Revelation of genetic diversity and genomic footprints of adaptation in Indian pig breeds

In the present study, the genetic diversity measures among four Indian domestic breeds of pig namely Agonda Goan, Ghurrah, Ghungroo, and Nicobari, of different agro-climatic regions of country were explored and compared with European commercial breeds, European wild boar and Chinese domestic breeds. The double digest restriction site-associated DNA sequencing (ddRADseq) data of Indian pigs (102) and Landrace (10 animals) were generated and whole genome sequencing data of exotic pigs (60 animals) from public data repository were used in the study. The principal component analysis (PCA), admixture analysis and phylogenetic analysis revealed that Indian breeds were closer in ancestry to Chinese breeds than European breeds. European breeds exhibited highest genetic diversity measures among all the considered breeds. Among Indian breeds, Agonda Goan and Ghurrah were found to be more genetically diverse than Nicobari and Ghungroo. The selection signature regions in Indian pigs were explored using iHS and XP-EHH, and during iHS analysis, it was observed that genes related to growth, reproduction, health, meat quality, sensory perception and behavior were found to be under selection pressure in Indian pig breeds. Strong selection signatures were recorded in 24.25-25.25 Mb region of SSC18, 123.25-124 Mb region of SSC15 and 118.75-119.5 Mb region of SSC2 in most of the Indian breeds upon pairwise comparison with European commercial breeds using XP-EHH. These regions were harboring some important genes such as EPHA4 for thermotolerance, TAS2R16, FEZF1, CADPS2 and PTPRZ1 for adaptability to scavenging system of rearing, TRIM36 and PGGT1B for disease resistance and CCDC112, PIAS1, FEM1B and ITGA11 for reproduction.

Impact of bioclimatic factors on physio-biochemical and molecular response of slow-growing poultry reared in tropics

Most of the climatic studies projected on heat stress have considered heat extremes, but not the humidity. Hence, this work was carried out to evaluate thermotolerance, production performance, physio-biochemical and immunological response of slow-growing poultry towards various temperature-humidity levels in coastal climate. A total of 240 straight run CARI-Debendra birds were reared in three groups based on temperature-humidity indices (THI > 80, = 75-80 and < 75). Significant difference (P < 0.01) in rectal and body surface temperatures was observed among treatment groups. Lowest body weight was observed in THI > 80 group as 1.45 kg at 12 weeks. There was no significant difference in feed intake and FCR; however, total water intake had increased in heat-stressed group. Birds under THI > 80 group had significantly low gizzard weight only at the 12th week compared to other groups. Significant differences (P < 0.05) in relative weight and length of intestine were noticed which was comparable between seasonal control and THI > 80 group but lower than THI < 75 group at the 6th week. However, at the 12th week, intestinal weight varied among the groups (P = 0.08), but intestinal size did not differ. Among immune organs, significant difference (P < 0.05) was noted only in weight of thymus. Except Cl^-, other biochemical indices such as cholesterol, lactate dehydrogenase, creatinine kinase, K⁺ and Na⁺ did not differ among treatment groups. Relative expression of HSP70 gene was differed significantly (P < 0.01) in the liver, intestine and breast muscles under different THI. The changes reported in seasonal control group during month of October to December revealed better thermotolerance capacity and adaptability of CARI-Debendra birds to coastal hot-humid climate. However, response of this breed to heat stress (THI > 80) reported decrease in growth, immune response and mineral balance attributable to heat loss efficacy in high humidity.

Assessment of diagnostic accuracy and effectiveness of trans-abdominal real-time ultrasound imaging for pregnancy diagnosis in breeding sows under intensive management

Early and accurate determination of pregnancy is critical to optimum reproductive performance in pigs and enables farmers to early rebreed or cull non-pregnant animals. Most of the conventional diagnostic methods are unsuitable for systematic application under practical conditions. The advent of real-time ultrasonography has made it possible to establish relatively more reliable pregnancy diagnosis. The present study was carried out to evaluate the diagnostic accuracy and effectiveness of trans-abdominal real-time ultrasound (RTU) imaging vis-à-vis pregnancy status in sows reared under intensive management. Trans-abdominal ultrasonographic examinations were performed using a mechanical sector array transducer and portable ultrasound system in crossbred sows from 20 days post-insemination for up to next 40 days. Animals were followed up for subsequent reproductive performance with farrowing data used as the definitive test for deriving predictive values. Accuracy for diagnosis was determined by diagnostic accuracy measures like sensitivity, specificity, predictive values, and likelihood ratios. Before 30 days of breeding, RTU imaging had 84.21% sensitivity and 75% specificity. Relatively higher false diagnosis rates were obtained in animals checked at or before 55 days after AI than in animals checked after 55 days (21.73% versus 9.09%). Negative pregnancy rate was low with 29.16% (7/24) false positives. Overall sensitivity and specificity, using farrowing history as the gold standard, were 94.74% and 70.83% respectively. The sensitivity of testing tended to be slightly lower in sows with litter size of less than 8 total born piglets, compared to sows with 8 or more piglets. Overall positive likelihood ratio was 3.25 while negative likelihood ratio was 0.07. The results indicate that pregnancy in swine herds can be reliably detected earlier in gestation by 30 days post-insemination using trans-abdominal RTU imaging. This non-invasive technique with portable imaging system can be used as an integral part of reproductive monitoring and sound management practices for profitable swine production systems.

Genetic evaluation of growth and reproductive performances of crossbred pigs reared under intensive system in tropical humid coastal climate

Pig farming is one of the most economically viable options for the rural backward and resource-poor farmers in Asian countries. Growth rate and litter size are the most important traits based on which the crossbreeding programs are typically planned in commercial pig farming. The modern system of farming with high yielding improved pig germplasm helps in economic growth in piggery enterprises. The present study was undertaken to evaluate the influence of various genetic and non-genetic factors on growth and reproductive performances of 75% crossbred progenies of Large White Yorkshire and indigenous Agonda Goan pigs. Body weights were recorded at birth, weaning, and at monthly intervals up to 10 months of age. Reproductive performances were also recorded for litter size and weights at birth and weaning stages, age at first farrowing, number of services per conception, farrowing interval, and pre-weaning mortality. The general linear model was used to estimate overall least square means of body weights at different ages considering the effects of different factors at certain levels viz., generation (i = first, second, third, fourth), sex (j = male, female), litter size at birth (k = 1-3, 4-6, 7-9, ≥10), parity (l = 1, 2, ≥3), season (m = summer, rainy, spring), and period of birth (n = 2012-2015, 2016-2019). The heritability and genetic correlations for different traits were estimated by restricted maximum likelihood (REML) method using WOMBAT software. The re(production) parameters were analyzed to assess the genetic improvement in successive generations. There was significant difference (p < 0.01) in body weights among different generations where animals belonging to latest generation showed maximum body weights indicating ideal selective breeding in the herd. Other fixed effects also had significant effects on growth performance which clearly signifies to the crucial influence of rearing environment and animal factors like parity of dams as well as litter size at birth. The overall birth weight, weaning weight, and weight at 10 months of age were 1.00 ± 0.01 kg, 7.57 ± 0.07 kg, and 81.58 ± 1.96 kg, respectively. Nevertheless, weaning weight and weight at marketing age (8 months) were 8.04 ± 0.27 kg and 75.48 ± 1.40 kg, respectively, in fourth generation, indicating higher post-weaning growth rate of 337.20 g/day. During this fourth generation, mean litter size at birth was 8.35 ± 0.43 and litter size at weaning was 7.79 ± 0.39 with lowest percentage of pre-weaning mortality (4.11 ± 1.51). The average age at first farrowing and farrowing interval was 293 ± 17.24 and 195 ± 4.78 days, respectively. There was apparently greater genetic gain in each generation except for the second generation which might be due to the environment and managemental issues that hindered reproductive performance traits and body growth. The heritability estimate for weaning weight was 0.45 and higher heritability values were observed for all the body weights except weight at third month. Genetic as well as phenotypic correlations were moderate to high among the growth traits. The heritability and genetic correlations at birth and weaning indicate the reliability of selection at an early age. The findings indicated that there is scope for improvement through genetic selection in later generations and the 75% crossbred pigs thrived well in the prevailing hot and humid tropical coastal climate. The improved germplasm could satisfy the farmers' need in a commercial venture with high economic return.

Signature of genome wide gene expression in classical swine fever virus infected macrophages and PBMCs of indigenous vis-a-vis crossbred pigs

The genetic basis of differential host immune response vis-à-vis transcriptome profile was explored in PBMCs of indigenous (Ghurrah) and crossbred pigs after classical swine fever vaccination and in monocyte derived macrophages (MDMs) challenged with virulent classical swine fever (CSF) virus. The humoral immune response (E2 antibody) was higher (74.87%) in crossbred than indigenous pigs (58.20%) at 21st days post vaccination (21dpv). The rate of reduction of ratio of CD4⁺/CD8⁺ was higher in crossbred pigs than indigenous pigs at 7th days post vaccination (7dpv). The immune genes IFIT1, IFIT5, RELA, NFKB2, TNF and LAT2 were up regulated at 7dpv in RNA seq data set and was in concordance during qRT-PCR validation. The Laminin Subunit Beta 1 (LAMB1) was significantly (p ≤ 0.05) down-regulated in MDMs of indigenous pigs and consequently a significantly (p ≤ 0.01) higher copy number of virulent CSF virus was evidenced in macrophages of crossbred pigs than indigenous pigs. Activation of LXR:RXR pathway at 60 h post infection (60hpi) in MDMs of indigenous versus crossbred pigs inhibited nuclear translocation of NF-κB, resulted into transrepression of proinflammatory genes. But it helped in maintenance of HDL level by lowering down cholesterol/LDL level in MDMs of indigenous pigs. The key immune genes (TLR2, TLR4, IL10, IL8, CD86, CD54, CASP1) of TREM1 signaling pathway were upregulated at 7dpv in PBMCs but those genes were downregulated at 60hpi in MDMs indigenous pigs. Using qRT-PCR, the validation of differentially expressed, immunologically important genes (LAMB1, OAS1, TLR 4, TLR8 and CD86) in MDMs revealed that expression of these genes were in concordance with RNA-seq data.

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 1 year 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 (895 bp) 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 (3 months) 6, 9 and 12 months 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.

Ultrasonographic Features of Ulnar Nerve Affected by Hansen's Disease

Leprosy continues to be a major public health problem in some areas of our country. It predominantly afflicts peripheral nerves and skin and may lead to deformities. Social stigma as a result of deformities further plagues the situation. Prompt and early diagnosis coupled with adequate treatment, concurrent rehabilitative strategies if deformities do occur, and health education help to control the problem. Definitive diagnosis of leprosy has traditionally been based on assessment of slit skin smears (SSS) after AFB-staining and characteristic histopathology after biopsyof the lesion. However, recently, thickening of the peripheral nerves has been demonstrated by ultrasonography and this can be used as a sensitive tool to assess and measure enlargement of peripheral nerves, which are hallmarks for leprosy especially in clinical settings. In this report, the ultrasonographic findings of ulnar nerve enlargement due to leprosy in a fourteen-year-old male patient are described.