Nilagiri Sheep Research Articles

Clustering of Dam’s Body Weight Based on Birth Weight of Lambs in Nilagiri Sheep

The population of Nilagiri breed of Sheep is threatened and required micro breeding strategy for conservation and genetic improvement. Data on 4,619 Nilagiri lambs born during the 28 years (1993-2021) at the Sheep Breeding Research Station (SBRS), Sandynallah of the Nilgiris district, Tamil Nadu, India were utilized for this investigation. Data on birth weight of lamb along with dam’s body weight at the time of lambing were collected. Relationship between different body weights of dam was investigated in terms of lamb’s birth weight using one-way ANOVA followed by post hoc test for different dam body weight pairwise comparison. Heatmap was drawn for P values between different dam’s body weights aiding in visualization of the possible compatibility between body weights of dam. The birth weight of lambs positively correlated with that of dam’s body weight. Heat map visual analysis revealed five different clusters viz. less than 23.00 kg, 23.01-26.00 kg, 26.01-29.00 kg, 29.01-32.00 kg and greater than 32.01 kg sets of patterns. This was the first study in sheep breed for applying heatmap tool for growth trait analysis.

Effects of inbreeding on reproduction and fitness traits in a closed flock of Nilagiri sheep, an endangered Indian breed

The objective of this study was to investigate the effect of inbreeding on reproductive and fitness traits in Nilagiri sheep. Information on pedigree of 6430 animals collected during the year of 1965–2015 by Sheep Breeding Research Station (SBRS) in Sandynallah were used for analysis. Inbreeding coefficient (F) was calculated from pedigree information using Wright’s method. The average inbreeding per cent was 1.82% in the whole population studies (6430 animals). The average inbreeding per cent was 3.9% for 3007 no. of inbred animals. The effect of inbreeding on most of the reproduction and fitness traits were significant and depression due to inbreeding was evident.The significant effect of inbreeding on reproduction traits viz., age at first service (AFS), weight at first service (WFS), age at first lambing (AFL) and fitness traits viz., tupping percent (TP), number of lambs weaned per ewe mated (NLWEM), number of lambs weaned per ewe lambing (NLWEL) and total lambs weaned per ewe over lifetime (TLWE) was studied using a general linear model, with individual inbreeding coefficient as covariate. The partial regression coefficient for AFC, WFS, AFL, TP, NLWEM, NLWEL and TLWE were 1.28 days, −0.25 kg, 8.13 days, −0.02%, −0.028, −0.017 and −0.182 per 1 per cent increase in inbreeding for Nilagiri sheep. Survival and litter size were not affected by inbreeding. In general, inbreeding had a depressive effect on most of the reproduction and fitness traits. Inbreeding in the population has to be restricted through methods such as introduction of unrelated animals or following co-ancestry based mating system.

Effect of Booroola fecundity (FeCB) gene on litter size and scope for use in restoration of Nilagiri sheep from threatened status

Effect of Booroola fecundity (FeCB) gene on litter size and scope for use in restoration of Nilagiri sheep from threatened status

Polymorphism of Keratin - Associated Protein (KAP) 6.1 gene and its association with wool traits of Sandyno and Nilagiri breeds of sheep

Polymorphic variants of keratin-associated protein (KAP) 6.1 gene with wool traits of Sandyno and Nilagiri breeds of sheep were investigated in this study. Genomic DNA was isolated from blood samples of 125 Sandyno, Nilagiri and Dorset x Nilagiri breeds of sheep along with 76 numbers of wool samples. A 528 bp segment was amplified by PCR using ovine specific primers for KAP 6.1 gene. SSCP analysis of KAP 6.1 gene in Dorset x Nilagiri crossbred sheep resulted in two genotypes for the A/B with no polymorphism. KAP 6.1 gene locus revealed allele frequencies of A, B, C, D and E in Sandyno sheep were 0.67, 0.23, 0.04, 0.01 and 0.04 and in Nilagiri were 0.75, 0.06, 0.11, 0.04 and 0.04 respectively. KAP 6.1 gene revealed departure from Hardy-Weinberg equilibrium. KAP 6.1 genes were found to have high degree of homozygosity (0.6667) in Nilagiri sheep. The effective number of alleles (Ne) for KAP 6.1 gene was 1.1690 and 1.7006 respectively in Sandyno and Nilagiri breeds of sheep. The PIC values for KAP 6.1 gene was 0.1341 and 0.3909 in Sandyno and Nilagiri breeds of sheep respectively. FIS values for KAP 6.1 gene was positive (0.1909) in Nilagiri breed and it was negative (– 0.0110) in Sandyno breed. Least squares analysis of variance showed significant (P less than 0.05) effect between genotypes and between sexes for wool traits like GFW (kg), CWY (%) and FD (µ). Significant (P less than 0.05) effect of breed (Sandyno and Nilagiri) was observed for all the wool traits (GFW, CWY, FD, SL and Medullation %). Significant (p less than 0.05) higher CWY production was recorded for AC genotype (62.00 ± 1.73 %) while low value was recorded for BB genotype (56.25 ± 1.74 %). FD was found to be high in genotype AC (24.29 ± 1.17 µ) than in AA genotype (23.24 ± 0.49 µ). The homozygote AA was found to have more Medullation (%) and SL. Genotypes BB had higher GFW and lower CWY. The heterozygous genotype AC yielded more FD and CWY with lower most Medullation (%) and SL values. From the study, it may be concluded that KAP 6.1 gene might be a potential molecular marker for genetic selection of wool traits in Sandyno and Nilagiri breeds of sheep.

Novel report on mutation in exon 3 of myostatin (MSTN) gene in Nilagiri sheep: an endangered breed of South India.

The variability in breeding program leads to rapid loss of genetic potential for which National Bureau of Animal Genetic Resources is emphasized to conserve the indigenous breeds. The variation in myostatin (MSTN) gene and its association with growth traits will throw light on its potential use as marker in selection. Hence, the study was conducted to detect polymorphism in exon 3 of MSTN, one of the most important growth regulatory gene and its association with growth in Nilagiri sheep breed. Blood samples were collected from Nilagiri sheep (n = 103) of South India and growth data up to 1year of age was recorded. Genomic DNA was isolated and amplified for part of MSTN gene; PCR products were genotyped by restriction digestion (MspI) and confirmed by sequencing. Restriction digestion has revealed a single nucleotide polymorphism at locus G5622C in exon 3 which was confirmed by sequencing. The wild-type DNA molecule (MM) cleaved by MspI produced 301-bp and 314-bp fragments and those with mutation (mm) would remain undigested. The genotypic frequencies were MM (0.689) and Mm (0.311) with complete absence of mm genotype; and allelic frequencies were M (0.8445) and m (0.1555). The locus was in Hardy-Weinberg equilibrium. The association analysis revealed that there was no significant difference in mean birth, weaning, 6-, 9-, and 12-month weight between MM and Mm genotypes at g.5622G>C locus of exon 3 of MSTN gene. This is the first report of mutation in exon 3 of MSTN gene. The non-significant effect and absence of mm genotype at this locus needs further studies based on large population size and haplotype analysis.

Polymorphism of growth hormone receptor (GHR) gene in Nilagiri sheep.

The allelic variation in the regulatory sequence of growth hormone receptor (GHR) gene influences the growth traits of sheep. A study was carried out to find out the polymorphisms associated with exon 10 of GHR gene and its association with growth traits of Nilagiri sheep. The blood samples were collected from Nilagiri sheep (n = 103) reared at Sheep Breeding Research Station, Sandynallah, Tamil Nadu, India. DNA was isolated using the phenol-chloroform extraction procedure and eight samples having amplified product of part of exon 10 (895bp) sequenced. The results indicated transitions of nucleotide G>A at loci G177624A and G177878A. The genotyping frequencies estimated using the tetra-primer amplification refractory mutation system-PCR for GG, GA and AA were 0.262, 0.544 and 0.194, and 0.349, 0.505 and 0.146, respectively. The estimated allele frequencies of G and A nucleotides were 0.5340 and 0.4660, and 0.6015 and 0.3985, respectively, at loci G177624A and G177878A. The effects of both the mutations on growth-related traits viz., birth, weaning (3months) 6, 9 and 12months weight in Nilagiri sheep were found to be non-significant. This can be a novel approach to assess growth of sheep using the mutation in GHR gene. Thus, this approach can be useful for further investigation as a molecular marker associated with genetic improvement.

Random regressions to model growth in Nilagiri sheep of South India

Random regression models (RRM) have been recognised as suitable for analysis of longitudinal data like growth. Growth in Nilagiri sheep was modeled using RRM to estimate genetic parameters and results obtained were compared with values already estimated using conventional methods A mixed RRM with contemporary group of year and season of birth, sex, litter size and age of dam at lambing, as fixed effects and direct additive, maternal genetic, maternal permanent environmental and individual permanent environmental factors, as random effect was used in different orders of fit. Age at recording of weight was included as the control variable. The RRM with fourth order for all random effects and heterogenous error variance (9 classes) was found to have the best fit. The pattern of variation over ages was similar for direct and maternal genetic variance, while maternal permanent environmental variance showed contrasting trend. Direct additive and maternal genetic variance showed a parabolic trend up to 36 months of age with maximum variance between 12 and 18 months. Phenotypic and individual permanent environmental variance showed similar increasing trend with age. The heritability estimates obtained through RRM for 3 month (3W), 6 month (6W), 9 month (9W), 12 month (12W), 18 month (18W) and 24 month (24W) body weights were 0.131, 0.240, 0.275, 0.254, 0.131 and 0.068, respectively. The values for 3W and 18W were similar to those obtained through univariate analysis, while other estimates were on the higher side. The trend of estimates over ages was similar between RRM and conventional methods Values of direct and maternal genetic correlations were positive and high. This finding of high positive genetic correlation among body weight at different ages was also evident from the trend of Eigen functions estimated from genetic (co)variance matrix. The correlation between breeding values estimated from RRM and conventional REML methods: were 0.904, 0.331, 0.774 and 0.771 for 3W, 6W, 9W and 12W, respectively. The estimates of heritability obtained were precise for ages up to 24 months and values indicate good scope for improvement through selection.

Genetic parameters for Kleiber ratio and its relation to other body weight traits in Nilagiri and Sandyno sheep

Kleiber ratio (KR) is an indicator of growth efficiency irrespective of body size. The trait was recommended as an efficient indirect selection criterion. The present study was done to estimate genetic parameters for KR and explore the possibility of its use as a selection criterion in Nilagiri and Sandyno sheep. KR for the pre-weaning (birth to 3-months) and post-weaning (3– 6, 6–9, 9–12 and 3–12 months) periods was studied. Pre-weaning KR was much higher than post-weaning KR in both the breeds. The mean pre-weaning KR for Nilagiri and Sandyno sheep was 14.37 and 14.52, respectively. All the post-weaning KR values were less than six. Animal model including or ignoring maternal effects was used to obtain REML estimates of (co)variances. The best model was chosen based on log-likelihood ratio test. Maternal effects and inbreeding were not significant for KR at any of the age intervals. Moderate estimates of heritability were obtained for pre-weaning KR in both the breeds. Among the post-weaning KR, the age interval from 3–6 months and 3–12 months showed moderate values in Nilagiri sheep. Post-weaning KR for Sandyno sheep showed negligible to low heritability estimates. The maximum heritability of 0.143 was for KR 3–6 months in Nilagiri sheep. In Nilagiri sheep, genetic correlation between pre-weaning KR and body weight traits ranged from 0.634 to 0.875. Similarly, in Sandyno sheep, the values ranged from 0.883 to 0.959. Thus pre-weaning KR could be used as a criterion for indirect selection to improve important body weight traits.

Effect of inbreeding and individual increase in inbreeding on growth in Nilagiri and Sandyno breeds of sheep

SummaryIndividual increase in inbreeding coefficients (ΔFi) has been recommended as an alternate measure of inbreeding. It can account for the differences in pedigree knowledge of individual animals and avoids overestimation due to increased number of known generations. The effect of inbreeding (F) and equivalent inbreeding (EF) calculated fromΔFi, on growth traits were studied in Nilagiri and Sandyno flocks of sheep. The study was based on data maintained at the Sheep Breeding Research Station, Sandynallah. The pedigree information and equivalent number of generations were less in Sandyno compared with Nilagiri sheep. The average F and EF for the Nilagiri population were 2.17 and 2.44, respectively and the corresponding values for Sandyno sheep were 0.83 and 0.84, respectively. The trend of inbreeding over years in both the populations indicated that EF was higher during earlier generations when pedigree information was shallow. Among the significant effects of inbreeding, the depression in growth per 1 percent increase in inbreeding ranged from 0.04 kg in weaning weight to 0.10 kg in yearling weight. In general, more traits were affected by inbreeding in Nilagiri sheep, in which greater regression of growth traits was noticed with F compared with EF. Higher values of EF than F in earlier generations in both the populations indicate that EF avoided the potential overestimation of inbreeding coefficient during recent generations. In the Sandyno population, the magnitude of depression noticed among growth traits with significant effects of inbreeding was higher. The differences in response to F and EF noticed in the two populations and possible causes for the trait wise differences in response to F and EF are appropriately discussed.

Direct and maternal components of variance for relative growth rate in Nilagiri and Sandyno sheep

A study was conducted to estimate genetic parameters of relative growth rate (RGR) and explore the possibility of its use as a selection criterion in Nilagiri and Sandyno sheep. RGR for the pre-weaning (birth to 3 months, n=6504) and post-weaning (3–6, 6–9, 9–12 and 3–12 months, n=4309, 3267, 2978 and 3257, respectively) periods were studied. The maximum RGR was noticed for the pre-weaning period and least during the latest age interval from 9 to 12 months. The ability of the trait to adjust for body size was evident from the effects of litter size, breed and age of dam on the trait. An animal model, including maternal effects was used to obtain REML estimates of (co)variances. Maternal genetic effects and inbreeding were not significant for RGR at any of the age intervals. Moderate estimates of heritability were obtained for pre-weaning RGR, with values of 0.126 and 0.103 for Nilagiri and Sandyno sheep, respectively. Among the post-weaning RGR, the age interval 3–6 months showed moderate value (0.140) in Nilagiri sheep. Post-weaning RGR for other intervals in Nilagiri and all intervals in Sandyno sheep showed negligible to low heritability estimates. The genetic correlations between pre-weaning RGR and body weight traits were high and positive in Nilagiri sheep. The estimates for the breed were found to decrease with age. Moderate heritability for pre-weaning RGR and high genetic correlation of the trait with other body weight traits provide scope for indirect selection using the trait in Nilagiri sheep. The result of the study supports the fact that RGR is able to adjust growth curve in such a way as to improve growth without affecting mature body size.

Genetic Polymorphism of Myostatin (MSTN) Gene in Sheep Breeds

Myostatin (MSTN) is one of the most important growth regulatory genes that resulted in higher growth of skeletal muscles in livestock species. So the study was undertaken to identify the polymorphism of myostatin (MSTN) gene as a genetic marker for growth traits in Madras Red, Mecheri and Nilagiri sheep breeds of Tamil Nadu. The blood samples were collected from unrelated animals of Madras Red (n = 127), Mecheri (n = 101) and Nilagiri (103) breeds of sheep from different agroclimatic regions of Tamil Nadu. Part of 5’UTR, exon 1 and part of intron 1 (797 bp) of MSTN gene was amplified with suitable primers. The amplified products were digested with the Msp I and Hae III restriction enzymes. But both the PCR-RFLP results of Msp I and Hae III was found to be monomorphic in all the three breeds of sheep indicating that the MSTN gene is highly conserved and of use in evolutionary studies.

Direct and maternal genetic components of variance for growth traits in Nilagiri and Sandyno Sheep of South India

The Nilagiri sheep is known for its prolificacy and adaptability to high altitudes of the Nilgiri hills. This breed was crossed with exotic sheep such as Rambouillet and Merino to develop a new synthetic sheep called Sandyno at Sheep Breeding Research Station, Sandynallah (Tamil Nadu). Both these breeds have been maintained as closed flocks in this station and growth data from 1992 to 2011 were utilized to estimate direct and maternal genetic (co)variance components for various growth traits viz., weight at birth (BW), 3 (3W), 6 (6W), 9 (9W), 12 (12W) and 18 (18W) months of age. An animal model including maternal effects was used to obtain restricted maximum likelihood estimates of (co)variances. The h2 values for BW, 3W, 6W, 9W, 12W and 18W were 0.140, 0.130, 0.074, 0.168, 0.129 and 0.166, respectively in Nilagiri sheep and 0.147, 0.114, 0.098, 0.141, 0.144 and 0.115 in Sandyno sheep. In Nilagiri sheep, maternal influence was significant (P<0.05) for BW, 3W, 6W and 9W and the maternal heritability values for the traits were 0.211, 0.050, 0.126 and 0.098, respectively. In Sandyno sheep, the maternal heritability values were significant (P<0.05) for BW, 3W, 6W, 9W and 18W with values of 0.285, 0.035, 0.054, 0.058 and 0.110, respectively. BW and 6W in Sandyno sheep were the only traits for which models with direct and maternal genetic correlation (σam) were significant (P<0.05). Genetic correlations among body weight traits were positive and moderate to high and ranged from 0.375 to 0.994 in Nilagiri and 0.553 to 0.952 in Sandyno sheep. Maternal effects were important with respect to growth traits in Nilagiri and Sandyno sheep. Moderate estimates of heritabilities and higher genetic correlations provide scope for further improvement in growth traits.

Screening for galway (FecXG), Inverdale (FecXI) and belclare (FecXB) mutations in BMP15 gene in Indian nilagiri sheep

Nilagiri sheep (n = 140) a prolific fine wool breed of India was screened for the presence of FecXG, FecXI and FecXB mutations in Bone Morphogenetic Protein 15 (BMP15)gene using Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) technique. The study revealed absence of these mutations in Nilagiri sheep and suggested that these mutations are not responsible for prolificacy in Nilagiri sheep.

Pedigree analysis of the Nilagiri sheep of South India

The Nilagiri sheep is a dual utility (fine wool and meat), native to the Nilagiri hills of Tamil Nadu. It is known for its adaptability to high altitude and low input system of rearing. At present, this breed is endangered with less than a thousand numbers existing, of which about 50 percent is maintained at Sheep Breeding Research Station, Sandynallah. Efforts are on to conserve the breed in-situ. Generation interval (GI), pedigree completeness level, inbreeding coefficient (F), average relatedness (AR), effective population size (Ne), and effective number of founders (fe) and ancestors (fa) were studied for the breed. Pedigree analysis was carried out using data available at the research station on 5 051 animals from 1965 onwards using ENDOG ver. 4.8. Higher values of pedigree completeness (more than 80 percent for 5th generation), balance in percent of ancestors between sire and dam pathways and higher equivalent complete generations (7.12) for the reference population were indicative of the depth in pedigree. The GI, F, and AR were 3.36 years, 2.17 and 3.45 percent, respectively. Ne based on maximum number of generations and individual increase in inbreeding was 298.83 and 97.25, respectively. fe and fa were 59 and 41, respectively, for the reference population. F was far from critical values of inbreeding and fe/fa ratio indicated absence of stringent bottlenecks. The effective population size was on the higher end of the range reported for endangered sheep breeds. The knowledge on genetic diversity and effective population size coefficients would support the cause of conservation.

Detection of Booroola (FecB) mutation in Indian sheep––Nilagiri

This study reports the status of Booroola (FecB) mutation in Indian sheep breed – Nilagiri. The discovery of FecB mutation in Nilagiri sheep will facilitate the use of FecB allele in improving the prolificacy and in conservation of this threatened breed. The Nilagiri sheep (n=145) was genotyped for the presence of FecB mutation by forced restriction fragment length polymorphism PCR technique. In the present study, FecB mutation was discovered in the Nilagiri sheep of Tamil Nadu, which is now the most prolific sheep of India after the Garole and Kendrapada. Out of 145 individuals of Nilagiri sheep, one was homozygous (BB), 38 heterozygous (B+) and 106 non-carriers (++) for the FecB mutation. The frequency of the FecB allele in this sample was 0.14. Results indicated that the frequency of the FecB mutation is moderate.

Molecular Characterisation of Nilagiri Sheep (Ovis aries) of South India Based on Microsatellites

Genetic variation in Nilagiri sheep, the only apparel wool breed in South India was studied using 25 FAO recommended ovine-specific microsatellite markers. The number of observed alleles ranged from 3 to 8 with a mean of 5 across all loci. The size of alleles ranged from 72 to 228 bp. The frequency of alleles ranged from 0.0104 to 0.5781. In total, 125 alleles were observed at the 25 loci studied. The effective number of alleles ranged from 2.18 to 6.49. The mean number of effective alleles was 3.84 across all loci. All the 25 loci were found to be highly polymorphic. The PIC values ranged from 0.4587 to 0.8277 with a mean of 0.6485. Of 25 microsatellites studied, 17 were in Hardy-Weinberg Equilibrium proportions. The observed heterozygosity ranged from 0.4222 to 1.000 with a mean value of 0.7610 whereas the expected heterozygosity ranged from 0.5415 to 0.8459 with a mean value of 0.7213. Except six loci, the other loci revealed negative within-population inbreeding estimates (F IS ) indicating excess of heterozygotes in the population ofNilagiri sheep.

Reproduction rate and viability of Merino, Nilagiri and halfbred Merino. II. Age specific replacement rate and net reproduction rate.

Age specific replacement rate, net reproduction rate and intrinsic rate of population increase were estimated from records over a period of 11 years of Merino, Nilagiri and halfbreds. On an average for every 1000 ewes mated 830 ewes lambed, 917 lambs were born, 898 lambs were weaned and 422 ewe lambs survived to joining age (one and a half years) in Nilagiri sheep. The corresponding figures were 665, 685, 590 and 228 in Merino and 664, 709, 691 and 341 in halfbreds. Nilagiri ewes in intermediate ages had more multiple births and older ewes weaned more lambs. The flock strength was not maintained unless the ewes were kept till the fifth lambing in Merino, third lambing in Nilagiri and fourth lambing in halfbred Merino. These results along with the culling levels indicated that the low reproductive efficiency in halfbreds may not be critical enough to avoid introduction of Merino for improvement in productivity. However, the poor reproductive efficiency of the Merino in this country may necessitate repeat importations of Merino rams for production of halfbreds.