Genomic inbreeding analysis reveals resilience and genetic diversity in Indian yak populations.

The yak (Bos grunniens), renowned for its adaptability to extreme cold and hypoxic conditions, stands as a remarkable domestic animal crucial for sustaining livelihoods in harsh climates. We conducted a comprehensive analysis of the whole genome sequence data from three distinct Indian yak populations: Arunachali yak (n = 10), Himachali yak (n = 10), and Ladakhi yak (n = 10). The genomic data for Indian yaks were meticulously generated by our laboratory and compared with their Chinese counterpart, the Jinchuan yak (n = 8), for a more nuanced understanding. Our investigation revealed a total of 37,437 runs of homozygosity (ROH) segments in 34 animals representing four distinct yak populations. The Jinchuan yak population exhibited the highest proportion, constituting 80.8 % of total ROHs, predominantly as small segments (<0.1 Mb), accounting for 63 % of the overall ROHs. Further analysis uncovered a significantly higher degree of inbreeding in Chinese yaks compared to their Indian counterparts. The Indian yak populations, in contrast, demonstrated relatively lower and consistent levels of inbreeding. Moreover, we identified ROH hotspots that covered at least 60 % of individuals in our study, indicating their pivotal role in environmental adaptation. A total of five hotspot regions were detected, housing genes such as ENSBGRG00000015023 (WNT2), YIPF4, SPAST, TLN2, and DSG4. These genes are associated with traits including hair follicle initiation, nutrient stress response, microtubule assembly, development of cardiac muscle, hair follicle, and coat color. This observation strongly suggests that there is substantial selection acting on these genes, emphasizing their important role in environmental adaptation among yak populations.

Identification of novel polymorphism in mammary-derived growth inhibitor gene of water buffalo and its expression analysis in the mammary gland.

Mammary-derived growth inhibitor (MDGI), a member of the lipophilic family of fatty acid-binding proteins, plays an important role in the development, regulation, and differentiation of the mammary gland. The aim of the study was to identify polymorphism in the MDGI gene and its expression analysis in the mammary gland at various stages of lactation, in Indian buffalo. Nucleotide sequence analysis of MDGI gene in different breeds of riverine and swamp buffaloes revealed a total of 16 polymorphic sites and one Indel. Different transcription factor binding sites were predicted for buffalo MDGI gene promoter sequence, using online tools and in-silico analysis indicating that the SNPs in this region can impact the gene expression regulation. Phylogenetic analysis exhibited the MDGI of buffalo being closer to other ruminants like cattle, yak, sheep, and goats. Further, the expression analysis revealed that buffalo MDGI being highly expressed in well-developed mammary glands of lactating buffalo as compared to involution/non-lactating and before functional development to start the milk production stage in heifers. Stage-specific variation in expression levels signifies the important functional role of the MDGI gene in mammary gland development and milk production in buffalo, an important dairy species in Southeast Asia.

Devising a selection strategy for the Jamunapari goat for improving lactation performance.

This study aimed to evaluate the genetic potential of the Jamunapari goat and formulate a selection strategy for improving lactation traits. The data set included 4049 phenotypic records for across parity milk yield at 90 days (MY90), 140 days (MY140), total milk yield (TMY), and lactation length (LL) obtained from the progeny of 83 sires and 1643 dams between the period 1990 and 2019. Animal model employing average information restricted maximum likelihood (AIREML) was used to estimate genetic parameters for milk yield traits and LL. The direct additive heritability estimates for across parity lactation traits that used repeatability model were 0.10 ± 0.03, 0.08 ± 0.03, and 0.12 ± 0.02 for MY90, MY140, and TMY, respectively, while it was low for LL (0.06 ± 0.02). The repeatability estimates were moderate ranging from 0.17 to 0.22 for milk yield traits and LL, indicating persistent performance over the parities. Animal permanent environment influence (c2) was significant in milk yield attributes, whereas direct maternal genetic effects were absent. As the early selection criteria based on first parity records are essential, we analyzed the data for the first parity separately and obtained moderate h2 estimates, viz., 0.26 ± 0.05, 0.16 ± 0.06, and 0.25 ± 0.06 for MY90, MY140, and TMY, respectively. These estimates augur further scope of selection in Jamunapari goats for higher milk yield. High and positive genetic correlation of MY90 with MY140 (0.97 ± 0.01) and TMY (0.91 ± 0.05) revealed the scope of using MY90 as the selection criterion. Based on these results, we recommend use of first parity MY90 as a single trait selection criterion for genetic improvement of all lactation traits in Jamunapari goat.

Genetic analysis of growth parameters and survival potential of Jamunapari goats in semiarid tropics.

Goats are adaptable to varied farming environments and contribute significantly towards sustainable livestock production and food security. Selective breeding of goats for improved performance is an important component of sustainable production. The objectives of the present study were to determine the most appropriate models of analysis for growth traits, to estimate genetic parameters, survival potential of kids from birth to 12 months of age and to estimate genetic trends for growth traits of Jamunapari kids at different ages. Genetic parameter estimates were obtained from 6590 records generated between 1982 and 2012 from 5922 animals with a pedigree covering over 13 generations. The most parsimonious model for early growth traits included permanent environmental effects due to the dam (PE) and litter effects. Similarly, the most appropriate model for early average daily gain (ADG) between birth and 3 or 6 months also included PE and litter effects. The estimates of heritability for survival from birth to 12 months of age ranged from 0.10 to 0.43. The estimates of heritability for ADG varied from 0.04 to 0.41. In general, higher estimates of heritability were observed when a sire model was fitted in the random effect. There was no genetic variation observed for survival between birth and 3 months of age. However, heritability estimates of between 0.18 and 0.39 were observed for survivability during post-weaning period to 12 months of age. The genetic trend at 9 months of age and 12 months of age was 0.144 kg 0.189 kg per year respectively. The genetic trend at all the ages was positive during the study period.

Estimation of genetic parameters and genetic trends for milk yield traits in Jamunapari goats in semiarid tropics.

The Jamunapari goats are reared as dairy animals in semi-arid conditions, therefore it is necessary to evaluate the genetic potential for the genetic improvement of milk production traits. The data comprised of 2217 phenotypic records for milk yield at 90 days (MY90) and 140 days (MY140), total milk yield (TMY) and lactation length (LL) obtained from the progeny of 173 sires and 446 dams during the period 1990-2013. The data were analysed using mixed linear models exploring random effects due to direct additive, maternal and permanent environment variance due to animal. The most appropriate genetic models for milk yield traits were those that included permanent environment effects due to the animal. The direct additive heritability estimates were 0.15 ± 0.05, 0.26 ± 0.07, 0.25 ± 0.08 for MY90, MY140 and TMY, respectively. The additive heritability estimate for LL was low and non-significant at 0.02 ± 0.03. The repeatability estimates were moderate to high ranging from 0.68 to 0.73 for milk yield traits. The repeatability for lactation length was 0.20 ± 0.03. Maternal variances were low ranging from 0.03 for MY90 to 0.13 for TMY. There was an increase in mean milk yield of 0.25, 0.70 and 0.72 kg/year respectively at 90 and 140 days, and for TMY. Genetic trends and phenotypic trends for MY90, MY140 and TMY were positive and indicated significant improvement in milk traits due to selective breeding.