Evaluation of genetic differentiation in Bos indicus cattle breeds from Marathwada region of India using microsatellite polymorphism

Morphometric characteristics and microsatellite markers based diversity and differentiation recognizes the first prospective cattle breed from the Jharkhand state of India

India is bestowed with immense cattle biodiversity with 50 registered breeds. However, the majority (59.3%) is yet not characterized. Identification and characterization are the gateways to the management of prized indigenous resources. Present research described a unique cattle population of Jharkhand state, managed under a traditional low-input, low-output system. It was characterized by morphological traits, performance parameters, and management practices. Animals have the characteristic pre-scapular location of the hump. Genetic variation within this population and its differentiation with the six closely distributed cattle breeds were evaluated using FAO recommended microsatellite markers. Jharkhandi cattle have substantial genetic variation based on gene diversity (>0.6) and the average number of alleles per locus (>8). The population did not suffer from a genetic bottleneck in the recent past. Pairwise Nei's genetic distance, phylogenetic relationship, population differentiation, and the correct assignment of all the animals to self group substantiated its separate genetic identity. Since gene flow (Nm = 2.8-7.32) was identified and admixture was indicated by the Bayesian analysis there is a pressing need for scientific management of this population. Results endow authorities with critical information for registering a new Indian cattle breed (Medini) that contributes to the food security, livelihood, and economic sustainability of rural tribal households.

Genetic diversity and differentiation of Thutho cattle from northeast India using microsatellite markers

Cattle are losing maximum breeds among the world's livestock. Genetic variability data is essentially required for conservation decision-making. Thutho is a recently registered Indian cattle breed (INDIA_CATTLE_1400_THUTHO_03047) from the northeast region (NE), a biodiversity hotspot. Genetic diversity in the Thutho population and its differentiation from the only other cattle breed of NE (Siri) and cattle (Bachaur) of the neighboring region was established using highly polymorphic, FAO-recommended microsatellite markers. Numerous alleles (253) were detected across the 25 loci. The mean observed and expected numbers of alleles in the population were 10.12 ± 0.5 and 4.5 ± 0.37, respectively. The observed heterozygosity (0.67 ± 0.04) was lower than the expected heterozygosity (0.73 ± 0.03) which indicated a departure from the Hardy-Weinberg equilibrium. A positive FIS value (0.097) confirmed the heterozygote deficiency in the Thutho population. Genetic distance, phylogenetic relationships, differentiation parameters, population assignment, and Bayesian analysis explicitly ascertained the unique genetic identity of the Thutho cattle. The population did not suffer any bottlenecks in the past. Thutho has minimum diversity among the three populations; hence, its scientific management needs to be initiated immediately. Interestingly, genetic variation is enough for formulating breeding programs for managing, improving, and conserving this precious indigenous cattle germplasm.

Genetic differentiation and structuration of the Gobra zebu cattle breeds reared in Senegal

The Gobra zebu genetic breeding program has resulted in the genetic improvement of a new population. This population gained genetic characteristics that set them apart from the other cattle populations reared in Senegal. The cause of these differences might be the reproductive isolation and selection to which this population of the "Centre de Recherches Zootechniques" of Dahra has been subjected since the 1950s. This study aimed to assess the genetic differentiation and structuration of this population compared to the main cattle breeds used in Senegal. A total of 180 individuals, selected from the Gobra selection nucleus and bovine populations from four main breeds in Senegal, were included in this study. We used a panel of 21 microsatellite markers among those recommended by the Food Agriculture Organization, to conduct the molecular genotyping of our sampled populations. The basic genetic parameters of differentiation and structuration were calculated using various bioinformatics software. The results of this study, particularly the degrees of genetic differentiation (Fst), the coefficient of genetic homogeneity (Gst), and the gene flow (Nm), show a significant genetic differentiation of the Gobra from the station compared to the other populations studied. Structuring and phylogeny analyses reveal a micro-structuring within the Gobra population as a novelty. This micro-structuring clearly identifies the Gobra individuals from Dahra's station among the other Gobra populations studied. The main causes of these observations would be reproductive isolation and the selection pressure exerted on this population for several decades.

Morphometric and microsatellite-based comparative genetic diversity analysis in Bubalus bubalis from North India

To understand the similarities and dissimilarities of a breed structure among different buffalo breeds of North India, it is essential to capture their morphometric variation, genetic diversity, and effective population size. In the present study, diversity among three important breeds, namely, Murrah, Nili-Ravi and Gojri were studied using a parallel approach of morphometric characterization and molecular diversity. Morphology was characterized using 13 biometric traits, and molecular diversity through a panel of 22 microsatellite DNA markers recommended by FAO, Advisory Group on Animal Genetic Diversity, for diversity studies in buffaloes. Canonical discriminate analysis of biometric traits revealed different clusters suggesting distinct genetic entities among the three studied populations. Analysis of molecular variance revealed 81.8% of genetic variance was found within breeds, while 18.2% of the genetic variation was found between breeds. Effective population sizes estimated based on linkage disequilibrium were 142, 75 and 556 in Gojri, Nili-Ravi and Murrah populations, respectively, indicated the presence of sufficient genetic variation and absence of intense selection among three breeds. The Bayesian approach of STRUCTURE analysis (at K = 3) assigned all populations into three clusters with a degree of genetic admixture in the Murrah and Nili-Ravi buffalo populations. Admixture analysis reveals introgression among Murrah and Nili-Ravi breeds while identified the Gojri as unique buffalo germplasm, indicating that there might be a common origin of Murrah and Nili-Ravi buffaloes. The study provides important insights on buffalo breeds of North India that could be utilized in designing an effective breeding strategy, with an appropriate choice of breeds for upgrading local non-descript buffaloes along with conservation of unique germplasm.

Genetic diversity and effective population sizes of thirteen Indian cattle breeds

Background

The genetic structure of a diverse set of 15 Indian indigenous breeds and non-descript indigenous cattle sampled from eight states was examined, based on 777 k single nucleotide polymorphism (SNP) genotypes obtained on 699 animals, with sample sizes ranging from 17 to 140 animals per breed. To date, this is the largest and most detailed assessment of the genetic diversity of Indian cattle breeds.

Results

Admixture analyses revealed that 109 of the indigenous animals analyzed had more than 1% Bos taurus admixture of relatively recent origin. Pure indigenous animals were defined as having more than 99% Bos indicus ancestry. Assessment of the genetic diversity within and between breeds using principal component analyses, F statistics, runs of homozygosity, the genomic relationship matrix, and maximum likelihood clustering based on allele frequencies revealed a low level of genetic diversity among the indigenous breeds compared to that of Bos taurus breeds. Correlations of SNP allele frequencies between breeds indicated that the genetic variation among the Bos indicus breeds was remarkably low. In addition, the variance in allele frequencies represented less than 1.5% between the Indian indigenous breeds compared to about 40% between Bos taurus dairy breeds. Effective population sizes (N_e) increased during a period post-domestication, notably for Ongole cattle, and then declined during the last 100 generations. Although we found that most of the identified runs of homozygosity are short in the Indian indigenous breeds, indicating no recent inbreeding, the high F_ROH coefficients and low F_IS values point towards small population sizes. Nonetheless, the N_e of the Indian indigenous breeds is currently still larger than that of Bos taurus dairy breeds.

Conclusions

The changes in the estimates of effective population size are consistent with domestication from a large native population followed by consolidation into breeds with a more limited population size. The surprisingly low genetic diversity among Indian indigenous cattle breeds might be due to their large N_e since their domestication, which started to decline only 100 generations ago, compared to approximately 250 to 500 generations for Bos taurus dairy cattle.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12711-021-00640-3.

Genetic characterization and population structure of different coat colour variants of Badri cattle

The present study aimed to genetically characterize the Badri cattle and its three colour variants and assess their population structure using 24 microsatellite markers. Out of 96 animals analyzed, 32 each were collected from grey (GVBC), brown (BrVBC) and black (BVBC) colour variants of Badri cattle (BC). The genetic diversity parameters including allele frequencies, observed and effective number of alleles, observed and expected heterozygosity, PIC, Shannon's indices and F-statistics were estimated using POPGENE software. Bottleneck analysis was performed using both qualitative and quantitative approaches. A total of 274 alleles (50 private and 224 shared) were scored for BC, GVBC, BrVBC and BVBC with mean number of 11.417, 9.083, 9.125 and 9.083 alleles, respectively. All populations exhibited average heterozygosity estimate > 0.5 indicating existence of substantial genetic variability, concurrent with revelations from Shannon's indices. Observed mean PIC estimates (> 0.74) were indicative of optimum informativeness of used microsatellite markers. The mean inbreeding estimates (F) in GVBC, BrVBC and BVBC were 0.041, - 0.024 and 0.016, respectively. The pair wise genetic (> 0.91) pointed towards similarity between different colour variant populations. STRUCTURE analysis also revealed clear admixture for the three Badri colour variants indicating absence of genetic differentiation. The present study revealed first-hand information that populations of Badri cattle with different phenotypes with respect to coat colour are genetically related and can be considered as a single breed. The comprehensive knowledge generated for Badri cattle will help in designing breeding plan for its genetic improvement and deciding the conservation priorities.

Genetic diversity status of only registered cattle breed of Chhattisgarh-Kosali

Assessment of diversity is essential for germplasm characterization and management. Kosali is the first and only registered breed of Chhattisgarh state which immensely contributes to the local economy of 70% farmers. Genomic microsatellite markers being valuable tool for estimating genetic diversity were selected for exploring existing genetic variability in Kosali cattle population. The standard metrics of genomic diversity detected high variability in this breed. All the loci were polymorphic resulting in 297 alleles. Mean values of observed and expected number of alleles were 11.423±0.877 and 4.989±0.372, respectively. Similarly, higher mean values of observed heterozygosity (0.693±0.031) also corroborated with the allelic diversity. Mean expected heterozygosity (0.765±0.02) under Hardy-Weinberg equilibrium (HWE) was higher than the observed values indicating some deviations from assumptions of the model. It can be attributed to the forces such as inbreeding. In fact a positive FIS value of 0.088±0.038 indicated some heterozygote deficiency in the population. Bottleneck analysis indicated that Kosali cattle have not suffered any population bottleneck event during evolutionary trajectory. This study is first to report the genetic diversity status of Kosali cattle based on microsatellite markers.The results imply the necessity of management programs in order to conserve the existing genetic variation and to avoid any escalation of inbreeding.

Identification of a new potential native Indian cattle breed by population differentiation based on microsatellite markers

India has a rich heritage of rearing cattle where farmers selected native cattle suitable to their local agro-ecological conditions for centuries. It is reflected in 50 indigenous breeds of cattle, besides many lesser known populations not explored so far. It is the need of the hour to characterize such populations to have prudent improvement and conservation options. Thus, present study was carried out to assess the genetic diversity and relationship between an unexplored local cattle population (Kathani) and four established cattle breeds of adjoining area (Gaolao, Kosali, Ongole and Motu) by using 20 FAO recommended microsatellite markers. High variability was recorded in the Kathani population with a total of 198 alleles that varied between 5 (ILSTS11, TGLA22, INRA05) and 17 (ILSTS34) with a mean of 9.9 ± 0.73. The average observed heterozygosity (Ho) was 0.658 ± 0.054. Heterozygote deficiency was not significant (F_IS = 0.029 ± 0.063) indicating random mating prevalent across this population. Mean estimates of observed number of alleles and heterozygosity over all the loci and five populations were 9.73 ± 0.421 and 0.617 ± 0.022, respectively. In the overall populations, the homozygote excess (F_IT) of 0.293 ± 0.032, was partly due to the homozygote excess within breeds (F_IS = 0.121 ± 0.025) and to a larger extent due to high (0.05 < F_ST < 0.15) genetic differentiation among them (F_ST = 0.195 ± 0.029). Substantial pairwise Nei's genetic distance and high population differentiation indicated towards separate genetic identity of Kathani cattle. The analysis of genetic structure based on Bayesian approach indicated that the most probable number of clusters is five confirming definitive genetic differentiation among all the popultions. Entire analysis showed that a significant amount of genetic variation is maintained in Kathani, a lesser known cattle population that is distinct from the recognized breeds in the proximity. As this autochthonous cattle plays role in the economic sustainability of a marginal and disadvantaged area, it is important to preserve and develop its breeding.