from five Chinese cattle breeds. The results showed that at the P1 locus, three observed genotypes (AA, AB and BB), two linked SNPs (G1267A and T1268C), and one missense mutation (S18N) within a putative signal peptide were determined. The frequencies of haplotypes A and B in the five breeds were 0.596–0.802 and 0.198–0.404, respectively. Polymorphism of the PRLR gene was shown to be significantly associated with growth traits in the Nanyang breed. Individuals with genotype BB had greater hucklebone width, body weight and average daily gain than those with genotype AA at 6 months old (P < 0.01), as well as better body height, body length and heart girth when 6 months (P < 0.05). This study revealed for the first time that the PRLR gene is a promising candidate gene that affects growth traits in cattle.     

Expression analysis, single nucleotide polymorphisms and combined genotypes in candidate genes and their associations with growth and carcass traits in Qinchuan cattle

The apolipoprotein E (ApoE) gene is an important component of plasma lipoprotein, and Fas apoptosis inhibitory molecule (FAIM) is a novel anti-apoptotic gene. In this study, we researched and discussed seven genes in eight different tissues in Qinchuan cattle by quantitative Real-time PCR. The result of analysis showed that ApoE and FAIM ₂ genes had a correlation with muscle and fat. PCR–RFLP was applied to analyze the genetic variations of the ApoE and FAIM ₂ genes and verify the effect on growth and carcass traits in a total of 365 Qinchuan cattles. The result of haplotype analysis showed that nine different haplotypes were identified among the four SNPs in ApoE and FAIM ₂ genes. The statistical analyses indicated that the four SNPs were significant association with growth and carcass traits (P < 0.05, N = 365); and the four SNPs were significant association between nine combined genotypes of candidate genes and growth and carcass traits. Taken together, our results provide the evidence that polymorphisms in candidate genes are associated with growth and carcass traits in Qinchuan cattle, and may be used as a possible candidate for marker-assisted selection and management in beef cattle breeding program.     

Association of IGF1 and KDM5A polymorphisms with performance, fatness and carcass traits in chickens

Two functional and positional candidate genes were selected in a region of chicken chromosome 1 (GGA1), based on their biological roles, and also where several quantitative trait loci (QTL) have been mapped and associated with performance, fatness and carcass traits in chickens. The insulin-like growth factor 1 (IGF1) gene has been associated with several physiological functions related to growth. The lysine (K)-specific demethylase 5A (KDM5A) gene participates in the epigenetic regulation of genes involved with the cell cycle. Our objective was to find associations of selected single-nucleotide polymorphisms (SNPs) in these genes with performance, fatness and carcass traits in 165 F₂ chickens from a resource population. In the IGF1 gene, 17 SNPs were detected, and in the KDM5A gene, nine SNPs were detected. IGF1 SNP c.47673G?>?A was associated with body weight and haematocrit percentage, and also with feed intake and percentages of abdominal fat and gizzard genotype × sex interactions. KDM5A SNP c.34208C?>?T genotype × sex interaction affected body weight, feed intake, percentages of abdominal fat (p?=?0.0001), carcass, gizzard and haematocrit. A strong association of the diplotype × sex interaction (p?<?0.0001) with abdominal fat was observed, and also associations with body weight, feed intake, percentages of carcass, drums and thighs, gizzard and haematocrit. Our findings suggest that the KDM5A gene might play an important role in the abdominal fat deposition in chickens. The IGF1 and KDM5A genes are strong candidates to explain the QTL mapped in this region of GGA1.     

Evaluation of Florina (Pelagonia) sheep breed for growth and carcass traits

Two experiments were conducted to evaluate the performance of growing Florina (Pelagonia) lambs fed a high concentrate diet, as well as the effect of slaughter weight on carcass characteristics. The assessment of the growth used 12 male and 12 female individually penned weaned lambs until they reached 60% of their mature body weight (BW), while assessment of the effect of slaughter weight at weaning (42 days of age), and at 30%, 45% and 60% of the mature BW, on carcass characteristics used 40 male and 40 female weaned lambs. In experiment 1, results showed that Florina lambs have good growth. Male lambs grew faster (P < 0.001) than female lambs, resulting in a lower (P < 0.001) feed conversion ratio (FCR) for males. Rate of gain, feed consumption and FCR increased (P < 0.001) as the experiment progressed. In experiment 2, results showed that degree of maturity affected (P < 0.001) fasted body weight and carcass weight, as well as all carcass characteristics and commercial cuts, except the steaks cut which did not differ. Florina lambs can be slaughtered in heavier carcass weights, heavier than the 15 kg as the present practice. The heavier carcasses can appeal to wider range of consumers due to the excellent muscle development and the reduced visible fat cover. Florina sheep raised for heavy carcass meat production may be more economically beneficial for the breeders and the increased meat produced locally can help reduce need for importing meat from abroad.     

Porcine insulin-like growth factor 1 (IGF1) gene polymorphisms are associated with body size variation

Previous studies have confirmed that insulin growth factor-1 (IGF1) plays important roles in growth and body size in humans and animals. However, whether single nucleotide polymorphisms (SNPs) within the IGF1 gene affects body size and growth in pigs has been unclear. We identified IGF1 SNPs among 5 pig breeds (Berkshire, Duroc, Landrace, Yorkshire and Korea Native Pig) and found that the G allele of SNP (c.G189A) was associated with higher body weight and was more predominant in western pig breeds, while the Korean Native Pig is the breed with the highest frequency of the A allele. Four haplotypes (–GA–, –GG–, –AG–, and –AA–) were constructed using the 2 identified SNPs. The GA haplotype was most frequently observed, except in the Berkshire breed. In addition, these SNPs and haplotypes were significantly associated with body size (final weight), average daily gain, and backfat thickness (P < 0.05) in 2 intercrossed F₂ pig populations (KNP × YS F₂ and KNP × LR F₂). Furthermore, the major GA haplotype had a significant additive effect on body size and average daily gain. In conclusion, specific SNPs within the porcine IGF1 gene may contribute to the smaller body size and lower growth rate of Korea Native Pigs.     

Melanocortin-4 receptor (MC4R) polymorphisms are associated with growth and meat quality traits in sheep

The involvement of melanocortin 4 receptor gene (MC4R) in food intake and body weight regulation is well characterized. MC4R mutations are the most frequent monogenic cause of human obesity. Significant associations have been revealed between MC4R mutations and productive traits in pigs, cattle and poultry. Herein, fluorescence-based conformation sensitive gel electrophoresis was used to identify two single nucleotide polymorphisms (SNPs) in the coding region (93G>A and 292G>A) and two SNPs in the 3′-UTR area (1016G>A and 1240T>C) of MC4R gene in 132 German Merino sheep. We found that the 1016G>A mutation in the 3′-UTR was significantly associated with body weight at 120 and 180 days, average daily gain, back fat thickness and loin-eye area. Allele A located at the 292th position of MC4R gene representing Arg98 was associated with significantly higher loin-eye area in sheep. For the synonymous 93G>A mutation, A allele carrier animals had higher back fat thickness. Our results provide evidence that the MC4R gene may be a candidate gene for growth and meat quality traits with MC4R SNPs being potentially valuable as genetic markers for economic traits in German Merino sheep.     

Fine mapping of genes on sheep chromosome 1 and their association with milk traits

On the basis of comparative mapping between cattle/sheep and human for milk trait quantitative trait loci (QTL) on BTA3/OAR1, annexin A9 (ANXA9) and solute carrier family 27 (fatty acid transporter), member 3 (SLC27A3) were selected as candidate genes for fat content (FC) in sheep milk. Two other genes in the same region, cingulin (CGN) and acid phosphatase 6, lysophosphatidic (ACP6), were also considered. DNA fragments of 1931 and 2790 bp corresponding to ANXA9 and SLC27A3 respectively were isolated, and 14 and 6 single nucleotide polymorphisms (SNPs) respectively were found in each gene. ANXA9, SLC27A3, CGN and ACP6 were localized to chromosome 1 between INRA006 and AE57 by linkage mapping using the International Mapping Flock. Across-family analyses of a daughter design comprising 13 sire families revealed significant sire and SLC27A3 genotype-nested-within-sire effects for FC. Within-family analyses indicated significant regression coefficients for FC in four of six heterozygous sires. These results could reflect the existence of a QTL for FC linked to SLC27A3 in sheep.     

Relationship of growth hormone and insulin-like growth factor-1 genotypes with growth and carcass traits in swine

The contribution of chromosomal regions linked to growth hormone (GH) and insulin-like growth factor-1 (IGF-1) loci to variation in preweaning average daily gain, postweaning average daily gain (ADG), 10th rib backfat, loin-eye area and muscle pH were evaluated. Offspring of four purebred sires (A–D; n = 150, 195, 148 and 136, respectively) and two crossbred sires (E and F; n = 157 and 145, respectively) were genotyped initially with GH and IGF-1 markers. When results of single marker analysis suggested possible linkage with a quantitative trait locus (QTL), additional flanking markers were typed for the family and interval mapping was performed. Growth hormone genotype was not associated with the traits evaluated in the study. Evidence suggestive of linkage was found for IGF-1 genotype and ADG in one sire family (lod = 2·3) where differences were 0.032 ± 0·01 kg/day for alternative sire alleles. Evidence for a putative ADG QTL was greatest in the interval between IGF-1 and Sw1071. A similar genomic region has been associated with growth variation in mice; however, QTL mapping precision in the current study is insufficient to establish similarity.