This article attempts to evaluate the present status and distribution of the ruminant genetic resources of Karnataka state vis-a-vis the exotic/crossbred and non-descript animals. The characteristics of the breeds of the ruminant species of the Karnataka state, including the new populations and breeds recently identified in the state like Dharwari and South Kanara buffaloes, Mouli and Yalga sheep and Nandidurga and Bidri goats, are also discussed. The total population of ruminant livestock, comprising cattle, buffalo, sheep and goat in Karnataka is 28.673 million. The density of 149.50 ruminants per km2 in this state is only marginally less than the national average of 160.15. However, the density of sheep at 57.62 per km2 is two and a half times than the national figure of 22.59. During 20012-2019, the total cattle and buffalo population have registered a decline of 11.01 and 14.00%, whereas, the sheep and goat population has shown an increase of 15.31 and 28.31%. During 2007-2012, periods for which the breed-wise data is available, the population of pure indigenous cattle, buffalo, sheep and goat have dwindled by 37.71, 32.93, 27.86 and 69.00%, compared to only -9.39, -19.79, 0.26 and -22.05% change in the total population of these species, respectively. Serious conservation efforts are required to arrest this decline in the ruminant genetic resources of the state of Karnataka.

The grey type donkeys of Braj region of Uttar Pradesh in India were genetically characterized using ten heterologous microsatellite loci. At these loci the PCR product size ranged from 75-95 bp at locus HTG6 to 251-277 bp at locus COR18. The observed number of alleles varied from 4 (HTG15) to 10 (HTG7 and AHT4) with a mean of 7.50 ± 1.96. The observed heterozygosity ranged from 0.46 (HTG6 and NVHEQ54) to 0.79 (COR18) with a mean of 0.66 ± 0.12. The mean genetic diversity estimate (FIS) was 0.157. When these donkeys were compared on the basis of allelic frequency data at these loci to the brown type donkeys of Ladakh, Spiti and Rayalseema regions in the union territories/states of Ladakh, Himachal Pradesh and Andhra Pradesh, respectively, they clustered independently from these three donkey populations in a dendrogram based on Goldstein's average square distances indicating their genetic distinctness.

The present status of goat population and production in India were analysed to decipher the trends in their geographic and demographic distribution across the country. India with 148.88 million goats holds the largest population of goats in the world. It is predicted that the overall population of goats will increase to 162.32 million in 2031. Only four states viz., Rajasthan, West Bengal, Uttar Pradesh and Bihar hold the 43.27% of the total goat population of the country. The region comprising three districts of Dinajpur Uttar, Dinajpur Dakshin and Maldah in North-central West Bengal has the highest density of 314.6 goats per Km2. Barmer district in Rajasthan has the highest population (2.947 million) of goats followed by Murshidabad in West Bengal (1.751 million), Jodhpur (1.641 million) in Rajasthan and Maldah (1.376 million) in West Bengal. In terms of population density per Km2, West Bengal has the highest density of goats (183.4.0/Km2) followed by Bihar (136.2/Km2), Jharkhand (114.4/Km2) and Tamil Nadu (76.0/Km2). The increasing trend observed in the states like West Bengal and Bihar that already have very high density of goat population may increase the pressure on already overgrazed and shrinking pastures. Contrarily, in the states like Himachal Pradesh, Arunachal Pradesh, Uttrakhand, Most North Eastern states and union territories of Jammu-Kashmir and Ladakh, that have comparatively larger forest areas/pastures available but comparatively lower goat density, popularizing the goat rearing especially among the weaker sections can be explored. During 2018–19 goats contributed 1.098 and 6.099 million tonnes of meat and milk, respectively. Black Bengal breed has the largest population (17.409 million) followed by Marwari (5.348 million), Osmanabadi (2.481 million) and Barbari (2.194 million). Although, the overall population of goats has decreased by 3.82% during 2007–12, the population of registered breeds has decreased more than five times as fast (21.7%) during this period. Therefore, serious conservation and improvement efforts are required to arrest decline in population and enhance productivity of the descript breeds of goats.

The objective of this study was to assess the genetic variability present across the Class II MHC DRB 3.2 gene locus in the Sangamneri goat breed of India. Sixty three single nucleotide variations were observed in CLA-DRB3.2 gene of eleven Sangamneri animals. Sixteen haplotypes with Haplotype diversity of 0.974 were found. Besides the snp(s) having two alleles, both triple and tetra allelic single nucleotide variations were present. Thus, the Class II DRB 3.2 gene of the Sangamneri goat breed animals (CLA-DRB3.2/ Cahi DRB3.2) was exhibiting a very high degree of genetic polymorphism. Of the sixty three single nucleotide variations, fifty variations were non-synonymous i.e. they resulted in a change in the corresponding amino acid encoded by the triplet codon in which they were existing. Both conservative and non-conservative amino acid changes were observed to occur. Rich diversity of the DRB3.2 gene reflected well on the ability of the Sangamneri animals to survive in the harsh climatic condition(s), exposed to all kinds of pathogen(s) existing in the environment.

Ability of a set of 24 microsatellite markers for individual identification and their potential for breed assignment of individuals was evaluated in 2 Indian pig populations. The cumulative probabilities of identity of 2 random individuals within a population, even with selected set of 5 loci (CGA, S0026, S0228, S0355, SW936) were 2.87×10–8 (Assamese) and 9.66×10–8 (Anakamali) and from 2 different population was 1.13×10–12. However, the population assignment precision even with all the 24 loci was only 80 (Assamese) and 88% (Ankamali). These results suggested that although this set of markers can be safely employed for identification of individuals but their utility for breed allocation in Indian pigs needs further authentication before they can be practically used for such purposes.

Ability of the microsatellite markers for individual identification and their potential for breed assignment of individuals was evaluated in three Indian donkey populations. The probability of identity of two random individuals within a population (G1), taking into consideration all eleven loci was 5.91×10–13, 1.06×10–12 and 3.67×10–14 in Ladakhi, Spiti and Andhra-brown donkeys, respectively. Similarly, the probability of identity of two random individuals from two different populations (G2) between Spiti and Ladakhi donkeys, the two most closely related populations, was only 8.05×10–21 . However, the population assignment precision using this set of 11 loci, the correct assignments ranged between 73.08 (Andhra-brown) to 96% (Ladakhi) with frequency method and between 88.46 (Andhra-brown) to 100% (Ladakhi) with Baysian approach. These results suggest that this set of markers can be a promising tool for identification of individuals and their products. Although G2 values were higher than the G1 values but when this set was specifically evaluated for breed allocation purposes, our results indicated that it may require further substantiation before this set can be safely employed for breed/population allocation of individuals in Indian donkey populations.

In India, the indigenous pigs are traditionally reared either by the poor, weaker and the tribal sections of the society. Although, the growth rates and feed conversion ratio of indigenous pigs are less than those of exotic or crossbred pigs, they have unique features like heat tolerance, disease resistance, early sexual maturity and ability to produce meat with less fat. In India, the total population of indigenous pigs is 78.35 lakhs constituting 76.14% of the total pig population of the country. Uttar Pradesh has the largest population of indigenous pigs (11.52 lakhs), followed by Assam (10.22 lakhs), Jharkhand (9.21 lakhs) and Bihar (6.26 lakhs). In studies conducted at various centres of All India Coordinated Research Project on pigs, the weight of these pigs at birth, weaning (8 weeks) and 32 weeks of age ranged from 0.44±0.01 to 0.83±0.01, 7.00±0.36 to 8.12±0.18 and 31.32±0.45 to 42.91±1.04 kg, respectively. Although, the indigenous pigs were largely clubbed as local or non-descript but in the last few years many population have been characterized. Some of them have been registered by ICAR-NBAGR as new breeds of indigenous pigs, like Ghoongroo, Niang Megha, Agondagoan, Tenyi Vo, Nicobari, Doom, Zovawk and Gurrah pigs. This review discusses the population trend, attributes and available breeds of indigenous pigs of India.

In India, the yaks are reared by the people residing between 3,000 and 5,000 meters above mean sea level in the states of Jammu-Kashmir, Himachal Pradesh, Uttrakhand, Sikkim, Arunachal Pradesh and West Bengal. Yaks thrive well in these extremely cold regions with hypoxic conditions providing milk, meat, hide, fibre, manure and draught power to the local population. They are able to withstand the fodder scarcity endemic to these regions in the winter months. The total yak population in our country is 0.76 lakhs. Jammu and Kashmir has the maximum population of yak (0.54 lakh), possessing about 71% of the total yak population of the country, followed by Arunachal Pradesh (18.34%) and Sikkim (5.26%). The milk yield per lactation in indigenous yaks is 250–500 kg in a lactation period of 260–300 days. The birth weight of indigenous yaks in males and females is 14.20±0.33 and 13.20±0.34 kg, which increases to 201.23±4.79 and 178.13±3.26 kg, respectively, at 2 years of age. Mainly, four types of Indian yaks have been described namely Arunachali, Ladakhi, Sikkimi and Himachali. Out of these, Arunachali yaks are the first and only recognized breed of Indian yaks. This review summarizes the population trends, attributes of indigenous yaks in general as well of specific types of indigenous yaks available in India.

The donkeys of Ladakh region of Jammu and Kashmir, are well adapted to the cold, arid and hypoxic conditions of this region. The genomic DNA, isolated from 25 blood samples collected from these donkeys, were amplified by PCR using FAM and HEX labeled primers and resolved for alleles on automatic DNA sequencer. Total 20 loci of the horse origin were tested and only 13 loci gave scorable results. Rest of the loci either did not amplify well (HMS3, HMS7, ASB17 and COR22) or showed less than four alleles (HMS5, HMS6, HTG4), in the studied population. At the 13 loci included in the final analysis, the PCR product size ranged from 79–85 bp at locus HTG6 to 257–275 bp at locus COR18. The observed number of alleles varied from 4 (HTG15, HTG6, HTG10 and VHL20) to 9 (HTG7 and COR71) with a mean of 5.92±1.80. The observed heterozygosity ranged from 0.44 (VHL209) to 0.90 (AHT5) with a mean of 0.76±0.13. The mean genetic diversity estimate (FIS) was –0.076. The cumulative exclusion probability (PE) of these loci was 0.999838 indicating their suitability for parentage testing in these donkeys. The sign test, standardized differences test, the Wilcoxon test using the allelic frequency data under two phased mutation model and sequential mutation model at the studied loci as well as normal ‘L’ shaped distribution of the allelic frequency indicated the absence of any recent genetic bottleneck in donkeys of Ladakh region. When these donkeys were compared to Spiti donkeys of Himachal Pradesh and Brown type donkeys of Andhra Pradesh on the basis of allelic frequency data at these loci, they showed Nei’s minimum genetic distances of 0.115 and 0.165, respectively, from these population.

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The Spiti donkeys distributed in Spiti and Yangthang regions of Himachal Pradesh were characterized for morphometric characteristics, management practices and utility. They were also evaluated for genetic diversity and bottlenecks using microsatellite markers. Spiti donkeys remain comparatively smaller in size with compact bodies usually covered with a thick coat of long hairs. The height at withers of male and female Spiti donkeys was 88.59±3.27 and 88.65±3.30 cm, respectively. The genomic DNA isolated from the blood samples collected from the 46 animals of this breed was amplified by PCR and resolved for alleles on automated DNA sequencer. The observed number of alleles ranged from 4 (VHL20, HTG6) to 10 (HTG7), with a mean of 6.33±1.72 alleles per locus. The observed heterozygosity ranged from 0.48 (NVHEQ54) to 0.89 (HTG7), with a mean value of 0.72±0.13. The mean FIS was 0.048 indicating moderate level of inbreeding. The normal 'L' shaped distribution of allelic frequency indicated towards absence of any recent genetic bottlenecks in the Spiti donkeys.

A set of 24 FAO recommended microsatellite markers was evaluated for parentage exclusion (PE) in three Indian pig types of Assamese, North-Indian and Ankamali. The genomic DNA from these three Indian pig types was amplified at these loci by polymerase chain reaction and resolved for alleles. The allelic frequency data was analysed to calculate the probability of paternity exclusion when one of the parents is to be excluded (PE1), when both the parents are to be excluded (PE2) and when only one parent is known and that is to be excluded (PE3) in these three Indian pig types using a set of minimum 5 loci and then increasing the number of loci in increments of 5 upto maximum of 24 loci. The cumulative PE1 values taking into consideration all the 24 loci varied from 1-2.07×10-10 in North Indian pigs to 1-3.95×10-11 in Ankamali pigs. The cumulative PE2 values taking into consideration all the 24 loci varied from 1-4.57×10-16 in Assamese pigs to 1-3.17×10-18 in Ankamali pigs. Similarly, cumulative PE3 values for all the 24 loci varied from 0.9999968 in Assamese pigs to 0.99999955 in Ankamali pigs. The cumulative PE values obtained, even with a set of 15 loci (CGA, IGF1, S0005, S0026, S0068, S0090, S0155, S0178, S0215, S0218, S0228, S0355, SW122, SW911, SW936), were clearly more than the required value of 0.9995 in all the three breeds with the minimum value of 0.99985 for PE3 in Assamese pigs. Clearly, this set of 15 loci or the sets with 20 or 24 loci can be safely employed for parentage exclusion purposes in the Indian pigs.

Toll-like receptor 9 protein, located in the endosomal compartment, is a nucleotide-sensing Toll-like receptor (TLR). It is activated by unmethylated cytidine-phosphate-guanosine dinucleotides (CpG ODN) in both viruses and bacteria, and is encoded by Toll-like receptor 9 gene, which was sequenced and characterized in the Bos indicus Sahiwal cattle breed. Eleven single nucleotide polymorphisms (SNPs) were detected within the 4.8 Kb region of the TLR9 gene. Eight of the SNPs were present in the coding region of the gene and the other 3 were present in the non-coding part of the gene. The SNP 2930(G>A) was non-synonymous leading to an amino acid change of G437E in the TLR9 protein. The other SNPs were synonymous. These SNPs led to generation of 11 most probable TLR9 gene haplotypes. The gene exhibited a nonsignificant value of Tajima's D which indicated it to be following the neutral mutation hypothesis.

The brown type donkeys of Andhra Pradesh, which are mainly concentrated in Kurnool and Anathapur districts, were evaluated for within breed genetic diversity and bottlenecks using heterologous microsatellite markers. The genomic DNA, isolated from 28 blood samples collected from Kurnool district, were amplified by PCR using FAM and HEX labeled primers and resolved for alleles on automatic DNA sequencer. In all, twenty loci of the horse origin were tested and only 12 loci gave scorable results. Rest of the loci either did not amplify (HMS3 and HMS7) or did not resolve properly (VHL20) or showed less than 4 alleles (HMS5, HMS6, HTG4, ASB17 and COR22) in the studied population. At the 12 loci included in the final analysis, the PCR product size range varied from 76-92 bp at locus HTG6 to 257-273 bp at locus COR18. The observed number of alleles varied from 4 (VHL209) to 10 (AHT5 and HTG7) with a mean of 6.92±1.83. The effective number of alleles ranged from 1.62 (VHL209) to 7.91 (AHT5) with a mean of 4.21±2.06. The observed heterozygosity ranged from 0.32 (HMS2) to 0.92 (AHT5) with a mean of 0.57±0.2. The expected heterozygosity ranged between 0.39 (VHL209) to 0.89 (AHT5 and HTG7) with a mean of 0.72±0.14. The mean genetic diversity estimate (FIS) was 0.21 indicating moderately high levels of inbreeding. The cumulative exclusion probability (PE) of these loci was 0.999892 indicating their suitability for parentage testing in these donkeys. The sign test, standardized differences test, the Wilcoxon test using the allelic frequency data at the studied loci as well as normal 'L' shaped distribution of the allelic frequency indicated the absence of any recent genetic bottleneck in Brown type donkeys of Andhra Pradesh. When these donkeys were compared to Spiti donkeys of Himachal Pradesh on the basis of allelic frequency data at these loci, they showed Nei's standard and unbiased genetic distances of 0.32 and 0.29, respectively.

Sangamneri, Osmanabadi, Berari and Konkan Kanyal are the known breeds of Maharashtra state of India. DNA from 50 unrelated goats of each breed was analysed to know the genetic diversity using 25 microsatellite markers. A total of 479 alleles (192 in Sangamneri, 153 in Osmanabadi, 294 in Berari and 255 in Konkan-Kanyal) were observed. Mean number of alleles per locus and observed heterozygosity were 7.68, 6.12, 11.76, 10.20 and 0.53, 0.42, 0.67 and 0.58 for Sangamneri, Osmanabadi, Berari and Kanyal goat populations respectively. The fixation coefficients of sub-populations within the total population (F-ST), varied from 0.04 (OarHH64) to 0.68 (OarJMP29) with a mean of 0.17. The L-shaped mode-shift curve indicated the absence of reduction in effective population size. The genetic distances between four breeds indicated the distinctness of Berari and Konkan Kanyal from Sangamneri and Osmanabadi. Berari and Konkan Kanyal although exists at different geographic locations but show some genetic overlapping. The Nei's genetic distance observed between breeds were 0.472 (Sangamneri and Osmanabadi), 0.667 (Sangamneri and Berari), 0.819 (Sangamneri and Konkan Kanyal), 0.797 (Osmanabadi and Berari), 0.994 (Osmanabadi and Konkan Kanyal) and 0.092 (Berari and Konkan Kanyal). Konkan Kanyal is genetically more distant from Osmanabadi and Sangamneri than Berari. Sangamneri and Osmanabadi goat breeds were assigned to cluster-3 where the proportion of membership for each breed was 0.975 (Sangamneri) and 0.992 (Osmanabadi). Kanyal and Berari goat populations were assigned to another cluster (Cluster 4). The proportion for their membership was 0.923 (Konkan Kanyal) and 0.869 (Berari).

The present study was undertaken to characterize the genetic variation present in lymphoxin A gene (LTA gene) encoding for the lymphotoxin A protein also known as tumor necrosis factor beta, a cytokine produced by lymphocytes, known to be cytotoxic for a wide range of tumor cells both in vitro and in vivo, and, which is essential for normal immunological development; in 40 animals of 5 diverse Bos indicus Indian zebu cattle breeds. These breeds survive under the harsh and tough tropical climatic conditions of various parts of the Indian subcontinent. The LTA gene in the present study was observed to contain 33 SNPs and 3 small insertion/deletion polymorphisms. Four SNPs occurred in the coding regions of the gene viz. g.1327A>G and g.1400C>T in exon 2 and g.1840C>T and g.1942C>T in exon 3, of which the SNP g.1327A>G in exon 2 resulted in a non-synonymous amino acid change G38D. This amino acid change was however predicted not be affecting the protein function in any manner. The gene contained putative transcription factor binding sites for the c-Re1 and for Pax-4 transcription factors. A putative promoter region was also predicted on the reverse DNA strand from position 894 to 644. Several repeat elements and microsatellite repeats were detected to be occurring across the 3.2kb LTA gene sequence. The study showed the occurrence of 40 genotypes and 48 most probable haplotypes. The genotypes at the observed SNP positions in the LTA gene were in near Hardy-Weinberg equilibrium. A negative Tajima's D value that was not significant statistically at P>0.10 indicated that the neutral mutation hypothesis could not be excluded. The genetic variations observed in the LTA gene in the present study have not been reported earlier and these could possibly be used as molecular markers for further studies involving association of the gene variability with disease resistance/tolerance traits.

Toll-like receptor 4 gene (TLR4) that recognizes the Gram negative bacterial ligand LPS was sequenced in the Bos indicus Sahiwal cattle breed. Ninety four single nucleotide polymorphisms (SNPs) were detected within 10.8kb gene region. Seventeen of the SNPs were in the coding regions and the one at position 9589(A>G) in exon3 resulted in an amino acid change from Valine to Isoleucine. These SNPs led to generation of 27 TLR4 gene haplotypes. All the Sahiwal animals studied presently showed the occurrence of the genotype CC at gene position 9662, which codes for the amino acid threonine at position 674 of the TLR4 protein, and which had been reported to be associated with lower somatic cell score and, therefore, a lower susceptibility to mastitis, in Taurus cattle. This nucleotide configuration of the Toll-like receptor 4 gene of the Bos indicus Sahiwal cattle breed could possibly indicate toward a lower susceptibility to mastitis in the Sahiwal animals. Monocyte chemo-attractant protein-1 (CCL2) gene encoding for small inducible cytokine A2 that belongs to the CC chemokine family was also sequence characterized in these Sahiwal animals. The CCL2 gene was observed to have 12 polymorphic sites in 3.3kb region of which one SNP at position 2500 (A>G) in exon 3 resulted in amino acid change from Valine to Isoleucine at position 46 of the mature CCL2 peptide. Seventeen haplotypes of the CCL2 gene were predicted corresponding to 12 genotypes detected.

The promoter region of hsp70 gene was characterized for cis-acting elements in zebu cattle of Hariana breed. The basal regulatory domain of CAAT box identified as CAAT/enhancer binding protein (C/EBP) and CAAT binding transcription factor (CTF) binding sites, as well as GC box identified as sp1 binding site, were localized in at least two regions in the hsp70 gene promoter. A highly conserved heat shock element was found between position -108 to -95, which exactly matched at all eight positions with the consensus sequence. These cis-acting elements were found to be conserved between Holstein-Friesian and studied zebu breed.

Productivity in dairy cattle and buffaloes depends on the genetic factors governing the production of milk and milk constituents as well as genetic factors controlling disease resistance or susceptibility. The immune system is the adaptive defense system that has evolved in vertebrates to protect them from invading pathogens and also carcinomas. It is remarkable in the sense that it is able to generate an enormous variety of cells and biomolecules which interact with each other in numerous ways to form a complex network that helps to recognize, counteract, and eliminate the apparently limitless number of foreign invading pathogens/molecules. The major histocompatibility complex which is found to occur in all mammalian species plays a central role in the development of the immune system. It is an important candidate gene involved in susceptibility/resistance to various diseases. It is associated with intercellular recognition and with self/nonself discrimination. It plays major role in determining whether transplanted tissue will be accepted as self or rejected as foreign.