Genetic diversity and relationship of Indian cattle inferred from microsatellite and mitochondrial DNA markers

Deciphering genetic diversity in conserved cattle bulls to achieve sustainable development goals

The primary objective of Sustainable Development Goal target 2.5 established by the United Nations is to ensure the preservation of genetic diversity in domesticated animals. The ICAR-National Bureau of Animal Genetic Resources in India has been actively engaged in the conservation of cattle and buffalo bull semen for long-term storage. This present study aimed to assess the genetic diversity present in the conserved cattle bull semen, which would aid in determining the most suitable strategy for future conservation management. A total of 192 bull semen belonging to 19 cattle breeds were selected to evaluate genetic diversity using 17 pairs of FAO recommended microsatellite primers. Total 267 alleles were detected across all the samples which indicates substantial amount of allelic variation is being maintained in conserved bulls. Further, all cattle bulls semen conserved showed higher observed heterozygosity than expected heterozygosity which indicates excess genetic diversity in all the populations. The FST, F IT and FIS value across the loci and population is 0.146 ± 0.009, 0.054 ± 0.038, and - 0.105 ± 0.035, respectively, which suggests lack of inbreeding in conserved cattle bull semen. This study has established genetic diversity in conserved cattle semen samples to achieve sustainable development goals. In addition, it provides compelling evidence that the current approach for conserving cattle bull semen is heading in the correct direction.

Interplay of hormones and metabolite excretion with fern pattern prove saliva as a potent indicator of male reproductive status in Kangayam breed cattle

Kangayam cattle are one of the drought breeds in India with distinct attributes. Agricultural transformation has led to a decline in many pure-breed indigenous cattle, including the Kangayam breed. Hence, a study on the reproductive physiology of male Kangayam breed cattle is necessary to disentangle problems in the area of livestock improvement. In this study, we investigated the relationship between serum hormones and bio-constituents and ascertained the potential of saliva as an indicator of the reproductive status of Kangayam cattle (Bos indicus). The present study confirms that cholesterol was higher in intact males and lower in prepubertal and castrated males. Testosterone levels were also higher in intact males than in castrated or prepubertal males. Hence, it can be inferred that high cholesterol levels contribute to active derivatization of testosterone in intact males. In contrast, reduced cholesterol availability leads to decreased testosterone synthesis in castrated and prepubertal males. Furthermore, it is reasonable to speculate that testosterone could have influenced salivary fern patterns in intact males, and thus, fern-like crystallization in the saliva was apparent. The unique salivary compounds identified through GC-MS across various reproductive statuses of Kangayam males may advertise their physiological status to conspecifics. In addition, the presence of odorant-binding protein (OBP) in saliva further supports its role in olfactory communication. This study attested to a posssible interlink between gonadal status and serum biochemical profiles. The salivary fern pattern revealed in this study can be used as a predictive tool, and the presence of putative volatiles and OBP adds evidence to the role of saliva in chemical communication.

Comparative assessment of the effective population size and linkage disequilibrium of Karan Fries cattle revealed viable population dynamics

OBJECTIVE

Karan Fries (KF), a high-producing composite cattle was developed through crossing indicine Tharparkar cows with taurine bulls (Holstein Friesian, Brown Swiss, and Jersey), to increase the milk yield across India. This composite cattle population must maintain sufficient genetic diversity for long-term development and breed improvement in the coming years. The level of linkage disequilibrium (LD) measures the influence of population genetic forces on the genomic structure and provides insights into the evolutionary history of populations, while the decay of LD is important in understanding the limits of genome-wide association studies for a population. Effective population size (Ne) which is genomically based on LD accumulated over the course of previous generations, is a valuable tool for e valuation of the genetic diversity and level of inbreeding. The present study was undertaken to understand KF population dynamics through the estimation of Ne and LD for the longterm sustainability of these breeds.

METHODS

The present study included 96 KF samples genotyped using Illumina HDBovine array to estimate the effective population and examine the LD pattern. The genotype data were also obtained for other crossbreds (Santa Gertrudis, Brangus, and Beefmaster) and Holstein Friesian cattle for comparison purposes.

RESULTS

The average LD between single nucleotide polymorphisms (SNPs) was r2 = 0.13 in the present study. LD decay (r2 = 0.2) was observed at 40 kb inter-marker distance, indicating a panel with 62,765 SNPs was sufficient for genomic breeding value estimation in KF cattle. The pedigree-based Ne of KF was determined to be 78, while the Ne estimates obtained using LD-based methods were 52 (SNeP) and 219 (genetic optimization for Ne estimation), respectively.

CONCLUSION

KF cattle have an Ne exceeding the FAO's minimum recommended level of 50, which was desirable. The study also revealed significant population dynamics of KF cattle and increased our understanding of devising suitable breeding strategies for longterm sustainable development.

Phenotypic and genetic characterization of unexplored, potential cattle population of Madhya Pradesh

Bawri or Garri, a non-descript cattle population managed under an extensive system in Madhya Pradesh state of India, was identified and characterized both genetically and phenotypically to check whether or not it can be recognised as a breed. The cattle have white and gray colour and are medium sized with 122.5 ± 7.5 cm and 109.45 ± 0.39 cm height at withers in male and female, respectively. Double-digest restriction site associated DNA (ddRAD) sequencing was employed to identify ascertainment bias free SNPs representing the entire genome cost effectively; resulting in calling 1,156,650 high quality SNPs. Observed homozygosity was 0.76, indicating Bawri as a quite unique population. However, the inbreeding coefficient was 0.025, indicating lack of selection. SNPs found here can be used in GWAS and genetic evaluation programs. Considering the uniqueness of Bawri cattle, it can be registered as a breed for its better genetic management.

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.

Assessment of genetic diversity of the fat-tailed Dumba sheep of India by mitochondrial and microsatellite markers

India has a centuries-old tradition of sheep production and breeding that accomplish economic, agricultural, and religious roles. In addition to the 44 registered sheep breeds, there is a fat-tailed sheep population referred to as Dumba. This study evaluated genetic variation in Dumba sheep and its differentiation from other Indian sheep breeds using mitochondrial DNA and genomic microsatellite loci. Haplotype and nucleotide diversity based on mitochondrial DNA analysis revealed substantially high maternal genetic diversity in Dumba sheep. Major ovine haplogroups A and B observed in sheep populations across the globe registered their presence in the Dumba sheep. The molecular genetic analysis using microsatellite markers also showed high measures of allele (10.125 ± 0.762) and gene diversity (0.749 ± 0.029). Results correspond to the non-bottleneck population that is near mutation-drift equilibrium despite some deficiency in the number of heterozygotes (FIS = 0.043 ± 0.059). Phylogenetic clustering confirmed Dumba to be a distinct population. Results of this study endow authorities with critical information imperative for sustainable utilization and conservation of Indian fat-tailed sheep, which is considered to be an untapped genetic resource contributing to the food security, livelihood, and economic sustainability of rural households in marginal areas of the country.

Estimation of microsatellite-based autozygosity and its correlation with pedigree inbreeding coefficient in crossbred cattle

In countries where farming is largely subsistence, no pedigree records of farm animals are maintained at farmers' herd and scientific mating plans are not observed which leads to the accumulation of inbreeding and loss of production potential. Microsatellites have been widely used as reliable molecular markers to measure inbreeding. We attempted to correlate autozygosity estimated from microsatellite data with the inbreeding coefficient (F) calculated from pedigree data in Vrindavani crossbred cattle developed in India. The inbreeding coefficient was calculated from the pedigree of ninety-six Vrindavani cattle. Animals were further grouped into three groups viz. acceptable/low (F: 0-5%), moderate (F: 5-10%) and high (F: ≥10%), based on their inbreeding coefficients. The overall mean of the inbreeding coefficient was found to be 0.070 ± 0.007. A panel of twenty-five bovine-specific loci were chosen for the study according to ISAG/FAO. The mean FIS, FST, and FIT values were 0.0548 ± 0.025, 0.012 ± 0.001 and 0.0417 ± 0.025, respectively. There was no significant correlation between the FIS values obtained and the pedigree F values. The locus-wise individual autozygosity was estimated using the method-of-moments estimator (MME) formula for locus-specific autozygosity. The autozygosities ascribing to CSSM66 and TGLA53 were found to be significantly (p < .01 and p < .05, respectively) correlated with pedigree F values.

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.

Genetic diversity analysis of cattle genetic groups of Kerala state using microsatellite data

Cattle belonging to seven different genetic groups in Kerala state, India were chosen for the study to find out the genetic diversity between the groups, which would aid in their sustainable improvement and conservation of native cattle. They included the native groups namely, Vechur, Kasaragod, Vadakara dwarf and Vilwadri, along with three different grades of crossbred cattle, based on milk production. Genomic DNA was isolated from 20 to 30 unrelated animals of each group and a panel of 25 microsatellite markers as suggested by FAO-ISAG, were amplified by multiplex PCR. The PCR amplicons were genotyped and the allelic data analyzed using suitable Bioinformatics softwares. The present study showed that the observed number of alleles was much more than the expected, in all populations. The mean PIC value obtained for the present study was 0.8912 and increased number of private alleles were observed, especially in Vilwadri and Kasaragod groups. Negative value of FIS (-0.055) indicated that the level of inbreeding was less. The FST value was 0.1442 indicating that the populations showed good genetic differentiation. The results of Structure analysis revealed admixture only in Vadakara population. The results obtained from the present study showed that Vilwadri and Kasaragod cattle showed distinct differences from other groups.

Genome sequencing and de novo and reference-based genome assemblies of Bos indicus breeds

BACKGROUND

Indian cattle breeds (Bos indicus) are known for their remarkable adaptability to hot and humid climates, higher nutritious quality of milk, better disease tolerance, and greater ability to perform in poor feed compared to taurine cattle (Bos taurus). Distinct phenotypic differences are observed among the B. indicus breeds; however, the whole genome sequences were unavailable for these indigenous breeds.

OBJECTIVE

We aimed to perform whole genome sequencing to construct the draft genome assemblies of four B. indicus breeds; Ongole, Kasargod Dwarf, Kasargod Kapila, and Vechur (the smallest cattle of the world).

METHODS

We sequenced the whole genomes using Illumina short-read technology, and constructed de novo and reference-based genome assemblies of these native B. indicus breeds for the first time.

RESULTS

The draft de novo genome assemblies of B. indicus breeds ranged from 1.98 to 3.42 Gbp. We also constructed the mitochondrial genome assemblies (~ 16.3 Kbp), and yet unavailable 18S rRNA marker gene sequences of these B. indicus breeds. The genome assemblies helped to identify the bovine genes related to distinct phenotypic characteristics and other biological processes for this species compared to B. taurus, which are plausibly responsible for providing better adaptive traits. We also identified the genes that showed sequence variation in dwarf and non-dwarf breeds of B. indicus compared to B. taurus.

CONCLUSIONS

The genome assemblies of these Indian cattle breeds, the 18S rRNA marker genes, and identification of the distinct genes in B. indicus breeds compared to B. taurus will help in future studies on these cattle species.

Progress and future perspectives of livestock genomics in India: a mini review

The field of genetics has evolved a lot after the emergence of molecular and advanced genomic technologies. The advent of Next Generation Sequencing, SNP genotyping platforms and simultaneous reduction in the cost of sequencing had opened the door to genomic research in farm animals. There are various applications of genomics in livestock, such as the use of genomic data: (i) to investigate genetic diversity and breed composition/population structure (ii) to identify genetic variants and QTLs related to economically important and ecological traits, genome-wide association studies (GWAS) and genomic signatures of selection; (iii) to enhance breeding programs by genomic selection. Compared to traditional methods, genomic selection is expected to improve selection response by increasing selection accuracy and reducing the generation interval due to early selection. Genomic selection (GS) in developed countries has led to rapid genetic gains, especially in dairy cattle, due to a well-established genetic evaluation system. Indian livestock system is still lagging behind developed nations in adopting these technologies. This review discusses the current status, challenges, and future perspectives of livestock genomics in India.

A. B. D. A, Abbas K, Hussain T, Ramasamy S, Manomohan V, Tapsoba ASR, Pichler R, Babar ME, Periasamy K. Indigenous cattle of Sri Lanka: Genetic and phylogeographic relationship with Zebu of Indus Valley and South Indian origin

The present study reports the population structure, genetic admixture and phylogeography of cattle breeds of Sri Lanka viz. Batu Harak, Thawalam and White cattle. Moderately high level of genetic diversity was observed in all the three Sri Lankan zebu cattle breeds. Estimates of inbreeding for Thawalam and White cattle breeds were relatively high with 6.1% and 7.2% respectively. Genetic differentiation of Sri Lankan Zebu (Batu Harak and White cattle) was lowest with Red Sindhi among Indus Valley Zebu while it was lowest with Hallikar among the South Indian cattle. Global F statistics showed 6.5% differences among all the investigated Zebu cattle breeds and 1.9% differences among Sri Lankan Zebu breeds. The Sri Lankan Zebu cattle breeds showed strong genetic relationships with Hallikar cattle, an ancient breed considered to be ancestor for most of the Mysore type draught cattle breeds of South India. Genetic admixture analysis revealed high levels of breed purity in Lanka White cattle with >97% Zebu ancestry. However, significant taurine admixture was observed in Batu Harak and Thawalam cattle. Two major Zebu haplogroups, I1 and I2 were observed in Sri Lankan Zebu with the former predominating the later in all the three breeds. A total of 112 haplotypes were observed in the studied breeds, of which 50 haplotypes were found in Sri Lankan Zebu cattle. Mismatch analysis revealed unimodal distribution in all the three breeds indicating population expansion. The sum of squared deviations (SSD) and raggedness index were non-significant in both the lineages of all the three breeds except for I1 lineage of Thawalam cattle (P<0.01) and I2 lineage of Batu Harak cattle (P<0.05). The results of neutrality tests revealed negative Tajima's D values for both the lineages of Batu Harak (P>0.05) and White cattle (P>0.05) indicating an excess of low frequency polymorphisms and demographic expansion. Genetic dilution of native Zebu cattle germplasm observed in the study is a cause for concern. Hence, it is imperative that national breeding organizations consider establishing conservation units for the three native cattle breeds to maintain breed purity and initiate genetic improvement programs.

ddRAD sequencing based genotyping of six indigenous dairy cattle breeds of India to infer existing genetic diversity and population structure

The present investigation aimed to identify genome wide SNPs and to carry out diversity and population structure study using ddRAD-seq based genotyping of 58 individuals of six indigenous milch cattle breeds (Bos indicus) such as Sahiwal, Gir, Rathi, Tharparkar, Red Sindhi and Kankrej of India. A high percentage of reads (94.53%) were mapped to the Bos taurus (ARS-UCD1.2) reference genome assembly. Following filtration criteria, a total of 84,027 high quality SNPs were identified across the genome of 6 cattle breeds with the highest number of SNPs observed in Gir (34,743), followed by Red Sindhi (13,092), Kankrej (12,812), Sahiwal (8956), Tharparkar (7356) and Rathi (7068). Most of these SNPs were distributed in the intronic regions (53.87%) followed by intergenic regions (34.94%) while only 1.23% were located in the exonic regions. Together with analysis of nucleotide diversity (π = 0.373), Tajima's D (D value ranging from - 0.295 to 0.214), observed heterozygosity (HO ranging from 0.464 to 0.551), inbreeding coefficient (FIS ranging from - 0.253 to 0.0513) suggested for the presence of sufficient within breed diversity in the 6 major milch breeds of India. The phylogenetic based structuring, principal component and admixture analysis revealed genetic distinctness as well as purity of almost all of the 6 cattle breeds. Overall, our strategy has successfully identified thousands of high-quality genome wide SNPs that will further enrich the Bos indicus representation basic information about genetic diversity and structure of 6 major Indian milch cattle breeds which should have implications for better management and conservation of valuable indicine cattle diversity.

Mitochondrial DNA diversity of D-loop region in three native Turkish cattle breeds

This study aimed to reveal the genetic variability of mitochondrial DNA (mtDNA) displacement-loop (D-loop) region in 62 animals belonging to three native Turkish cattle breeds, namely Anatolian Black (AB), East Anatolian Red (EAR) and Zavot (ZAV), and to conduct phylogenetic relationship analyses to obtain deeper information on their genetic origin and breeding history by comparison of 6 taurine and 11 indicine breeds, together with 66 polymorphic sites, a total of 31 haplotypes, of which 15, 10 and 6 were detected in AB, EAR and ZAV, respectively. Mean nucleotide and haplotype diversity were 0.01 and 0.891, respectively, whereas the genetic differentiation derived from Wright's F ST index was 0.174 across the breeds. A significant level of total variation (17.42 %) was observed among breeds in molecular variance analysis. Six main haplogroups (T, T1, T2, T3, Q and I2) were detected in Anatolian cattle populations, where T3 was the most frequent among breeds (43.55 %), whereas I2, an indicine specific haplogroup, was observed only in ZAV. At the breed level, phylogenetic analyses supported by 198 sequences of 17 cattle breeds and 3 outgroup species retrieved from the GenBank clustered native Turkish cattle breeds with the taurine group rather than the indicine one, as expected. However, indicine admixture at low frequency (8.89 %) was detected in the ZAV breed for the first time due to more likely gene flow from indicine cattle breeds raised in neighbour countries, particularly Iran. This finding should be further investigated in all native Turkish and indicine cattle breeds from nearby countries to clarify gene flow and indicine admixture in Anatolian cattle.

Genetic diversity evaluation of Sojat goat population of India

Sojat goat forms the part and parcel of the lives of the farmers in the Barmer region of Rajasthan. These are large-sized goats, white in colour, and have dual utility. These goats fetch premium price during the Eid festival. Assessment of diversity is essential for germplasm characterization and management. Genomic microsatellite markers being a valuable tool for estimating genetic diversity were selected for exploring existing genetic variability in the Sojat goat population. The standard metrics of genomic diversity detected moderate variability with a total of 162 alleles across 22 loci in this lesser-known population. The expected number of alleles had a mean value of 3.40±0.39. Similarly, a moderate magnitude of diversity was recorded in the Sojat population as the mean observed heterozygosity was 0.54±0.05. Expected heterozygosity was higher than the observed (0.60±0.06), indicating a deviation from Hardy-Weinberg Equilibrium (HWE) and the possibility of inbreeding due to the non-random mating in the population. Accordingly, significant heterozygote deficiency was noticed (F=0.08±0.03). The population did not suffer a reduction in effective population size in the last few generations. Mutation drift equilibrium did not reveal significant heterozygosity excess under different models of microsatellite evolution and no shift was recorded in the frequency distribution of alleles. To conclude, the results provided the first insights into the genetic diversity of Sojat goats. A moderate genetic variability with heterozygote deficiency within the population warrants immediate attention for scientific management of this unique goat population to conserve the existing genetic variation and to avoid any escalation of inbreeding.

Legacies of domestication, Neolithic diffusion and trade between Indian subcontinent and Island Southeast Asia shape maternal genetic diversity of Andaman cattle

Andaman cattle is a precious indigenous livestock species endemic to Andaman and Nicobar Islands, India. Till date, origin and genetic makeup of the breed which is warranted for breed conservation is not known. Moreover, the spread of zebu cattle from Indus valley to different parts of Island Southeast Asia (ISEA) is not properly understood. Here, we report the genetic diversity, population structure of Andaman cattle and their evolution in the context of epicentre of zebu domestication and ISEA. High genetic diversity in complete mitochondrial D-loop sequences indicated the ability of the breed to withstand impending climate change. Total 81 haplotypes were detected and all of them except three belonged to Bos indicus. The presence of taurine haplotypes in Andaman cattle indicate introgression by European-derived cattle. A poor phylogenetic signal of Andaman cattle with genetic affinities with cattle of Indian subcontinent and ISEA was observed. The poor phylogenetic structure may be due to multidirectional gene flow from Indian subcontinent and ISEA, with which Andaman shares a close cultural and trade relationship from Neolithic age. We hypothesize that Andaman cattle is the outcome of Neolithic diffusion from centre of zebu domestication along with multidirectional commercial exchange between Indian subcontinent and ISEA.

Whole-genome resequencing of Chinese pangolins reveals a population structure and provides insights into their conservation

Poaching and trafficking have a substantial negative impact on the population growth and range expansion of the Chinese pangolin (Manis pentadactyla). However, recently reported activities of Chinese pangolins in several sites of Guangdong province in China indicate a promising sign for the recovery of this threatened species. Here, we re-sequence genomes of 15 individuals and perform comprehensive population genomics analyses with previously published 22 individuals. These Chinese pangolins are found to be divided into three distinct populations. Multiple lines of evidence indicate the existence of a newly discovered population (CPA) comprises entirely of individuals from Guangdong province. The other two populations (CPB and CPC) have previously been documented. The genetic differentiation of the CPA and CPC is extremely large (F_ST = 0.541), which is larger than many subspecies-level differentiations. Even for the closer CPA and CPB, their differentiation (F_ST = 0.101) is still comparable with the population-level differentiation of many endangered species. Further analysis reveals that the CPA and CPB populations separate 2.5–4.0 thousand years ago (kya), and on the other hand, CPA and CPC diverge around 25–40 kya. The CPA population harbors more runs of homozygosity (ROHs) than the CPB and CPC populations, indicating that inbreeding is more prevalent in the CPA population. Although the CPC population has less mutational load than CPA and CPB populations, we predict that several Loss of Function (LoF) mutations will be translocated into the CPA or CPB populations by using the CPC as a donor population for genetic rescue. Our findings imply that the conservation of Chinese pangolins is challenging, and implementing genetic rescue among the three groups should be done with extreme caution.

Whole-genome resequencing of Chinese pangolins reveals a new population CPA that is genetically distinct from and harbor more homozygosity than CPB and CPC populations, indicating prevalence in inbreeding and implying challenges in conservation.

Assessment of genetic diversity and relationship of the two Sanga type cattle of Botswana based on microsatellite markers

The study was performed to evaluate genetic variation on two Sanga type cattle found in Botswana: Tswana and Tuli using twelve microsatellite markers. All amplified loci were polymorphic with 75 and 77 alleles genotyped in the Tswana and Tuli populations, respectively. The total number of alleles per locus ranged from 2 (BM1818) to 10 (TGLA227) with total mean of 6.25 for Tswana and 6.43 for Tuli population. Almost all the markers showed high polymorphic information content (PIC) apart from BM1818 (0.375) and INRA23 (0.393) which were moderately informative in Tswana population. Most of the markers were in Hardy-Weinberg equilibrium except for CSSRM60 and CSSM66 loci in Tswana population and ETH10, ETH225 and CSSM66 loci in Tuli population. A total of 103 unique alleles were genotyped across the two breeds with 49-shared, and 26 and 28 were unique to Tswana and Tuli populations, respectively. The expected heterozygosity (He) values were higher than the observed heterozygosity (Ho) in both populations: Tswana (He = 0.7895 ± 0.033 vs Ho = 0.631 ± 0.091) and Tuli (He = 0.8123 ± 0.033 vs Ho = 0.556 ± 0.021). The inbreeding coefficient was 0.200 ± 0.002 and 0.332 ± 0.001 in Tswana and Tuli populations, respectively. Analysis of molecular variance revealed 6.8% of the total genetic variation corresponding to differences between the two breeds and 93.2% within populations. The genetic identity between the two breeds was 56% and there were similar levels of multilocus heterozygosity and allelic diversity in the two breeds. The use of Tswana and Tuli breeds in a crossbreeding programme is likely to result in minimal heterosis and therefore not recommended.

Genetic diversity and population structure of four Nigerian indigenous cattle breeds

A total of thirty-eight (38) Nigerian indigenous cattle were used to evaluate the genetic relatedness, diversity, and population structure of four indigenous cattle breeds. Blood samples were collected from the experimental animals into vacutainer tubes containing EDTA, and genomic DNA extracted, quantified, and evaluated for integrity. Fourteen (14) microsatellite primers were used for polymerase chain reaction (PCR) and PCR amplification performed under standard conditions followed by electrophoresis in 2.5% Metaphor Agarose gel. Genomic parameter estimates included allele number (Na), observed (H_o) and expected (H_e) heterozygosity, polymorphism information content (PIC), test of Hardy-Weinberg equilibrium, and genetic diversity; pairwise Nei's genetic distance, Wright's F-statistics (FIT, FST, and FIS), and gene flow (Nm); and breed relationship, population structure, and degree of admixture. A total of 112 alleles were detected and mean number of alleles was 4.02 ± 0.190, while mean fixation index was 0.461 ± 0.068. Mean H_o and H_e were 0.352 ± 0.05 and 0.605 ± 0.018, respectively. Pairwise estimates of genetic differentiation, F_ST, were significantly different (p < 0.001) implying distinct breeds. Estimates of Nm were less than 4 but greater than 1, indicating that the cattle breeds do not belong to one panmictic population. Estimates of pairwise genetic distance revealed that White Fulani and Sokoto Gudali were more closely related than Muturu and N'Dama. The results of STRUCTURE, principal coordinate, and phylogenetic analyses revealed four clusters which implies that the breeds were genetically distinct. It is recommended that the four cattle breeds can be used to develop composites with higher genetic potentials for beef production and resistance to endemic diseases and pests. Further efforts should be made to conserve and genetically improve these breeds to meet present and future production and breeding imperatives.

Do Pharaohs' cattle still graze the Nile Valley? Genetic characterization of the Egyptian Baladi cattle breed

Egyptian Baladi cattle is one of the few native taurine breeds which remain in the original domestication area of Bos taurus, the Nile Valley (Upper Egypt). Apart from its evolutive relevance, the breed is well-adapted and integrated into the traditional family farming systems, with great potentialities for local sustainable rural development. The diversity and structure of the Baladi population were assessed using 28 genetic microsatellite markers. Within and between-breeds diversity, its relations with other cattle breeds, and an inference on its origin and evolution, were analyzed. Results reported high levels of diversity, with an average number of alleles (Na) of 11.39, observed heterozygosity (Ho) of 0.68, and expected heterozygosity (He) of 0.75. The studied population was in Hardy-Weinberg disequilibrium, which could be ascribed to its internal structure. The comparison between breeds using factorial correspondence analysis, Reynolds genetic distance evaluation, and genetic structure analysis suggested slight influences of Bos indicus. Upper Egypt's rural communities have preserved the Baladi cattle breed, protecting this historical and biological heritage against the constant and indiscriminate introduction of exotic genetic resources along the history of development of the breed. Developing and implementing conservation and breeding programs is crucial for the preservation and improvement of the breed.HIGHLIGHTSBaladi cattle breed is a well-defined and highly diverse breed.Higher diversity levels are found in northern and central governorates.A clear geographical cluster is formed around the Nile Delta.Baladi cattle may be reminiscent of the ancient 'pharaoh' cattle.Assiut's population acted as the most ancestral population nucleus.

Genetic differentiation of Indian dromedary and Bactrian camel populations based on mitochondrial ATP8 and ATP6 genes

Camelids are acknowledged worldwide to endure hostile conditions prevalent in the hot as well cold deserts across the globe. Adaptations to climatic extremes have been associated with mitochondrial protein variants such as ATP8 and ATP6 in different species. The camel genetic resources of India are represented by 9 breeds of dromedary camels which inhabit hot arid and semi-arid zones of the country and a small population of Bactrian camels found in the cold desert of Ladakh. In this study, within and between breed genetic diversity in Indian dromedaries and their divergence from Bactrian camels was investigated based on ATP8/6 genes. Sequence analysis of a mitochondrial DNA fragment encompassing ATP8 and ATP6 genes identified 15 haplotypes in the dromedaries of India and 3 haplotypes in Bactrian camels. The values of haplotype diversity and nucleotide diversity were 0.647 and 0.00187 in the former and 0.679 and 0.00098, respectively in the latter. AMOVA analysis revealed 97.81% variance between the two species. Median-Joining network delineated three distinct mitochondrial haplogroups for Camelus dromedarius, Camelus ferus and Camelus bactrianus. Clear demarcation of the old world (Dromedary and Bactrian camels) and new world camelids (Alpaca, llama, guanaco and vicugna) was evident through the phylogenetic analysis.

Microsatellite markers based genetic diversity and differentiation of Balangir goat population of Odisha

This study was executed to investigate the genetic diversity of Balangir, a local goat population from Odisha, and its differentiation from the geographically closest registered goat breeds, Ganjam and Black Bengal by utilizing 22 polymorphic microsatellite markers. The genotypic status of individuals at each locus was identified by an automated DNA sequencer and allelic data was analyzed for genetic diversity parameters. It resulted in the acquisition of original and comparable information confirming the genetic distinctness of the Balangir goat population. The observed number of alleles varied between 4 (RM4) and 16 (OMHC1) with 8.23±0.64 alleles per locus in Balangir goats. A moderate level of observed heterozygosity (0.57±0.05) indicated sufficiently existing genetic diversity in this goat population which varied between 0.09 (OarJMP29) and 1 (ILSTS22). Expected heterozygosity (0.64±0.04) oscillated between 0.18 (ILSTS34) and 0.89 (OMHC1). Within the population, heterozygosity deficiency estimate (FIS) was significantly positive (0.13±0.05) and 73% of the investigated loci contributed towards the homozygote excess. Consequently, significant deviation from Hardy–Weinberg equilibrium was observed at 12 of 22 analyzed loci. Assessment of Balangir goat population for mutation drift equilibrium indicated that the population did not suffer a reduction in effective population size in the last few generations. Four different approaches utilized to study genetic relationships (F statistics, analysis of molecular variance, phylogenetic relationship genetic distance, and individual assignment) indicated that the Balangir goat population was genetically differentiated from the two registered goat breeds. The study highlighted that Balangir is discrete Indian goat germplasm with sufficient genetic variability and needs to be registered as a goat breed of India.

Characterization of a new potential goat breed (Palamu) from Jharkhand, India

Palamu goat forms the part and parcel of the lives of the farmers and tribes of Jharkhand. Palamu goat also known as Medini is named after its distribution area (Palamu, Latehar and Garhwa) in Jharkhand. This small size goat is reared in Jharkhand since time immemorial. Average flock size is 5.36±0.19 and varies from 1 to 31. Twinning is common except in first kidding. Head profile is convex, ears are pendulous, and horns are straight with backward and upward orientation. Muzzle, eyelids and hooves are black, body is cylindrical, udder is small and pendulous and teats are conical shaped. Age at first mating in males is 8.32±0.86 (months) that vary between 7.2– 9.2 months. Corresponding values for female are 7.22±1.35 months varying between 6.7–7.7 months. Diversity status of the population was explored using 25 microsatellite markers. A total of 190 alleles were detected and sufficient polymorphism was evident from the allele frequency data. ILSTS82 showed the highest number of observed alleles per locus (20) while RM4 and ILSTS05 showed the lowest (4) with 9.14±2.0 as mean number of alleles. Expected number of alleles varied from 1.49 (ILSTS065) to 7.55 (ILSTS30) with the mean value of 4.15±0.91. Palamu goat had substantial genetic variation based on its gene diversity in addition to the average number of alleles per locus. The observed and expected heterozygosity values were 0.64±0.14 and 0.69±0.15, respectively. Observed heterozygosity was lower than expected showing a departure from Hardy-Weinberg Equilibrium (HWE) and possibility of inbreeding. Population has heterozygote deficiency to the tune of 9% (FIS value=0.09). Population did not suffer from recent genetic bottleneck (last 40–80 generations). The results suggest existence of a distinct goat population harboring sufficient genetic variation for scientific management.

An Overview of the Use of Genotyping Techniques for Assessing Genetic Diversity in Local Farm Animal Breeds

Simple Summary

The number of local farm animal breeds is declining worldwide. However, these breeds have different degrees of genetic diversity. Measuring genetic diversity is important for the development of conservation strategies and, therefore, various genomic analysis techniques are available. The aim of the present work was to shed light on the use of these techniques in diversity studies of local breeds. In summary, a total of 133 worldwide studies that examined genetic diversity in local cattle, sheep, goat, chicken and pig breeds were reviewed. The results show that over time, almost all available genomic techniques were used and various diversity parameters were calculated. Therefore, the present results provide a comprehensive overview of the application of these techniques in the field of local breeds. This can provide helpful insights into the advancement of the conservation of breeds with high genetic diversity.

Abstract

Globally, many local farm animal breeds are threatened with extinction. However, these breeds contribute to the high amount of genetic diversity required to combat unforeseen future challenges of livestock production systems. To assess genetic diversity, various genotyping techniques have been developed. Based on the respective genomic information, different parameters, e.g., heterozygosity, allele frequencies and inbreeding coefficient, can be measured in order to reveal genetic diversity between and within breeds. The aim of the present work was to shed light on the use of genotyping techniques in the field of local farm animal breeds. Therefore, a total of 133 studies across the world that examined genetic diversity in local cattle, sheep, goat, chicken and pig breeds were reviewed. The results show that diversity of cattle was most often investigated with microsatellite use as the main technique. Furthermore, a large variety of diversity parameters that were calculated with different programs were identified. For 15% of the included studies, the used genotypes are publicly available, and, in 6%, phenotypes were recorded. In conclusion, the present results provide a comprehensive overview of the application of genotyping techniques in the field of local breeds. This can provide helpful insights to advance the conservation of breeds.

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.

Legacy of draught cattle breeds of South India: Insights into population structure, genetic admixture and maternal origin

The present study is the first comprehensive report on diversity, population structure, genetic admixture and mitochondrial DNA variation in South Indian draught type zebu cattle. The diversity of South Indian cattle was moderately high. A significantly strong negative correlation coefficient of -0.674 (P<0.05) was observed between the effective population size of different breeds and their estimated F_IS. The genetic structure analysis revealed the distinctness of Kangayam, Vechur and Punganur cattle from the rest of the zebu breeds. The results showed the influence of Hallikar breed in the development of most Mysore type cattle breeds of South India with the exception of Kangayam. Bayesian clustering analysis was performed to assess the taurine admixture in South Indian zebu cattle using purebred Jersey and Holstein-Friesian as reference genotypes. Relatively high levels of taurine admixture (>6.25%) was observed in Punganur, Vechur, Umblachery and Pulikulam cattle breeds. Two major maternal haplogroups, I1 and I2, typical of zebu cattle were observed, with the former being predominant than the later. The pairwise differences among the I2 haplotypes of South Indian cattle were relatively higher than West Indian (Indus valley site) zebu cattle. The results indicated the need for additional sampling and comprehensive analysis of mtDNA control region variations to unravel the probable location of origin and domestication of I2 zebu lineage. The present study also revealed major concerns on South Indian zebu cattle (i) risk of endangerment due to small effective population size and high rate of inbreeding (ii) lack of sufficient purebred zebu bulls for breeding and (iii) increasing level of taurine admixture in zebu cattle. Availability of purebred semen for artificial insemination, incorporation of genomic/molecular information to identify purebred animals and increased awareness among farmers will help to maintain breed purity, conserve and improve these important draught cattle germplasms of South India.

Genetic Diversity and Population Structure of Dromedary Camel-Types

The dromedary camel is a unique livestock for its adaptations to arid-hot environments and its ability to provide goods under extreme conditions. There are no registries or breed standards for camels. Thus, named camel populations (i.e., camel-types) were examined for genetic uniqueness and breed status. Camel populations are generally named based on shared phenotype, country or region of origin, tribal ownership, or the ecology of their habitat. A dataset of 10 Short-Tandem Repeat markers genotyped for 701 individual camels from 27 camel-types was used to quantify genetic diversity within camel-types, compare genetic diversity across camel-types, determine the population genetic structure of camel-types, and identify camel-types that may represent true breeds. Summary statistics (genotyping call rate, heterozygosity, inbreeding coefficient FIS, and allelic frequencies) were calculated and population-specific analyses (pairwise FST, neighbor-joining tree, relatedness, Nei's genetic distance, principal coordinate analysis [PCoA], and STRUCTURE) were performed. The most notable findings were 1) little variation in genetic diversity was found across the camel-types, 2) the highest genetic diversity measure was detected in Targui and the lowest was in Awarik, 3) camel-types from Asia (especially the Arabian Peninsula) exhibited higher genetic diversity than their counterparts in Africa, 4) the highest DeltaK value of population structure separated camel-types based on geography (Asia vs. Africa), 5) the most distinct camel-types were the Omani, Awarik, and the Gabbra, 6) camel-types originating from the same country did not necessarily share high genetic similarity (e.g., camel-types from Oman), and 7) camel-type names were not consistently indicative of breed status.

Evaluation of Genetic Diversity and Structure of Turkish Water Buffalo Population by Using 20 Microsatellite Markers

The present study was aimed to investigate the genetic diversity among 17 Turkish water buffalo populations. A total of 837 individuals from 17 provincial populations were genotyped, using 20 microsatellites markers. The microsatellite markers analyzed were highly polymorphic with a mean number of alleles of (7.28) ranging from 6 (ILSTS005) to 17 (ETH003). The mean observed and expected heterozygosity values across all polymorphic loci in all studied buffalo populations were 0.61 and 0.70, respectively. Observed heterozygosity varied from 0.55 (Bursa (BUR)) to 0.70 (Muş (MUS)). It was lower than expected heterozygosity in most of the populations indicating a deviation from Hardy-Weinberg equilibrium. The overall value for the polymorphic information content of noted microsatellite loci was 0.655, indicating their suitability for genetic diversity analysis in buffalo. The mean F_IS value was 0.091 and all loci were observed significantly deviated from Hardy-Weinberg Equilibrium (HWE), most likely based on non-random breeding. The 17 buffalo populations were genetically less diverse as indicated by a small mean F_ST value (0.032 ± 0.018). The analysis of molecular variance (AMOVA) analysis indicated that about 2% of the total genetic diversity was clarified by population distinctions and 88 percent corresponded to differences among individuals. The information produced by this study can be used to establish a base of national conservation and breeding strategy of water buffalo population in Turkey.

Genomic scans for selection signatures revealed candidate genes for adaptation and production traits in a variety of cattle breeds

Domestication and selection are the major driving forces responsible for the determinative genetic variability in livestock. These selection patterns create unique genetic signatures within the genome. BovineSNP50 chip data from 236 animals (seven indicine and five taurine cattle breeds) were analyzed in the present study. We implemented three complementary approaches viz. iHS (Integrated haplotype score), ROH (Runs of homozygosity), and F_ST, to detect selection signatures. A total of 179, 56, and 231 regions revealed 518, 277, and 267 candidate genes identified by iHS, ROH, and F_ST methods, respectively. We found several candidate genes (e.g., NCR3, ARID5A, HIST1H2BN, DEFB4, DEFB7, HSPA1L, HSPA1B, and DNAJB4) related to production traits and the adaptation of indigenous breeds to local environmental constraints such as heat stress and disease susceptibility. However, further studies are warranted to refine the findings using a larger sample size, whole-genome sequencing, and/or high density genotyping.

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.

Molecular and phenometric characterization of Bhakarwali goat breed of India

Bhakarwali is recently registered as 34th goat breed of India. It is distributed in the hilly tracts of Jammu and Kashmir. The breed is distinct with superior qualities such as high temperature resistance and milk, meat and fiber productivity under the low input system. It’s characterization at phenotypic level was carried out by surveying the breeding tract and at genotypic level by microsatellite markers. Information on body traits, performance traits and managemental practices were collected by interviewing the goat keepers. All the microsatellite loci selected for diversity analysis were polymorphic and a total of 190 alleles were identified across the 23 microsatellite loci. OMHC1 depicted the highest number of alleles (15) while ILSTS065 had the lowest (2) with 8.26±0.663 mean number of alleles per locus. Expected number of alleles ranged from 1.065 (ILSTS044) to 6.755 (OMHC1) with a mean value of 3.613±0.367 alleles per locus. The observed heterozygosity ranged from 0.063 (ILSTS044) to 0.915 (OMHC1) with a mean of 0.629±0.045. Corresponding values of expected heterozygosity varied between 0.061 (ILSTS044) to 0.852 (OMHC1) with a mean of 0.639±0.043. Heterozygote deficiency was negligible as average FIS value was only 0.002±0.033. Bottleneck was examined using all the three mutations models and was found to be absent. Normal L-shaped curve indicated lack of mode shift in the population. This is the first-hand report on current diversity status of Bhakarwali goat and is expected to be useful in planning conservation and in facilitating their effective use in future breeding programs.

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.

Microsatellite Diversity and Phylogenetic Relationships among East Eurasian Bos taurus Breeds with an Emphasis on Rare and Ancient Local Cattle

We report the genetic analysis of 18 population samples of animals, which were taken from cattle (Bos taurus) breeds of European and Asian origins. The main strength of our study is the use of rare and ancient native cattle breeds: the Altai, Ukrainian Grey, Tagil, and Buryat ones. The cattle samples studied have different production purposes, belong to various eco-geographic regions, and consequently have distinct farming conditions. In order to clarify the genetic diversity, phylogenetic relationships and historical origin of the studied breeds, we carried out an analysis of the genetic variation of 14 high-variability microsatellite loci at 1168 genotyped animals. High levels of heterozygosity and allelic richness were identified in four of the ancient local breeds, namely the Kalmyk, Tagil, Kyrgyz native, and Buryat breeds. The greatest phylogenetic distances from a common ancestor were observed for the Yakut and Ukrainian Grey breeds, while the Tagil breed showed the smallest difference. By using clustering approaches, we found that the Altai cattle is genetically close to the Kyrgyz one. Moreover, both the Altai and Kyrgyz breeds exposed genetic divergences from other representatives of the Turano-Mongolian type and genetic relationships with the Brown Swiss and Kostroma breeds. This phenomenon can be explained by the extensive use of the Brown Swiss and Kostroma breeds in the breeding and improvement processes for the Kyrgyz breeds, which have been involved in the process of keeping the Altai cattle. Our results can be valuable for conservation and management purposes.

Genome-wide assessment of genetic diversity, linkage disequilibrium and haplotype block structure in Tharparkar cattle breed of India

Knowledge about genetic diversity is very essential for the management and sustainable utilization of livestock genetic resources. In this study, we presented a comprehensive genome-wide analysis of genetic diversity, ROH, inbreeding, linkage disequilibrium, effective population size and haplotype block structure in Tharparkar cattle of India. A total of 24 Tharparkar animals used in this study were genotyped with Illumina BovineSNP50 array. After quality control, 22,825 biallelic SNPs were retained, which were in HWE, MAF > 0.05 and genotyping rate >90%. The overall mean observed (H_O) and expected heterozygosity (H_E) were 0.339 ± 0.156 and 0.325 ± 0.129, respectively. The average minor allele frequency was 0.234 with a standard deviation of ± 0.131. We identified a total of 1832 ROH segments and the highest autosomal coverage of 13.87% was observed on chromosome 23. The genomic inbreeding coefficients estimates by F_ROH, F_HOM, F_GRM and F_UNI were 0.0589, 0.0215, 0.0532 and 0.0160 respectively. The overall mean linkage disequilibrium (LD) for a total of 133,532 pairwise SNPs measured by D' and r² was 0.6452 and 0.1339, respectively. In addition, we observed a gradual decline in effective population size over the past generations.

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.

Detection of estrous biomarkers in the body exudates of Kangayam cattle (Bos indicus) from interplay of hormones and behavioral expressions

Behavioral expressions and biochemical composition of body exudates are significantly altered in concert with the endocrine status, which are all clear indicators of physiological conditions of animals. In this study, we sought to infer about the reproductive physiological status of Kangayam cattle (Bos indicus) by analyzing behaviors, endocrine pattern, and body exudates and further to discover estrous biomarkers so as to facilitate timely artificial insemination/mating and to aid in aspects of conservation of the species. Therefore, in this study, we followed Kangayam cows through pre-estrous to post-estrous phases to correlate the endocrine dependence of biochemical constituents in urine and cervical mucus and sought to identify estrous biomarkers. Behavioral estrus was confirmed in 10 cows, from which urine samples were collected and subjected to determination of LH, FSH, estrogens, progesterone, proteins, and lipids. Furthermore, urinary fatty acids and proteins were profiled using gas chromatography and SDS-PAGE, respectively. The volatile compounds in the urine and cervical mucus were identified by gas chromatography-mass spectrometry analysis. The data revealed that LH, FSH, and estrogen levels increased significantly in estrous urine compared with nonestrous urine, whereas progesterone status was vice versa (P < 0.05). The lipid content was also significantly higher in estrous urine than in pre- and post-estrous urines (P < 0.05). There were also cyclical variations of volatiles and fatty acid profiles across phases of the estrous cycle. More acidic compounds were present in estrous urine, rendering it more acidic, than in pre- and post-estrous urines. Interestingly, oleic acid, which was present as a fatty acid in estrous and post-estrous urines, appeared to be a volatile in post-estrous urine and estrous cervical mucus. In addition, octanoic and butanoic acids were specific to both estrous urine and cervical mucus, indicating their possible candidature as estrous biomarkers. SDS-PAGE analysis showed pronounced expression of a 98 kDa protein in post-estrous urine, which in matrix-assisted laser desorption ionization-time of flight mass spectrometry was identified as albumin. Our results demonstrate multiple biomarkers in estrous urine and specific volatiles in cervical mucus that offer scope to develop viable estrus detection kits for Kangayam cows.

Comprehensive analysis of mitochondrial DNA based genetic diversity in Indian goats

Thirty four distinct breeds and many non-descript populations represent the caprine diversity of India. Genetic characterization of breeds is an essential element in designing breeding strategies and preserving genetic diversity. Considering the popularity of mitochondrial DNA for phylogeographical studies, this study involved an extensive analysis of population structure and genetic diversity of 28 defined breeds and 5 lesser known populations representing all four major agro-climatic zones of India using mitochondrial DNA markers. Analysis of hypervariable region 1 of mtDNA control region in 443 goats together with 22 reference sequences, delineated 341 distinct haplotypes belonging to four maternal haplogroups; A, B, C and D, with haplogroup A representing 90% of the individuals. The haplotype and nucleotide diversity indices of Indian goats were 0.998 ± 0.001 and 0.028 ± 0.001, respectively indicating abundant genetic variability. Estimates of population demographic parameters from mismatch analysis suggested a relatively good fit to the model of either spatial or demographic expansion of Indian goats. AMOVA analysis and topology of MJ network suggested lack of phylogeographic structure in domestic goats, which can be attributed to unstructured animal breeding, dwindling pastures and nomadic pastoralism. Genetic differentiation between goats from different agro-ecological regions was in accordance with their geographical propinquity.

Y-chromosome genetic diversity of Bos indicus cattle in close proximity to the centre of domestication

Y-chromosome genetic diversity in and around its domestication origin and a better understanding of indicine-specific microsatellite alleles are imperative concerns but less -targeted. We analysed Y-chromosome markers in 301 bulls representing 19 native Indian cattle (Bos indicus) and identified new alleles and haplotypes. Compared to other indicine studies, the high Y-haplotype diversity found in Indian cattle supports the hypothesis of greater genetic variability across the centre of origin decreasing along migratory routes with increasing distance. Hence, a considerable paternal genetic diversity of Indian cattle appears to have been lost in transboundary commercial indicine breeds. The Khillar and Gir are the most diversified populations where the first tends to be the well-differentiated traditional breed carrying strikingly distinct Y-lineages with typical BM861-158 bp allele, characteristics of taurine cattle, while retaining standard indicine lineages for all other markers. Geographical distribution found to be an unreliable predictor of parental variation, and Y-lineages seemed closely related to Indian breed function/utility. The comprehensive Y-chromosome information will be useful to examine the demographic expansion/spread of Bos indicus lineages from close proximity to the domestication centre across different countries worldwide and such diversity should be preserved through effective management and conservation programs.

Short Tandem Repeat (STR) based assessment of genetic diversity of Alambadi - A draught cattle breed of Tamil Nadu

Alambadi is one of the five indigenous draught type cattle breeds of Tamil Nadu. The present study was undertaken to establish baseline genetic diversity information and evaluate its genetic relationship with Bargur cattle. The results suggested moderate levels of allelic diversity and observed heterozygosity with an overall mean of 6.52 and 0.666 respectively. Estimates of FIS showed significant heterozygosity deficit (0.056) indicating relatively higher levels of inbreeding in Alambadi cattle. The test for Hardy-Weinberg equilibrium revealed 11.1% (3 out of 27) of the investigated loci showing significant deviations due to heterozygosity deficit. Estimation of global F statistics revealed low genetic differentiation between Alambadi and Bargur cattle. The global FST indicated only 3% of the total variation being explained by between breed differences, while the remaining 97% was explained by within breed variability. Principal components analysis revealed separate clustering of Alambadi and Bargur cattle, although admixture was observed among few animals from both the breeds. The test for mutation drift equilibrium revealed no evidences for the occurrence of genetic bottleneck in Alambadi and Bargur cattle in the recent past. Considering the rapid decline in the population of Alambadi cattle, the results of the present study is expected to help planning the strategy for genetic conservation and breed improvement.

Population genetic structure and maternal lineage of South African crossbred Nguni cattle using the cytochrome b gene in mtDNA

The Nguni cattle breed predominates South Africa and is endowed with traits favourable against environmental stressors such as heat stress and resistance to diseases. Interventions to improve production have led to the erosion of the genetic integrity of local breeds and the introduction of exotic breeds has proved ineffective as they fail to perform well due to different climatic conditions and production systems. In this study, the genetic structure and genetic lineage of Nguni crossbreds from 6 populations were assessed using the mitochondrial cytochrome b gene. Twelve polymorphic sites were detected resulting in 11 haplotypes with haplotype and nucleotide diversities of 0.550 ± 0.135 and 0.0019 ± 0.0011, respectively. Only 2 of the 6 populations displayed recent population expansion events, whereas the majority adhered to neutral evolution. The basal haplotype contained approximately 60% of the studied populations and there were four unique haplotypes that were revealed. A possible Nguni descript haplotype was uncovered, and this haplotype was found in all populations but was however devoid of individuals from around the world. The genetic structure of the populations was rather low (average pairwise F_ST = 0.066 and Slatkins F_ST = 0.094), and approximately 96% of the total genetic variation was accounted for by differences within populations. Phylogenetic analyses supported the clustering of all the samples within the Bos taurus clade and no Bos indicus haplotype was detected. Furthermore, no intermediate haplotype of taurine and indicine was detected. Overall, the maternal lineage of the crossbreds points to a taurine origin and the low genetic diversity depicts the retention of the Nguni genetic pool and possibly its superior adaptive traits.

Population structure and genetic diversity in Colombian Simmental cattle

A vital requirement to design and implement a breeding program is to know the structure and genetic diversity of a population. The aim of this study was to characterize population structure and genetic diversity of the Colombian Simmental cattle. The pedigree file included 27,985 animals born from 1975 to 2017. The level of genetic diversity and breed structure was evaluated through probabilities of gene origin expressed via effective number of founders, ancestors and founders genomes. The inbreeding rates and the degree of genetic connectivity were estimated using a regression analysis and a genetic drift variance analysis, respectively. The lowest effective number of founders and ancestors were 50 and 38 by year, respectively. The average inbreeding by year of birth decreased from 5.06% in 1980 to 2.25% in 2017. The dairy line genetic contributions in the overall population increased significantly in the last 37 years, and the beef line contribution decreased. Regarding the genetic connectivity, Colombian regions (administrative divisions) with the largest cattle population had higher values. The results indicate that the availability of European and North American bulls contributes to genetic diversity by increasing the effective number of founders over time in the Colombian Simmental cattle population. However, the intensive use of relatively few founders causes an unbalanced genetic contribution and the loss of genetic diversity by gene pool erosion.

Genetic diversity and relationships among three Southern African Nguni cattle populations

The Nguni cattle breed has distinct populations that are adapted to the different ecological zones of Southern Africa. This study was carried out to assess genetic diversity and establish the relationships among South African (SA), Mozambican (Landim), and Swazi Nguni cattle populations, using 25 microsatellite markers. Genotypic data were generated from deoxyribonucleic acid (DNA) samples of 90 unrelated individuals of the three cattle populations, collected from government conservations and stud herds. DNA profiles of five local beef breeds were used as the reference populations. Most of the 25 microsatellite markers were highly polymorphic across the studied populations, with an overall polymorphic information content (PIC) mean of 0.676. Genetic diversity within populations was high with expected heterozygosity varying from 0.705 ± 0.024 (Landim) to 0.748 ± 0.021 (SA Nguni) and mean number of alleles being highest in the SA Nguni (7.52 ± 0.42). Average observed heterozygosity (0.597 ± 0.046) compared to the expected heterozygosity (0.719 ± 0.022) was lowest for the Swazi Nguni, which also had a high number of Hardy-Weinberg Equilibrium (HWE) deviated loci (13), confirming the relatively high level of inbreeding (0.158 ± 0.058) in that population. Analysis of molecular variance revealed only 9.61% of the total variation between the populations and 90.39% within populations. A short genetic distance (0.299) was observed between Landim and Swazi Nguni, with the SA Nguni (> 0.500) being the most genetically distant population. The distant relationship between SA Nguni and the other two Nguni cattle populations was further confirmed by a principal coordinates analysis. The three Nguni populations clustered independently from each other, despite some evidence of admixture. Therefore, it can be concluded that SA Nguni, Landim, and Swazi Nguni populations in Southern Africa exhibit high levels of genetic diversity and are genetically distant; with the two latter populations being less genetically apart. These results present useful information for the development of strategies for regional management of animal genetic resources, through conservation and sustainable utilisation.

Evaluation of 17 microsatellite markers for parentage testing and individual identification of domestic yak (Bos grunniens)

BACKGROUND

Yak (Bos grunniens) is the most important domestic animal for people living at high altitudes. Yak ordinarily feed by grazing, and this behavior impacts the accuracy of the pedigree record because it is difficult to control mating in grazing yak. This study aimed to evaluate the pedigree system and individual identification in polled yak.

METHODS

A total of 71 microsatellite loci were selected from the literature, mostly from the studies on cattle. A total of 35 microsatellite loci generated excellent PCR results and were evaluated for the parentage testing and individual identification of 236 unrelated polled yaks. A total of 17 of these 35 microsatellite loci had polymorphic information content (PIC) values greater than 0.5, and these loci were in Hardy-Weinberg equilibrium without linkage disequilibrium.

RESULTS

Using multiplex PCR, capillary electrophoresis, and genotyping, very high exclusion probabilities were obtained for the combined core set of 17 loci. The exclusion probability (PE) for one candidate parent when the genotype of the other parent is not known was 0.99718116. PE for one candidate parent when the genotype of the other parent is known was 0.99997381. PE for a known candidate parent pair was 0.99999998. The combined PEI (PE for identity of two unrelated individuals) and PESI (PE for identity of two siblings) were >0.99999999 and 0.99999899, respectively. These findings indicated that the combination of 17 microsatellite markers could be useful for efficient and reliable parentage testing and individual identification in polled yak.

DISCUSSION

Many microsatellite loci have been investigated for cattle paternity testing. Nevertheless, these loci cannot be directly applied to yak identification because the two bovid species have different genomic sequences and organization. A total of 17 loci were selected from 71 microsatellite loci based on efficient amplification, unambiguous genotyping, and high PIC values for polled yaks, and were suitable for parentage analysis in polled yak populations.

Suitability of existing commercial single nucleotide polymorphism chips for genomic studies in Bos indicus cattle breeds and their Bos taurus crosses

Bos indicus cattle breeds are genetically distinct from Bos taurus breeds. We examined the performance of three SNP arrays, the Illumina BovineHD BeadChip (777k; Illumina Inc.), the Illumina BovineSNP50 BeadChip (50k) and the GeneSeek 70k Indicus chip (75Ki; GeneSeek) in four B. indicus breeds (Gir, Kankrej, Sahiwal and Red Sindhi) and their B. taurus crosses, along with two B. taurus breeds, Holstein and Jersey. More SNPs on both Illumina SNP chips were monomorphic in B. indicus breeds (average 20.3%-29.3% on the 777k chip, 35.5%-45.5% on the 50k chip) than in Holstein (19.7% on the 777k chip, 17.1% on the 50k chip). The proportion of monomorphic SNPs on the 75Ki chip was much lower, 4% (2.8%-7%) in B. indicus breeds, while it was 33.5% in Holstein. With on average 164,357 heterozygous loci in B. indicus breeds, the 777k SNP chip has sufficient heterozygous loci to design a chip customized for B. indicus breeds. Principal component analysis clearly differentiated B. indicus from B. taurus breeds. Differentiation among B. indicus breeds was only achieved by plotting the third and fifth principal components using 777k genotype data. Admixture analysis showed that many B. indicus animals, previously believed to be of pure origin, are in fact had mixed ancestry. The extent of linkage disequilibrium showed comparatively higher effective population sizes in four B. indicus breeds compared to two B. taurus breeds. The results of admixture analyses show that it is important to assess the genomic composition of a bull before using it in a breeding programme.

Whole-genome SNP analysis elucidates the genetic structure of Russian cattle and its relationship with Eurasian taurine breeds

BACKGROUND

The origin of native and locally developed Russian cattle breeds is linked to the historical, social, cultural, and climatic features of the diverse geographical regions of Russia. In the present study, we investigated the population structure of nine Russian cattle breeds and their relations to the cattle breeds from around the world to elucidate their origin. Genotyping of single nucleotide polymorphisms (SNPs) in Bestuzhev (n = 26), Russian Black-and-White (n = 21), Kalmyk (n = 14), Kholmogor (n = 25), Kostromsky (n = 20), Red Gorbatov (n = 23), Suksun (n = 20), Yakut (n = 25), and Yaroslavl cattle breeds (n = 21) was done using the Bovine SNP50 BeadChip. SNP profiles from an additional 70 breeds were included in the analysis as references.

RESULTS

The observed heterozygosity levels were quite similar in eight of the nine studied breeds (H_O = 0.337-0.363) except for Yakut (Ho = 0.279). The inbreeding coefficients F_IS ranged from -0.028 for Kalmyk to 0.036 for Russian Black-and-White and were comparable to those of the European breeds. The nine studied Russian breeds exhibited taurine ancestry along the C1 axis of the multidimensional scaling (MDS)-plot, but Yakut was clearly separated from the European taurine breeds on the C2 axis. Neighbor-Net and admixture analyses, discriminated three groups among the studied Russian breeds. Yakut and Kalmyk were assigned to a separate group because of their Turano-Mongolian origin. Russian Black-and-White, Kostromsky and Suksun showed transboundary European ancestry, which originated from the Holstein, Brown Swiss, and Danish Red breeds, respectively. The lowest level of introgression of transboundary breeds was recorded for the Kholmogor, Yaroslavl, Red Gorbatov and Bestuzhev breeds, which can be considered as an authentic genetic resource.

CONCLUSIONS

Whole-genome SNP analysis revealed that Russian native and locally developed breeds have conserved authentic genetic patterns in spite of the considerable influence of Eurasian taurine cattle. In this paper, we provide fundamental genomic information that will contribute to the development of more accurate breed conservation programs and genetic improvement strategies.