Associations between variants of bone morphogenetic protein 7 gene and growth traits in chickens

1. Enhancing bone strength to solve leg disorders in poultry has become an important goal in broiler production. Bone morphogenetic protein 7 (BMP7), a member of the BMP family, represents an attractive therapeutic target for bone regeneration in humans and plays critical roles in skeletal development.

2. The objective of this study was to investigate the relationship between BMP7 gene expression, single-nucleotide polymorphisms (SNPs) and growth traits in chickens. Here, a SNP (c.1995T>C) in the chicken (Gallus gallus) BMP7 gene was identified, that was associated with growth and carcass traits.

3. Genotyping revealed that the T allele occurred more frequently in breeds with high growth rates, whereas the C allele was predominant in those with low growth rates. The expression level of BMP7 in the thigh bone of birds with the TT genotype was significantly higher than in those with the CC genotype at 21, 42 and 91 d of age.

4. These findings suggest that selecting the birds with the TT genotype of SNP c.1995T>C could improve bone growth, could reduce leg disorders in fast-growing birds. The SNP c.1995T>C may serve as a selective marker for improving bone growth and increasing the consistency of body weights in poultry breeding.     

A note on cloning and analysis of the osteopontin gene with egg quality traits in two Chinese domestic ducks

ABSTRACT

1. Osteopontin (OPN) is a highly phosphorylated acidic glycoprotein that plays a crucial role in eggshell formation. In this study, an 893-bp cDNA sequence of the OPN gene, which encodes 180 amino acids, was obtained.

2. Polymorphisms of the OPN gene were analysed with DNA sequencing and polymerase chain reaction-single-strand conformation polymorphism methods in two Chinese domestic laying ducks (Jingding n = 100, Youxian n = 478, respectively).

3. One polymorphism was identified in exon 7 (NM_ 004676534.1:c.267T>C) of the OPN gene, with three genotypes: TT (both T allels weren’t mutated (wild type)), TC (one T allel was mutated to C (heterozygote genotype)) and CC. (both T allels were mutated to C (homozygote 20 genotype)) Association analysis with egg quality traits in the two Chinese domestic laying ducks showed that the ducks with the CC genotype had significantly greater eggshell strength and eggshell thickness (p < 0.05). Hence, the exon 7 267T>C polymorphism of the OPN gene is a potentially valuable genetic marker for laying duck breeding programmes.     

UTS2R gene polymorphisms are associated with fatty acid composition in Japanese beef cattle

Fatty acid composition of beef adipose tissue is one of its important traits because a high proportion of monounsaturated fatty acid is related to favorable beef flavor and tenderness. In this study, we searched polymorphisms in full length coding DNA sequence of urotensin 2 recepter and investigated the effects on fatty acid composition (C14:0, C14:1, C16:0, C16:1, C18:0, C18:1, C18:2, monounsaturated fatty acid, saturated fatty acid). Eight single nucleotide polymorphisms (SNP) were identified by sequence comparison among eight animals, including five Japanese Black and three Holstein cattle. One of these SNP (c.866C>T) was predicted to cause amino acid substitutions (P289L) and the other seven synonymous SNP, including c.267C>T, were presumed to be in linkage disequilibrium. Therefore we selected two SNP (c.267C>T and c.866C>T) for further analysis. We investigated associations between these genotypes and fatty acid composition in three Japanese Black populations (n = 560, 245 and 287) and a Holstein population (n = 202). Tukey‐Kramer's honestly significant difference test revealed that CC genotype in c.267C>T indicated lower C14:0 and higher C18:1 than the other genotypes in Japanese Black cattle and CC genotype in c.866C>T showed lower C16:1 than CT genotype in Holstein cattle (P < 0.05). These results suggested that these genotypes would contribute to production of high‐grade meat as selection markers in beef cattle.     

黔东南小香鸡MEF2C基因外显子多态性及其与体重、体尺性状的关联分析

【目的】探究肌细胞增强因子2C（myocyte enhancer factor 2C,MEF2C）基因多态性对黔东南小香鸡体重和体尺性状的影响。【方法】试验以251羽300日龄黔东南小香鸡为研究对象,利用PCR扩增和直接测序技术对MEF2C基因全部（15个）外显子进行单核苷酸多态性（single nucleotide polymorphism,SNP）位点筛选,并运用SPSS 18.0统计分析软件对不同SNPs位点所对应的基因型与黔东南小香鸡的体重、体尺性状进行相关性分析。【结果】黔东南小香鸡群体中仅在MEF2C基因外显子12上发现3个SNPs位点：g.1819 T＞C、g.2426 T＞C和g.2543 C＞T,在其他外显子中未发现多态位点。χ²检验结果表明,3个SNPs在黔东南小香鸡群体中均偏离Hardy-Weinberg平衡状态（P＞0.05）。关联分析结果显示,g.1819 T＞C位点TC基因型个体体斜长、胸深和胫围均极显著高于TT和CC基因型,体重极显著高于TT基因型（P＜0.01）;TC基因型个体胫长显著高于TT和CC基因,龙骨长显著高于TT基因型（P＜0.05）。g.2426 T＞C和g.2543 C＞T位点互为连锁平衡位点,对胫围有极显著影响（P＜0.01）。【结论】黔东南小香鸡MEF2C基因外显子具有较强的保守性,g.1819 T>C位点可以作为黔东南小香鸡分子标记辅助选育参考位点。     

Association between novel variants in BMPR1B gene and litter size in Mongolia and Ujimqin sheep breeds

Prolificacy is an important trait of animals, specifically for sheep. The Bone morphogenetic protein receptor 1B (BMPR1B) is a major gene affecting the litter size of many sheep breeds. The well-known FecB mutation (Q249R) was associated fully with the hyper prolific phenotype of Booroola Merino. However, the identification of variation in all exonic regions of BMPR1B was rare. In this study, we sequenced all exonic regions of BMPR1B gene of Mongolia sheep breed, and ten novel variants were detected by direct sequencing. Among them, the litter size of the Mongolia ewes with the CC genotype was significantly higher (0.34 additional lambs, p < .05) than those with the TT genotype of the g.29346567C>T single nucleotide polymorphism (SNP). The litter size of the Mongolia ewes with the TT genotype was significantly higher (0.19 additional lambs, p < .05 and .31 additional lambs, p < .01, respectively) than those with the GT and GG genotypes of the c.1470G>T SNP. The silent c.1470G>T mutation is predicted to increase the stability of the mRNA secondary structure through reducing minimum free energy and is predicted to change the mRNA secondary structure of BMPR1B. Our findings may give potentially useful genetic markers for increasing litter size in sheep.     

A single-nucleotide polymorphism in the 3′ untranslated region of the LPIN1 gene and association analysis with performance traits in chicken

1. A single nucleotide polymorphism (SNP), c.*77C>G, was found in the 3′ UTR of the chicken LPIN1 gene by DNA sequencing. In total, 860 chickens were genotyped by polymerase chain reaction–restriction fragment length polymorphism (PCR-RFLP) in a F2 resource population obtained by crossing F0 Gushi chickens and Anka broilers, and the associations of this polymorphism with chicken growth, carcass, muscle fibre traits and serum biochemistry parameters were analysed.

2. Significant associations were found between the polymorphism and breast muscle fibre diameter (FDB). Comparison of the different genotypes of c.*77C>G in the F2 resource population showed that the GG genotype had significantly higher values than that of CG genotype in FDB. c.*77C>G was predicted to cause changes to multiple microRNA (miRNA) binding sites. But the total mRNA level of chicken LPIN1, LPIN1-;α and LPIN1-β in liver and muscle tissues did not show significant difference among GG, CG and CC genotypes, respectively.

3. The results suggested that chicken LPIN1 has a potential effect on muscle fibre development, but no effect on other studied traits.     

ADSL基因启动子区遗传变异与鸡肉冻藏新鲜度的相关性分析

试验旨在探究鸡腺苷琥珀酸裂解酶（adenylosuccinate lyase,ADSL）基因启动子区多态性及其与鸡肉冻藏新鲜度的相关性。以161只青脚麻鸡为研究对象,通过DNA混池测序法检测ADSL基因启动子区遗传变异。采用等位基因特异性PCR完成个体基因型分析,并分析了各基因型与鸡胸肌肉色、体重及胸肌冷冻60 d后新鲜度K值和pH的相关性。结果显示,在ADSL基因启动子区ATG上游1 670 bp处发现1个SNP位点（c.-1670 C>A）,其AA基因型个体肌肉冷冻60 d后新鲜度K值（23.61%）极显著低于CA（33.00%）和CC（33.56%）基因型（P<0.01）,即冻藏60 d后AA基因型个体肌肉较CA和CC基因型新鲜,CA和CC基因型间新鲜度K值差异不显著（P>0.05）;各基因型间鸡体重、胸肌肉色及胸肌冷冻60 d后pH均无显著差异（P>0.05）。生物信息学预测发现,c.-1670 C>A导致ADSL基因启动子区转录因子结合位点的显著改变,该突变位点可能造成ADSL基因的表达差异。综上,ADSL基因启动子区c.-1670 C>A与青脚麻鸡胸肌冷冻60 d后新鲜度K值具有显著相关性,该位点可作为青脚麻鸡肉品新鲜度的候选分子遗传标记。     

中国美利奴羊IGFBP-3基因内含子4区的PCR-RFLP多态性分析

本研究针对在绵羊IGFBP-3基因内含子4区新发现的1个SNP位点(C218T),建立了PCR-RFLP的基因分型方法。利用该方法对353只中国美利奴羊(新疆军垦型)进行了多态性检测,结果显示,有CC（249 bp）、CT（249/216/33 bp）和TT（216/33 bp）3种基因型,基因型频率分别为0.52、0.41和0.07;有C、T 2种等位基因,等位基因频率分别为0.72、0.28。多重比较结果表明,不同基因型对中国美利奴部分羊毛生产性能有一定的影响,CC基因型个体的毛丛长度显著短于TT基因型个体(P＜0.05),其毛囊密度显著高于CT和TT基因型个体(P＜0.05)。     

Association Analysis Between Polymorphism of IGF1 Gene and Growth Traits in Rabbit

This study was aimed to analyze the association of insulin-like growth factor 1 (IGF1) gene polymorphisms with growth traits in rabbit. The technology of DNA pooling, PCR-SSCP and direct sequencing were used to detect the SNP of IGF1 gene. The results showed that T365C was detected in IGF1 gene exon 3 of rabbit. The SNP (C/T) was devised into three genotypes:TT, TC and CC. The relationships between genotypes and growth traits revealed that the birth weight and the weight at 28 days of age in New Zealand rabbit of TT genotype of T365C locus were significantly higher than TC and CC genotypes (P<0.05), the birth weight, the weight at 90 days of age and average daily gain form birth to 90 days of age in Belgian rabbit of TT genotype of T365C locus were significantly higher than TC and CC genotypes (P<0.05), there were no significant difference of the growth traits in other rabbit breeds (P>0.05).The consequence indicated that IGF1 gene was primarily deduced to be a potential major gene or linked to major gene effecting the growth traits of rabbit, and this SNP (T365C) might be a candidate molecular genetic markers to improve the growth traits of rabbit.     

Effects of forage type,body condition and single‐nucleotide polymorphisms in the bovine cytochrome P450 regulatory region on cow productivity*

Single‐nucleotide polymorphisms (SNP) in the coding sequence of cytochrome p450 (CYP3A28) have been associated with milk yield and composition, and calving traits in cows. In this study, we aimed to determine whether (i) the CYP3A28 regulatory region was polymorphic and (ii) SNP genotype, forage type, body condition and their interactions affect cow productivity. Primers for CYP3A28 promoter were designed to amplify a 483‐bp segment by PCR. Amplicon sequences revealed seven SNP (T‐318C, T‐113A, C‐189T, T‐78G, A6G, G17A and T21C) in Brahman (38 cows), Brahman x Angus reciprocal crosses (47 cows) and crossbreds (98 cows). Angus cows (n = 41) appeared to be fixed at those SNP locations. Genotype and forage {endophyte‐infected tall fescue [KY+; Lolium arundinaceum (Schreb.) S. J. Darbyshire] vs. bermudagrass [Cynodon dactylon (L.) Pers.]} effects on lifetime (8‐years) calving rate, and calf weaning weights and heights were determined in Herd 1 (126 cows); genotype and BC (low vs. moderate) effects on calving date and calving percent were determined in Herd 2 (98 cows). Four SNP (T‐318C, T‐113A, A06G and T21C) appeared to be related to cattle productivity, CC cows at T‐318C having a lower (p < 0.05) lifetime calving rate than TC or TT cows (65%, 85% and 81% respectively). Cows that grazed KY+ and were TT at T‐318C produced calves that tended (p < 0.07) to weigh less than their contemporaries. Moreover, calves of TT cows were shorter (p < 0.05) at weaning than calves of CC or TC cows. In Herd 2, moderate‐BC cows that were TT or AA at T‐318C, T‐113A, T‐78G, A6G and T21C had greater (p < 0.05) calving rates (74–80%) than heterozygous cows (46–60%), and low‐BC cows that were AA at G17A calved at least 6 days earlier (p < 0.05) than heterozygous cows. Our findings suggest that SNP in the CYP3A28 regulatory region of Brahman‐influenced cows are associated with cattle productivity.     

Molecular characteristics of MC1R gene in tile-grey plumage of domestic chicken

ABSTRACT

1. Tile-grey plumage is a unique and rare feather type of local chicken breeds in China, but its genetic mechanism and corresponding genes remain unknown.

2. In order to identify the genetic basis and molecular characteristics of tile-grey plumage, this experiment investigated variations of melanocortin 1 receptor (MC1R) gene in Yunnan Piao chickens with typical tile-grey plumage characteristics in contrast with three Yunnan local breeds as well as two standard breeds with different plumage colour, and analysed the association between genic variation and tile-grey plumage.

3. Through sequencing and comparison of the entire coding region of the MC1R gene, a total of 10 SNP loci were detected, of which eight were non-synonymous mutations that cause amino acid changes. The gene frequency and genotype frequency of the MC1R mutation sites in different breeds and different plumage colour groups revealed that C69T, T212C and A274G were significantly associated with tile-grey plumage. Eighteen haplotypes of the MC1R gene were constructed based on 10 nucleotide variations and eight amino acid variations. Haplotype distribution and the median joining network in breeds and plumage colour groups revealed a main haplotype (hap2) for tile-grey plumage. Hap2 is unique to the tile-grey feather of Piao chicken, and the individuals carrying this haplotype account for 62.96% of the whole tile-grey chicken.

4. The results of this study are of significance for further analysis of the molecular basis of tile-grey plumage and the selective breeding of tile-grey plumage.     

家兔IGF1基因多态性与生长性状的关联分析

本研究旨在探讨胰岛素样生长因子1（insulin-like growth factor 1,IGF1）基因SNP与家兔生长性状的关联性。采用DNA池、PCR-SSCP方法对家兔IGF1基因的外显子进行多态性检测,结果发现,在家兔IGF1基因的外显子3中检测到1个SNP位点T365C,表现为3种基因型：TT、TC和CC。IGF1基因不同基因型与家兔生长性状的关联分析结果发现,新西兰兔TT基因型个体的初生重、28日龄体重均显著高于TC和CC基因型个体（P<0.05）;比利时兔TT基因型个体的初生重、90日龄体重和初生至90日龄的平均日增重均显著高于TC和CC基因型个体（P<0.05）;其余品种的各生长性状指标在该位点均没有达到显著水平（P>0.05）。结果提示,IGF1基因可能是影响家兔生长性状的主效基因或与主效基因连锁,T365C位点有望作为提高家兔个体生长性状的分子遗传标记。     

Association of ADSL gene polymorphisms with meat quality and carcass traits in domestic pigeons (Columba livia)

ABSTRACT

1. Adenylosuccinate lyase (ADSL) plays an important role in the synthesis of inosine monophosphate (IMP). In this trial, a total of 200 pigeons were sampled and slaughtered. Seven meat quality traits and 11 carcass traits were measured. DNA sequencing was used to detect nucleotide mutations, and associations between ADSL gene polymorphisms and meat quality and carcass traits were analysed.

2. Sequencing results showed that 9 nucleotide mutations were found in the exons of the ADSL gene. All the mutations were synonymous except C13065G, which caused a change in amino acids (Ser to Arg). In addition, two of the detected single nucleotide polymorphisms (SNPs) had significant associations with meat quality and carcass traits.

3. For the C13065G SNP located in exon11, the IMP content of breast muscle in AA and AB genotype was higher than in the BB genotype (P < 0.01). The SNP G10696A located in exon10 was significantly associated with carcass rate, in which AA and AB genotype were higher than the BB genotype (P < 0.01).

4. The results indicated that the ADSL gene has a close association with meat quality and carcass traits in domestic pigeons, and G10696A and C13065G SNPs could be applied as genetic markers in molecular marker-assisted breeding of pigeons.     

Functional identification of an exon 1 substitution in the myostatin gene and its expression in breast and leg muscle of the Bian chicken

1. The objective of this study was to verify the functional effects of the c.234G>A substitution in the myostatin (MSTN) gene and ascertain the mechanism by which the variant affects growth traits in the Bian chicken.

2. The c.234G>A substitution was detected by PCR-RFLP analysis in the 7th-generation Bian chickens and three genotypes (AA, AG and GG) were identified. Results showed that the substitution was significantly associated with all studied growth traits, except first-d-weight, in female Bian chickens.

3. Based on these results, the substitution was used in gene-assisted selection for growth traits and thus fast-growth (AA genotype) and slow-growth (GG genotype) lines were successfully established. Significant differences in growth traits were detected between the fast-growth and slow-growth lines from 6 to 16 weeks of age. Furthermore, all slaughter traits, except leg muscle rate, were significantly different between the fast-growth and slow-growth lines.

4. Expression analysis showed that the relative expression level of MSTN in chickens with GG and AG genotypes were significantly higher than that in chickens with an AA genotype, both in breast and leg muscle. Chickens in the slow-growth line had significantly higher relative expression level of MSTN compared to chickens in the fast-growth line, both in breast and leg muscle.

5. The results suggest that the c.234G>A substitution in the myostatin (MSTN) gene negatively regulates the expression of MSTN in the Bian chicken and that it may be used in marker-assisted selection to accelerate the chicken breeding process.     

Variation in the chicken LPIN2 gene and association with performance traits

1. The objective of the study was to investigate the distribution of LPIN2 variants and haplotypes among breeds and perform an association analysis of the variants and haplotypes with the broiler traits in chickens.

2. Six breeds were used to study the variation and distribution of chicken LPIN2, and an F₂ resource population was used to measure growth traits, carcass traits, meat quality traits and serum biochemistry parameters.

3. A c.-599G>A variant was located in the promoter region of LPIN2 and c.444G>A and c.1730A>T (E577D) coding variant mutations were detected. Linkage disequilibrium tests showed that these three variants were under moderate linkage disequilibrium in the 6 breeds and 7 haplotypes were constructed. The distribution of variation/haplotypes presented clear differences among breeds.

4. Association analysis showed that c.-599G>A was associated with leg muscle weight, jejunum length, ileum length, leg muscle fibre density and leg muscle fibre diameter; c.444G>A was associated with spleen weight, ileum length, body weight at hatch and metatarsus length at 8 weeks; c.1730T>A had significant effects on chicken liver weight, heart weight, body weight at 10 weeks, serum albumin and glucose.

5. Diplotypes were significantly associated with body weight at hatch, heart weight, pancreas weight, duodenum length, leg muscle fibre density and lactate dehydrogenase.

     

Comparison of the effects explained by variations in the bovine PLAG1 and NCAPG genes on daily body weight gain,linear skeletal measurements and carcass traits in Japanese Black steers from a progeny testing program

The c.1326T>G single nucleotide polymorphism (SNP) in the NCAPG gene, which leads to an amino acid change of Ile442 to Met442, was previously identified as a candidate causative variation for a bovine carcass weight quantitative trait loci (QTL) on chromosome 6, which was associated with linear skeletal measurement gains and daily body weight gain at puberty. Recently, we identified the stature quantitative trait nucleotides (QTNs) in the PLAG1‐CHCHD7 intergenic region as the causative variations for another carcass weight QTL on chromosome 14. This study aimed to compare the effects of the two QTL on growth and carcass traits using 768 Japanese Black steers from a progeny testing program and to determine whether a genetic interaction was present between them. The FJX_250879 SNP representing the stature QTL was associated with linear skeletal measurements and average daily body weight gain at early and late periods during adolescence. A genetic interaction between FJX_250879 and NCAPG c.1326T>G was detected only for body and rump lengths. Both were associated with increased carcass weight and Longissimus muscle area, and NCAPG c.1326T>G was also associated with reduced subcutaneous fat thickness and increased carcass yield estimate. These results will provide useful information to improve carcass weight in Japanese Black cattle.