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 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.     

Identification of a novel 43-bp insertion in the heparan sulfate 6-O-sulfotransferase 3 (HS6ST3) gene and its associations with growth and carcass traits in chickens

Previous studies have revealed a significant association between SNPs found within the heparan sulfate 6-O-sulfotransferase 3 (HS6ST3) gene and obesity. This study identified a novel 43-bp indel polymorphism in intron 1 of HS6ST3 in 1963 chickens from nine different breeds, and three genotypes, designated II, ID and DD, were observed. The frequency of the ‘I’ (0.62–0.87) allele was higher than that of the ‘D’ (0.13–0.38) allele. A total of 777 individuals of the Gushi-Anka F₂ resource population were used for the analysis of associations according to growth traits, carcass traits, serum variables and meat quality traits. The results showed that the 43-bp indel polymorphism was significantly associated with the body weight at 4 and 6 weeks of age, chest depth at 4 and 12 weeks of age and shank girth at 12 weeks of age (P?<?0.05). In terms of the carcass traits, the indel polymorphism was significantly associated with breast muscle weight, heart weight and leg weight (P?<?0.05). These findings suggested that this indel polymorphism has the potential to become a new target for the marker-assisted selection of chicken growth and carcass traits.     

A novel single-nucleotide polymorphism of thevisfatin gene and its associations with performance traits in the chicken

Visfatin is a peptide that is predominantly expressed in visceral adipose tissue and is hypothesized to be related to obesity and insulin resistance. In this study, a novel silent single-nucleotide polymorphism (SNP) was found in exon 7 of the chickenvisfatin gene (also known asPBEF1) by single-stranded conformation polymorphism (SSCP) and DNA sequencing. In total, 836 chickens forming an F₂ resource population of Gushi chicken crossed with Anka broiler were genotyped by XbaI forced RFLP, and the associations of this polymorphism with chicken growth, carcass characteristics, and meat quality were analyzed. Significant associations were found between the polymorphism and 4-week body weight (BW4), 6-week body weight (BW6), 4-week body slanting length (BSL4), fat bandwidth (FBW), breast muscle water loss rate (BWLR) and breast muscle fiber density (BFD) (P < 0.05), as well as 4-week breastbone length (BBL4) (P < 0.01). These observations suggested that the polymorphism in exon7 of thevisfatin gene had significant effects on the early growth traits of chicken.     

Genome-wide association study of shank length and diameter at different developmental stages in chicken F2 resource population

In order to find SNPs and genes affecting shank traits, we performed a GWAS in a chicken F2 population of eight half-sib families from five hatches derived from reciprocal crosses between an Arian fast-growing line and an Urmia indigenous slow-growing chicken. A total of 308 birds were genotyped using a 60K chicken SNP chip. Shank traits including shank length and diameter were measured weekly from birth to 12 weeks of age. A generalized linear model and a compressed mixed linear model (CMLM) were applied to achieve the significant regions. The value of the average genomic inflation factor (λ statistic) of the CMLM model (0.99) indicated that the CMLM was more effective than the generalized linear model in controlling the population structure. The genes surrounding significant SNPs and their biological functions were identified from NCBI, Ensembl and UniProt databases. The results indicated that 12 SNPs at 12 different ages passed the LD-adjusted 5% Bonferroni significant threshold. Two SNPs were significant for shank length and nine SNPs were significant for shank diameter. The significant SNPs were located near to or inside 11 candidate genes. The results showed that a number of significant SNPs in the middle ages were higher than the rest. The MXRA8 gene was related to the significant SNP at week 1 that promotes proliferation of growth plate chondrocytes. A unique SNP of Gga_rs16689511 located on chicken Z chromosome within the LOC101747628 gene was related to shank length at three different ages of birds (weeks 8, 9 and 11). The significant SNPs for shank diameter were found at weeks 4 and 7 (four and five SNPs respectively). The identifications of SNPs and genes here could contribute to a better understanding of the genetic control of shank traits in chicken.     

One novel SNP of growth hormone gene and its associations with growth and carcass traits in ducks

In this study, the growth hormone (GH) gene was studied as a candidate gene for growth and carcass traits of three duck populations (Cherry Valley duck, Muscovy duck and Jingjiang duck). Three pairs of primers were designed to detect single nucleotide polymorphisms of introns 2, 3 and 4 of the GH gene by polymerase chain reaction-restriction fragment length polymorphism and sequencing methods. Only the products amplified from intron 2 displayed polymorphism. The results showed one novel polymorphism: a variation in intron 2 of GH gene (C172T, JN408701 and JN408702). It was associated with some growth and carcass traits in three duck populations including birth weight, 8-week weight, carcass weight, breast muscle weight, leg muscle weight, eviscerated weight, lean meat rate, dressing percentage, etc. And the TT and CT genotypes were associated with superior growth and carcass traits in carcass weight, dressing percentage and percentage of eviscerated weight. Therefore, the variation in intron 2 of GH may be a molecular marker for superior growth and carcass traits in above duck populations.     

Genetic association of <Emphasis Type="Italic">Phosphodiesterase 1B</Emphasis> (PDE1B) with carcass traits in Korean cattle

Quantitative trait loci for fat deposition and carcass traits have been identified in the vicinity of the gene encoding phosphodiesterase 1B (PDE1B) on bovine chromosome 5. Therefore, the PDE1B gene can be considered as a positional and functional candidate gene for carcass traits in beef cattle. This study aimed to identify single nucleotide polymorphisms (SNPs) in the PDE1B gene and to evaluate their associations with carcass traits in Korean cattle. Eight SNPs, g.440T>G, g.17122A>G, g.17507A>C, g.17575A>G, g.17607T>C, g.17609C>A, g.17692C>T, and g.17707C>G, were identified in the region ranged from exon 1 to intron 6. Five of them were used for association analysis because of their availability of restriction fragment length polymorphisms. As a result, g.17122A>G in intron 3 was significantly associated with backfat thickness (BFT), and g.17507A>C in exon 5 was associated with longissimus dorsi muscle area (LMA, P < 0.05). Animals with the AG genotype of g.17122 had thicker BFT than those with the AA genotype. Animals with the AA or AC genotype of g.17507A>C had larger LMA than those with the CC genotype. We suggested the PDE1B gene as a candidate gene for carcass traits of beef cattle. Fine mapping would be required for application to marker-assisted selection.     

An SNP in the MyoD1 Gene Intron 2 Associated with Growth and Carcass Traits in Three Duck Populations

Myogenic differentiation 1 (MyoD1) genes belong to the MyoD gene family and play key roles in growth and muscle development. This study was designed to investigate the effects of variants in the MyoD1 gene on duck growth and carcass traits. Three duck populations (Cherry Valley, Jingjiang, and Muscovy) were sampled, their growth and carcass traits were measured, and they were genotyped using the PCR–RFLP method. The results showed one novel polymorphism, an alteration in intron 2 of the MyoD1 gene (A to T). It was associated with the traits of weight at 8?weeks, carcass weight, breast muscle weight, leg muscle weight, eviscerated percentage, percentage of leg muscle weight, dressing percentage, and lean meat percentage. This alteration in intron 2 of MyoD1 may be linked with potential major loci or genes affecting some growth and carcass traits.     

Polymorphisms and expression of the chicken POU1F1 gene associated with carcass traits

POU1F1 is an essential factor that regulates the development and reproduction of animal. The objective of the current research was to screen for polymorphism, expression of POU1F1 and their association with carcass quality traits. A total of 126 Erlang mountainous chickens from two strains (SD02 and SD03) were employed for testing. Seventeen single nucleotide polymorphisms (SNPs) were detected, but only two SNPs (g.96217999 T > C and g.96219442 C > T) were associated with carcass quality traits. In SD03 chicken, g.96217999 T > C genotypes were significantly associated with body weight (BW), carcass weight (CW), eviscerated weight (EW), and semi-eviscerated weight (SEW; P < 0.05), and was highly significantly associated with breast muscle weight (BMW) and abdominal fat weight (AW; P < 0.01). g.96219442 C > T was significantly associated with BW, EW, SEW (P < 0.05). However, these two SNPs were not significantly associated with any carcass traits in SD02 chicken. Diplotypes showed that in SD03 chicken, the haplotype [C: C] was the most favorable haplotype because it was associated with higher BW, CW, SEW, EW, BMW, and AW (P < 0.05). On the contrary, haplotype [T: T] was associated with lower carcass quality traits (P < 0.01). In addition, qRT-PCR revealed that at 13 weeks, the POU1F1 mRNA expression was significantly higher in breast muscle of cock compared to that of hens (P < 0.05), whereas there was no significant correlation between POU1F1 expression and carcass traits. These results suggested that POU1F1 could be a potential candidate gene for carcass traits in chicken.     

Sequence variants of the <Emphasis Type="Italic">LCORL</Emphasis> gene and its association with growth and carcass traits in Qinchuan cattle in China

Molecular marker-assisted selection is a better way to satisfy the growing customer requirement with the development of beef cattle growth and breeding research. For now, quantitative trait locus (QTL) for cattle growth and carcass traits, just like body height, body length and carcass weight have been detected on bovine chromosome 6. In this study, ligand-dependent nuclear receptor corepressor-like (LCORL) was selected as the potential positional candidate gene located in chromosome 6 which is closely connected with the bovine growth and carcass traits. A total of 450 Qinchuan beef cattle were used to detect mutations in exon and its neighbouring region, and the promoter region of the bovine LCORL gene. The methods for SNPs detection were polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and created restriction site PCR (CRS-PCR), and the results of this study show that there were two variations in intron regions, the other four variations were located in the promoter region. Linkage disequilibrium analysis and haplotype analysis indicated that L78-Q4 had strong linkage disequilibrium, A T G C G C (16.2%) and G C G C A T (16.7%) had higher haplotype frequencies, G C A C A C (0.8%) and G T A C A T (0.7%) had lower haplotype frequencies. Correlation analysis indicated that SNP g. INT + 52098A >G was significantly associated with slaughter weight and carcass weight. Based on the research, we selected LCORL as the candidate gene that can contribute to improved marker-assisted selection for the meat performance of Qinchuan beef cattle.     

Sequencing and genotypic analysis of the triosephosphate isomerase (TPI1) locus in a large sample of long-lived Germans

Background

With crucial roles on the differentiation of anterior pituitary and the regulation of the prolactin (PRL), growth hormone (GH) and thyroid-stimulating hormone-β (TSH-β) genes, the chicken PIT1 gene is regarded as a key candidate gene for production traits. In this study, five reported polymorphisms (MR1-MR5) of the PIT1 gene were genotyped in a full sib F₂ resource population to evaluate their effects on growth, carcass and fatty traits in chickens.

Results

Marker-trait association analyses showed that, MR1 was significantly associated with shank diameters (SD) at 84 days (P < 0.05), hatch weight (HW) and shank length (SL) at 84 days (P < 0.01), MR2 was significantly associated with BW at 28, 42 days and average daily gain (ADG) at 0–4 weeks (P < 0.05), and MR3 was significantly associated with ADG at 4–8 weeks (P < 0.05). MR4 was associated with SL at 63, 77, 84 days and BW at 84 days (P < 0.05), as well as SD at 77 days (P < 0.01). Significant association was also found of MR5 with BW at 21, 35 days and SD at 63 days (P < 0.05), BW at 28 days and ADG at 0–4 weeks (P < 0.01). Both T allele of MR4 and C allele of MR5 were advantageous for chicken growth. The PIT1 haplotypes were significantly associated with HW (P = 0.0252), BW at 28 days (P = 0.0390) and SD at 56 days (P = 0.0400). No significant association of single SNP and haplotypes with chicken carcass and fatty traits was found (P > 0.05).

Conclusion

Our study found that polymorphisms of PIT1 gene and their haplotypes were associated with chicken growth traits and not with carcass and fatty traits.     

钙蛋白酶Ⅰ(CAPN1)基因多态性与鸡肉嫩度和屠体性状的相关研究

为了探讨CAPN1基因作为影响鸡肌肉嫩度候选基因的可能性, 寻找与鸡嫩度性状相关的分子标记, 对钙蛋白酶Ⅰ(CAPN1)基因的CDS区进行SNPs 检测, 分析不同基因型在5个优质肉鸡纯品系和3个配套系间分布规律。利用测序和单链构象多态(SSCP)的方法进行SNPs 检测和基因型的分析, 计算等位基因频率、各位点多态信息含量。结果发现2546位(位点A) 处发生点突变由C→T和3535位(位点B)处发生点突变由G→A。各位点的3 种基因型与肉鸡生产性状的最小二乘分析结果表明,各位点的各种基因型个体在肌纤维密度和部分屠体性状指标存在显著差异(P< 0.05)。初步推断CAPN1基因可能是影响鸡嫩度性状潜在的主效基因或与主效基因连锁, 并且这些位点具有成为分子标记的潜在可能。     

The novel 5bp deletion polymorphism in the promoter region of bovine <Emphasis Type="Italic">ACRP30</Emphasis> gene

ACRP30 gene was located nearby the QTL affecting the marbling, ribeye muscle area and fat thickness on the BAT1 in Angus. In this study, a 5bp deletion mutation within the bovine ACRP30 gene was firstly detected and confirmed in 991 cattle by PCR-SSCP, DNA sequencing and direct PCR amplification. The deletion mutation was appeared in Qinchuan, Nanyang, Jiaxian and Hasake, but was not found in Jinnan, Chinese Holsteins and Angus. The association of the deletion polymorphism with growth traits (including birth weight, body weight, average daily gain and body sizes in different growth periods (6/12/18/24 month-old)) was analyzed in 224 Nanyang cattle. No signification association of the deletion polymorphism with growth traits were observed (P > 0.05). The deletion was located in the promoter region and it resulted in a new putative CCAAT/enhancer binding protein-β response element (C/EBP-RE).     

High diversity of the chicken growth hormone gene and effects on growth and carcass traits

The chicken growth hormone (cGH) gene plays a crucial role in controlling growth and metabolism, leading to potential correlations between cGH polymorphisms and economic traits. In this study, DNA from four divergent chicken breeds were screened for single nucleotide polymorphisms (SNPs) in the cGH gene using denaturing high-performance liquid chromatography and sequencing. A total of 46 SNPs were identified, of which 4 were in the 5' untranslated region, 1 in the 3' untranslated region, 5 in exons (two of which are nonsynonymous), with the remaining 36 in introns. The nucleotide diversity in the cGH gene ( theta = 2.7 x 10(-3)) was higher than that reported for other chicken genes, even within the same breeds. The associations of five of these SNPs and their haplotypes with chicken growth and carcass traits were determined using polymerase chain reaction-restriction fragment length polymorphism analysis in a F2 resource population cross of two of the four chicken breeds (White Recessive Rock and Xinghua). This analysis shows that, among other correlations, G+1705A was significantly associated with body weight at all ages measured, shank length at three of four ages measured, and average daily gain within weeks 0 to 4. Thus, this cGH polymorphism, or another polymorphism that is in linkage disequilibrium with G+1705A, appears to correspond to a significant growth-related quantitative trait locus difference between the two breeds used to construct the resource population.     

Mutations in Leptin (LEP) Gene Are Associated with Carcass and Meat Quality Traits in Crossbreed Rabbits

Leptin is a hormone synthesized and secreted primarily in adipose cells that help to regulate energy balance. This study examined the associations of single nucleotide polymorphisms in the rabbit leptin gene with growth traits, slaughter traits and physicochemical parameters of New Zealand White (NZW) and Belgian Giant Grey (BGG) crossbreed rabbits. In total, 320 crossbreed animals were genotyped for polymorphisms within exon 2—g.16081633T>C, intron 1_2—g.16081420C>T, and within UTR—g.16079636C>G for association analysis. Identified polymorphisms within rabbits leptin gene showed significant differences for dissectible fat percentage in carcass and dissectible fat weight in intermediate part (g.16081633T>C). Moreover, meat traits like protein content (g.16081633T>C; g.16079636C>G), intramuscular fat content (g.16081633T>C; g.16079636C>G, g.16081420C>T), dry matter (g.16081420C>T), ash (g.16081420C>T), water (g.16081420C>T), and cohesiveness (g.16081420C>T, g.16079636C>G) were affected by polymorphisms in leptin gene. We conclude that polymorphism in the rabbit leptin gene influences important carcass and meat traits of NZW?×?BGG crossbreeds. Therefore, polymorphisms identified in this study may be used in selection as a meat trait markers.     

Associations of <Emphasis Type="Italic">GHSR</Emphasis> gene polymorphisms with chicken growth and carcass traits

Ghrelin receptor (GHSR), or growth hormone secretagogue receptor, modulates many physiological effects by binding to its ligand and therefore is a candidate gene for chicken production performance. In this study, five polymorphisms (four SNP and a ‘GGTACA’ indel) of GHSR gene were genotyped in a F₂ full sib chicken population to investigate their associations with production traits. Results showed that c.739 + 726T > C (M2) was significantly associated with body weight (BW) at 28 days (BW28), BW90, dressed weight, eviscerated weight, eviscerated weight with giblet, breast muscle weight and leg muscle weight (P < 0.05). Meanwhile, T allele rather than C was positive for chicken body weight gain as individuals with CC had the lowest value of all traits. Otherwise, no significant association of c.264G > A (M1), c.3211-196_3211-181delGGTACA (M3), c.3211 + 75C > T (M4), and c.3211 + 150C > T (M5) with any growth and carcass traits was found. Haplotypes based on five polymorphisms were significantly associated with hatch weight, BW7, BW14, BW21 and breast angle (P < 0.05), as well as BW28 (P < 0.01). Therefore, it was concluded that M2 of the GHSR gene and the analyzed haplotypes were associated with some chicken growth and carcass traits.     

Polymorphisms in chicken extracellular fatty acid binding protein gene

In this study, we report the investigation of extracellular fatty acid binding protein gene (Ex-FABP) genetic polymorphism in a sample of 360 chicken individuals. The screening of the coding regions with their intron–exon boundaries and the proximal flanking regions was performed through a PCR-SSCP strategy. Following sequence analysis revealed 35 novel single nucleotide polymorphisms (SNPs) of chicken Ex-FABP gene. Among the 35 SNPs, twenty-five were found in the introns. And the remaining seven and three SNPs were in the coding region and the 5′UTR, respectively. Two SNPs in the coding region caused two missense mutants and the other five did not result in any amino acid changes. The nature and the distribution of Ex-FABP mutations in three chicken breeds were analyzed. Variations detected here might have an impact on Ex-FABP activity and function and underpin the development of gene markers for chicken fatty deposition and metabolism. The polymorphism, generated by C4715T mutation in exon5, was significantly associated with thickness of subcutaneous fat plus skin in cocks. Subcutaneous fat plus skin of cocks was more thick in TT genotype than in CC genotype (P < 0.05). The Ex-FABP gene could be a candidate locus or linked to a QTL that significantly affects fatty deposition and metabolism in chicken.