The Mongolian cattle are one of the most widespread breeds with strictly Bos taurus morphological features in northern China. In our current study, we presented a diversity of mitochondrial DNA (mtDNA) D-loop region and Y chromosome SNP markers in 25 male and 8 female samples of Mongolian cattle from the Xinjiang Uygur autonomous region in Western China, and detected 21 B. taurus and four Bos indicus (zebu) mtDNA haplotypes. Among four B. indicus mtDNA haplotypes, two haplotypes belonged to I1 haplogroup and the remaining two haplotypes belonged to I2 haplogroup. In contrast, all 25 male Mongolian cattle samples revealed B. taurus Y chromosome haplotype and no B. indicus haplotypes were found. Historical and archeological records indicate that B. taurus was introduced to Xinjiang during the second millennium BC and B. indicus appeared in this region by the second century AD. The two types of cattle coexisted for many centuries in Xinjiang, as depicted in clay and wooden figurines unearthed in the Astana cemetery in Turfan (3rd-8th century AD). Multiple lines of evidence suggest that the earliest B. indicus introgression in the Mongolian cattle may have occurred during the 2nd-7th centuries AD through the Silk Road around the Xinjiang region. This conclusion differs from the previous hypothesis that zebu introgression to Mongolian cattle happened during the Mongol Empire era in the 13th century.

Forkhead box A2 (Foxa2) has been recognized as one of the most potent transcriptional activators that is implicated in the control of feeding behavior and energy homeostasis. However, similar researches about the effects of genetic variations of Foxa2 gene on growth traits are lacking. Therefore, this study detected Foxa2 gene polymorphisms by DNA pool sequencing, PCR-RFLP and PCR-ACRS methods in 822 individuals from three Chinese cattle breeds. The results showed that four sequence variants (SVs) were screened, including two mutations (SV1, g. 7005 C>T and SV2, g. 7044 C>G) in intron 4, one mutation (SV3, g. 8449 A>G) in exon 5 and one mutation (SV4, g. 8537 T>C) in the 3'UTR. Notably, association analysis of the single mutations with growth traits in total individuals (at 24months) revealed that significant statistical difference was found in four SVs, and SV4 locus was highly significantly associated with growth traits throughout all three breeds (P<0.05 or P<0.01). Meanwhile, haplotype combination CCCCAGTC also indicated remarkably associated to better chest girth and body weight in Jiaxian Red cattle (P<0.05). We herein described a comprehensive study on the variability of bovine Foxa2 gene that was predictive of molecular markers in cattle breeding for the first time.

The Longlin goat is one of the most valuable livestock species in Guangxi Autonomous Region of China, but its genomic diversity and selective signals are not clearly elucidated. Here we compared 20 genomes of Longlin goat to 66 genomes of other seven goat breeds worldwide to analyze patterns of Longlin goat genetic variation. We found the lowest linkage disequilibrium at the large distances between SNPs associated with the highest effective population size in the recent generations ago in Longlin goat. The eight goat breeds could be divided into Euro-African and East Asian goat population. Interestingly, like East Asian taurine, the same two migration phases might have occurred in the history of East Asian goat. More importantly, we identified selective signals implicated in immune resistance to disease, especially for skin disease, in Longlin goat. Our findings will not only help understand the evolutionary history and breed characteristic but can provide valuable resources for conservation of germplasm resources and implementation of crossbreeding programs.

Previous, studies have shown that the dynein transporter compound has a role in diseases such as intellectual disability and cerebral malformations. However, the study of CNV in DYNC1I2 gene has not been reported. Q-PCR and data association analysis were used for DYNC1I2 gene copy in this study. In this study, blood samples were collected from five breeds of Chinese cattle (Qingchuan cattle, Xianan cattle, Yunling cattle, Pinan cattle and Guyuan cattle) for DYNC1I2 gene CNV type detection. SPSS 20.0 software and method of ANOVA were used to analyzed the association between types of CNV and growth traits. Results reveal that the distribution of different copy number types in different cattle breeds is different. Association analysis indicate that CNV of DYNC1I2 gene showed a positive effect in cattle growth: in XN cattle, individuals with deletion types showed better performance on height at hip cross (P < 0.05); individuals with duplication types have better performance on body length (P < 0.05) in PN cattle; individuals with deletion types was significantly correlated with chest width and Hucklebone width (P < 0.05) in QC cattle; individuals with duplication types in Yunling cattle were better than the normal types, and there was a significant correlation between copy number variant and chest depth (P < 0.05). The results showed that CNV markers closely related to cattle production traits were detected at DNA level, which could be used as an important candidate molecular marker for marker-assisted selection of growth traits in Chinese cattle, and provided a new research basis for genetics and breeding of Chinese beef cattle.

Copy number variations (CNVs) are an important source of genetic variation, which can affect a wide range of economic traits by diverse mechanisms. KMT2D (Lysine methyltransferase 2D) is an important positional candidate for growth traits. Quantitative trait loci (QTLs) with large effects on economically important traits cover the KMT2D gene. The KMT2D gene overlays a CNV within its exons, hence it was chosen as a crucial candidate gene to study the association between CNV and growth traits. Further, KMT2D, a major mammalian histone H3K4 mono-methyltransferase, plays a critical role in regulating development, differentiation, metabolism, and tumor suppression. Therefore, we proposed the hypothesis that KMT2D CNV may have phenotypic effects on sheep growth traits. In our study, KMT2D CNVs in three Chinese sheep breeds were detected by quantitative polymerase chain reaction (qPCR), and the loss copy was found to be the dominant genotype. Association analysis between growth traits and KMT2D CNV was also performed, which revealed that individuals with the median copy showed better performance than those with the loss copy in all three breeds. This research suggested that KMT2D CNV can be used as a promising marker for sheep molecular breeding.

SLC45A2 is involved in the synthesis of melanin transporters. We investigated the association between single nucleotide polymorphisms (SNPs) of the SLC45A2 gene and humidity and hot conditions in indigenous cattle habitat. According to the Bovine Genome Variation Database and Selective Signatures (BGVD), we explored the frequency distribution of a missense mutation (NC_037347.1: c.1543A > G, p.ser515gly) in the SLC45A2 gene in Chinese indigenous cattle. This variation from serine to glycine caused a significant change in the protein modeling structure. PCR and partial DNA sequencing were used to genotype 541 individuals, including 28 Chinese indigenous cattle breeds as well as Angus and zebu. From our results, the mutant allele frequency of this SNP in Chinese native cattle increases gradually from north to south, which is consistent with the distribution of climatic conditions in China. In addition, according to association analysis of a missense mutation (NC_037347.1: c.1543A > G) (rs525805167) in Chinese cattle, it is closely related to the annual average temperature (T), relative humidity (RH), temperature and humidity index (THI) and solar radiation time (P < 0.01). Based on the statistical analysis of the data, we assumed that rs525805167 was associated with heat tolerance traits. Simple Summary: The characteristics of Chinese indigenous cattle are closely related to their climatic environment. In China, Bos taurus is mainly distributed in the northern regions; Bos indicus is mainly distributed in southern China. In addition, the average temperature is higher in the south than in the north, and there are many mixed ancestry breeds of B. taurus and B. indicus in the middle area. The SLC45A2 gene is related to melanin synthesis, which may be closely related to heat tolerance in cattle. The purpose of our study was to investigate whether the SLC45A2 gene is related to heat tolerance in Chinese indigenous cattle.

Copy number variation, as a kind of genetic submicroscopic structural variation, refers to the deletion or repetition of a large segment of genomic DNA, involving a segment size ranging from 50 bp to several MB. Mitochondrial fusion protein (MFN1) gene regulates the fusion of mitochondrial outer membrane in cells and maintains the dynamic needs of reticular mitochondria in cells. In this study, we conducted to tested the dstribution characteristics of MFN1-CNV in 522 cattles across Xianan cattle (XN), Pinan cattle (PN), Qinchuan cattle (QC), Jiaxian cattle (JX), Yunling cattle (YL), and correlated it with phenotypic traits. Then we observed the expression of MFN1 in various tissues of QC cattle (n = 3), and the expression levels were higher in lung and muscle. The results showed that there was significant correlation between MFN1 gene CNV and hucklebone width of QC cattle, hip width and height at sacrum of JX red cattle, chest width and rump length of YL cattle (P < 0.05). Individuals with duplication type were better than the type of normal or deletion in phenotypic traits. In conclusion, our data showed the correlation between MFN1 gene and growth traits of Chinese cattle. MFN1 gene can be used as a molecular marker for cattle selection and breeding, and accelerate the improvement of Chinese cattle.

The aim of this study was to examine the association of cofilin2 (CFL2) gene polymorphisms with growth traits in Chinese Qinchuan cattle. Three single nucleotide polymorphisms (SNPs) were identified in the bovine CFL2 gene using DNA sequencing and (forced) PCR-RFLP methods. These polymorphisms included a missense mutation (NC_007319.5: g. C 2213 G) in exon 4, one synonymous mutation (NC_007319.5: g. T 1694 A) in exon 4, and a mutation (NC_007319.5: g. G 1500 A) in intron 2, respectively. In addition, we evaluated the haplotype frequency and linkage disequilibrium coefficient of three sequence variants in 488 individuals in QC cattle. All the three SNPs in QC cattle belonged to an intermediate level of genetic diversity (0.250.33). Association analysis indicated that SNP G 1500 A, T 1694 A and C 2213 G were significantly associated with growth traits in the QC population. The results of our study suggest that the CFL2 gene may be a strong candidate gene that affects growth traits in the QC cattle breeding program.

The KRT75 gene (Keratin 75) is a member of the type II epithelial α-keratin gene family which plays a key role in hair and nail formation. And the coat conformation affects heat tolarence in mammals. Therefore, the aim of this study was to identify novel single nucleotide polymorphisms (SNPs) of the KRT75 gene and further evaluate its relation to heat stress in Chinese cattle. A missense mutation (NC_037332.1: g.1052 T > C) of the bovine KRT75 was identified using the Bovine Genome Variation Database (BGVD). The g.1052 T > C variant was then genotyped in 519 individuals of 22 cattle breeds. Further analyses showed that the frequency of T allele in Chinese indigenous cattle breeds gradually diminished from northern groups to southern groups, whereas the frequency of C allele displayed a contrary patternl. Simultaneously, the frequency of the CC and CT genotype for southern groups was much greater than that of the TT genotype. Additionally, association analysis showed the genotypes were remarkably associated with mean annual temperature (T), relative humidity (RH) and temperature humidity index (THI) (P < 0.01). Our results demonstrated that the KRT75 gene might be a candidate gene associated with the heat stress in Chinese cattle.

Qinchuan cattle is one of the five yellow cattle breeds in China with good performance of meat. The proliferation and differentiation level of muscle and fat are closely related to the growth and development of the organism and are the key factors affecting the quality of meat. In order to study the effect of lncRNA on the fat tissues of Qinchuan cattle, six calf and adult bovine adipose tissues were selected for high-throughput sequencing. We obtained 3,716 lncRNA candidates from calves and adult cattle fat samples, among them 789 lncRNA were annotated and 2,927 lncRNA were novel lncRNA. A number of lncRNAs were highly abundant, and 119 lncRNA were differentially expressed between two developmental stages. We further validated several differentially expressed lncRNAs using qPCR, and the results were consistent with the sequencing data. Therefore, we conclude that lncRNA may play an important role in adipose tissue in different age groups of cattle.

Transmembrane protein 95 (TMEM95) is closely related to male reproductive performance in cattle, but does not affect semen quality. Alternative splicing plays an important role in regulating biological function as well as in generating proteomic and functional diversity in metazoan organisms. Thus, the aim of this study was to clone and identify transcripts of the TMEM95 gene in cattle using RT-PCR, characterize them via bioinformatics analysis, and detect their expression patterns using qRT-PCR. Two transcripts of TMEM95 were identified in cattle, including TMEM95-SV1 and TMEM95-SV2. Bioinformatics predicted that TMEM95-SV1 has a leucine-rich repeat C-terminal domain and a Pfam: IZUMO. These regions are closely related to protein interactions and the acrosome reaction, respectively. Interestingly, the two transcripts were exclusively expressed in the testes and brain in male fetus cattle, and TMEM95-SV1 was expressed in the brain at significantly higher levels than in the testis (P<0.05, 4.06-fold) and TMEM95-SV2 in the brain (P<0.05, 4.95-fold). These findings enrich the understanding of the TMEM95 gene function and benefit for enhancing male reproduction in cattle industry.

Domestic buffalo is an important livestock in the tropical and sub-tropical region, including two types: swamp and river buffalo. The swamp buffalo is mainly used as draft animal, while the river buffalo is raised for milk production. In this study, based on the new high-quality buffalo reference genome UOA_WB_1, we firstly investigated the copy number variants in buffalo using whole-genome Illumina sequencing. A total of 3,734 CNV regions (CNVRs) were detected in 106 buffalo population with a total length of 23,429,066 bp, corresponding to ∼ 0.88% of the water buffalo genome (UOA_WB_1). Our results revealed a clear population differentiation in CNV between swamp and river buffalo. In addition, a total of 667 highly differentiated CNVRs (covering 886 genes) were detected between river and swamp buffalo population. We detected a set of CNVR-overlapping genes associated with exercise, immunity, nerve, and milk trait which exhibited different copy numbers between swamp and river buffalo population. This study provides valuable genome variation resources for buffalo and would contribute to understanding the genetic differences between swamp and river buffalo.

Bovine leukocyte antigen, class II, DO beta (BoLA-DOB) is related to antigen presentation, which can triggered by multicul factors. And the condition of immune function determines how much cattle load to heat stress. To evaluate the relationship between heat-resistance and single nucleotide polymorphisms (SNPs) in BoLA-DOB gene, our study has taken further analysis in Chinese indigenous cattle for the first time. A missense single nucleotide polymorphism (rs464874590) was detected in BoLA-DOB gene. We directly sequenced rs464874590 (NM_001013600.1 g.7122762 A > G) in BoLA-DOB gene of 522 individuals of 26 cattle breeds. The frequency of allele G gradually decreases from south to north with distinct climatic distribution characteristics. Further association analysis was carried out between different genotypes and environmental parameters, including annual mean temperature (T), relative humidity (RH), and temperature-humidity index (THI). The result showed that three genotypes were significantly correlated with T, H, and THI (P < 0.01), indicating that GG genotype was distributed in areas with hot and moist conditions. Therefore, our results suggested that the rs464874590 could be applied as a genetic marker to detect the heat-resistance of Chinese indigenous cattle.

Pituitary homeobox 2 (PITX2) plays crucial roles in embryogenesis, ontogenesis, growth, and development via the Wnt/beta-catenin and POU1F1 pathways. To better understand the characteristics and genetic effects of the cattle PITX2 gene, we identified alternative PITX2 splicings, examined the effects of the spliced variants on mRNA expression levels in tissues, and then used association analyses to explore the relationships between a PITX2 deletion genetic variant and growth traits in 750 native Chinese cattle. An unreported spliced variant of PITX2, designated here as PITX2-V1, was identified in cattle using in silico cloning and RT-PCR. The entire coding sequence of PITX2 is 978 bp, encoding 325 amino acids, whereas that of PITX2-V1 is 357 bp encoding 118 amino acids. Cattle PITX2 exhibited both a perfect homeodomain and an OAR domain, but PITX2-V1 lacked the homeodomain. Analyses with qRT-PCR showed that the expression level of PITX2 in cattle testis was very low, and PITX2-V1 was only very slightly expressed in the brain and testis. Furthermore, a 24 bp deletion was detected within PITX2 intron, and the different genotypes were significantly associated with growth traits (e.g., body height, body length, heart girth) in four cattle breeds (P < 0.05). These results are of direct benefit to future cattle breeding, and provide new insights into the characteristics and functions of cattle PITX2 gene.

Angiopoietin-like protein 6, which is encoded by ANGPTL6 gene (also known as angiopoietin growth factor, AGF), has been extensively characterized with regard to its proposed functions as angiogenesis and energy metabolism. The present results showed the occurrence of alternative splicing by intron retention (IR) event in the bovine ANGPTL6 gene (bANGPTL6). By means of RT-PCR, TA clone and sequencing, we have shown that the bANGPTL6 gene has a splice variant generated by the retention of its partial intron 3. The computational analysis of the bANGPTL6 genomic sequence showed that its intron 3 has a high percentage of GC (62.31%) and a length of 199 nt, characteristics that have been associated with an IR event. The IR event does not interfere with the coding region as the bANGPTL6 prepropeptide is entirely coded in the third exon. Additionally, both the intronless (namely, bANGPTL6α) and intron-retaining (namely, bANGPTL6β) ANGPTL6 transcripts are constitutively co-expressed in the bovine liver. Further, the relative expression level of different variants in liver was tested by both semi-RT-PCR and RT-qPCR methods. The results suggested bANGPTL6β are significantly higher than bANGPTL6α. Overall, our findings will be helpful for studies on the molecular mechanism of IR events and the functions of ANGPTL6 gene. Specially, bANGPTL6β gene probably contributes to a new target for treatment of obesity and obesity-related diseases.