Local Ancestry and Adaptive Introgression in Xiangnan Cattle

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, FST, 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.

The effects and mechanisms of heat stress on mammalian oocyte and embryo development

The sum of nonspecific physiological responses exhibited by mammals in response to the disruption of thermal balance caused by high-temperature environments is referred to as heat stress (HS). HS affects the normal development of mammalian oocyte and embryos and leads to significant economic losses. Therefore, it is of great importance to gain a deep understanding of the mechanisms underlying the effects of HS on oocyte and embryonic development and to explore strategies for mitigating or preventing its detrimental impacts in the livestock industry. This article provides an overview of the negative effects of HS on mammalian oocyte growth, granulosa cell maturation and function, and embryonic development. It summarizes the mechanisms by which HS affects embryonic development, including generation of reactive oxygen species (ROS), endocrine disruption, the heat shock system, mitochondrial autophagy, and molecular-level alterations. Furthermore, it discusses various measures to ameliorate the effects of HS, such as antioxidant use, enhancement of mitochondrial function, gene editing, cultivating varieties possessing heat-resistant genes, and optimizing the animals'rearing environment. This article serves as a valuable reference for better understanding the relationship between HS and mammalian embryonic development as well as for improving the development of mammalian embryos and economic benefits under HS conditions in livestock production.

Functional transcriptome analysis revealed upregulation of MAPK-SMAD signalling pathways in chronic heat stress in crossbred cattle

Animal geneticists and breeders have the impending challenge of enhancing the resilience of Indian livestock to heat stress through better selection strategies. Climate change's impact on livestock is more intense in tropical countries like India where dairy cattle crossbreeds are more sensitive to heat stress. The main reason for this study was to find the missing relative changes in transcript levels in thermo-neutral and heat stress conditions in crossbred cattle through whole-transcriptome analysis of RNA-Seq data. Differentially expressed genes (DEGs) identified based on the minimum log twofold change value and false discovery rate 0.05 revealed 468 up-regulated genes and 2273 down-regulated significant genes. Functional annotation and pathway analysis of these significant DEGs were compared based on Gene Ontology (Biological process), Kyoto Encyclopedia of Genes and Genome (KEGG), and Reactome pathways using g: Profiler, ShinyGO v0.76, and iDEP.951 web tools. On finding network visualization, the most over-represented and correlated pathways were neuronal and sensory organ development, calcium signalling pathway, Mitogen-activated protein kinase (MAPK) and Smad signalling pathway, Ras-proximate-1, or Ras-related protein 1 (Rap 1) signalling pathway, apoptosis, and oxidative stress. Similarly, down-regulated genes were most expressed in mRNA processing, immune system, B-cell receptor signalling pathway, Nucleotide oligomerization domain (NOD)-like receptors (NLRs) signalling pathway and nonsense-mediated decay (NMD) pathway. The heat stress-responsive genes identified in this study will facilitate our understanding of the molecular basis for climate resilience and heat tolerance in Indian dairy crossbreeds.

TRPM4 gene variation associated with climatic conditions in Chinese cattle

The transient receptor potential (TRP) superfamily has been reported to play an important role in heat tolerance pathways. Based on the Bovine Genome Variation Database and Selective Signatures, a missense mutation (NC_037345.1: c.2237A > G: p. His746Arg) (rs209689836) was identified in the transient receptor potential cation channel subfamily M member 4 (TRPM4) gene, a member of the TRP family, corresponding to heat tolerance. Here, we explored the prevalence of this variant in 19 native Chinese cattle (comprised of 404 individuals) to determine its possible association with heat tolerance in Chinese cattle by using PCR and DNA sequencing. The distribution of alleles of NC_037345.1: c.2237A > G: p. His746Arg displays significant geographical differences across native Chinese cattle breeds, consistent with the distribution of indicine and taurine cattle in China. Additionally, the association analysis indicated that the G allele was significantly associated with mean annual temperature (T), relative humidity (RH) and temperature humidity index (THI) (p < .05), suggesting that cattle carrying allele G were distributed in regions with higher T, RH, and THI. In conclusion, our results suggested that the mutation of the TRPM4 gene in Chinese cattle might be a candidate locus associated with heat tolerance.

Genes related to heat tolerance in cattle-a review

Heat stress is described as the cumulative detrimental effect caused by an imbalance between heat production within the body and heat dissipation. When cattle are exposed to heat stress with skin surface temperatures exceeding 35 °C, gene networks within and across cells respond to environmental heat loads with both intra and extracellular signals that coordinate cellular and whole-animal metabolism changes to store heat and rapidly increase evaporative heat loss. In this study, we examined evidence from genes known to be associated with heat tolerance (Hsp70, HSF1, HspB8, SOD1, PRLH, ATP1A1, MTOR, and EIF2AK4). This information could serve as valuable resource material for breeding programs aimed at increasing the thermotolerance of cattle.

Expression profile and bioinformatics analysis of circRNA and its associated ceRNA networks in longissimus dorsi from Lufeng cattle and Leiqiong cattle

This paper aims to explore the role of circRNA expression profiles and circRNA-associated ceRNA networks in the regulation of myogenesis in the longissimus dorsi of cattle breeds surviving under subtropical conditions in southern China by RNA sequencing and bioinformatics analysis. It also aims to provide comprehensive understanding of the differences in muscle fibers in subtropical cattle breeds and to expand the knowledge of the molecular networks that regulate myogenesis. With regard to meat quality indicators, results showed that the longissimus dorsi of LQC had lower pH (P < 0.0001), lower redness (P < 0.01), lower shear force (P < 0.05), and higher brightness (P < 0.05) than the longissimus dorsi of LFC. With regard to muscle fiber characteristics, the longissimus dorsi of LQC had a smaller diameter (P < 0.0001) and higher density of muscle fibers (P < 0.05). The analysis results show that the function of many circRNA-targeted mRNAs was related to myogenesis and metabolic regulation. Furthermore, in the analysis of the function of circRNA source genes, we hypothesized that btacirc_00497 and btacirc_034497 may regulate the function and type of myofibrils by affecting the expression of MYH6, MYH7, and NEB through competitive linear splicing.

Heat Stress: A Serious Disruptor of the Reproductive Physiology of Dairy Cows

Global warming is a significant threat to the sustainability and profitability of the dairy sector, not only in tropical or subtropical regions but also in temperate zones where extreme summer temperatures have become a new and challenging reality. Prolonged exposure of dairy cows to high temperatures compromises animal welfare, increases morbidity, and suppresses fertility, resulting in devastating economic losses for farmers. To counteract the deleterious effects of heat stress, cattl e employ various adaptive thermoregulatory mechanisms including molecular, endocrine, physiological, and behavioral responses. These adaptations involve the immediate secretion of heat shock proteins and cortisol, followed by a complex network of disrupted secretion of metabolic and reproductive hormones such as prolactin, ghrelin, ovarian steroid, and pituitary gonadotrophins. While the strategic heat stress mitigation measures can restore milk production through modifications of the microclimate and nutritional interventions, the summer fertility records remain at low levels compared to those of the thermoneutral periods of the year. This is because sustainment of high fertility is a multifaceted process that requires appropriate energy balance, undisrupted mode of various hormones secretion to sustain the maturation and fertilizing competence of the oocyte, the normal development of the early embryo and unhampered maternal-embryo crosstalk. In this review, we summarize the major molecular and endocrine responses to elevated temperatures in dairy cows, as well as the impacts on maturing oocytes and early embryos, and discuss the consequences that heat stress brings about in dairy cattle fertility.

Distribution of a missense mutation (rs525805167) within the SLC45A2 gene associated with climatic conditions in Chinese cattle

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.

CNV analysis of VAMP7 gene reveals variation associated with growth traits in Chinese cattle

Copy number variant (CNV), a common genetic polymorphism, is closely related to the phenotypic variation traits of organisms. Vesicle-associated membrane protein 7 gene (VAMP7) codes a protein, which is a member of the SNARE proteins family and plays an important role in the process of intracellular vesicle transport. In this study, a total of four cattle breeds (Yunling cattle, Xianan cattle, Pinan cattle, Jiaxian red cattle) were used to investigate the copy numbers, and we found an association relationship between CNV of VAMP7 gene and growth traits of cattle by SPSS 20.0 software. The results showed that the CNV type of VAMP7 gene in four cattle breeds had the same distribution, Duplication type occupies a dominant position among the four varieties. In Yunling cattle, the Duplication type of VAMP7 is significantly related to the height at the hip cross (p < 0.05), Individuals with Duplication type commonly have less performance on growth and development, which indicates that the Duplication type of the VAMP7 gene may have a negative effect on cattle growth. Individuals with the other two CNV types may become the breeding direction of the VAMP7 gene. This study provided a new perspective and basic material for the molecular genetics of the CNV of the VAMP7 gene, and also promoted the breeding progress of Chinese local cattle.

A novel missense mutation (rs464874590) within BoLA-DOB gene associated with the heat-resistance in Chinese cattle

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.

A novel missense mutation within KRT75 gene strongly affects heat stress in Chinese cattle

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.

A novel SNP of MYO1A gene associated with heat-tolerance in Chinese cattle

With the advent of global climate change, heat-tolerance is becoming more and more important to the sustainability of animal husbandry production systems. Previous studies have shown that MYO1A gene associated with pigmentation may be closely related to heat-tolerance in cattle. In this study, a novel missense mutation (NC_037332.1 g.56390345 A > G) was first detected in MYO1A in 891 individuals of 35 cattle breeds, which transformed the amino acid isoleucine into valine. The purpose of this study was to determine the allele frequencies distribution of this locus in Chinese indigenous cattle and to analyze the relationship between this locus and heat-tolerance. Further analysis showed that frequency of wild allele A decreased gradually from northern cattle to southern cattle, whereas frequency of mutant type allele G showed the opposite pattern, which was consistent with the distribution of various climatic conditions of China. Additionally, association analysis was carried out between genotypes and four climatic conditions (annual mean temperature (T), relative humidity (H), temperature-humidity index (THI) and average annual sunshine hours (100-cloudiness) (SR)). Analysis results showed that genotypes were significantly correlated with climatic conditions. Therefore, our results suggest that the novel SNP (rs209559414) is related to heat-tolerance trait of Chinese indigenous cattle.

Selection signatures of Fuzhong Buffalo based on whole-genome sequences

BACKGROUND

Fuzhong buffalo, a native breed of Guangxi Zhuang Autonomous Region, is traditionally used as a draft animal to provide farm power in the rice cultivation. In addition, the Fuzhong buffalo also prepared for the bullfighting festival organized by the locals. The detection of the selective signatures in its genome can help in elucidating the selection mechanisms in its stamina and muscle development of a draft animal.

RESULTS

In this study, we analyzed 27 whole genomes of buffalo (including 15 Fuzhong buffalo genomes and 12 published buffalo genomes from Upper Yangtze region). The ZHp, ZFst, π-Ratio, and XP-EHH statistics were used to identify the candidate signatures of positive selection in Fuzhong buffalo. Our results detected a set of candidate genes involving in the pathways and GO terms associated with the response to exercise (e.g., ALDOA, STAT3, AKT2, EIF4E2, CACNA2D2, TCF4, CDH2), immunity (e.g., PTPN22, NKX2-3, PIK3R1, ITK, TMEM173), nervous system (e.g., PTPN21, ROBO1, HOMER1, MAGI2, SLC1A3, NRG3, SNAP47, CTNNA2, ADGRL3). In addition, we also identified several genes related to production and growth traits (e.g., PHLPP1, PRKN, MACF1, UCN3, RALGAPA1, PHKB, PKD1L). Our results depicted several pathways, GO terms, and candidate genes to be associated with response to exercise, immunity, nervous system, and growth traits.

CONCLUSIONS

The selective sweep analysis of the Fuzhong buffalo demonstrated positive selection pressure on potential target genes involved in behavior, immunity, and growth traits, etc. Our findings provided a valuable resource for future research on buffalo breeding and an insight into the mechanisms of artificial selection.

Association of HSF1 Genetic Variation with Heat Tolerance in Chinese Cattle

The heat shock factor 1 (HSF1) gene is a regulator of the heat stress response, maximizing HSP protein expression survival. In this research, we explored the frequency distribution of a missense mutation (NC_037341.1 g.616087A > G, rs135258919) in the HSF1 gene in Chinese cattle with amino acid substitution, valine to alanine. This mutation could be related to the heat tolerance in Bos indicus. A total of 941 individuals representing 35 Chinese native cattle breeds, combining pure taurine (Angus) and indicine cattle, were used to determine the genotypes of the mutation through PCR and partial DNA sequencing. The results showed significant differences in allele frequencies and their genotypes amongst Chinese cattle from different regions. Allele G or indicine-specific allele frequency diminished from south to north China, while allele A (genotype AA) or the taurine-specific allele had a contrary pattern, which agreed with the distribution of taurine and indicine cattle. According to the association analysis, the NC_037341.1 g.616087A > G (rs135258919) of the bovine HSF1 gene, annual temperature (T), relative humidity (RH), and the temperature humidity index (THI) (p < 0.01) were interrelated closely, which indicated that the NC_037341.1 g.616087A > G of the HSF1 gene is associated with heat tolerance in indicine cattle.

MTOR Variation Related to Heat Resistance of Chinese Cattle

With the inexorable rise of global temperature, heat stress deserves more and more attention in livestock agriculture. Previous studies have shown that the mechanistic target of rapamycin (MTOR) (NC_037343.1:c.2062G>C) gene contributes to the repair of DNA damage repair and is associated with the adaptation of camels in dry and hot environments. However, it is unknown whether this mutation is related to the heat tolerance of Chinese cattle. In this study, PCR and sequencing were used to type the mutation locus in 1030 individuals of 37 cattle breeds. The analysis results showed that the frequency of G allele of the locus gradually diminished from the northern group to the southern group of native Chinese cattle, whereas the frequency of the C allele showed an opposite pattern, displaying a significant geographical difference across native Chinese cattle breeds. Additionally, an analysis of the locus in Chinese indigenous cattle revealed that this SNP was significantly associated with mean annual temperature (T), relative humidity (RH) and temperature humidity index (THI) (p < 0.01), suggesting that cattle with C allele was distributed in regions with higher T, RH and THI. In conclusion, this study proved that the mutation of MTOR gene in Chinese cattle could be associated with the heat tolerance.

A SNP in PLAG1 is associated with body height trait in Chinese cattle

Stature is an important quantitative trait for cattle performance, which influences herd productivity. Previous studies have reported that an SNP (AC_000171.1:g.25015640G>T, rs109815800) in Pleomorphic adenoma gene 1 (PLAG1) on chromosome 14 (CHR14) is associated with bovine stature. To validate whether rs109815800 is associated with the body height of Chinese cattle, we carried out an association analysis using 558 adult cattle samples from seven populations. Then, 1038 samples from 38 Chinese cattle breeds were used to show the geographical distribution of this variant in China. The results showed that the Q allele (G allele) increased the height of cattle. Furthermore, the frequencies of Q allele in Chinese native breeds tend to decrease from northern China to southern China, and the frequency of Q allele in two Chinese beef cattle breeds is much higher than that in another 36 Chinese local cattle breeds. Our data suggest that the prevalence of the Q allele is correlated with latitude in China.

A Missense Mutation of the HSPB7 Gene Associated with Heat Tolerance in Chinese Indicine Cattle

Simple Summary

A missense mutation (NC_037329.1: g.136054902 C > G: p. Ala69Gly) was identified in the heat shock protein family B (small) member 7 (HSPB7) gene in indicine cattle, which might be a candidate mutation associated with the heat tolerance. Here, Polymerase Chain Reaction and DNA sequencing methods were used to detect this mutation in 774 individuals belonging to 32 Chinese indigenous cattle breeds. The distribution of alleles of NC_037329.1: g.136054902 C > G displays significant geographical difference across native Chinese cattle breeds and cattle carrying allele G distributed in regions with higher mean annual temperature, relative humidity, and temperature humidity index. Our results demonstrate that the mutation of the HSPB7 gene in Chinese indicine cattle might be a candidate gene associated with the heat tolerance.

Abstract

The small heat shock proteins (HSPB) are expressed in response to heat stress, and the heat shock protein family B (small) member 7 (HSPB7) gene has been reported to play an important role in heat tolerance pathways. Only a missense mutation (NC_037329.1: g.136054902 C > G: p.Ala69Gly) was identified in the HSPB7 gene in indicine cattle, which might be a candidate mutation associated with the heat tolerance. Here, we explore the allele frequency of this mutation in 774 individuals belonging to 32 Chinese indigenous cattle breeds using polymerase chain reaction (PCR) and DNA sequencing methods. The distribution of alleles of NC_037329.1: g.136054902 C > G displays significant geographical difference across native Chinese cattle breeds that the allele C was dominant in northern cattle groups, while allele G was dominant in southern indicine cattle groups. Additionally, the association analysis indicated that the G allele was significantly associated with mean annual temperature (T), relative humidity (RH), and temperature humidity index (THI) (p < 0.01), suggesting that cattle carrying allele G were distributed in regions with higher T, RH, and THI. Our results demonstrate that the mutation of the HSPB7 gene in Chinese indicine cattle might be a candidate gene associated with the heat tolerance.

A Novel SNP in EIF2AK4 Gene Is Associated with Thermal Tolerance Traits in Chinese Cattle

Simple Summary

China harbors two lineages of cattle (Bos taurus and Bos indicus) that display pronounced geographical distribution differences. Northern Chinese cattle predominantly belong to B. taurus and southern Chinese cattle belong to B. indicus. Both B. taurus and B. indicus contribute to the admixture of cattle in central China. Thermal stress induces oxidative stress and DNA damage in mammals. In general, B. indicus are more resistant to thermal stress than B. taurus. Eukaryotic translation initiation factor 2-alpha kinase 4 (EIF2AK4), which pertains to the family of serine–threonine kinase, is a candidate gene for thermal stress. However, the effects of the bovine EIF2AK4 gene on the thermal tolerance traits of Chinese cattle breeds remain unknown. Our results suggest that a variant of the EIF2AK4 gene is associated with thermal tolerance traits in Chinese cattle.

Abstract

Eukaryotic translation initiation factor 2-alpha kinase 4 (EIF2AK4, also known as GCN2), which pertains to the family of serine–threonine kinase, is involved in oxidative stress and DNA damage repair. A missense single-nucleotide polymorphism (SNP) (NC_037337.1 g.35615224 T > G) in exon 6 of the EIF2AK4 gene which encodes a p.Ile205Ser substitution was observed in the Bovine Genome Variation Database and Selective Signatures (BGVD). The purpose of the current study is to determine the allelic frequency distribution of the locus and analyze its association with thermal tolerance in Chinese indigenous cattle. In our study, the allelic frequency distribution of the missense mutation (NC_037337.1 g.35615224 T > G) in Chinese cattle was analyzed by sequencing 1105 individuals of 37 breeds including 35 Chinese indigenous cattle breeds and two exotic breeds. In particular, association analysis was carried out between the genotypes and three environmental parameters including annual mean temperature (T), relative humidity (RH), and temperature–humidity index (THI). The frequency of the mutant allele G (NC_037337.1 g.35615224 T > G) gradually decreased from the southern cattle groups to the northern cattle groups, whereas the frequency of the wild-type allele T showed an opposite pattern, consistent with the distribution of indicine and taurine cattle in China. In accordance with the association analysis, genotypes were significantly associated with T (P < 0.01), RH (P < 0.01), and THI (P < 0.01), suggesting that the cattle with genotype GG were found in regions with higher T, RH, and THI. Thus, our results suggest that the mutation (NC_037337.1 g.35615224 T > G) of the EIF2AK4 gene is associated with thermal tolerance traits in Chinese cattle.