Indicus Breeds Research Articles

Genomic variants identified from whole-genome resequencing of indicine cattle breeds from Pakistan.

The primary goal of cattle genomics is the identification of genome-wide polymorphism associated with economically important traits. The bovine genome sequencing project was completed in 2009. Since then, using massively parallel sequencing technologies, a large number of Bos taurus cattle breeds have been resequenced and scanned for genome-wide polymorphisms. As a result, a substantial number of single nucleotide polymorphisms (SNPs) have been discovered across European Bos taurus genomes, whereas extremely less number of SNPs are cataloged for Bos indicus breeds. In this study, we performed whole-genome resequencing, reference-based mapping, functional annotation and gene enrichment analysis of 20 sires representing eleven important Bos indicus (indicine) breeds of Pakistan. The breeds sequenced here include: Sahiwal, Red Sindhi, Tharparkar and Cholistani (tropically adapted dairy and dual purpose breeds), Achai, Bhagnari, Dajal and Lohani (high altitude adapted dual and drought purpose breeds); Dhanni, Hisar Haryana and Gabrali (dairy and light drought purpose breeds). A total of 17.4 billion QC passed reads were produced using BGISEQ-500 next generation sequencing platform to generate 9 to 27-fold genome coverage (average ~16×) for each of the 20 sequenced sires. A total of 67,303,469 SNPs were identified, of which 3,850,365 were found novel and 1,083,842 insertions-deletions (InDels) were detected across the whole sequenced genomes (491,247 novel). Comparative analysis using coding region SNPs revealed a close relationship between the best milking indicine breeds; Red Sindhi and Sahiwal. On the other hand, Bhagnari and Tharparkar being popular for their adaptation to dry and extremely hot climates were found to share the highest number of SNPs. Functional annotation identified a total of 3,194 high-impact (disruptive) SNPs and 745 disruptive InDels (in 275 genes) that may possibly affect economically important dairy and beef traits. Functional enrichment analysis was performed and revealed that high or moderate impact variants in wingless-related integration site (Wnt) and vascular smooth muscle contraction (VSMC) signaling pathways were significantly over-represented in tropically adapted heat tolerant Pakistani-indicine breeds. On the other hand, vascular endothelial growth factor (VEGF) and hypoxia-inducible factor 1 (HIF-1) signaling pathways were found over-represented in highland adapted Pakistani-indicine breeds. Similarly, the ECM-receptor interaction and Jak-STAT signaling pathway were significantly enriched in dairy and beef purpose Pakistani-indicine cattle breeds. The Toll-like receptor signaling pathway was significantly enriched in most of the Pakistani-indicine cattle. Therefore, this study provides baseline data for further research to investigate the molecular mechanisms of major traits and to develop potential genomic markers associated with economically important breeding traits, particularly in indicine cattle.

Genotyping of Indigenous Cattle Breeds and their Exotic Crosses for beta -casein Milk Type using PCR-RFLP and Sequencing

The role of A1 and A2 s casein milk variants and human health is a subject of concern for scientific investigations. The status of A1/A2 s-casein variants in Bos taurus cattle breeds from several countries have shown presence of A1 variant in European cattle, which has been linked to range of illness. However, information on A1/A2 s-casein variants in Bos indicus and their crosses is limited. Bulls can influence the population structure more profoundly. Hence, the intend of the study was to know the prevalence of variants of s-casein (β-CSN2) in Gir and Kankrej, prominent Bos indicus breeds of the country and crossbred bulls (HF crossbreds) used for artificial insemination. Semen/ blood samples of 226 Gir, 88 Kankrej and 263 crossbred bulls and cows were collected from three semen stations and three non-government breeding farm, in Gujarat. PCR–RFLP and allele specific PCR analysis of the s casein region revealed all three genotypes suggesting prevalence of A1 variant in Gir and Kankrej also. Frequency of A1 allele in the indigenous breeds was much higher than believed earlier. We also report the first case of A1A1 Gir bull. This is probably the first report of prevalence of A1A1 genotype in any of the zebu Bos indius breeds. Crossbred cattle showed prevalence of both variants, A1 and A2 with higher frequency of A2. Further, allelic frequencies confirmed deviation from H-W equilibrium in HF crossbreds but not in Gir and Kankrej. The sequence analysis confirmed SNP ‘C’ to ‘A’ causing replacement of proline by histidine between A1 and A2 s casein. The present study confirmed the earlier theory that A2 allele of s casein is predominant in Bos indicus.

Variable sialic acid content in milk of Indian cattle and buffalo across different stages of lactation.

The aim of this Research Communication was to contribute to the knowledge of milk sialic acid concentration of bovines with specific focus on India. Sialic acids (SA) are important constituents of mammalian milks. Buffaloes are the main milk producing species in India, therefore, our research focused on both cow and buffalo. Two Indian cattle (Bos indicus) breeds (Sahiwal, Tharparkar), one cross bred cattle - Karan Fries (Tharparkar × Holstein Friesian) and a buffalo breed (Murrah) were selected. Systematic comparisons of the total, free and bound form of SA and also its distribution over the course of lactation- colostrums and mature milk (120-140 d) was generated. Animal management, sample collection and methodology of SA estimation were identical for the different groups. Colostrum had the highest concentration of SA, which declined with the progress of lactation in all the groups. Majority of the SA existed in bound form. No significant (P < 0.05) difference was recorded in the total, bound or free SA across all the groups. However, differences were obvious in the total and bound SA level in the mature milk. Indian cattle, Sahiwal and Tharparkar were equivalent, but had higher concentration of total and bound SA than crossbred cattle. Milk of buffalo had SA equivalent to that of crossbred cattle. The mean (se) levels of total SA was 23.4 (0.8), 25.8 (2.4), 20.3 (0.6) and 20.2 (1.2) in Sahiwal, Tharparkar, cross bred and Murrah buffalo, respectively. The findings suggested that milk of indigenous cattle may be a potential source of SA, a bioactive compound with beneficial effect on human health and a potential functional ingredient in foods. Results add value to the currently declining indigenous cattle of India.

Animal and management factors associated with weight gain in dairy calves and heifers on smallholder dairy farms in Kenya

Calf growth is an important determinant of dairy herd productivity, particularly in countries where the dairy industry is expanding, such as Kenya. Our objective was to determine factors associated with weight gain in randomly selected dairy calves and heifers in smallholder dairy farms (SDF) in Kenya.A cross-sectional study on a census of 321 calves and heifers (dairy calves and heifers up to 36 months of age), sampled from 200 randomly selected SDF in Naari, Kenya, formed the study population. Youngstock management was recorded using a questionnaire. Biodata were obtained through subsequent physical examination and heart girth measurement. Descriptive statistical analyses were conducted, and mixed model regression was used for identification of factors associated (p < 0.05) with the natural log transformation of estimated average daily weight gain (ADG).Median and mean ADG of the youngstock were 360 and 443 (s.d. = 375) g day−1, respectively. In the final model, ADG was highest in pre-weaned calves and declined with age. Supplementing with quality hay during the dry season at least weekly was associated with increased ADG. There was an interaction between breed and historical disease on ADG such that disease was associated with decreased ADG in Bos taurus breeds, while ADG in Bos indicus breeds was not affected by disease. There was a significant interaction between education levels of the husband and wife caretakers; when the man’s education was low (having less than or equal to primary school), ADG was highest when the woman had not completed primary school, but was lower when the woman had completed primary, secondary or tertiary education, possibly because such women worked off-farm more often.General growth performance of animals on these farms was lower than benchmarked standards recommended for optimum dairy production but within previously reported ranges for the East African region. Supplementation of diets (with hay and/or concentrates) is recommended for optimum growth in calves and heifers, especially in the dry season. If nutritional management of Bos taurus youngstock is not improved, crosses of Bos indicus could be better suited for the current nutritional management systems in SDF in Meru having calf disease problems. Interventions to support educating women (the primary caretakers of the cattle) and men in the community on calf management should be initiated, preferably with shared on-farm responsibilities. Training in better management, even for learned farmers, would be critical to better calf growth.

Can the antral follicular count modulate the gene expression of bovine oviducts in Aberdeen Angus and Nelore heifers?

The number of visible ovarian antral follicles (antral follicle count—AFC) is repeatable in bovine individuals, but highly variable between animals, and with differences between Bos taurus and Bos indicus breeds. Several studies have tried to determine the correlation between AFC and increased fertility in cattle. While the impacts of AFC on embryo production, hormonal levels, and pregnancy rates have been described, the molecular effects of AFC on bovine oviducts have not yet been investigated. Here, the aim was to investigate the impact of breeds, such as Aberdeen Angus and Nelore heifer with high or low AFC, on abundance of transcripts and protein related to oviductal transport, sperm reservoir formation, monospermy control, and gamete interaction in the oviducts. In summary, the ovulation side was the major factor that affected transcript abundance on bovine oviducts. However, a discreet effect among AFC and cattle breeds was also observed. Based on this, we concluded and reinforced here that differential microenvironments between ipsilateral and contralateral oviducts have a major effect on modulating the transcripts related to oviductal transport, sperm reservoir formation, monospermy control, and gamete interaction. However, we cannot exclude that there is minimal effect of AFC or breed on regulation of some genes (such as AGTR1, ACE1, FUCA1, and VEGFA) in bovine oviducts.

Complete mitogenome reveals genetic divergence and phylogenetic relationships among Indian cattle (Bos indicus) breeds

Indigenous cattle of India belong to the species, Bos indicus and they possess various adaptability and production traits. However, little is known about the genetic diversity and origin of these breeds. To investigate the status, we sequenced and analyzed the whole mitochondrial DNA (mtDNA) of seven Indian cattle breeds. In total, 49 single-nucleotide variants (SNVs) were identified among the seven breeds analyzed. We observed a common synonymous SNV in the COII gene (m.7583G > A) of all the breeds studied. The phylogenetic analysis and genetic distance estimation showed the close genetic relationship among the Indian cattle breeds, whereas distinct genetic differences were observed between Bos indicus and Bos taurus cattle. Our results indicate a common ancestor for European Zwergzebu breed and South Indian cattle. The estimated divergence time demonstrated that the Bos indicus and Bos taurus cattle lineages diverged 0.92 million years ago. Our study also demonstrates that ancestors of present zebu breeds originated in South and North India separately ∼30,000 to 20,000 years ago. In conclusion, the identified genetic variants and results of the phylogenetic analysis may provide baseline information to develop appropriate strategies for management and conservation of Indian cattle breeds.

Identification of differentially expressed microRNAs in Sahiwal (Bos indicus) breed of cattle during thermal stress.

microRNAs (miRNAs) are a class of small non-coding RNAs that play key roles in post transcriptional gene regulation that influence various fundamental cellular processes, including the cellular responses during environmental stresses. However, perusal of literatures revealed few reports on the differential expression of miRNA during thermal stress in Indian native (Bos indicus) cattle breeds. The present investigation aimed to identify differentially expressed miRNAs during thermal stress in Sahiwal (Bos indicus) dairy cattle breed of India, adapted with tropical climate over a long period of time. Stress responses of the animals were characterized by determining various physiological as well as biochemical parameters and differential expression profile of major heat shock protein genes. Ion Torrent deep sequencing and CLC-genomic analysis identified a set of differentially expressed miRNAs during summer and winter seasons. Most of the identified differentially expressed miRNAs were found to target heat shock responsive genes especially members of heat shock protein (HSP) family. Real-time quantification-based analysis of selected miRNAs revealed that bta-mir-1248, bta-mir-2332, bta-mir-2478, and bta-mir-1839 were significantly (p < 0.01) over expressed while bta-mir-16a, bta-let-7b, bta-mir-142, and bta-mir-425 were significantly (p < 0.01) under expressed during summer in comparison to winter. The present study enlists differentially expressed miRNAs at different environmental temperatures in Sahiwal (Bos indicus) that may be importance for further understanding the role of miRNAs on thermo-regulatory mechanisms.

Fatores relacionados ao desenvolvimento reprodutivo em novilhas Nelore: Revisão

The intensification of beef cattle production systems, aiming to increase production rates, requires the use of technologies that favor the rational exploitation of livestock. Among the animal indicators, reproductive efficiency stands out because it is closely associated with the conditions of nutrition, management and sanity, which together with the genetic pattern influence the general enjoyment of the herd. Among the Bos taurus indicus breeds used in Brazilian meat production systems, the Nellore breed occupies a prominent place, mainly due to its adaptation to the tropical climate. However, animals of this genetic group are usually sexually late than those of Bos taurus taurus bulls, even when bred in similar conditions. And within this context the age at first calving is one of the aspects that directly reflect the determination of the reproductive efficiency of the herd. Based on this assumption, the inclusion of heifers at younger ages to reproduction, providing improvements in profitability. This review aims to address some aspects related to reproductive development in Nellore heifers, such as the influence of live weight, nutrition, hormone therapy and reproductive tract morphology. According to a bibliographical survey presented in this review, it is concluded that the attainment of puberty in Nellore heifers is multifactorial and varies according to the general management of the herd and the genetic composition of the animals.

Likelihood of pregnancy after the transfer of embryos derived from follicle aspiration and in vitro embryo production sessions with different relative efficiencies

The aim of the present study was to evaluate the likelihood of pregnancy of in vitro-produced (IVP) embryos from batches with distinct relative efficiencies. Data were retrospectively analyzed from 605 transvaginal ultrasonic-guided follicle aspiration sessions (OPU) followed by in vitro embryo production (IVEP) and 2456 fresh embryo transfers (ET), performed between 2008 and 2012 in individuals of the Gir (dairy Bos indicus) breed. The OPU and IVEP were performed using standard procedures by a single group of technicians at the same laboratory facility. Records were stratified into quartiles (I to IV) according to the total of cumulus-oocytes complexes (COC) produced per donor, or in percentile ranges (0%–25%, 26%–50%, 51%–75%, and 76%–100%) for endpoints related to COC quality or efficiency of embryo production. Pregnancy per embryo transfer (P/ET) was compared among quartiles or ranges using the chi-squared test. Donors producing a greater number of total COC (quartile I) also had more viable and grade I COC, and a greater number of embryos than donors ranked in quartiles II, III or IV, respectively (P < 0.0001). Nevertheless, P/ET did not differ (P > 0.05) among embryos produced by donors ranked in Quartiles I to IV. Similarly, there was no difference (P > 0.05) in P/ET for embryos derived from OPU sessions with a relatively greater or lesser percentage of viable or Grade I COC. Cleavage and blastocyst rates within each IVEP batch had no effect (P > 0.05) on P/ET. In conclusion, data suggest that there is no relationship among oocyte yield after OPU, or efficiency of IVEP, and the likelihood of pregnancy after ET of fresh IVP embryos.

Comparison of longissimus thoracis physical quality traits and the expression of tenderness-related genes between Goudali zebu breed and Italian Simmental × Goudali crossbreed

The aim of this trial was to compare some meat physical quality traits and the expression of some tenderness-related genes between Goudali (G, Bos indicus) breed and Italian Simmental × Goudali (SimGoud, SG, Bos taurus x Bos indicus) crossbreed. Ten G and 12 SG bulls, aged 31 ± 0.49 months, bred in the same farm and conditions in Western Highland Plateau Savannah of Cameroon were considered. Physical quality traits of longissimus thoracis (LT) muscle such as water losses, colour parameters and rheological properties were determined together with ultimate pH (pHu). The mRNA early post-mortem abundance of calpain-1 (Capn1), calpain-2 (Capn2), calpastatin (Cast), caspase 3 (Casp3), caspase 9 (Casp9), αB-crystallin (Cryab), heat shock proteins 27 (Hsp27), 40 (Hsp40) and 70 (Hsp70) was detected by qPCR. The Capn1, Cast, Hsp27 and Hsp70, early post-mortem protein content was determined by ELISA. The meat of G bulls had greater values of lightness (p < .05) and cooking loss (p < .05) than SG. The expression of Hsp70 in G was greater at mRNA (p < .05) level than SG. None of the other variables considered was significantly different between G and SG breeds. Whereas crossbreeding with Italian Simmental breed changed the colour and ameliorated the water retention capacity of G meat, tenderness and the expression of tenderness-related genes, both at mRNA and at protein level, were not significantly different between the pure local breed and the crossbreed. In comparison with pure Goudali, crossbreeding Goudali with Italian Simmental breed has a limited impact on meat traits in tropical conditions.

Novel extraction of high quality genomic DNA from frozen bovine blood samples by using detergent method.

DNA is the prerequisite for life’s inception that transfers hereditary information, past several years; various types of commercial kits are made available which vary depending on the type of the biological sample being used. The present study is focused on developing an improvised methodology for the isolation of genomic DNA from stored bovine blood samples. DNA was isolated by using the conventional Phenol: Chloroform: Isoamyl alcohol (PCI) method and Detergent method. The aim of the study was to make a comparative analysis and evaluation of these two methods to identify the one that gives a superior quality and quantity of genomic DNA. Total (n=48) each duplicate blood samples from three different buffalo(Bubalus bubalis) breeds Banni, Surti, Murrah, three zebu cattle (Bos indicus) breeds Kankerj, Gir, Sahiwal were collected from the jugular vein. The quantity, purity of the genomic DNA was assessed based on the total DNA yield, purity ratios, spectral profile, agarose gel electrophoresis analysis and polymerase chain reaction amplification of MC1R gene product without any inhibitors. The results of our study suggest that detergent method is also suitable for extraction of genomic DNA from the bovine blood and results were significant (*P>0.05). The total mean yield was found to be 329.05±11 μg/5ml for all six breeds while the PCI method was employed. The total mean yield of the gDNA for all six breeds was 406.6±43 μg/5ml of blood when the detergent method was used. One way ANOVA test showed that the total DNA yield varied depending on the isolation method used. The DNA yield obtained from the DG method was (***P< 0.001) significant as compared to the PCI method (**P<0.01).

134 Effects of Gas Tension During Culture upon Development of Bovine Embryos from Beef (Nellore) and Dairy (Girolando) Breeds

Culture of bovine embryos is a critical step during in vitro embryo production (IVEP) and, as such, has been the focus of numerous studies on cattle IVEP. Improvements of culture conditions to mimic the in vivo maternal microenvironment involves studying the optimal gas tension for pre-implantation embryonic development. In the commercial conditions, there is great variability in results, in part because of the difference between breeds and donors. The objective of this study was to evaluate the effects of culture in high or low oxygen tension upon the development of embryos from a crossbred dairy breed (Girolando F1; Gir × Holstein) and a beef Bos indicus breed, Nellore. We collected data from an IVEP commercial operation located in a tropical area of southeastern Brazil (Minas Gerais State) from February to May 2017. The study was designed in a 2 × 2 factorial arrangement of treatments: 2 O2 tensions during culture (5%, low O2 v. 20%, high O2) and 2 breeds (Nellore, beef v. Girolando F1, dairy). Thus, the following 4 groups were studied: Nellore-high O2 (n = 86 donors), Nellore-low O2 (n = 107 donors), Girolando F1-high O2 (n = 114 donors), and Girolando F1-low O2 (n = 110 donors). Outcome variables were the number of cleaved embryos 72 h post-insemination (hpi), cleavage rate relative to the total number cumulus–oocyte complexes (COC) put in culture, number and percentage of blastocysts 192 hpi relative to the structures kept in culture. Variables that were not normally distributed were transformed using the formula log(y + 0.05). Data were analysed using the GLM procedure of SAS (SAS Institute Inc., Cary, NC, USA) for the main effects of gas tension (low v. high O2) and breed (Girolando F1 v. Nelore). Results are shown as mean ± SEM. Gas tension affected the number of cleaved embryos (10.52 ± 0.92 v. 8.33 ± 0.72 for high and low O2, respectively; P &lt; 0.01) and cleavage rates (40.58 ± 2.49 v. 44.41 ± 2.88 for high and low O2; P &lt; 0.01 in Nellore), but did not affect these variables in Girolando F1 donors (13.23 ± 1.33 v. 10.76 ± 0.76 cleaved embryos, for high and low O2; P = 0.63; 58.01 ± 2.00 v. 60.19 ± 1.97 cleavage rate, for high and low O2; P = 0.80). Nonetheless, the number and percentage of blastocysts were not affected by gas tension in either breed. Results for Nellore were 4.99 ± 0.56 v. 3.51 ± 0.38 blastocysts in high and low O2, respectively (P = 0.051) and 41.92 ± 3.91% v. 39.81 ± 3.77% blastocysts, in high and low O2 (P = 0.11). For Girolando F1, numbers of blastocysts were 5.84 ± 0.66 v. 4.24 ± 0.39 in high and low O2 (P = 0.19) and percentage of blastocysts 49.14 ± 2.97% v. 49.11 ± 3.40% in high and low O2 (P = 0.46). These results suggest that oxygen tension during culture affects IVEP differently depending on breed. The initial period of culture, recognised as critical in IVEP, seemed more sensitive to high O2 tension, particularly in Nellore.

A PLAG1 mutation contributed to stature recovery in modern cattle

The recent evolution of cattle is marked by fluctuations in body size. Height in the Bos taurus lineage was reduced by a factor of ~1.5 from the Neolithic to the Middle Ages, and increased again only during the Early Modern Ages. Using haplotype analysis, we found evidence that the bovine PLAG1 mutation (Q) with major effects on body size, weight and reproduction is a >1,000 years old derived allele that increased rapidly in frequency in Northwestern European B. taurus between the 16th and 18th centuries. Towards the 19th and 20th centuries, Q was introgressed into non-European B. taurus and Bos indicus breeds. These data implicate a major role of Q in recent changes in body size in modern cattle, and represent one of the first examples of a genomic sweep in livestock that was driven by selection on a complex trait.

Genetic diversity, population structure, and correlations between locally adapted zebu and taurine breeds in Brazil using SNP markers.

Genetic diversity is one of the most important issues in studies on conservation of cattle breeds and endangered species. The objective of this study was to estimate the levels of genetic differentiation between locally adapted taurine (Bos taurus taurus) and zebu (Bos taurus indicus) breeds in Brazil, which were genotyped for more than 777,000 SNPs. The fixation index (F ST), principal component analysis (PCA), and Bayesian clustering were estimated. The F ST highlighted genetic differentiation between taurine and zebu breeds. The taurine lines, Caracu and Caracu Caldeano, had significant genetic differentiation (F ST close to 5%) despite their recent selection for different uses (meat and milk). This genetic variability can be used for conservation of locally adapted animals, as well as for breeding programs on zebu breeds. Introgression of zebu in locally adapted breeds was identified, especially in Curraleiro Pé-Duro breed. The Gyr breed, however, had low breed purity at genomic level due to its very heterogeneous mixing pattern.

PCR diagnosis of tick-borne pathogens in Maharashtra state, India indicates fitness cost associated with carrier infections is greater for crossbreed than native cattle breeds.

Tick-borne pathogens (TBP) are responsible for significant economic losses to cattle production, globally. This is particularly true in countries like India where TBP constrain rearing of high yielding Bos taurus, as they show susceptibility to acute tick borne disease (TBD), most notably tropical theileriosis caused by Theileria annulata. This has led to a programme of cross breeding Bos taurus (Holstein-Friesian or Jersey) with native Bos indicus (numerous) breeds to generate cattle that are more resistant to disease. However, the cost to fitness of subclinical carrier infection in crossbreeds relative to native breeds is unknown, but could represent a significant hidden economic cost. In this study, a total of 1052 bovine blood samples, together with associated data on host type, sex and body score, were collected from apparently healthy animals in four different agro-climatic zones of Maharashtra state. Samples were screened by PCR for detection of five major TBPs: T. annulata, T. orientalis, B. bigemina, B. bovis and Anaplasma spp.. The results demonstrated that single and co-infection with TBP are common, and although differences in pathogen spp. prevalence across the climatic zones were detected, simplistic regression models predicted that host type, sex and location are all likely to impact on prevalence of TBP. In order to remove issues with autocorrelation between variables, a subset of the dataset was modelled to assess any impact of TBP infection on body score of crossbreed versus native breed cattle (breed type). The model showed significant association between infection with TBP (particularly apicomplexan parasites) and poorer body condition for crossbreed animals. These findings indicate potential cost of TBP carrier infection on crossbreed productivity. Thus, there is a case for development of strategies for targeted breeding to combine productivity traits with disease resistance, or to prevent transmission of TBP in India for economic benefit.

Functional confirmation of PLAG1 as the candidate causative gene underlying major pleiotropic effects on body weight and milk characteristics

A major pleiotropic quantitative trait locus (QTL) located at ~25 Mbp on bovine chromosome 14 affects a myriad of growth and developmental traits in Bos taurus and indicus breeds. These QTL have been attributed to two functional variants in the bidirectional promoter of PLAG1 and CHCHD7. Although PLAG1 is a good candidate for mediating these effects, its role remains uncertain given that these variants are also associated with expression of five additional genes at the broader locus. In the current study, we conducted expression QTL (eQTL) mapping of this region using a large, high depth mammary RNAseq dataset representing 375 lactating cows. Here we show that of the seven previously implicated genes, only PLAG1 and LYN are differentially expressed by QTL genotype, and only PLAG1 bears the same association signature of the growth and body weight QTLs. For the first time, we also report significant association of PLAG1 genotype with milk production traits, including milk fat, volume, and protein yield. Collectively, these data strongly suggest PLAG1 as the causative gene underlying this diverse range of traits, and demonstrate new effects for the locus on lactation phenotypes.

Whole genome scan reveals the genetic signature of African Ankole cattle breed and potential for higher quality beef

BackgroundAfrica is home to numerous cattle breeds whose diversity has been shaped by subtle combinations of human and natural selection. African Sanga cattle are an intermediate type of cattle resulting from interbreeding between Bos taurus and Bos indicus subspecies. Recently, research has asserted the potential of Sanga breeds for commercial beef production with better meat quality as compared to Bos indicus breeds. Here, we identified meat quality related gene regions that are positively selected in Ankole (Sanga) cattle breeds as compared to indicus (Boran, Ogaden, and Kenana) breeds using cross-population (XP-EHH and XP-CLR) statistical methods.ResultsWe identified 238 (XP-EHH) and 213 (XP-CLR) positively selected genes, of which 97 were detected from both statistics. Among the genes obtained, we primarily reported those involved in different biological process and pathways associated with meat quality traits. Genes (CAPZB, COL9A2, PDGFRA, MAP3K5, ZNF410, and PKM2) involved in muscle structure and metabolism affect meat tenderness. Genes (PLA2G2A, PARK2, ZNF410, MAP2K3, PLCD3, PLCD1, and ROCK1) related to intramuscular fat (IMF) are involved in adipose metabolism and adipogenesis. MB and SLC48A1 affect meat color. In addition, we identified genes (TIMP2, PKM2, PRKG1, MAP3K5, and ATP8A1) related to feeding efficiency. Among the enriched Gene Ontology Biological Process (GO BP) terms, actin cytoskeleton organization, actin filament-based process, and protein ubiquitination are associated with meat tenderness whereas cellular component organization, negative regulation of actin filament depolymerization and negative regulation of protein complex disassembly are involved in adipocyte regulation. The MAPK pathway is responsible for cell proliferation and plays an important role in hyperplastic growth, which has a positive effect on meat tenderness.ConclusionResults revealed several candidate genes positively selected in Ankole cattle in relation to meat quality characteristics. The genes identified are involved in muscle structure and metabolism, and adipose metabolism and adipogenesis. These genes help in the understanding of the biological mechanisms controlling beef quality characteristics in African Ankole cattle. These results provide a basis for further research on the genomic characteristics of Ankole and other Sanga cattle breeds for quality beef.

Parametrization of the Davis Growth Model using data of crossbred Zebu cattle

The system of differential equations proposed by Oltjen et al. [1986, named Davis Growth Model (DGM)] to represent cattle growth has been parameterized with data from Bos taurus (British) and Bos indicus (Nellore) breeds. The DGM has been successfully used for simulation and decision support in the United States. However, the effect of about 30 years of genetic improvement and the use of different breeds may affect the model parameter values, which also may need to be re-estimated for crossbred animals. The aim of this study was to estimate parameter values and confidence intervals for the DGM with growth and body composition data from Zebu crossbred animals. Confidence intervals and asymptotic distribution were generated through nonparametric bootstrap with data from a field experiment conducted in Brazil. The parameters showed normal probability distribution for most scenarios. The rate constant for deoxyribonucleic acid (DNA) synthesis had a minimum increase of 156 % and the maximum of 389 %, compared to the original values and the maintenance requirement had a minimum increase of 126 % and maximum of 160 % compared to the original values. Lower limits of 95 % confidence intervals for the parameters related to maintenance and protein accretion rates were higher than the original estimates of the DGM, evidencing genetic differences of the Zebu crossbred animals in relation to the original DGM parameters.

Breed composition does not influence the performance of Holstein-Gyr crossbred as oocyte donors for OPU/IVP.

Holstein-Gyr crossbred cattle are strategic for dairy systems in tropical countries, since they combine milk yield genetics with adaptability to tropical climate. However, Holstein (Bos taurus) and Gyr (Bos indicus) breeds present remarkable differences regarding reproductive physiology. Brazil stands out as the world’s largest user of embryo in vitro production (IVP) in bovine, and the use of this technique is increasing in dairy systems. As Holstein-Gyr crossbreds are important oocyte donors for IVP, the present work aimed at investigating whether increased Gyr or Holstein breed composition influences donor’s performance. Sixteen Holstein-Gyr crossbred females presenting increased (HG, 71.4 to 87.5% Holstein; n = 9) or decreased (GH, 40.2 to 46.6% Holstein; n = 7) Holstein composition were submitted to three ovum pick up (OPU) sessions. We observed similar (P = 0.2946) antral follicle count between HG and GH donors (24.8 ± 3.2 vs 29.4 ± 2.8 respectively; mean ± SEM). Groups also display similar morphological oocyte grading (Grade I: 0.1 ± 0.1 vs 0.1 ± 0.1 – P = 0.9680; Grade II: 0.9 ± 0.5 vs 1.9 ± 0.5 – P = 0.1942; Grade III, 4.0 ± 1.2 vs 7.2 ± 1.4 – P = 0.1047, HG vs GH respectively; mean ± SEM). Additionally, the proportion of viable oocyte was similar between HG and GH groups (27.8% vs 31.9%, respectively, P = 0.3500) and oocyte lipid area fraction (6.8% vs 9.5%, respectively; P = 0.1539). Our results indicate that the individual variation has more influence than breed composition of crossbred oocyte donors.

Intrafollicular oestradiol production, expression of the LH receptor (LHR) gene and its isoforms, and early follicular deviation in Bos indicus.

The aim of the present study was to characterise the roles of intrafollicular oestradiol production and granulosa cell (GC) expression of the LH receptor (LHR) gene and its isoforms during follicular deviation in Bos indicus. Follicular wave emergence was synchronised in heifers from a Bos taurus dairy (Holstein; n=10) and a B. indicus dairy breed (Gir; n=10). Follicles were aspirated individually at sizes corresponding to the periods of predeviation, deviation and postdeviation. Intrafollicular oestradiol (IF-E2) and progesterone (IF-P4) concentrations were determined in the follicular fluid (FF) by radioimmunoassay, and relative expression of P450 aromatase (CYP19A1) and LHR forms was evaluated in GC using real-time quantitative-polymerase chain reaction. Despite differences in the size of the dominant follicle at deviation, changes in CYP19A1 expression and IF-E2 concentrations were similar in follicles of the same diameter in both breeds. A peak in total LHR expression occurred after follicular deviation in association with low expression of LHR isoforms. The results suggest that regulation of LHR function by sequential changes in the expression pattern of LHR isoforms may play a role in the early deviation of the dominant follicle, as observed in B. indicus breeds.