Association of SCD1 and DGAT1 SNPs with the intramuscular fat traits in Chinese Simmental cattle and their distribution in eight Chinese cattle breeds

Intramuscular fat (IMF) is a key parameter for evaluation of nutritional quality of beef, with its endogenous synthesis regulated by stearoyl CoA desaturase (SCD1) and diacylglycerol-acyl transferase 1 (DGAT1) genes in cattle. The object of this research was to evaluate the effect of SCD1 and DGAT1 polymorphisms on IMF trait in beef cattle and to estimate the frequency distribution of SNPs in the two genes in Chinese cattle populations. The SCD1 and DGAT1 polymorphisms were detected by PCR-single strand conformation polymorphism (PCR-SSCP) method in Chinese Simmental cattle and their associations with IMF traits were analyzed using the general linear model (GLM). The frequency distribution of SNPs in SCD1 and DGAT1 genes were detected by PCR-SSCP method and analyzed in seven other cattle populations. The results showed significant associations of SNPs SCD1-878, SCD1-762, and DGAT1 10433 and 10434 with IMF (%) and shearing force values (SFV; kg) in Chinese Simmental cattle. A haplotype combining SCD1-878C, SCD1-762T, and DGAT1 10433 and 10434-GC had the highest IMF, marbling score and shearing force. The polymorphic investigation indicated that the frequency of SCD1-878C or SCD1-762T was significantly higher in Chinese southern cattle (Leiqiong, Yunnan High pump, BMY or Minnan Cattle) than in Chinese northern cattle (Chinese Simmental, Luxi Cattle, Bohai Black or Chinese Holstein), while the frequency of DGAT1 10433 and 10434-GC in Chinese indigenous breed (Leiqiong, Yunnan High pump, BMY, Luxi Cattle, Bohai Black, or Minnan Cattle) was significantly lower than breeds with imported blood (Chinese Simmental or Chinese Holstein). These findings demonstrated that both the SCD1 and DGAT1 SNPs were prospect genetic markers for IMF traits, and the SCD1 SNPs could be used as a genetic marker for southern or northern blood in Chinese cattle.     

Novel single nucleotide polymorphisms and haplotypes within the bovine<Emphasis Type="Italic"> CXCR2</Emphasis> gene

The objectives of this study were to identify single nucleotide polymorphisms (SNPs) and resulting haplotypes in the bovine CXCR2 gene. A 311-bp segment of the bovine CXCR2 gene was amplified and sequenced. Five SNPs at positions 612, 684, 777, 858, and 861 were expressed in both Holstein and Jersey dairy cattle. Four SNPs resulted in synonymous substitutions, while a non-synonymous switch at position 777 (GC) resulted in a glutamine to histidine substitution at amino acid residue 245. Strong linkage disequilibrium was exhibited for both breeds among all five loci (P<0.001). Both allele and genotype frequencies differed significantly with respect to breed at four of the five loci (P<0.001). The five polymorphisms generated ten distinct haplotypes. Six haplotypes were common between the two breeds, while Holsteins and Jerseys each uniquely expressed two haplotypes. Of the six common haplotypes, two represented 83% of the Jersey population; whereas four of these haplotypes represented 95% of the Holstein population.     

Polymorphisms in OATP-C: identification of multiple allelic variants associated with altered transport activity among European- and African-Americans

The human organic anion transporting polypeptide-C (OATP-C) (gene SLC21A6) is a liver-specific transporter importantly involved in the hepatocellular uptake of a variety of endogenous and foreign chemicals. In this study, we demonstrate the presence of multiple functionally relevant single-nucleotide polymorphisms (SNPs) in OATP-C in a population of African- and European-Americans. Moreover, examination of 14 nonsynonymous polymorphisms indicated that genotypic frequencies were dependent on race. Functional assessment of 16 OATP-C alleles in vitro revealed that several variants exhibited markedly reduced uptake of the OATP-C substrates estrone sulfate and estradiol 17beta-d-glucuronide. Specifically, alterations in transport were associated with SNPs that introduce amino acid changes within the transmembrane-spanning domains (T217C (Phe-73 --> Leu), T245C (Val-82 --> Ala), T521C (Val-174 --> Ala), and T1058C (Ile-353 --> Thr)) and also with those that modify extracellular loop 5 (A1294G (Asn-432 --> Asp), A1385G (Asp-462 --> Gly), and A1463C (Gly-488 --> Ala)). Cell surface biotinylation experiments indicated that the altered transport activity of some OATP-C variants was due, in part, to decreased plasma membrane expression. Given the relatively high genotypic frequency of the T521C (14%) transition in European-Americans and the G1463C (9%) transversion in African-Americans, SNPs in OATP-C may represent a heretofore unrecognized factor influencing drug disposition.     

Identification of three SNPs in the porcine myostatin gene (MSTN)

Thirteen pairs of primers were designed for the entire porcine MSTN gene to enable PCR amplification for the detection of single nucleotide polymorphisms (SNPs) by a PCR-SSCP approach. Altogether 96.5% (1089/1128) of the encoding regions and 971 bp of the non-coding regions were screened. A total of three polymorphisms were identified with PCR-SSCP. They were located in the promoter, intron one and exon three regions of the gene. These polymorphisms were then confirmed to be point mutations (T --> A transversion, G --> A transition and C --> T transition respectively) by sequencing. Allele frequencies were determined for all three SNPs in several different pig breed populations. The polymorphisms were found to be rare in Western breeds, but much more common in Chinese breeds. Whether they have any relationship with the marked difference in lean meat mass between Western and Chinese breeds requires further study.     

SNP detection and haplotype analysis in partial sequence of MSTN gene in sheep

Polymerase chain reaction (PCR) products of the MSTN gene amplified from sixty sheep of nine Chinese indigenous sheep breeds and one imported sheep breed were sequenced to identify the single-nucleotide polymorphisms (SNPs) in a 378-bp fragment including intron 2 and exon 3 of the MSTN gene. A total of fifteen SNPs (A1937C, T1942G, C1956T, A1972C, A1990G, A2008C, A2011G, C2019T, A2025C, A2027C, T2085G, T2173C, C2198T, C2210T and C2213T) were detected among the sixty sequenced individuals and they were all located in intron 2. Twelve haplotypes were identified from these fifteen SNPs, of which haplotype I (CGTCGCGTCCGCTTT) and VIII (ATCAAAACAATTCCC) were the two major and basic ones with frequencies of 12.25% and 77.80%, respectively. Haplotype VIII was distributed in all sheep breeds and all individuals of the meat or meat-wool type sheep breeds were homozygous with respect to this haplotype. This suggests that haplotype VIII might be related to meat production traits in sheep. Haplotype I was only distributed in the fur, lambskin type and fur-meat type sheep breeds. This suggests that haplotype I may have some relationship with fur traits in sheep.     

Genotyping of Novel SNPs in BMPR1B,BMP15, and GDF9 Genes for Association with Prolificacy in Seven Indian Goat Breeds

Goats form the backbone of rural livelihood and financial security systems in India but their population is showing decreasing trend. Improvement of reproductive traits such as prolificacy offers a solution to stabilize the decreasing goat population and to meet the nutritional needs of growing human population. In the present study, six novel SNPs in three candidate genes for prolificacy (BMPR1B, BMP15, and GDF9) were genotyped in seven breeds of Indian goats to evaluate their association with litter size. Tetra primer ARMS-PCR and PCR-RFLP based protocols were developed for genotyping six novel SNPs, namely, T(-242)C in BMPR1B; G735A and C808G in BMP15; and C818T, A959C, and G1189A in GDF9 gene. The effect of breed was highly significant (p ≤ 0.01) on litter size but the effect of genotype was nonsignificant. The effect of parity on litter size was also significant in the prolific Black Bengal breed. The litter size differences observed between breeds are attributed to breed differences. Novel mutations observed at different loci in GDF9, BMP15, and BMPR1B genes do not contribute to the reproductive capability of the investigated breeds. Further studies with more number of breeds and animals exploring association of these novel SNPs with reproductive traits may be fruitful.     

Differences in the rumen methanogen populations of lactating Jersey and Holstein dairy cows under the same diet regimen

In the dairy cattle industry, Holstein and Jersey are the breeds most commonly used for production. They differ in performance by various traits, such as body size, milk production, and milk composition. With increased concerns about the impact of agriculture on climate change, potential differences in other traits, such as methane emission, also need to be characterized further. Since methane is produced in the rumen by methanogenic archaea, we investigated whether the population structure of methanogen communities would differ between Holsteins and Jerseys. Breed-specific rumen methanogen 16S rRNA gene clone libraries were constructed from pooled PCR products obtained from lactating Holstein and Jersey cows, generating 180 and 185 clones, respectively. The combined 365 sequences were assigned to 55 species-level operational taxonomic units (OTUs). Twenty OTUs, representing 85% of the combined library sequences, were common to both breeds, while 23 OTUs (36 sequences) were found only in the Holstein library and 12 OTUs (18 sequences) were found only in the Jersey library, highlighting increased diversity in the Holstein library. Other differences included the observation that sequences with species-like sequence identity to Methanobrevibacter millerae were represented more highly in the Jersey breed, while Methanosphaera-related sequences and novel uncultured methanogen clones were more frequent in the Holstein library. In contrast, OTU sequences with species-level sequence identity to Methanobrevibacter ruminantium were represented similarly in both libraries. Since the sampled animals were from a single herd consisting of two breeds which were fed the same diet and maintained under the same environmental conditions, the differences we observed may be due to differences in host breed genetics.     

五指山猪IGF2基因5′调控区单核苷酸多态性分析

利用PCR产物直接测序法, 对五指山猪、滇南小耳猪、香猪、梅山猪和大白猪共60个样本的IGF2基因5＇调控区部分片段的单核苷酸多态性进行了研究。找到13个SNP, 分别是: C5872T、C5888T、A5976G、C6010T、T6029A、C6037T、C6043T、C6063T、C6112T、C6164T、G13520A、G13563A和G13669A。T6029A为T←→A碱基颠换, A5976G、G13520A、G13563A和G13669A为A←→G转换, 其他均为C←→T转换。针对13个SNP位点得到23种组合基因型。统计各位点等位基因和基因型以及各组合基因型在总群体与各品种内的分布频率, 发现3个小型猪在A5976G、C6164T和G13669A位点上的优势等位基因均分别为G、T和A, 而梅山猪和大白猪的优势等位基因均分别为A、C和G; H19型为3个小型猪的特征组合基因型, 而另两个猪品种为H15型。同时对123头五指山猪IGF2基因C5888T位点进行了PCR-RFLP分析, 研究表明该位点C为优势等位基因(0.8536), CC为优势基因型(0.7235)。卡方检验表明该位点处于Hardy-Weinberg平衡状态。这些结果可为五指山猪等小型猪的生长发育规律、矮小机制等方面的研究提供遗传学依据。     

Polymorphism of intron 2 of the SDF1 gene in Galloway, Hereford, and Russian Black Pied cattle

The region of intron 2 of the SDF1 gene encoding a chemokine of the CXC subfamily has been resequenced in Galloway, Hereford, and Black Pied cattle. Five of the single-nucleotide polymorphisms (SNPs) that were earlier detected by other authors in various breeds of cattle in North America (99C/G, 128T/C, 206C/T, 267C/G and 313C/T) have been found. The 270insC polymorphic marker has proved to be monomorphic in Russian cattle breeds. Hereford cattle significantly differ from Galloway and Black Pied cattle in the frequencies of some SNP variants and their combinations. The number of SNP combinations in Hereford and Galloway cattle exceeds that in Black Pied cattle.     

The complementary neighborhood patterns and methylation-to-mutation likelihood structures of 15,110 single-nucleotide polymorphisms in the bovine genome

Bayesian analysis was performed to examine the single-nucleotide polymorphism (SNPs) neighborhood patterns in cattle using 15,110 SNPs, each with a flanking sequence of 500 bp. Our analysis confirmed three well-known features reported in plants and/or other animals: (1) the transition is the most abundant type of SNPs, accounting for 69.8% in cattle; (2) the transversion occurs most frequently (38.56%) in cattle when the A + T content equals two at their immediate adjacent sites; and (3) C <--> T and A <--> G transitions have reverse complementary neighborhood patterns and so do A <--> C and G <--> T transversions. Our study also revealed several novel SNP neighborhood patterns that have not been reported previously. First, cattle and humans share an overall SNP pattern, indicating a common mutation system in mammals. Second, unlike C <--> T/A <--> G and A <--> C/G <--> T, the true neighborhood patterns for A <--> T and C <--> G might remain mysterious because the sense and antisense sequences flanking these mutations are not actually recognizable. Third, among the reclassified four types of SNPs, the neighborhood ratio between A + T and G + C was quite different. The ratio was lowest for C <--> G, but increased for C <--> T/A <--> G, further for A <--> C/G <--> T, and the most for A <--> T. Fourth, when two immediate adjacent sites provide structures for CpG, it significantly increased transitions compared to the structures without the CpG. Finally, unequal occurrence between A <--> G and C <--> T in five paired neighboring structures indicates that the methylation-induced deamination reactions were responsible for approximately 20% of total transitions. In addition, conversion can occur at both CpG sites and non-CpG sites. Our study provides new insights into understanding molecular mechanisms of mutations and genome evolution.     

牛HTR1B基因的分子遗传特性研究

用PCR-SSCP技术研究了涉及肉牛和奶牛共计7品种HTR1B基因的编码区和3′侧翼区的多态性,以期为牛性情的标记辅助选择积累数据。扩增得到4个片段, 有3个片段存在(SSCP)多态性。对不同的SSCP带型对应片段进行测序, 共发现6个SNP多态位点(G205T、C507T、C546G、C744T、G816A和G942A)。各遗传群体内G205T、C744T、G816A和G942A 位点均处于Hardy-Weinberg平衡, 而C507T和C546G位点只有鲁西牛处于Hardy-Weinberg平衡。奶牛205T等位基因频率显著高于其他肉牛品种(χ2 = 6.87)。奶牛G205T位点多态信息含量为0.25, 其余各位点在不同群体内均小于0.10, 说明牛HTR1B基因较保守。     

Improvement of Prediction Ability for Genomic Selection of Dairy Cattle by Including Dominance Effects

Dominance may be an important source of non-additive genetic variance for many traits of dairy cattle. However, nearly all prediction models for dairy cattle have included only additive effects because of the limited number of cows with both genotypes and phenotypes. The role of dominance in the Holstein and Jersey breeds was investigated for eight traits: milk, fat, and protein yields; productive life; daughter pregnancy rate; somatic cell score; fat percent and protein percent. Additive and dominance variance components were estimated and then used to estimate additive and dominance effects of single nucleotide polymorphisms (SNPs). The predictive abilities of three models with both additive and dominance effects and a model with additive effects only were assessed using ten-fold cross-validation. One procedure estimated dominance values, and another estimated dominance deviations; calculation of the dominance relationship matrix was different for the two methods. The third approach enlarged the dataset by including cows with genotype probabilities derived using genotyped ancestors. For yield traits, dominance variance accounted for 5 and 7% of total variance for Holsteins and Jerseys, respectively; using dominance deviations resulted in smaller dominance and larger additive variance estimates. For non-yield traits, dominance variances were very small for both breeds. For yield traits, including additive and dominance effects fit the data better than including only additive effects; average correlations between estimated genetic effects and phenotypes showed that prediction accuracy increased when both effects rather than just additive effects were included. No corresponding gains in prediction ability were found for non-yield traits. Including cows with derived genotype probabilities from genotyped ancestors did not improve prediction accuracy. The largest additive effects were located on chromosome 14 near DGAT1 for yield traits for both breeds; those SNPs also showed the largest dominance effects for fat yield (both breeds) as well as for Holstein milk yield.     

A novel polymorphisms in intron 12 of the bovine <Emphasis Type="Italic">calpastatin</Emphasis> gene

Calpastatin (CAST) is a specific inhibitor of the ubiquitous calcium-dependent proteases-mu-calpain and m-calpain, found in mammalian tissues. This proteolytic system plays a key role in the tenderization process that occurs during post-mortem storage of meat under refrigerated conditioning. Fragments of the bovine CAST gene including intron 12 were amplified and subjected to SSCP analysis. Four new SNPs were found within intron 12 of the CAST gene: a transition T/C at position 3893+155* A/G at position 3893+163, a transversion T/A at position 3893+223 and a substitution A/G at position 3893+428 (consensus sequence--GenBank AY834771). The genetic variants in the bovine CAST gene can be analyzed with RFLP method and was studied in 375 bulls of six breeds, including Hereford, Aberdeen-angus, Simmental, Charolaise, Limousine and Polish Black-and-White (BW; Fresian) breeds.     

Molecular characterization of porcine hyaluronidase genes 1, 2, and 3 clustered on SSC13q21

Hyaluronidase genes (HYAL) encode hyaluronidase enzymes required for hyaluronan degradation. Both in humans and in mouse, clustered hyaluronidase genes have been identified. Here, the porcine hyaluronidase cluster consisting of genes HYAL1, HYAL2 and HYAL3 was characterized. The porcine cDNA sequences and proteins share homologies to human orthologs of 85 and 81% for HYAL1, 87 and 89% for HYAL2 and 86 and 83% for HYAL3, respectively. The porcine hyaluronidase proteins approximately share a 40% homology with each other. Furthermore, genes FUS1 and FUS2 were found within this cluster, which was assigned to SSC13q21. A total of seven SNPs were detected in the genes (four in HYAL1, two in HYAL2 and one in HYAL3). Three of the four SNPs in HYAL1 led to amino acid exchanges (C622G --> Asp24 to Glu; C633T --> Pro28 to Leu, and G1298T --> Ala250 to Ser). The amino acid replacements induce putative changes in the extended strand at Asp24, in the extended strand and the random coil at Pro28, and finally in the random coil and the alpha helix at Ala250. Frequency estimations for four SNPs located in genes HYAL1 and HYAL3 using animals (n = 295) of nine European and six Chinese pig breeds indicated several significant deviations. For example, there were no significant differences in allele frequencies between pigs representing breeds Hampshire and Jiangquhai at SNP C633T (HYAL1), but between Hampshire respectively Jiangquhai animals and Rongchang pigs. Analysis of the same breeds at SNP C588T (HYAL3) indicates significant differences between Hampshire and Jiangquhai respectively Rongchang, but not between Jiangquhai and Rongchang. The breed G?ttingen Minipig displayed significant differences concerning two SNPs with respect to the other European pig breeds tested. For all three hyaluronidase genes, N-glycosylation sites are typical. For HYAL2 the lysosomal character was proven. The catalytic site responsible for HAase activity is conserved in the three enzymes. Expression of hyaluronidases was determined by RT-PCR and quantitative PCR. Broad gene expression was observed in different tissues for the three genes, respectively.     

Hydrogen-exchange stabilities of RNase T1 and variants with buried and solvent-exposed Ala --> Gly mutations in the helix

Hydrogen-exchange rates were measured for RNase T1 and three variants with Ala --> Gly substitutions at a solvent-exposed (residue 21) and a buried (residue 23) position in the helix: A21G, G23A, and A21G + G23A. These results were used to measure the stabilities of the proteins. The hydrogen-exchange stabilities (DeltaG(HX)) for the most stable residues in each variant agree with the equilibrium conformational stability measured by urea denaturation (DeltaG(U)), if the effects of D(2)O and proline isomerization are included [Huyghues-Despointes, B. M. P., Scholtz, J. M., and Pace, C. N. (1999) Nat. Struct. Biol. 6, 210-212]. These residues also show similar changes in DeltaG(HX) upon Ala --> Gly mutations (DeltaDeltaG(HX)) as compared to equilibrium measurements (DeltaDeltaG(U)), indicating that the most stable residues are exchanging from the globally unfolded ensemble. Alanine is stabilizing compared to glycine by 1 kcal/mol at a solvent-exposed site 21 as seen by other methods for the RNase T1 protein and peptide helix [Myers, J. K., Pace, C. N., and Scholtz, J. M. (1997) Proc. Natl. Acad. Sci. U.S.A. 94, 3833-2837], while it is destabilizing at the buried site 23 by the same amount. For the A21G variant, only local NMR chemical shift perturbations are observed compared to RNase T1. For the G23A variant, large chemical shift changes are seen throughout the sequence, although X-ray crystal structures of the variant and RNase T1 are nearly superimposable. Ala --> Gly mutations in the helix of RNase T1 at both helical positions alter the native-state hydrogen-exchange stabilities of residues throughout the sequence.     

鸭脂联素基因单核苷酸多态性检测及群体遗传分析

以昆山麻鸭、樱桃谷鸭、高邮鸭、荆江麻鸭、金定鸭, 山麻鸭、龙白鸭和白羽番鸭8个鸭品种为实验材料, 根据鸭脂联素基因开放阅读框序列设计5对引物, 用PCR-SSCP方法进行单核苷酸多态性分析,并对不同品种群体进行群体遗传学分析。结果发现引物4扩增片段上共存有7个单碱基突变, 第430、457、523处的G-A 、A-G、T-C单碱基突变导致第144、153、175个氨基酸分别由丙氨酸（A）变为苏氨酸（T）、异亮氨酸（I）变为缬氨酸(V)、酪氨酸(Y)变为组氨酸(H); 而C507T, T540C, C576T和C597T 4个单碱基突变为沉默突变。鸭群中表现出AA、AB、AC、BB、BC、CC、DD、DE 8种基因型。8种基因型在8个鸭品种间分布存在极显著的差异(P<0.01)。除金定鸭外, 其他品种均处于Hardy-Weinberg平衡状态。群体遗传分析表明金定鸭的纯合度最高, 高邮鸭最低, 其他各群体的纯合度较相近; 金定鸭为低度多态, 高邮鸭为高度多态, 其他品种为中度多态。表明鸭脂联素基因不同品种中具有丰富的单核苷酸多态性, 可以进一步作为候选基因来分析其与脂肪性状的相关性。     

Novel SNPs in the caprine stearoyl-CoA desaturase (SCD) and decorin (DCN) genes that are associated with growth traits in Chinese goat breeds

Stearoyl-CoA desaturase (SCD) is an iron-containing enzyme involving in the biosynthesis of monounsaturated fatty acids (MUFA) in mammary gland and adipose tissue, while decorin (DCN) consists of a protein core and a single dermatan or chondroitin sulfate glycosaminoglycan chain, contributing multifunctionally to matrix assembly, modulation of the activity of growth factors and cell migration and proliferation. However, few studies have focused on the genetic variability of them in goat. Herein, five Chinese goat breeds (1229 animals) were analyzed. Based on DNA pooling and PCR-RFLP, three nucleotide substitutions, one of which caused a amino acid substitution, were detected in SCD gene and three haploids (A, B, C) were constructed. According to SSCP analysis and DNA sequencing methods, a 2-bp deletion and two other SNPs were found existing in another analyzed gene DCN, and three haploids (X, Y, Z) were built. Associations between the genotypes and the growth traits (body length, body height, chest circumference, cannon circumference) were also analyzed. For SCD gene, genotype CC individuals had significant greater body height in Guanzhong and body length in both Guanzhong and Xinong saanen than genotype BC individuals (P < 0.05). For DCN gene, individuals with genotype XX was obviously higher than that with genotype XY (P < 0.05). These results indicated that genotype CC of SCD gene and genotype XX of DCN gene could be used for the breeding of new breeds of goat in China.     

Genetic effects of stearoyl-coenzyme A desaturase (SCD) polymorphism on milk production traits in the Chinese dairy population

Stearoyl-CoA desaturase (SCD) is a multifunctional complex enzyme important in the cellular biosynthesis of fatty acids. The present study was to investigate the association of the SCD gene with milk production traits in dairy cattle. Two single nucleotide polymorphisms (SNPs) (g.6926A>G and g.8646A>G) in introns 3 and 4, and three SNPs (g.10153A>G, g.10213T>C and g.10329C>T) in exon 5 were identified with pooled DNA sequencing and genotyped using matrix-assisted laser desorption/ionization time of flight mass spectrometry assay in 752 Chinese Holstein cows. Polymorphism g.10329C>T was predicted to result in an amino acid replacement from alanine to valine in the SCD protein. With a mixed animal model, the significant associations of the five SNPs with 305-day milk, fat and protein yields and protein percentage were determined. We further demonstrated cows with heterozygous genotypes (A/G or C/T) had highest 305 day milk yield, fat yield, protein yield and lowest protein percentage. Heterozygous cows with genotype AG at the g.6926A>G locus showed the greatest milk yield (P < 0.0001), fat yield (P < 0.0001) and protein yield (P < 0.0001) among other heterozygous genotypes at any of the loci. Dominance effects of all identified SNPs on milk, fat and protein yields and protein percentage were significant. Moreover, significant allele substitution effects at g.6926A>G locus on milk yield and at g.10213T>C on protein yield were observed. Five-locus haplotypes and strong linkage disequilibrium (D' > 0.9) between the five SNPs were also observed. The results suggest that identified polymorphisms could be potential genetic markers to improve the production performance of Chinese Holstein.     

SNPs in the porcine <Emphasis Type="Italic">PPARGC1a</Emphasis> gene: Interbreed differences and their phenotypic effects

Due to its function, the peroxisome proliferative activated receptor-γ, coactivator-1α (PPARGC1A) gene is a candidate in the search for genes that may affect production traits in the pig. The purpose of this study was to screen for new SNPs in exon 8 of the porcine PPARGC1A gene and to test their possible association with production traits. Altogether 736 pigs representing five breeds Polish Landrace, n=242; Polish Large White, n=192; Hampshire, n=27; Duroc, 21; Pietrain, n=12) and synthetic line 990 (n=242) were scanned via SSCP assay. Four SNPs were found; two new ones: C/G (His338Gln) and G/A Thr359Thr), and two previously reported ones: C/A (Arg369Arg) and T/A Cys430Ser). The missense T/A and C/G SNPs demonstrated pronounced interbreed variability in terms of allele frequencies, including the exclusive presence of the C/G substitution in the Hampshire breed. The tested SNPs occurred in five putative haplotypes, and their frequency also differed substantially between breeds. The association of the SNPs with production traits was tested for G/A (Thr359Thr), C/A (Arg369Arg) and T/A (Cys430Ser) substitutions in Polish Large White, Polish Landrace and line 990. The analysis revealed only breed-specific associations. The T/A (Cys430Ser) SNP was related to the feed conversion ratio in the Polish Large White (P=0.02), and the silent G/A and C/A substitutions were respectively associated with abdominal fat in line 990 and backfat thickness in Polish Landrace (P=0.04). The combined effects of the substitutions were estimated as haplotype effects. Three significant contrasts between haplotypes were calculated, but the observed associations were again only breed-specific.     

Associations of the bovine major histocompatibility complex DRB3 (BoLA-DRB3) alleles with occurrence of disease and milk somatic cell score in Canadian dairy cattle

Potential associations were investigated between bovine leucocyte antigen (BoLA) alleles and occurrence of disease. Cows (Holstein n = 835; Jersey n = 66) were examined for polymorphisms of the second exon of the BoLA-DRB3 gene, using the polymerase chain reaction (PCR), followed by digestion of the amplified fragments with three restriction endonucleases. Disease occurrences were recorded for each cow throughout one lactation. Milk somatic cell count data were retrieved through the Dairy Herd Improvement records and converted to somatic cell score (SCS). There were no effects of BoLA alleles on SCS in Jersey cows, but BoLA-DRB3·2* 16 was significantly associated ( P ≤ 0·05) with lower SCS in Holsteins. Since the number of Jerseys was relatively small and prevalence of diseases in this population was low, health records of Jerseys were not analyzed further. BoLA associations with occurrence of disease in Holsteins were investigated using a log-linear model. There was a significant ( P ≤ 0·05) association between BoLA-DRB3.2* 23 and occurrence of severe mastitis, from which coliforms were the most commonly isolated bacteria. The BoLA allele *3 was associated with a lower risk of retained placenta ( P ≤ 0·05) and alleles *16 ( P ≤ 0·05) and *22 ( P ≤ 0·05) with a lower risk of cystic ovarian disease. Although more studies are required to confirm the present findings, it can be concluded that BoLA alleles may have potential usefulness as genetic markers of higher or lower risk of disease occurrence in cows.