Search Results (20)

Bos frontalis (Mithun) and Bos grunniens (yak) are crucial to the culture, food security, and economy of Southeast Asia, especially in India and China, respectively. Their genetic closeness to Bos indicus (indicine cattle) and Bos taurus (taurine cattle) necessitates precise methods for meat origin authentication. This study introduces a DNA-based technique to distinguish Mithun and yak species using the alkaline lysis (AL) protocol for DNA extraction, followed by species-specific polymerase chain reaction (PCR) to amplify unique mitochondrial D-loop regions, yielding 489 bp and 422 bp amplicons, respectively. The AL-PCR method showed high specificity for both species, with no cross-amplification with other related species. The method’s effectiveness was validated across various sample preparations, including raw, cooked, autoclaved, microwaved, and fried samples. The AL-PCR assay is highly sensitive, detecting as little as 1 pg of Mithun DNA and 100 pg of yak DNA, and can identify down to 0.1% of these species in binary mixtures. This approach is rapid and cost-effective, offering significant benefits for consumer protection, promoting Mithun and yak farming, and addressing food safety and traceability issues. Full article

Exploring the genetic landscape of native cattle is an exciting avenue for elucidating nuanced patterns of genetic variation and adaptive dynamics. Xiangnan cattle, a native Chinese cattle breed mainly produced in Hunan Province, are well adapted to the high temperature and humidity of the local environment and exhibit strong disease resistance. Herein, we employed whole-genome sequences of 16 Xiangnan cattle complemented by published genome data from 81 cattle. Our findings revealed that Xiangnan cattle are pure East Asian indicine cattle with high genetic diversity and low inbreeding. By annotating the selection signals obtained by the CLR, θπ, F_ST, and XP-EHH methods, genes associated with immunity (ITGB3, CD55, OTUD1, and PRLH) and heat tolerance (COX4I2, DNAJC18, DNAJC1, EIF2AK4, and ASIC2) were identified. In addition, the considerable introgression from banteng and gaur also contributed to the rapid adaptation of Xiangnan cattle to the environment of Southern China. These results will provide a basis for the further conservation and exploitation of Xiangnan cattle genetic resources. Full article

Linkage disequilibrium (LD) maps are fundamental tools for exploring the genetic basis of traits of interest in any species. Quantifying LD patterns in cattle breeds has been made possible due to the availability of huge quantities of SNPs through modern sequencing technology. The present research aims to determine and compare linkage disequilibrium levels at different distances on the genome of Sistani domestic cattle and subspecies of Bos taurus and Bos indicus based on genome SNP data. A total of 60 Bos indicus Sahiwal (dairy) and Nellore (beef), Bos taurus Hereford (beef) and Holstein (dairy), and Sistani cattle were sampled and genotyped using Illumina Bovine HD 770 k chip. To ensure the caliber of the sequencing, 10 samples (genetically sequenced cattle) were randomly chosen among all breeds represented. LD was evaluated at distances of 1–50 Kb, 50–100 Kb, 100–500 Kb, and 0.5–1 Mb, and average r² values for all autosomes were calculated within distance classes. For all breeds, the average r² was over 0.2 at distances less than 100 Kb, while for Sistani, Nellore, and Sahiwal, the average r² was above 0.2 between 100 and 500 Kb. Furthermore, for all breeds, the average r² exceeding 0.3 was noted at distances smaller than 50 Kb, while this amount for Holstein and Hereford was observed at distances between 50 and 100 Kb. In various breeds, greater changes in LD levels were observed (at <10 Kb distance). In this study, the Sistani breed showed LD decay patterns similar to indicine cattle (Nellore and Sahiwal), which may be due to the geographic proximity of the Sistan and Baluchestan province to Pakistan, the origin of indicine breeds (they may have had genetic or kinship relationships over a long historical period), or due to ascertainment bias in the SNP chips used. Full article

The Pingliang red cattle, an outstanding indigenous resource in China, possesses an exceptional breeding value attributed to its tender meat and superior marbling quality. Currently, research efforts have predominantly concentrated on exploring its maternal origin and conducting conventional phenotypic studies. However, there remains a lack of comprehensive understanding regarding its genetic basis. To address this gap, we conducted a thorough whole-genome analysis to investigate the population structure, phylogenetic relationships, and gene flows of this breed using genomic SNP chip data from 17 bovine breeds. The results demonstrate that Pingliang red cattle have evolved distinct genetic characteristics unique to this breed, clearly distinguishing it from other breeds. Based on the analysis of the population structure and phylogenetic tree, it can be classified as a hybrid lineage between Bos taurus and Bos indicus. Furthermore, Pingliang red cattle display a more prominent B. taurus pedigree in comparison with Jinnan, Qinchuan, Zaosheng, Nanyang, and Luxi cattle. Moreover, this study also revealed closer genetic proximity within the Chinese indigenous cattle breed, particularly Qinchuan cattle, which shares the longest identical by descent (IBD) fragment with Pingliang red cattle. Gene introgression analysis shows that Pingliang red cattle have undergone gene exchange with South Devon and Red Angus cattle from Europe. Admixture analysis revealed that the proportions of East Asian taurine and Chinese indicine in the ancestry of Pingliang red cattle are approximately 52.44% and 21.00%, respectively, while Eurasian taurine, European taurine, and Indian indicine account for approximately 17.55%, 7.27%, and 1.74%. Our findings unveil distinct genetic characteristics in Pingliang red cattle and attribute their origin to B. taurus and B. indicus ancestry, as well as contributions from Qinchuan cattle, South Devon, and Red Angus. Full article

During embryo development, the endoplasmic reticulum (ER) acts as an important site for protein biosynthesis; however, in vitro culture (IVC) can negatively affect ER homeostasis. Therefore, the aim of our study was to evaluate the effects of the supplementation of tauroursodeoxycholic acid (TUDCA), an ER stress inhibitor, in the IVC of bovine embryos. Two experiments were carried out: Exp. 1: an evaluation of blastocyst rate, hatching kinetics, and gene expression of hatched embryos after being treated with different concentrations of TUDCA (50, 200, or 1000 μM) in the IVC; Exp. 2: an evaluation of the re-expansion, hatching, and gene expression of hatched embryos previously treated with 200 µM of TUDCA at IVC and submitted to vitrification. There was no increase in the blastocyst and hatched blastocyst rates treated with TUDCA in the IVC. However, embryos submitted to vitrification after treatment with 200 µM of TUDCA underwent an increased hatching rate post-warming together with a down-regulation in the expression of ER stress-related genes and the accumulation of lipids. In conclusion, this work showed that the addition of TUDCA during in vitro culture can improve the cryotolerance of the bovine blastocyst through the putative modulation of ER and oxidative stress. Full article

Dehong humped cattle are precious livestock resources of Yunnan Province, China; they have typical zebu traits. Here, we investigated their genetic characteristics using whole-genome resequencing data of Dehong humped animals (n = 18). When comparing our data with the publicly-available data, we found that Dehong humped cattle have high nucleotide diversity. Based on clustering models in a population structure analysis, Dehong humped cattle had a mutual genome ancestor with Chinese and Indian indicine cattle. While using the RFMix method, it is speculated that the body sizes of Dehong humped cattle were influenced by the Chinese indicine segments and that the immune systems of Dehong humped cattle were affected by additional ancestral segments (Indian indicine). Furthermore, we explored the position selection regions harboring genes in the Dehong humped cattle, which were related to heat tolerance (FILIP1L, ABHD6) and immune responses (GZMM, PRKCZ, STOML2, LRBA, PIK3CD). Notably, missense mutations were detected in the candidate gene ABHD6 (c.870C>A p.Asp290Glu; c.987C>A p.Ser329Arg). The missense mutations may have implications for Dehong humped cattle adaptation to hot environments. This study provides valuable genomic resource data at the genome-wide level and paves the way for future genetic breeding work in the Dehong humped cattle. Full article

Dabieshan cattle are a typical breed of southern Chinese cattle that have the characteristics of muscularity, excellent meat quality and tolerance to temperature and humidity. Based on 148 whole-genome data, our analysis disclosed the ancestry components of Dabieshan cattle with Chinese indicine (0.857) and East Asian taurine (0.139). The Dabieshan genome demonstrated a higher genomic diversity compared with the other eight populations, supported by the observed nucleotide diversity, linkage disequilibrium decay and runs of homozygosity. The candidate genes were detected by a selective sweep, which might relate to the fertility (GPX5, GPX6), feed efficiency (SLC2A5), immune response (IGLL1, BOLA-DQA2, BOLA-DQB), heat resistance (DnaJC1, DnaJC13, HSPA4), fat deposition (MLLT10) and the coat color (ASIP). We also identified the “East Asian taurine-like” segments in Dabieshan cattle, which might contribute to meat quality traits. The results revealed by the unique and valuable genomic data can build a foundation for the genetic improvement and conservation of genetic resources for indigenous cattle breeds. Full article

Shades of grey and brown are a dominant component in mammal coat colours, representing a fundamental trait involved in a great number of processes including cryptism, sexual selection and signalling. The genetic mechanisms of the grey colouration in mammals are very complex and controlled by hundreds of genes whose effects and interactions are still largely unclear. In this study, we adopted a robust multi-cohort F_st outlier approach based on pairwise contrasts between seven grey indicine cattle breeds and both taurine and indicine non-grey cattle breeds in order to find genomic regions potentially related to the grey colouration. On the basis of three main drawn settings, built in order to control both the effect of the sample size and the genetic structure, we have identified some signals common to those obtained in a previous work employing only taurine cattle. In particular, using the top 1% F_st approach, we detected a candidate region (22.6–23.8 megabases) on chromosome 14 in which genes related to pigmentation have been already documented. In addition, when we constructed a phylogenetic tree using the significant markers identified in this study and including also the genotyping data at these loci of both the grey taurine and the extinct wild auroch, we found a topological repartition consistent with breed colour pattern rather than with the known bovine evolutionary history. Thus, on the basis of this evidence, together with the geographical distribution of the current taurine grey cattle, an ancestral indicine origin for the grey phenotype would seem to be a conceivable interpretation. In this context, a higher thermo-tolerance and less UV-induced damage of the grey phenotype might have favoured the retention of advantageous genes into the taurine genome during the post-Neolithic human-mediated cattle expansions. Full article

Immune adaptation plays an essential role in determining pregnancy, which has been shown to be dependent on sufficient immunological tolerance mediated by FOXP3⁺ regulatory T cells. Recently, an X-linked maternal single-nucleotide polymorphism (SNP), located 2175 base pairs upstream of the start codon in the bovine FOXP3 gene (NC_037357.1: g.87298881A>G, rs135720414), was identified in Japanese Black (JB: Bos taurus) cows in association with recurrent infertility. However, with the exception of JB cows, the frequency of this SNP has yet to be studied in other cow populations. In this study, we thus aimed to evaluate the frequency of this SNP in different cow breeds. Between 2018 and 2021, a total of 809 DNA samples were obtained from 581 JB, 73 Holstein Friesian (HF: B. taurus), 125 Korean Hanwoo (KH: B. taurus coreanae), and 30 Indonesian Madura (IM: a crossbreed between B. indicus and B. javanicus) cows, which were genotyped using a TaqMan probe-based real-time polymerase chain reaction assay designed in this study. The frequency of the G allele was found to be relatively high in local IM (0.700), moderate in dairy HF (0.466), and low in beef JB (0.250) and KH (0.112) cows, with differences in the frequencies between each group being shown to be statistically significant (p < 0.005) using Fisher’s exact test. The results obtained in this study indicate that the G allele frequencies of the identified the SNP differ markedly in different breeds of taurine and indicine cattle. Given these findings, it would thus be important to evaluate the relationships between high frequencies of the G allele and infertility in different breeds. Full article

Bohai Black cattle are one of the well-known cattle breeds with black coat color in China, which are cultivated for beef. However, no study has conducted a comprehensive analysis of genomic diversity and selective pressures in Bohai Black cattle. Here, we performed a comprehensive analysis of genomic variation in 10 Bohai Black cattle (five newly sequenced and five published) and the published whole-genome sequencing (WGS) data of 50 cattle representing five “core” cattle populations. The population structure analysis revealed that Bohai Black cattle harbored the ancestry with European taurine, Northeast Asian taurine, and Chinese indicine. The Bohai Black cattle demonstrated relatively high genomic diversity from the other cattle breeds, as indicated by the nucleotide diversity (pi), the expected heterozygosity (H_E) and the observed heterozygosity (H_O), the linkage disequilibrium (LD) decay, and runs of homozygosity (ROH). We identified 65 genes containing more than five non-synonymous SNPs (nsSNPs), and an enrichment analysis revealed the “ECM-receptor interaction” pathways associated with meat quality in Bohai Black cattle. Five methods (CLR, θπ, F_ST, θπ ratio, and XP-EHH) were used to find several pathways and genes carried selection signatures in Bohai Black cattle, including black coat color (MC1R), muscle development (ITGA9, ENAH, CAPG, ABI2, and ISLR), fat deposition (TBC1D1, CYB5R4, TUSC3, and EPS8), reproduction traits (SPIRE2, KHDRBS2, and FANCA), and immune system response (CD84, SLAMF1, SLAMF6, and CDK10). Taken together, our results provide a valuable resource for characterizing the uniqueness of Bohai Black cattle. Full article

This study investigated polymorphisms in the milk protein genes CSN1S1, CSN2, CSN1S2, CSN3, LALBA, and LGB, and casein haplotypes in Beninese indigenous cattle. Considering 67 animals, DNA sequencing of the genes’ exons, flanking regions and parts of the 5?-upstream regions identified 1058 genetic variants including 731 previously unknown. In addition, four novel milk protein variants were detected, including CSN3^K (p.Ala66Val), LALBA^F (p.Arg58Trp), LGB^B1 (p.Ala134Val) and LGB^K (p.Thr92Asnfs*13). CSN3^K is caused by a novel SNP (BTA6:85656526C>T, exon 4) whereas LALBA^F and LGB^B1 are due to rs714688595C>T (exon 1) and rs109625649C>T (exon 4), respectively. Regarding LGB^K, a frameshift insertion of one adenine residue at BTA11:103257980 (exon 3) induces a premature translation termination resulting in a 46% reduction of the reference protein sequence. The casein polymorphisms formed five main CSN1S1-CSN2-CSN1S2-CSN3 haplotypes including B-A1-A-B, B-A1-A-A and C-A2-A-B which are predominant in the investigated cattle breeds. Moreover, in silico analyses of polymorphisms within the 5?- and 3?- untranslated regions of all six milk proteins revealed effects on microRNA and transcription factor binding sites. This study suggests a large genetic variation of milk protein genes in Beninese cattle, which should be investigated in further studies for their effects on milk production, including quality and yield traits. Full article

Understanding the genetic basis of locally adapted indigenous cattle populations is essential to design appropriate strategies and programs for their genetic improvement and conservation. Here, we report genetic diversity measures, population differentiation, and structure of 218 animals sampled from six indicine cattle populations of Bangladesh. Animals were genotyped with Illumina Bovine SNP50K BeadChip along with genotyped data of 505 individuals included from 19 zebu and taurine breeds worldwide. The principal component analysis (PCA) showed clear geographic separation between taurine and indicine lineages where Bangladeshi indigenous cattle clustered with South Asian zebu populations. However, overlapped clusters in PCA, heterozygosity estimates, and Neighbor-Joining phylogenetic tree analysis revealed weak genetic differentiation among the indigenous cattle populations of Bangladesh. The admixture analysis at K = 5 and 9 suggests distinct genetic structure of the studied populations along with 1 to 4% of taurine ancestry. The effective population size suggested a limited pool of ancestors particularly for Sahiwal and North Bengal Grey cattle. In conclusion, these findings shed insights into the genetic architecture of six indigenous cattle populations of Bangladesh for the first time and suggested as distinct gene pools without potential admixture with zebu or taurine populations. Full article

Long non-coding RNA (lncRNA) can regulate several aspects of gene expression, being associated with complex phenotypes in humans and livestock species. In taurine beef cattle, recent evidence points to the involvement of lncRNA in feed efficiency (FE), a proxy for increased productivity and sustainability. Here, we hypothesized specific regulatory roles of lncRNA in FE of indicine cattle. Using RNA-Seq data from the liver, muscle, hypothalamus, pituitary gland and adrenal gland from Nellore bulls with divergent FE, we submitted new transcripts to a series of filters to confidently predict lncRNA. Then, we identified lncRNA that were differentially expressed (DE) and/or key regulators of FE. Finally, we explored lncRNA genomic location and interactions with miRNA and mRNA to infer potential function. We were able to identify 126 relevant lncRNA for FE in Bos indicus, some with high homology to previously identified lncRNA in Bos taurus and some possible specific regulators of FE in indicine cattle. Moreover, lncRNA identified here were linked to previously described mechanisms related to FE in hypothalamus-pituitary-adrenal axis and are expected to help elucidate this complex phenotype. This study contributes to expanding the catalogue of lncRNA, particularly in indicine cattle, and identifies candidates for further studies in animal selection and management. Full article

Reproductive efficiency plays a major role in the long-term sustainability of livestock industries and can be improved through genetic and genomic selection. This study aimed to estimate genetic parameters (heritability and genetic correlation) and identify genomic regions and candidate genes associated with anti-Müllerian hormone levels (AMH) and antral follicle populations measured after estrous synchronization (AFP) in Nellore cattle. The datasets included phenotypic records for 1099 and 289 Nellore females for AFP and AMH, respectively, high-density single nucleotide polymorphism (SNP) genotypes for 944 animals, and 4129 individuals in the pedigree. The heritability estimates for AMH and AFP were 0.28 ± 0.07 and 0.30 ± 0.09, and the traits were highly and positively genetically correlated (r_G = 0.81 ± 0.02). These findings indicated that these traits can be improved through selective breeding, and substantial indirect genetic gains are expected by selecting for only one of the two traits. A total of 31 genomic regions were shown to be associated with AMH or AFP, and two genomic regions located on BTA1 (64.9–65.0 Mb and 109.1–109.2 Mb) overlapped between the traits. Various candidate genes were identified to be potentially linked to important biological processes such as ovulation, tissue remodeling, and the immune system. Our findings support the use of AMH and AFP as indicator traits to genetically improve fertility rates in Nellore cattle and identify better oocyte donors. Full article

Guangxi Province is located in the southernmost region of China, adjacent to the hotspot that is considered to be the putative migratory corridor or domestication area for Chinese indicine cattle. Here, we investigated the evolutionary status of Guangxi native breeds, Longlin (n = 21), Nandan (n = 18), and Weizhou cattle (n = 17) using mitogenome sequencing. Our results show that Bos indicus sub-haplogroup I1a predominates in Guangxi cattle breeds. Population structure by multidimensional-scaling analysis significantly differentiates Weizhou from the other two breeds (Longlin and Nandan). Moreover, the mtDNA haplotype composition and F_ST values indicate that the formation of Longlin and Nandan breeds may have been affected by Indian indicine, whereas, Weizhou island might have preserved pure Chinese indicine cattle due to its geographical isolation. We speculate that following the initial entry of zebu into southern China, the subsequent introgression of Indian indicine may have influenced the matrilineal origin of local breeds in southwestern China. Full article