Genetic analysis of Thai cattle reveals a Southeast Asian indicine ancestry

Carcass characteristics, meat quality, sensory palatability and chemical composition of Thai native cattle grazing in lowland and Phu Phan mountain forest

OBJECTIVE

The aim of this study was to assess the effect of Thai native cattle grazing in the lowland or mountain forest on carcass characteristics, meat quality, sensory palatability, and chemical composition.

METHODS

Twelve male Thai native cattle with an average weight of 110±10 kg are allowed to be grazing in the lowland or Phu Phan mountain forest during the rainy season in northeastern Thailand.

RESULTS

The carcass characteristics, meat pH, and meat color were unaffected by treatment (p>0.05). The boiling loss was lower in the cattle grazing on the mountain forest (p = 0.027). The cattle grazing in the mountain forest had increased shear force (p = 0.039), tenderness (p = 0.011), and flavor intensity (p = 0.003). The protein and fat were higher (p<0.001 and p = 0.035, respectively) in cattle grazing in the mountain forest. The different grazing systems of the cattle had no effect (p>0.05) fatty acids in meat, except for capric acid (C10:0) and lauric acid (C12:0), which were higher (p = 0.046 and p = 0.049, respectively) when the cattle were grazing in the mountain forest. The different grazing systems did not influence (p>0.05) the unsaturated fatty acids in meat.

CONCLUSION

Thai native cattle grazing in the Phu Phan mountain forest in the rainy season improves meat quality, sensory evaluation, and chemical composition.

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.

Effect of coated cysteamine hydrochloride and probiotics supplemented alone or in combination on feed intake, nutrients digestibility, ruminal fermentation, and blood metabolites of Kamphaeng Saen beef heifers

This study aimed to determine the effects of coated cysteamine hydrochloride (CSH) and probiotics (PB) supplemented alone or in combination on feed intake, digestibility, ruminal fermentation, and blood metabolites of heifer beef cattle. Sixteen heifers (body weight = 210 ± 41 kg; age = 9 ± 2 months) were assigned according to a randomized complete block design in a 2 × 2 factorial arrangement. All animals were fed the basal diet, which contained an 82:17 concentrate-to-forage ratio, and the forage source was rice straw. The treatments were as follows: (1) 0% PB + 0 g/d CSH, (2) 0.1% PB + 0 g/d CSH, (3) 0% PB + 20 g/d CSH, and (4) 0.1% PB + 20 g/d CSH. The main effect of CSH supplementation has been found to improve feed intake (P < 0.05). There were no treatment interactions with nutrient digestibility or rumen fermentation parameters. Supplementation of CSH did not affect any of the variables evaluated, while probiotics supplementation increased DM digestibility due to the increases in CP and fiber fraction digestibility. Compared to controls and CSH, at 16 h post-feeding, heifers receiving probiotics tended (P = 0.07) to show 17% greater ruminal NH3-N concentration, but this effect was not evident at 2 h post-feeding. However, the main effects of probiotic supplementation showed a tendency to increase the number of total bacteria and fungal zoospores in the rumen at 2 h post-feeding. The blood triglyceride (BTG) concentration of heifers fed a diet supplemented with 20 g/d CSH and 0.1% probiotics was found to be greater than those fed CSH alone (P < 0.1) at 16 h post-feeding, and then, there were greater BTG concentrations than other treatments (P < 0.05) at 2 h post-feeding. In conclusion, the combination of CSH and PB did not potentiate the effects of probiotics on digestibility and rumen fermentation and had minimal effects on blood parameters.

1H NMR Metabolic Profiling and Meat Quality in Three Beef Cattle Breeds from Northeastern Thailand

The increasing need for effective analytical tools to evaluate beef quality has prompted the development of new procedures to improve the animal sector's performance. In this study, three beef breeds-Thai native (TN), crossbred Brahman × Thai native (BT), and crossbred Charolais × Brahman (CB)-were compared in terms of their physicochemical and metabolic profiles. The findings demonstrated that TN beef was lighter and tougher than other beef. Beef odor was stronger in BT. In addition, CB beef was the most tender and had the highest intramuscular fat content. Twenty-one different metabolites were found overall through NMR and chemometric approaches. The primary factors contributing to the difference in OPLS-DA loading plots were acetylcholine, valine, adenine, leucine, phosphocreatine, β-hydroxypyruvate, ethanol, adenosine diphosphate, creatine, acetylcholine, and lactate. The multivariate analysis indicated that these metabolites in beef cattle breeds could be distinguished using NMR spectroscopy. The results of this study provide valuable information on the quality and meat metabolites of different breeds. This could help in the development of a more accurate assessment of the quality of beef in future research.

Kouprey (Bos sauveli) genomes unveil polytomic origin of wild Asian Bos

The evolution of the genera Bos and Bison, and the nature of gene flow between wild and domestic species, is poorly understood, with genomic data of wild species being limited. We generated two genomes from the likely extinct kouprey (Bos sauveli) and analyzed them alongside other Bos and Bison genomes. We found that B. sauveli possessed genomic signatures characteristic of an independent species closely related to Bos javanicus and Bos gaurus. We found evidence for extensive incomplete lineage sorting across the three species, consistent with a polytomic diversification of the major ancestry in the group, potentially followed by secondary gene flow. Finally, we detected significant gene flow from an unsampled Asian Bos-like source into East Asian zebu cattle, demonstrating both that the full genomic diversity and evolutionary history of the Bos complex has yet to be elucidated and that museum specimens and ancient DNA are valuable resources to do so.

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We generated two genomes from the likely extinct kouprey (Bos sauveli)

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Extensive mt and nuclear-genome-wide incomplete lineage sorting across wild Asian Bos

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Initial polytomic diversification of the wild Asian Bos—kouprey, banteng, and gaur

Meat quality, post-mortem proteolytic enzymes, and myosin heavy chain isoforms of different Thai native cattle muscles

OBJECTIVE

This study investigated the meat quality characteristics, endogenous proteolytic enzymes, collagen content, and myosin heavy chain (MyHC) isoforms of different muscles of Thai native cattle (TNC).

METHODS

Infraspinatus (IF), Longissimus thoracis (LT), and Supraspinatus (SS) muscles were obtained from two TNC breeds, Kho-Lan (KL, n = 7) and Kho-Isaan (KI, n = 7). The muscle and meat characteristics of TNC breeds and their relationship with MyHC expression were examined.

RESULTS

Three MyHC isoforms namely MyHC I, MyHC IIa, and MyHC IIx were detected in the muscles. The KL had higher (p<0.05) MyHC IIx than the KI. The IF muscle had higher (p<0.05) MyHC I compared to other muscles. The LT muscle had the least MyHC I. The LT had higher (p<0.05) MyHC IIx than the IF and SS muscles. The IF presented the least MyHC IIx. The KL had higher (p<0.05) lightness and moisture content and lower crude protein, redness, cooking loss, shear force, and calpastatin than the KI. The glycogen, total collagen, soluble collagen, crude protein, ash contents, and troponin T degradation product of IF and SS were lower (p<0.05) than that of LT. Ether extract in LT was lower (p<0.05) than that of IF and SS. The percentage of MyHC I, MyHC IIa, and MyHC IIx were significantly correlated with muscle and meat characteristics of TNC.

CONCLUSION

These results suggest that the differences in the MyHC isoforms may partly account for the variation in meat quality between breeds and among muscles of TNC.

An insight into the evolutionary history of Indonesian cattle assessed by whole genome data analysis

The domestication of Indonesian cattle was investigated through a study of their genetic diversity, up to the genome level. Little documentation exists regarding the history of domestication of Indonesian cattle and questions remain despite a growing body of molecular evidence. In this study, we genotyped seven Indonesian cattle breeds using an Illumina BovineSNP50 Bead Chip to provide insight into their domestication and demographic history in a worldwide population context. Our analyses indicated the presence of hybrid cattle, with Bos javanicus and Bos indicus ancestries being most prevalent, as well as purebred cattle. We revealed that all the breeds were interconnected through several migration events. However, their demographic status varied widely. Although almost all the Indonesian cattle had an effective population size higher than the minimum level required to ensure breed fitness, efforts are still needed to maintain their genetic variability and purity.

Evolution and domestication of the Bovini species

Domestication of the Bovini species (taurine cattle, zebu, yak, river buffalo and swamp buffalo) since the early Holocene (ca. 10 000 BCE) has contributed significantly to the development of human civilization. In this study, we review recent literature on the origin and phylogeny, domestication and dispersal of the three major Bos species - taurine cattle, zebu and yak - and their genetic interactions. The global dispersion of taurine and zebu cattle was accompanied by population bottlenecks, which resulted in a marked phylogeographic differentiation of the mitochondrial and Y-chromosomal DNA. The high diversity of European breeds has been shaped through isolation-by-distance, different production objectives, breed formation and the expansion of popular breeds. The overlapping and broad ranges of taurine and zebu cattle led to hybridization with each other and with other bovine species. For instance, Chinese gayal carries zebu mitochondrial DNA; several Indonesian zebu descend from zebu bull × banteng cow crossings; Tibetan cattle and yak have exchanged gene variants; and about 5% of the American bison contain taurine mtDNA. Analysis at the genomic level indicates that introgression may have played a role in environmental adaptation.

Feeding pineapple waste silage as roughage source improved the nutrient intakes, energy status and growth performances of growing Myanmar local cattle

Objective

The aim of this experiment was to determine the effect of feeding pineapple waste silage (PWS) as the source of roughage replaced in Napier grass silage (NGS) on the nutrient intakes, energy status, and growth performances of growing Myanmar local cattle.

Materials and methods

Eight growing Myanmar local cattle were randomly allocated into two groups, which were adjusted for age, sex, and body weight. Treatments were control (70% NGS + 30% concentrate) and PWS (45% NGS + 25% PWS + 30% concentrate). This experiment lasted for 6 weeks, including adaptation, and feed intake, energy status, and body weight gain were measured.

Results

The higher (p < 0.05) intakes of dry matter, crude protein, non-fiber carbohydrate, neutral detergent fiber and energy, and energy balance were observed in the PSW group than in the control group. Although the initial and final body weights of both groups were not different (p > 0.05), the body weight gain and average daily gain were significantly higher (p < 0.05) in the PSW group than in the control group. Feeding PWS as a roughage source at 25% of diet improved the nutrient intake, energy balance, and body weight gain of growing Myanmar local cattle.

Conclusion

Thus, PWS could be used as the source of roughage replaced in NGS in Myanmar local cattle with the improvement of productive performances.

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.

Origin of prehistoric cattle excavated from four archaeological sites in central and northeastern Thailand

Cattle have been domesticated in Southeast Asia, including Thailand, for thousands of years, but the history of cattle domestication in the region remains unclear. To date, only genetic studies of modern Thai cattle DNA have been reported. To gain some insight into cattle domestication in the country, a total of 56 cattle remains excavated from four archaeological sites (dated to between 3550 and 1700 years before present (YBP)) in northeastern and central Thailand were analysed in this study. Of 56, the 157-bp D-loop fragment was successfully generated from 26 samples, all of which belonged to Bos taurus in haplogroup T/T3. One haplotype contained 19 members from all four archaeological sites and clustered with the ancient B. taurus from Iran, Turkey and China. Other haplotypes have not shared haplotype with B. taurus from other countries but they showed close relationship to those from China. This represents the first genetic evidence that B. taurus was domesticated in Thailand between 3550 and 1700 YBP. In addition, the close relationship among ancient Thai, Iranian and Chinese taurines suggests that cattle from the Near East were introduced into North China, and were subsequently brought into Thailand thousands of years ago.

Genomic Selection and Use of Molecular Tools in Breeding Programs for Indigenous and Crossbred Cattle in Developing Countries: Current Status and Future Prospects

Genomic selection (GS) has resulted in rapid rates of genetic gains especially in dairy cattle in developed countries resulting in a higher proportion of genomically proven young bulls being used in breeding. This success has been undergirded by well-established conventional genetic evaluation systems. Here, the status of GS in terms of the structure of the reference and validation populations, response variables, genomic prediction models, validation methods, and imputation efficiency in breeding programs of developing countries, where smallholder systems predominate and the basic components for conventional breeding are mostly lacking is examined. Also, the application of genomic tools and identification of genome-wide signatures of selection is reviewed. The studies on genomic prediction in developing countries are mostly in dairy and beef cattle usually with small reference populations (500-3,000 animals) and are mostly cows. The input variables tended to be pre-corrected phenotypic records and the small reference populations has made implementation of various Bayesian methods feasible in addition to GBLUP. Multi-trait single-step has been used to incorporate genomic information from foreign bulls, thus GS in developing countries would benefit from collaborations with developed countries, as many dairy sires used are from developed countries where they may have been genotyped and phenotyped. Cross validation approaches have been implemented in most studies resulting in accuracies of 0.20-0.60. Genotyping animals with a mixture of HD and LD chips, followed by imputation to the HD have been implemented with imputation accuracies of 0.74-0.99 reported. This increases the prospects of reducing genotyping costs and hence the cost-effectiveness of GS. Next-generation sequencing and associated technologies have allowed the determination of breed composition, parent verification, genome diversity, and genome-wide selection sweeps. This information can be incorporated into breeding programs aiming to utilize GS. Cost-effective GS in beef cattle in developing countries may involve usage of reproductive technologies (AI and in-vitro fertilization) to efficiently propagate superior genetics from the genomics pipeline. For dairy cattle, sexed semen of genomically proven young bulls could substantially improve profitability thus increase prospects of small holder farmers buying-in into genomic breeding programs.

Current situation and future prospects for beef production in Thailand - A review

Thailand is a country of native beef cattle resource farming. It has undergone rapid social and economic change in the past decade. Agricultural growth has been maintained by increasing the production of rice and cassava. Changing economic status also provides opportunities for beef cattle producers to meet increasing consumer demand for beef. Finishing beef cattle numbers in Thailand were about 1.0 M head in 2015. Beef produced in Thailand has exclusively been for domestic consumption. Only 1% of Thailand’s beef cattle are for the premium market which is based on marbling score, 40% are sold into modern markets that consider muscling of cattle, and the remainder enter traditional markets. Cross-bred cattle for the premium market are raised within intensive systems. Most producers of premium beef are members of beef cooperatives, or have invested in their enterprises at high levels. Culled cow (native or cross-bred cattle) are mainly for small holder farm production. Malaysia, Indonesia, and other members of the Asian Economic Community (AEC) are set to become the largest beef market, which has been confirmed by 2015 through 2020 forecasts for consumption of beef that must increasingly be halal. These circumstances are likely to be challenging for beef producers in Thailand to gain a share of this market. Integration across all sectors involved in beef production in Thailand will be required.

Species composition and environmental adaptation of indigenous Chinese cattle

Indigenous Chinese cattle combine taurine and indicine origins and occupy a broad range of different environments. By 50 K SNP genotyping we found a discontinuous distribution of taurine and indicine cattle ancestries with extremes of less than 10% indicine cattle in the north and more than 90% in the far south and southwest China. Model-based clustering and f4-statistics indicate introgression of both banteng and gayal into southern Chinese cattle while the sporadic yak influence in cattle in or near Tibetan area validate earlier findings of mitochondrial DNA analysis. Geographic patterns of taurine and indicine mitochondrial and Y-chromosomal DNA diversity largely agree with the autosomal cline. The geographic distribution of the genomic admixture of different bovine species is proposed to be the combined effect of prehistoric immigrations, gene flow, major rivers acting as genetic barriers, local breeding objectives and environmental adaptation. Whole-genome scan for genetic differentiation and association analyses with both environmental and morphological covariables are remarkably consistent with previous studies and identify a number of genes implicated in adaptation, which include TNFRSF19, RFX4, SP4 and several coat color genes. We propose indigenous Chinese cattle as a unique and informative resource for gene-level studies of climate adaptation in mammals.