Assessment of association between variants and haplotypes of the IGF2 gene in beef cattle

Insulin-like growth factor 2 (IGF2) is a fetal growth and differentiation factor that plays an important role in muscle growth and in myoblast proliferation and differentiation. The aim of this study was to examine the association of the IGF2 polymorphism with growth traits in beef cattle breed. Four single nucleotide polymorphisms (SNPs: 1–4) were identified in the bovine IGF2 by sequencing pooled DNA samples (Pool-Seq) and forced polymerase chain reaction–restriction fragment length polymorphism (Forced PCR–RFLP) methods. The result of haplotype analysis of four SNPs showed that eight haplotypes and eighteen combined genotypes were revealed, and the linkage disequilibrium and evolutionary relationship were assessed in 1522 individuals representing four purebred cattle breeds from China. The statistical analyses indicated that the 4 SNPs and 18 combined genotypes or haplotypes are associated with the body weight at 18 and 24 months in Jiaxian cattle population (P < 0.05 or P < 0.01). Our results provide evidence that polymorphisms in the IGF2 gene are associated with growth traits, and may be used for marker-assisted selection in beef cattle breeding program.     

Haplotype distribution in the GLI3 gene and their associations with growth traits in cattle

The glioma-associated oncogene family zinc finger 3 gene (GLI3) mediates in all vertebrates hedgehog (Hh) signaling that plays an essential role in the induction and patterning of numerous cell types during invertebrate and vertebrate development. In this study, a total of 6 single nucleotide polymorphisms (SNPs: 1–6) were identified by polymerase chain reaction–single stranded conformational polymorphism (PCR–SSCP) and DNA pool sequencing, including all 13 exons and 12 exon–intron boundaries within the bovine GLI3 gene. 16 haplotypes and 13 combined genotypes were revealed and the linkage disequilibrium was assessed in 708 individuals representing three main cattle breeds from China. The statistical analyses indicated that the SNP2, 3 and 4 are associated with the body weight at birth and 6 months in Nanyang cattle population (P < 0.05). No significant association was detected between 11 combined genotypes and body weight at five different ages. Our results provide evidence that polymorphisms in the GLI3 gene are associated with growth traits, and may be used for marker-assisted selection in beef cattle breeding program.     

Novel polymorphisms of the APOA2 gene and its promoter region affect body traits in cattle

Apolipoprotein A-II (APOA2) is one of the major constituents of high-density lipoprotein and plays a critical role in lipid metabolism and obesity. However, similar research for the bovine APOA2 gene is lacking. In this study, polymorphisms of the bovine APOA2 gene and its promoter region were detected in 1021 cows from four breeds by sequencing and PCR-RFLP methods. Totally, we detected six novel mutations which included one mutation in the promoter region, two mutations in the exons and three mutations in the introns. There were four polymorphisms within APOA2 gene were analyzed. The allele A, T, T and G frequencies of the four loci were predominant in the four breeds when in separate or combinations analysis which suggested cows with those alleles to be more adapted to the steppe environment. The association analysis indicated three SVs in Nangyang cows, two SVs in Qinchun cows and the 9 haplotypes in Nangyang cows were significantly associated with body traits (P < 0.05 or P < 0.01). The results of this study suggested the bovine APOA2 gene may be a strong candidate gene for body traits in the cattle breeding program.     

Proopiomelanocortin gene polymorphisms and its association with meat quality traits by ultrasound measurement in Chinese cattle

Ultrasound technology was used to measure live animal meat traits instead of true carcass meat traits for beef production and cattle breeding by an increasing number of institutions. In this study, we analyzed the association between genetic polymorphisms of proopiomelanocortin (POMC) and ultrasound measurement traits in Chinese cattle. Using direct DNA sequencing in 322 individuals of 7 different cattle subpopulation, 7 SNPs were identified for genotyping within 790 bp region of intron 2 and exon 3 of POMC. 6586 T>G in intron 2 and 6769 C>T and 7216 C>T in exon 3 were significantly associated with ultrasound backfat thickness (UBF) (P < 0.05) and ultrasound loin muscle area (ULMA) (P < 0.01) in the total population; 6694 C>T, 6706 T>C, 6796 C>T and 6810 C>T in exon 3 were significantly associated with ULMA (P < 0.0001) in the total population. These results clearly suggest that these SNPs of POMC be benefit for selection of individuals with good quality meat in Chinese cattle breeding program. Following validation in other populations and breeds, these markers could be incorporated into breeding programs to increase the rate of improvement in carcass and meat quality traits.     

Haplotypes and effects on growth traits of bovine Wnt7a gene in Chinese Qinchuan cattle

Wnt7a is a member of the WNT gene family, which encodes secreted signaling proteins and responds to many biological processes. Specifically Wnt7a influences satellite stem cells and regulates the regenerative potential of the muscle. However, similar researches about the bovine Wnt7a gene are lacking. Therefore, in this study, polymorphisms of the bovine Wnt7a gene were detected in 488 individuals from Chinese Qinchuan cattle by DNA pooling, forced PCR-RFLP, and DNA sequencing methods. 3 novel SNPs were identified, two SNPs (g.T4926C and g.A21943G) were in the intron and the last one (g.C63777T) was in the exon. Five haplotypes involved in these three variant sites in the Wnt7a gene were identified and their effects on growth traits were analyzed. The results revealed that haplotype 1 had the highest haplotype frequencies and was highly significantly associated with body height (P < 0.01), body weight (P < 0.05), chest width (P < 0.05) and height at hip cross (P < 0.01) respectively.     

Association between JY-1 gene polymorphisms and reproductive traits in beef cattle

Reproductive traits have a high economic value and it is interesting to include them in the selection objectives of an animal breeding program. These traits generally show low heritability and molecular markers may therefore be used in genetic evaluations to improve the accuracy of predictions. The JY-1 gene is expressed in the oocyte and it is associated with folliculogenesis and early embryo development. It has been suggested to affect reproductive traits. In this study, exons 1 and 2 of the JY-1 gene were studied in 385 Nellore females by PCR-sequencing. Seventeen polymorphisms were identified. After analysis of linkage disequilibrium, association tests were performed between eight SNPs and the occurrence of early pregnancy, age at first calving, days to calving, and reconception of primiparous heifers. Seven SNPs were significant for three traits. The most significant was chr29:12,999 T/A (p = 0.003) which was associated with the occurrence of early pregnancy. This SNP might be involved in protein translation inhibition since it affects the initial methionine codon. The JY-1, an oocyte specific gene, influences reproductive traits; further studies investigating other regions of the gene or other genes expressed in tissues of the female reproductive system would be interesting to be performed.     

Effect of genetic variations within the SH2B2 gene on the growth of Chinese cattle

As an adaptor protein, apart from potentiating Janus kinase 2 (JAK2) activation and promoting the insulin signaling pathway, Src homology 2 B 2 (SH2B2) indirectly takes part in the regulation of glucose uptake through the c-Cb1/CAP/TC10 pathway, which can in turn affect growth. In this study, we identified a 4 bp indel mutation and three single nucleotide polymorphisms (SNPs) within the SH2B2 gene in 959 individuals from five Chinese cattle breeds by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and sequencing. Based on the four variations, 12 haplotypes were identified. Additionally, there was a tendency that in every population pair-wise linkages increased progressively from V1–V2 to V3–V4. By association analysis, positive effects of genotypes CC and CT (snp1220 locus), DI (4 bp indel locus), and CC (snp21049 locus) on growth traits were obtained. Furthermore, when combined, individuals with the combination CCDITTCC showed the best performance at an early age. These results were suggestive of an association of snp1220, 4 bp indel and snp12049 with growth performance in Nanyang cattle, indicating possibly the candidate role of the SH2B2 gene in marker assisted selection in a beef cattle breeding program.     

Genetic variants in BMP8B gene are associated with growth traits in Chinese native cattle

As a signaling molecule, bone morphogenetic protein 8B (BMP8B) plays an essential role in bone metabolism and is able to regulate thermogenesis and energy balance, which suggests that BMP8B gene may be a new candidate for growth traits. Here, to characterize the effects of BMP8B gene on growth traits, we first used three Chinese indigenous cattle breeds (n = 845) to detect single nucleotide polymorphisms (SNPs). Five novel SNPs of BMP8B gene (g.− 242C>T, g.2164C>T, g.2639T>C, g.2900C>G and g.10817C>T) were identified by DNA pool sequencing and forced PCR–RFLP. And then we associated the five SNPs with four growth traits (body weight, body length, heart girth, and hucklebone width). Results from association analysis showed that the SNPs 1, 2, and 3 affected growth trait(s) markedly (P < 0.05). Further, 6 combined haplotypes were constructed to guarantee the reliability of analysis results. There were also significant differences in body length, heart girth and body weight between the 6 combined haplotypes (P < 0.05), but not in hucklebone width (P > 0.05). Collectively, our results suggest a modulatory role of BMP8B gene in cattle growth and development, and 3 SNPs could be used as molecular markers in early marker assisted selection (MAS) in beef cattle breeding program.     

Identification of bovine NPC1 gene cSNPs and their effects on body size traits of Qinchuan cattle

NPC1 gene is an important gene closely related to the Niemann–Pick type C (NPC). Mutations in the NPC1 gene tend to cause Niemann–Pick type C, a lysosomal storage disorder. Previous studies have shown that NPC1 protein plays an important role in subcellular lipid transport, homeostasis, platelet function and formation, which are basic metabolic activities in the process of development. In this study, to explore the association between the NPC1 gene variation and body size traits in Qinchuan cattle, we detected four novel coding single nucleotide polymorphisms (cSNPs) in the bovine NPC1 gene, including one missense mutation (SNP1) and three synonymous mutations (SNP2, SNP3 and SNP4). Population genetic analyses of 518 individuals and association correlations between cSNPs and bovine body size traits were conducted in this research. A missense mutation at SNP1 locus was found to be significantly related to the heart girth, hip width and body weight (P < 0.01 or P < 0.05, 3.5-year-old). Two synonymous mutations at SNP2 and SNP3 loci also showed significant effects on hip width (P < 0.05, 3.5-year-old). One synonymous mutation at SNP4 locus showed significant effect on body weight (P < 0.05, 2.0-year-old). Combined haplotypes H₂H₆ and H₆H₆ showed significant effects on body size traits such as heart girth, hip width, and body weight (3.5-year-old, P < 0.01 or P < 0.05). This study provides evidence that the NPC1 gene might be involved in the regulation of bovine growth and body development, and may be considered as a candidate gene for marker assisted selection (MAS) in beef cattle breeding industry.     

Genetic variations in insulin-like growth factor binding protein acid labile subunit gene associated with growth traits in beef cattle (Bos taurus) in China

The insulin-like growth factor binding protein acid labile subunit (IGFALS) gene encodes a serum protein that binds to IGFs and regulates growth, development, and other physiological processes. We have found that sequencing of the IGFALS gene in Chinese Qinchuan beef cattle (n = 300) revealed four SNP loci in exon two of the gene (g1219: T>C, g1893: T>C, g2612: G>A, and g2696: A>G). The SNP g2696: A>G resulted in a change from asparagine to aspartic acid (p. N574D) in the leucine-rich repeat region in the carboxyl-terminal domain of IGFALS. Four SNPs were in low linkage disequilibrium, and 12 different haplotypes were identified in the population. Association analysis suggested that SNP g1219: T>C had a significant association with hip width (P < 0.05) and SNP g2696: A>G displayed a significant association with stature (P < 0.05). The results from our investigation indicated that polymorphisms in the IGFALS gene were associated with growth traits of bovine, and may serve as a genetic marker for selection of beef cattle for growth traits, including stature.     

Identification and genetic effect of haplotype in the bovine BMP7 gene

Bone morphogenetic proteins (BMPs) are peptide growth factors belonging to the transforming growth factor-beta (TGF-β) superfamily, and some members of the BMP family support white adipocyte differentiation. In this study, we focused on the BMP7 which singularly promotes the differentiation of brown preadipocytes. Haplotypes involving 5 single nucleotide polymorphism (SNP) sites in the bovine BMP7 gene were identified and their effect on body weight was analyzed. 16 haplotypes and 18 combined haplotypes were revealed and the linkage disequilibrium was assessed in the cattle population with 602 individuals representing three main cattle breeds from China. The results showed that haplotypes 3, 10 and 14 were predominant and accounted for 75.64%, 69.85%, and 83.36% in Nanyang, Qinchuan and Jiaxian cattle breeds, respectively. The statistical analyses indicated that the SNP 1, 4, and 5 are associated with the body weight, body length, and heart girth at 12 and 24 months in Nanyang cattle population (P < 0.05), whereas there is no significant association between their 16 haplotypes and 18 combined haplotypes. Our results provide evidence that some SNPs and haplotypes in BMP7 are associated with growth traits, and may be utilized as a genetic marker in marker-assisted selection for beef cattle breeding programs.     

Effects of a novel SNP of IGF2R gene on growth traits and expression rate of IGF2R and IGF2 genes in gluteus medius muscle of Egyptian buffalo

Insulin-like growth factor 2 receptor (IGF2R) is responsible for degradation of the muscle development initiator, IGF2, and thus it can be used as a marker for selection strategies in the farm animals. The aim of this study was to search for polymorphisms in three coding loci of IGF2R, and to analyze their effect on the growth traits and on the expression levels of IGF2R and IGF2 genes in the gluteus medius muscle of Egyptian buffaloes. A novel A266C SNP was detected in the coding sequences of the third IGF2R locus (at nucleotide number 51 of exon 23) among Egyptian water buffaloes. This SNP was non-synonymous mutation and led to replacement of Y (tyrosine) amino acid (aa) by D (aspartic acid) aa. Three different single-strand conformation polymorphism patterns were observed in the third IGF2R locus: AA, AC, and CC with frequencies of 0.555, 0.195, and 0.250, respectively. Statistical analysis showed that the homozygous AA genotype significantly associated with the average daily gain than AC and CC genotypes from birth to 9 mo of age. Expression analysis showed that the A266C SNP was correlated with IGF2, but not with IGF2R, mRNA levels in the gluteus medius muscle of Egyptian buffaloes. The highest IGF2 mRNA level was estimated in the muscle of animals with the AA homozygous genotype as compared to the AC heterozygotes and CC homozygotes. We conclude that A266C SNP at nucleotide number 51 of exon 23 of the IGF2R gene is associated with the ADG during the early stages of life (from birth to 9 mo of age) and this effect is accompanied by, and may be caused by, increased expression levels of the IGF2 gene.     

SNP identification in FBXO32 gene and their associations with growth traits in cattle

The F-box protein 32 (FBXO32), also known as Atrogin-1, is one of the four subunits of the ubiquitin protein ligase complex. FBXO32 has been previously shown to be involved in regulation of initiation and development of muscle mass. In the present study, we investigated the polymorphism of FBXO32 gene in 1313 cattle from seven bovine breeds using DNA sequencing, polymerase chain reaction–restriction fragment length polymorphism (PCR–RFLP) and PCR-based amplification-created restriction site (PCR-ACRS) methods. Four novel single nucleotide polymorphisms (SNPs) were identified within bovine FBXO32, and were deposited in the GenBank database. The association studies between these four SNPs and growth traits were performed in NanYang cattle. Notably, the SNPs ss411628932 and ss411628936 were shown to be significantly associated with body length of 24-month-old NanYang cattle. Based on the above four SNPs, 16 haplotypes were identified. The main haplotype was AATA, which occurred at a frequency of more than 40%. Additionally, phylogenetic analysis showed that geographical distance was essential to gene flow among seven cattle breeds. Indigenous bovine breeds displayed genetic difference in comparison to hybrid bovine breeds that have foreign origins. We herein describe for the first time a comprehensive study on the variability of bovine FBXO32 gene that is predictive of genetic potential for body length phenotype.     

Novel polymorphisms of SIX4 gene and their association with body measurement traits in Qinchuan cattle

Sine oculis homeobox homolog 4 (SIX4) gene belongs to the sine oculis/SIX gene family, which includes six members in vertebrates. SIX4 gene plays a crucial role in skeletal myogenesis, and its genetic variations or deficiency may cause hypopituitarism, suggesting that SIX4 gene is a potential candidate gene affecting body measurement traits (BMTs) in animals. Herein, the objectives of this study were to identify genetic polymorphisms of bovine SIX4 gene and to analyze potential association between single nucleotide polymorphisms (SNPs) and body measurement traits in Qinchuan cattle. In the present study, we investigated polymorphisms of SIX4 gene in 426 Qinchuan cattle using DNA sequencing and polymerase chain reaction–restriction fragment length polymorphisms. Three novel SNPs were identified within bovine SIX4 gene. Associations between body measurement traits and SIX4 gene polymorphisms were investigated, and significant statistical associations were found between polymorphisms of these three SNPs and body measurement traits (P < 0.05). Hence, based on results obtained from this study, we conjectured that SIX4 gene may have potential effects on body measurement traits in Qinchuan cattle population and could be used for marker-assisted selection.     

ZBTB38 gene polymorphism associated with body measurement traits in native Chinese cattle breeds

Body measurement traits, influenced by genes and environmental factors, play numerous important roles in the value assessment of productivity and economy. In this study, we investigated the association between genetic polymorphisms of the zinc finger and BTB domain containing 38 gene (ZBTB38) and body measurement traits in native Chinese cattle. Using direct DNA sequencing in 423 individuals of 8 different cattle subpopulations, 9 novel polymorphisms were identified for genotyping within 647 bp region of exon 1 of ZBTB38. Linkage disequilibrium and association analysis revealed that two coding exon polymorphisms (2323 G>A and 2325 C>T polymorphisms), missense mutations valine GTC(T) to isoleucine ATC(T), were associated with body length (BL), withers height (WH) and rump length (RL). Furthermore, the analysis of 2323 G>A and 2325 C>T SNP markers shows that there are significant effects on the BL (P = 0.0488), WH (P = 0.0044) and RL (P = 0.0314) in the total population. These results clearly suggest that the ZBTB38 gene is among the target genes for body measurement traits in bovine breeding, and provide data for establishment of an animal model using cattle to study big animal body type.     

Association of TLR and TREM-1 gene polymorphisms with risk of coronary artery disease in a Russian population

Atherosclerosis, manifesting itself as acute coronary syndrome, stroke, and peripheral arterial diseases, is a chronic progressive inflammatory disease which is driven by responses of both innate and adaptive immunity. Toll-like receptors (TLRs) and Triggering Receptor Expressed on Myeloid Cells-1 (TREM-1) are important effectors of the innate immune system, and polymorphisms within genes encoding them may increase risk of occurrence of various pathologies including cardiovascular disorders. Thus, we carried out a genetic association study on the sample of 702 consecutive Caucasian (Russian) patients with coronary artery disease (CAD) and 300 age-, sex-, and ethnicity-matched healthy controls. We revealed that the C/C genotype of the TLR1 rs5743551 polymorphism was significantly associated with a reduced risk of CAD according to the recessive model (OR = 0.41, 95% CI = 0.20–0.84, P = 0.017, adjusted by age and gender). Concerning TREM-1 gene polymorphisms, we found that A/A genotype of the rs2234237 polymorphism, the G/G genotype of the rs6910730 polymorphism, the C/C genotype of the rs9471535 polymorphism, and the T/T genotype of the rs4711668 polymorphism were significantly associated with elevated CAD risk according to the recessive model (OR = 5.52, 95% CI = 1.17–25.98, P = 0.011; OR = 4.28, 95% CI = 1.09–16.81, P = 0.021; OR = 5.55, 95% CI = 1.18–26.09, P = 0.011, and OR = 1.66, 95% CI = 1.10–2.52, P = 0.014, respectively, adjusted by age and gender). Conversely, the G allele of the rs1817537 polymorphism, the T allele of the rs2234246 polymorphism, and the T allele of the rs3804277 polymorphism significantly correlated with similarly decreased risk of CAD according to the dominant model (OR = 0.57, 95% CI = 0.40–0.81, P = 0.0013; OR = 0.59, 95% CI = 0.42–0.84, P = 0.003, and OR = 0.58, 95% CI = 0.41–0.81, P = 0.0014, respectively, adjusted by age and gender). We conclude that certain TLR and TREM-1 gene polymorphisms may be associated with CAD in Russian population; however, their significance as predictive and pathogenic markers of CAD should be interpreted with caution in other populations.