Exosomal RNAs: Novel Potential Biomarkers for Diseases-A Review.

Exosomes are a subset of nano-sized extracellular vesicles originating from endosomes. Exosomes mediate cell-to-cell communication with their cargos, which includes mRNAs, miRNAs, lncRNAs, and circRNAs. Exosomal RNAs have cell specificity and reflect the conditions of their donor cells. Notably, their detection in biofluids can be used as a diagnostic marker for various diseases. Exosomal RNAs are ideal biomarkers because their surrounding membranes confer stability and they are detectable in almost all biofluids, which helps to reduce trauma and avoid invasive examinations. However, knowledge of exosomal biomarkers remains scarce. The present review summarizes the biogenesis, secretion, and uptake of exosomes, the current researches exploring exosomal mRNAs, miRNAs, lncRNAs, and circRNAs as potential biomarkers for the diagnosis of human diseases, as well as recent techniques of exosome isolation.

A novel duplicated insertion/deletion (InDel) of the CPT1a gene and its effects on growth traits in goat.

Carnitine palmitoyltransferase 1a (CPT1a) is a rate-limited enzyme in the mitochondrial fatty acid ß-oxidation pathway. It acts as a bridge between PPARα and the fatty acid oxidation pathways and is closely related to ruminant growth and development. In this study, one 12 bp InDel polymorphism of the CPT1a gene was identified in 700 goats, and we designated these three genotypes II, ID, and DD. Association analysis showed that the InDel polymorphism was closely associated with trunk index (p = 0.008) and body length index (p = 0.034) in Hainan black goats, and body length (p = 0.010), chest circumference (p = 0.004), chest depth (p = 0.029), and huckle bone width (p = 0.002) in Nubian goats, as well as the chest circumference (p = 0.016) in the Fuqing goat breed. In both kids and adult goats, qRT-PCR results showed that the CPT1a gene was expressed in all tissues, showing the highest mRNA levels in the liver, lung, spleen, and kidney, followed by the adipose tissue and brain. This indicates an association between the InDel of the CPT1a gene and growth traits in selected goat breeds, which may facilitate marker-assisted selection in goat genetics and breeding.

Transcriptional regulation of the bovine FGFR1 gene facilitates myoblast proliferation under hypomethylation of the promoter.

DNA methylation, which can affect the expression level of genes, is one of the most vital epigenetic modifications in mammals. Fibroblast growth factor receptor 1 (FGFR1) plays an important role in muscle development; however, DNA methylation of the FGFR1 promoter has not been studied to date in cattle. Our study focused on methylation of the FGFR1 promoter and its effect on bovine myoblast proliferation and differentiation. We identified the FGFR1 core promoter by using luciferase reporter assays; we then studied FGFR1 expression by reverse transcription quantitative polymerase chain reaction, and the methylation pattern in the FGFR1 core promoter by bisulfite sequencing polymerase chain reaction in bovine muscle tissue at three different developmental stages. We used RNAi strategy to investigate the function of FGFR1 in myoblast proliferation and differentiation. Results showed that the FGFR1 core promoters were located at the R2 (-509 to ~-202 bp) and R4 (-1295 to ~-794 bp) regions upstream of the FGFR1 gene. FGFR1 expression level was negatively associated with the degree of methylation of the FGFR1 core promoter during the developmental process. In addition, we found that FGFR1 can promote myoblast proliferation, but had no effect on myoblast differentiation. In conclusion, our results suggest that FGFR1 can promote myoblast proliferation and its transcription can be regulated by the methylation level of the core promoter. Our findings provide a mechanistic basis for the improvement of animal breeding.

Detection of InDel variations within seven candidate genes and their associations with phenotypic traits in three cattle breeds.

The Xinjiang brown cattle, Red steppe cattle, and Yunling cattle are indigenous cultivated cattle breeds in Chinese frontier provinces, and they produce high-grade beef and milk products, however, their genetic diversity in many important genes related to excellent meat and milk production is still unknown. Our previous studies have found that several candidate genes (e.g., SREBP1c and PAX7) were associated with bovine economically important phenotypic traits, but none has been reported in the above-mentioned three cattle breeds. Since the InDel (insertion/deletion) marker becomes a useful tool applied in the animal molecular breeding, herein, we firstly found that the InDel variations of seven candidate genes in these cattle. Results showed that the genotypic and allelic distributions of these seven genes were remarkably different among these three cattle (p < 0.05 or p < 0.01). Furthermore, the InDel variations of SREBP1c and PAX7 genes were significantly associated with eight phenotypic traits in Xinjiang brown cattle (p < 0.05 or p < 0.01), respectively, suggesting that they can become the useful DNA markers.

Determination of genetic effects of SERPINA3 on important growth traits in beef cattle.

Serine protease inhibitor protein 3 (serpin peptidase inhibitor, clade A, member 3, SERPINA3) is a member of the serpin superfamily, probably related to the yield and quality of muscle. This study focuses on the relationship between SERPINA3 gene polymorphism and growth traits in beef cattle. The study first uses sequencing pooled DNA samples (Pool-Seq), PCR-RFLP and Tetra-primer ARMS-PCR techniques to determine the genetic polymorphisms of SERPINA3 in 765 beef cattle. Then, the polymorphic loci were correlated with the growth characters of cattle. Five SNPs (SNP1:A-648G, SNP2:T6496A, SNP3:G2495A, SNP4:T2595A, SNP5:A2615G) were found, located in the promoter, introns 5 and SNP 3, 4, 5 were in exons 2, respectively. The observed He was from 0.44 to 0.5, Ne were approaching 2 (1.78 to 2.00). The maximum and minimum PIC (polymorphism information content) values were 0.37 and 0.34, respectively. The association analysis results showed that the SNPs had a significant height in the chest girth and body length. (p < 0.05 or p < 0.01). This will provide important information for the rapid breeding of Chinese yellow cattle and the establishment of a molecular genetic marker database.

Genetic Variants in ADD1 Gene and their Associations with Growth Traits in Cattle.

The α-adducin (ADD1) is a subunit of adducin which is a cytoskeleton heterodimeric protein. Adducin participates in oocytes chromosome meiosis of mice, prompting adducin has an effect on embryonic development. Adducin gene mutation has significantly functional change. So the present study was to identify and characterize polymorphisms within the coding region of the bovine ADD1 gene among different cattle breeds. Here, 11 novel single nucleotide polymorphisms (SNPs 1-11) were identified by DNA sequencing and polymerase chain reaction-single stranded conformational polymorphism, there were one synonymous mutation in exon 1 (SNP1); four missense mutations in exons 4, 7, and 8 (SNPs 3-6); and six mutations in introns 4, 12, 13, and 14 (SNPs 2, 7-10). The statistical analyses indicated that the some SNPs are associated with the growth traits (body length, body height, chest circumference, and hucklebone width) in Chinese Jiaxian cattle population. Our results provide evidence that polymorphisms in the ADD1 gene are associated with growth traits, and may be used for marker-assisted selection in beef cattle breeding program.

Comparative microRNAome analysis of the testis and ovary of the Chinese giant salamander.

MicroRNAs (miRNAs) are 18-24 nucleotides non-coding RNAs that regulate gene expression by post-transcriptional suppression of mRNA. The Chinese giant salamander (CGS, Andrias davidianus), which is an endangered species, has become one of the important models of animal evolution; however, no miRNA studies on this species have been conducted. In this study, two small RNA libraries of CGS ovary and testis were constructed using deep sequencing technology. A bioinformatics pipeline was developed to distinguish miRNA sequences from other classes of small RNAs represented in the sequencing data. We found that many miRNAs and other small RNAs such as piRNA and tsRNA were abundant in CGS tissue. A total of 757 and 756 unique miRNAs were annotated as miRNA candidates in the ovary and testis respectively. We identified 145 miRNAs in CGS ovary and 155 miRNAs in CGS testis that were homologous to those in Xenopus laevis ovary and testis respectively. Forty-five miRNAs were more highly expressed in ovary than in testis and 21 miRNAs were more highly expressed in testis than in ovary. The expression profiles of the selected miRNAs (miR-451, miR-10c, miR-101, miR-202, miR-7a and miR-499) had their own different roles in other eight tissues and different development stages of testis and ovary, suggesting that these miRNAs play vital regulatory roles in sexual differentiation, gametogenesis and development in CGS. To our knowledge, this is the first study to reveal miRNA profiles that are related to male and female CGS gonads and provide insights into sex differences in miRNA expression in CGS.

Correlation between ZBED6 Gene Upstream CpG Island methylation and mRNA expression in cattle.

DNA methylation is essential for the regulation of gene expression and important roles in muscle development. To assess the extent of epigenetic modifications and gene expression on the differentially methylated region (DMR) in ZBED6, we simultaneously examined DNA methylation and expression in six tissues from two different developmental stages (fetal bovine and adult bovine). The DNA methylation pattern was compared using bisulfite sequencing polymerase chain reaction (BSP) and combined bisulfite restriction analysis (COBRA). The result of quantitative real-time PCR (qPCR) analysis showed that ZBED6 has a broad tissue distribution and is highly expressed in adult bovine (P < 0.05 or P < 0.01). The DNA methylation level was significantly different in liver, lung and spleen between the two cattle groups (P < 0.05 or P < 0.01). The adult bovine group exhibited a significantly higher mRNA level and lower DNA methylation level than the fetal bovine group in liver, lung, and spleen. No significant association was detected between DNA methylation level and muscle, heart, and kidney at two different stages. In this study, the statistical analyses indicated that DNA methylation patterns are associated with mRNA level in some tissues, these results may be a useful parameter to investigate muscle developmental in cattle and as a model for studies in other species, potentially contributing to an improvement of growth performance selection in beef cattle breeding program.

Effect of Genetic Variations within the I-mfa Gene on the Growth Traits of Chinese Cattle.

I-mfa (inhibitor of the MyoD family a) is a transcription modulator that binds to MyoD family members and inhibits their transcriptional activities. It is highly expressed in the sclerotome and plays an important role in the patterning of the somite early in development. In this study, the polymorphisms of the bovine I-mfa gene were detected by polymerase chain reaction-single stranded conformational polymorphism (PCR-SSCP) and DNA pool sequencing methods in 541 individuals from three Chinese cattle breeds. The results showed that P3 locus had two novel complete linked single nucleotide polymorphisms (NC_007324.4:g.12284A>G and g.12331T>C), resulting in a missense mutation p.S(AGC)113G(GGC) and a synonymous mutation p.H(CAT)128H(CAC), respectively. P4 locus had a novel SNP (NC_007324.4: g.16432C>A), which resulted in a nonsense mutation p.C(TGC)241X(TGA). The statistical analyses indicated that the three SNPs, are associated with the phenotypic traits in Luxi (LX), Qinchuan (QC), and Jiaxian (JX) cattle population (P < 0.05 or P < 0.01). The mutant-type variants were superior for growth traits; the heterozygote diplotype was associated with higher growth traits compared to wild-type homozygote. Our results provide evidence that polymorphisms in the I-mfa gene are associated with growth traits and may be used for marker-assisted selection in beef cattle breeding program.

miR-30-5p Regulates Muscle Differentiation and Alternative Splicing of Muscle-Related Genes by Targeting MBNL.

MicroRNAs (miRNAs), a class of single stranded, small (~22 nucleotides), non-coding RNAs, play an important role in muscle development. We focused on the role of the miR-30-5p family during bovine muscle development from previous high-throughput sequencing results and analyzed their expression profiles. MHC and MyoG mRNAs expression as well as their proteins were suppressed in differentiated C2C12 cells, suggesting the importance of miR-30-5p in muscle development. MBNL, the candidate target of miR-30-5p, is an alternative splicing regulation factor. MBNL1 and MBNL3 have opposite effects on muscle differentiation. Our results confirmed that miR-30a-5p and miR-30e-5p repress the expression of MBNL1, MBNL2 and MBNL3, whereas miR-30b-5p inhibits MBNL1 and MBNL2 expression. This provides direct evidence that MBNL expression can be flexibly regulated by miR-30-5p. Previous studies showed that MBNL1 promotes exon inclusion of two muscle-related genes (Trim55 and INSR). Through RNA splicing studies, we found that miR-30-5p had an effect on their alternative splicing, which means miR-30-5p via MBNL1 could be integrated into muscle signaling pathways in which INSR or Trim55 are located. In conclusion, miR-30-5p could inhibit muscle cell differentiation and regulate the alternative splicing of Trim55 and INSR by targeting MBNL. These results promote the understanding of the function of miRNAs in muscle development.

SNP and haplotype analysis reveal IGF2 variants associated with growth traits in Chinese Qinchuan cattle.

Insulin-like growth factor 2 (IGF2) is a potent cell growth and differentiation factor and is implicated in mammals' growth and development. The objective of this study was to evaluate the effects of the mutations in the bovine IGF2 with growth traits in Chinese Qinchuan cattle. Four single nucleotide polymorphisms (SNPs) were detected of the bovine IGF2 by DNA pool sequencing and forced polymerase chain reaction-restriction fragment length polymorphism (forced PCR-RFLP) methods. We also investigated haplotype structure and linkage disequilibrium (LD) coefficients for four SNPs in 817 individuals representing two main cattle breeds from China. The result of haplotype analysis showed eight different haplotypes and 27 combined genotypes within the study population. The statistical analyses indicated that the four SNPs, combined genotypes and haplotypes are associated with the withers height, body length, chest breadth, chest depth and body weight in Qinchuan cattle population (P < 0.05 or <0.01). The mutant-type variants and mutant haplotype (Hap 8: ATGG; likely to be the beneficial QTN allele) was superior for growth traits; the heterozygote diplotype was associated with higher growth traits compared to wild-type homozygote. 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.

Expression, SNP identification, linkage disequilibrium, and haplotype association analysis of the growth suppressor gene ZBED6 in Qinchuan beef cattle.

Zinc finger, BED-type containing 6 (ZBED6) is a novel transcription factor that was identified and shown to act as a repressor of IGF2 transcription in skeletal muscle myogenesis and development. The aims of this study were to determine ZBED6 expression level and examine the association of the ZBED6 polymorphism with growth traits in Qinchuan beef cattle. The bovine ZBED6 mRNA was detected in eight tissues by quantitative real-time PCR (qPCR), being highly expressed in skeletal muscle. Three single nucleotide polymorphisms (SNPs) were identified the bovine ZBED6 by sequencing pooled DNA samples (Pool-Seq) and forced polymerase chain reaction-restriction fragment length polymorphism (forced PCR-RFLP) methods. In this study, we reported one mutation in the promoter and two missense mutations in the coding regions within the bovine ZBED6 gene, and the haplotype variability and extent of linkage disequilibrium (LD) in 817 individuals from the Qinchuan (QC) and Chinese Holstein (CH). We also investigated haplotype structure and linkage disequilibrium coefficients for three SNPs of ZBED6 in the study populations. The result of haplotype analysis of three SNPs showed that eight different haplotypes were identified in two breeds. The wild-type haplotype (Hap 1: GCA) and mutant-type haplotype (Hap 8: AGG) shared by two populations accounted for 29.8%, 57.5%, and 8.6%, 0% of all haplotypes observed in QC and CH, respectively. The statistical analyses indicated that three SNPs, 23 combined genotypes, and 8 haplotypes were significantly associated with different growth traits in the QC cattle population (P < 0.05 or P < 0.01). The mutant-type variants and mutant haplotype were superior for growth traits; the heterozygote diplotype was associated with higher growth traits compared to the wild-type homozygote. The results of this study suggest that the ZBED6 gene possibly is a strong candidate gene that affects growth traits in QC beef cattle breeding program.

Comparative analysis of the IGF2 and ZBED6 gene variants and haplotypes reveals significant effect of growth traits in cattle.

Muscle growth is a complex phenomenon regulated by many factors, whereby net growth results from the combined action of synthesis and turnover. 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; Zinc finger, BED-type containing 6 (ZBED6) is a novel transcription factor that was identified and shown to act as a repressor of IGF2 transcription in skeletal muscle. In this study, a total of seven single nucleotide polymorphisms (SNPs) were identified, four SNPs in intron 8 of IGF2 and one promoter SNP and two missense mutations in the coding region of ZBED6, two of which were in complete linkage disequilibrium (LD) in the bovine IGF2. The 58 haplotypes were inferred in 1522 individuals representing four purebred cattle breeds from China. The seven SNPs, 79 and 66 combined diplotypes were revealed for association with body mass in Nanyang and Jiaxian cattle populations at five different ages (P < 0.05 or 0.01). The mutant-type variants and haplotype 58 (likely in LD with the beneficial quantitative trait nucleotide allele) was superior for body mass; the heterozygote diplotype of the most common haplotypes 58 was associated with higher body mass compared to either heterozygote or homozygote. The statistical analyses indicated that the mutant-type variants and haplotypes are significantly associated with body mass in study cattle populations at different ages. These data demonstrate that variants and haplotypes are associated with growth traits, and these results may provide important biological insights into the phenotypic differentiation that is associated with adaptation and specialization of cattle breeds.

The effect of haplotype variation in the bovine PAX6 gene.

The transcription factor paired box 6 gene (PAX6) plays a key role during the early development of various organs. In this study, three single nucleotide polymorphisms (SNPs) have been identified in the introns 2, 8 and 11 of the bovine PAX6 gene. 8 haplotypes and 13 diplotypes were revealed and the linkage disequilibrium (LD) was assessed in 817 cows representing four main cattle breeds from China (Nanyang, NY; Qinchuan, QC; Jiaxian, JX; Chinese Holstein, CH). The LD analysis revealed that the additional three SNPs were not in strong LD, the wild haplotype (Hap 1: CTT) and mutant haplotype (Hap 8: TCC) have a frequency of 9.36, 35.61, 18.32, 57.15 % and 15.60, 14.19, 0.83, 0 % in the four cattle populations. The statistical analyses indicated that the SNP2 and 3 are associated with the body weight at birth, 6 and 12 months in NY and JX cattle population (P < 0.01 or P < 0.05); and significant association was detected between 19 (NY) or 13 (JX) diplotype (combined genotypes) and body weight at different ages (birth, 6 and 12 months). Our results provide evidence that some polymorphisms in PAX6 are associated with growth traits at some ages, and may be used as candidates for marker-assisted selection in beef cattle breeding program.

Y chromosome diversity and paternal origin of Chinese cattle.

To determine the Y chromosome genetic diversity and paternal origin of Chinese cattle, 369 bulls from 17 Chinese native cattle breeds and 30 bulls from Holstein and four bulls from Burma were analyzed using a recently discovered USP9Y marker that could distinguish between taurine and indicine cattle more efficiently. In total, the taurine Y1, Y2 haplogroup and indicine Y3 haplogroup were detected in 7 (1.9 %), 193 (52.3 %) and 169 (45.8 %) individuals of 17 Chinese native breeds, respectively, although these frequencies varied amongst the Chinese native cattle breeds examined. Y2 dominates in northern China (91.4 %), while Y3 dominates in southern China (81.2 %). Central China is an admixture zone with Y2 predominating overall (72.0 %). Our results demonstrate that Chinese cattle have two paternal origins, one from B. taurus (Y2) and the other from B. indicus (Y3). The Y1 haplogroup may originate from the imported beef cattle breeds in western countries. The geographical distributions of the Y2 and Y3 haplogroup frequencies reveal a pattern of male indicine introgression from south to north China, and male taurine introgression from north to south China.

A novel c.-274C>G polymorphism in bovine SIRT1 gene contributes to diminished promoter activity and is associated with increased body size.

SIRT1, a mammalian homologue for yeast silent information regulator 2 (SIR2), is a NAD(+) -dependent deacetylase that belongs to the class III histone deacetylases. It plays an important role in diverse cellular processes, including stress resistance, mitochondrial function, suppression of inflammation and DNA repair. In this study, we screened and identified a novel polymorphism (c.-274C>G) in the SIRT1 promoter region. In silico prediction reveals that this SNP is in the core of cell cycle-dependent element (CDE)-binding motif. Interestingly, the G allele abolished a CDE-binding site, which suggested its functional significance. In the luciferase assay system, we found that the G allele-containing construct displayed a strikingly lower promoter activity compared with the C allele, which may downregulate SIRT1 expression levels. Additionally, we observed a significant association between the c.-274C>G polymorphism and growth traits in Nanyang cattle, suggesting that anomalous transcription factor-based repression of SIRT1 may increase bovine fat mass and body size.

Genotype and haplotype analysis of the AZGP1 gene in cattle.

Zinc-a2-glycoprotien (AZGP1) involved in lipid metabolism and associated with adipose tissue atrophy in cachexia. And it also related to sperm motility and in turn fertilization. To ascertain whether there were mutations in the bovine AZGP1 gene, this study investigated variation of the AZGP1 gene through PCR-SSCP and sequencing. Four missense mutations were identified in 649 cattle from six independent populations. Haplotype frequencies and linkage disequilibrium (LD) coefficients of these SNPs in three Chinese indigenous cattle breeds were analyzed. One LD block was found in three cattle breeds. The statistical analyses indicated that AC genotype of Z4 locus was associated with the high body weight, body length and chest girth in Jiaxian cattle breed (P < 0.05). Our results provided evidence that polymorphisms in the AZGP1 gene were associated with growth traits, and may be used for marker-assisted selection and management in cattle breeding program.

Effects of ghrelin gene genotypes on the growth traits in Chinese cattle.

Ghrelin is an important peptide that stimulates food intake and regulates energy balance of animals. Single nucleotide polymorphisms of ghrelin gene in three Chinese cattle populations were investigated through PCR-SSCP and DNA sequencing. Five over-lapped DNA fragments were analyzed and a total of three ones exhibited different genotypes. Three genotypes and four SNPs (-415 A > G, -414 T > C, -321 C > A, and -172 A > G) were found on the -544 to +35 bp region (G-1) of ghrelin gene. On the locus of -1037 to -509 bp (G-2), two genotypes and one SNP (-726 A > T) were discovered. And in the exon1, exon2, and intron1 (G-4 locus, (+4 to +427)), two genotypes and one SNP were detected (+205 C > T, located in intron1). Positions of the five SNPs in the 5' regulatory region might be the transcription factor binding sites. The SNPs at -415 and -414 in the core binding sequence were found to cause the change of the site. Though the SNP at -172 did not change the binding site, it generated one new site at the same time. The frequencies of the genotypes varied differently in the three breeds. Results of ANOVA showed that G-1 was correlative to the ischium width (IW) of Nanyang cattle aged 18 months (p = 0.043). The least square analysis between genotypes at G-1 locus and growth traits in Nanyang cattle showed that the individuals (aged 18 months) with C genotype had greater IW than that of the other two genotypes. The C genotype might serve as one potential candidate genetic marker for cattle growth and development.

Genetic variations of ANGPTL6 gene and their associations with growth traits and slaughter traits in Qinchuan cattle.

Angiopoietin-like protein 6 (ANGPTL6), which plays an important role in angiogenesis and energy metabolism as a circulating orphan peptide secreted by liver, could produce a potential effect on growth and development of animals. The objective of this study was to detect genetic variations of ANGPTL6 gene in 732 Qinchuan cattle, as well as to analyze their associations with growth traits and carcass weight. Herein, three novel mutations (T2359C, C2403A and G3258T) were identified in cattle for the first time. Chi-square test showed T2359C and C2403A loci were in Hardy-Weinberg equilibrium except G3258T locus. Haplotype with TCG (wild type) was dominant with frequency of 40.0 % among eight different haplotypes. Statistical analysis showed body height (BH) and hucklebone width (HW) of individuals with genotype CC were significant higher than other genotypes in T2359C locus (P < 0.05). In the C2403A locus, chest girth (CG), chest depth (CD), and chest breadth (CB) of individuals with genotype CA were all extremely significant higher (P < 0.01) while BH was significant higher (P < 0.05) than genotype CC. The association analysis of combined sites showed BH, CG, CB and HW of individuals with combined genotype TC-CA were significant higher than other combined genotypes (P < 0.05) in ScaI-VspI site. BH, CG and CB of individuals with genotype CA-GG were significant higher (P < 0.05) as well as CD was extremely significant higher (P < 0.01) than other genotypes in VspI-RsaI site. For ScaI-VspI-RsaI site, CD and HW of individuals with genotype TC-CA-GG were significant higher (P < 0.05) than those of other combined genotypes. Slaughter test also revealed that the effect of the combined genotypes was extremely significant on the carcass weight. Carcass weight of individuals with genotype TT-CA and TT-CA-GT were extremely significant heavier than other combined genotypes (P < 0.01) in the ScaI-VspI and ScaI-VspI-RsaI sites. And those with genotype TT-GT of ScaI-RsaI were significantly heavy (P < 0.05) as well as the individuals with genotype CA-GT of VspI-RsaI. In conclusion, the present results provided evidence that polymorphisms of ANGPTL6 gene were associated with growth and slaughter traits, and may apply to Qinchuan cattle breeding program as a possible candidate for marker-assisted selection (MAS).

Haplotype combination of SREBP-1c gene sequence variants is associated with growth traits in cattle.

The aim of this study was to examine the association of the SREBP-1c polymorphism with growth traits in cattle breeds. Five sequence variants (SVs) were identified within the bovine sterol regulatory element-binding protein-1c gene (SREBP-1c), using DNA sequencing, PCR, PCR­RFLP, and forced PCR­RFLP methods. These polymorphisms include three missense mutations (SV1, SV4, and SV5) in exons 7, 9, and 12, a silent mutation (SV3) in exon 9, and a large deletion (SV2) in intron 7. Overall, we report the validation of polymorphisms within the bovine SREBP-1c gene, and the haplotype variability and extent of linkage disequilibrium (LD) in 1061 individuals representing the five main cattle breeds from China. We also investigated haplotype frequencies and LD coefficients for five SVs in all study populations. LD and haplotype structure of SREBP-1c were different between breeds. The result of haplotype analysis of five SVs showed that 27 different haplotypes were identified by all breeds. Two haplotypes (Hap1 and Hap2) shared by all five populations accounted for 42.75%, 35.68%, 36.44%, 25.43%, and 96.26% of all haplotypes observed in the cattle breeds Nanyang, Qinchuan, Jiaxian, Jinnan, and Chinese Holstein, respectively. The statistical analyses indicated that one single SV and 38 combined haplotypes were significantly associated with growth traits in the Nanyang cattle population (P < 0.05 or P < 0.01). The results of this study suggest that the SREBP-1c gene possibly is a strong candidate gene that affects growth traits in the Chinese beef cattle breeding program.