Shared SNP effects across breeds increase the genomic prediction accuracy for numerically small breeds.

Genomic selection has proven effective for accelerating genetic improvement in livestock, but its application in developing countries faces challenges, particularly for numerically small breeds, wherein, establishing large, single-breed reference population is difficult. To address this limitation, current study aimed to investigate the effectiveness of multi-breed reference populations to improve the genomic prediction accuracy in numerically small breeds with limited phenotypic and genomic resources. Genotypic and phenotypic data from 1,298 Gir, 1,291 Sahiwal, and 500 Kankrej indigenous cattle were used to enhance the genomic prediction accuracy in Kankrej, utilizing a multi-breed reference population.

Exploring genomic signatures of selection for adaptation and resilience in nomadic Belahi cattle in the tropical climate.

Background: Indigenous cattle in India are known for their resilience to diseases, parasites, and heat stress. Belahi is a newly registered indigenous breed reared by pastoralist communities in the North Himalayan foothills (Shivalik range). It has been naturally selected for adaptability to nomadic grazing, disease resistance, and milk production.

Optimizing multi-breed joint genomic prediction issues in numerically small breeds for sex-limited trait in a loosely structured dairy cattle breeding system.

Genomic prediction is crucial in the developed dairy industry, but implementing it in resource-poor regions with numerically small breeds and with no historic pedigree information is challenging. This study explores possibilities for joint genomic prediction, using genomic best linear unbiased prediction (GBLUP) across four closely related breeds for sex-limited traits when recently collected genomic information and phenotypes are available. The data was simulated to cover low (0.

De-novo assembled mitochondrial genome of Bhadawari buffalo (Bubalus bubalis) reveals close divergence to Egyptian buffalo.

Background: The objective of this study was to assemble the mitochondrial genome of Bhadawari buffalo and do phylogenetic analysis of it. We assembled the complete mitochondrial sequence of Bhadawari buffalo de novo from short Illumina sequences generated from the paired-end library. Phylogenetic analysis was done on 24 assembled mitochondrial genomes from the Bovidae family using the Maximum Likelihood method and General Time Reversible Substitution Model.

Chronic heat stress upregulates pyruvate metabolic process and gluconeogenesis but downregulates immune responses in Sahiwal cattle.

Climate change and growing population and their strain on animal production are the impending challenges that the developing countries, like India, need to tackle in the coming days. This study aimed to detect and analyze the uncharacterized variation in the gene expression patterns with the change of condition, from thermoneutral to chronic hot-humid, in the Sahiwal cattle, one of the best breeds of milk-producing cattle in India, known for being heat-tolerant. Using RNA-Seq analysis on peripheral blood mononuclear cells (PBMCs), 4021 differentially expressed mRNAs (2772 upregulated, 1249 downregulated) and 1303 differentially expressed long non-coding RNAs (769 upregulated, 534 downregulated) were identified, with the thresholds of false discovery rate < 0.

Assessing genetic parameters for first parity reproductive traits for early selection in Saanen × Beetal goats of India.

The present study aimed to evaluate the genetic parameters of first parity reproductive traits. Information on 762 reproductive records on Saanen × Beetal (S × B) goats reared for approximately five decades was collected from ICAR-National Dairy Research Institute, Karnal, Haryana (1973-2020). For genetic analysis, single-trait and multiple-trait animal models were used.

Genome-wide comparative analyses highlight selection signatures underlying saline adaptation in Chilika buffalo.

Chilika, a native buffalo breed of the Eastern coast of India, is mainly distributed around the Chilika brackish water lake connected with the Bay of Bengal Sea. This breed possesses a unique ability to delve deep into the salty water of the lake and stay there to feed on local vegetation of saline nature. Adaptation to salinity is a genetic phenomenon; however, the genetic basis underlying salinity tolerance is still limited in animals, specifically in livestock.

Functional transcriptome analysis revealed upregulation of MAPK-SMAD signalling pathways in chronic heat stress in crossbred cattle.

Animal geneticists and breeders have the impending challenge of enhancing the resilience of Indian livestock to heat stress through better selection strategies. Climate change's impact on livestock is more intense in tropical countries like India where dairy cattle crossbreeds are more sensitive to heat stress. The main reason for this study was to find the missing relative changes in transcript levels in thermo-neutral and heat stress conditions in crossbred cattle through whole-transcriptome analysis of RNA-Seq data.

Weighted single step GWAS reveals genomic regions associated with economic traits in Murrah buffaloes.

The objective of the present study was to identify genomic regions influencing economic traits in Murrah buffaloes using weighted single step Genome Wide Association Analysis (WssGWAS). Data on 2000 animals, out of which 120 were genotyped using a double digest Restriction site Associated DNA (ddRAD) sequencing approach. The phenotypic data were collected from NDRI, India, on growth traits, viz.

Diversity assessment of a lesser known buffalo population from Central India and its comparative evaluation reveals presence of sufficient genetic variation and absence of selection.

Planned breeding and conservation strategies for a lesser-known population require an assessment of complete genetic diversity and population structure analysis in addition to its morphometric characteristics. In the present study, a comparative analysis of the genetic structure of a rare buffalo population, namely Chhattisgarhi, was extensively studied using a panel of FAO-recommended microsatellite markers along with well-established breeds namely Murrah, Nili-Ravi, Gojri, Kalahandi, and Nagpuri. Mode shift analysis indicated the absence of genetic bottleneck in the recent past.

Modelling the lactation curve in Alpine × Beetal crossbred dairy goats using random regression models fitted with Legendre polynomial and B-spline functions.

The current study sought to genetically assess the lactation curve of Alpine × Beetal crossbred goats through the application of random regression models (RRM). The objective was to estimate genetic parameters of the first lactation test-day milk yield (TDMY) for devising a practical breeding strategy within the nucleus breeding programme. In order to model variations in lactation curves, 25,998 TDMY records were used in this study.

Discriminant analysis reveals differences in breed structure in river buffaloes of Maharashtra (India).

Buffaloes are a major milch species of India, and owning a true-to-breed buffalo herd is a reverie for livestock keepers, as it substantiates their incomes. Multivariate discriminate analysis is an efficient methodology to classify different farm animal populations based on canonical discriminant function. The present study was conducted on 392 adult buffaloes using 18 body biometric traits.

TWAS revealed significant causal loci for milk production and its composition in Murrah buffaloes.

Milk yield is the most complex trait in dairy animals, and mapping all causal variants even with smallest effect sizes has been difficult with the genome-wide association study (GWAS) sample sizes available in geographical regions with small livestock holdings such as Indian sub-continent. However, Transcriptome-wide association studies (TWAS) could serve as an alternate for fine mapping of expression quantitative trait loci (eQTLs). This is a maiden attempt to identify milk production and its composition related genes using TWAS in Murrah buffaloes (Bubalus bubalis).

Optimizing selection strategy for enhancing reproduction efficiency in Indian crossbred goats using milk productivity as a selection criterion.

The present study was aimed at optimizing the selection strategy for enhancing reproductive efficiency and milk productivity of Alpine × Beetal crossbred goats. The data set included 2949 milk trait records across parities and 1389 milk records from first parity and corresponding reproductive traits. The traits included for analysis were 150-day milk yield (150DMY), days in milk (DIM), peak yield (PY) and total milk yield (TMY).

Exome-wide comparative analyses revealed differentiating genomic regions for performance traits in Indian native buffaloes.

In India, 20 breeds of buffalo have been identified and registered, yet limited studies have been conducted to explore the performance potential of these breeds, especially in the Indian native breeds. This study is a maiden attempt to delineate the important variants and unique genes through exome sequencing for milk yield, milk composition, fertility, and adaptation traits in Indian local breeds of buffalo. In the present study, whole exome sequencing was performed on Chhattisgarhi (n = 3), Chilika (n = 4), Gojri (n = 3), and Murrah (n = 4) buffalo breeds and after stringent quality control, 4333, 6829, 4130, and 4854 InDels were revealed, respectively.

Explicating the genetic diversity and population structure of Saanen × Beetal goats using pedigree analysis.

Pedigree analysis is required to assess the genetic diversity and population structure of a close breeding population in order to effectively manage the breeding program and keep inbreeding under acceptable limits. Saanen × Beetal is a crossbred population of goats, reared at the National Dairy Research Institute (NDRI), Karnal, for the last five decades. This germplasm has been acclimated to a tropical climate and has a higher milk potential and prolificacy.

Estimation of genetic parameters and genetic change of first parity reproductive traits in Alpine × Beetal goats.

The study of reproductive traits is crucial for improving genetic potential of goats because of their significant utility in meat production. Hence, genetic analysis was conducted for reproductive traits on Alpine × Beetal goats using animal model for first parity data. Information on 1462 reproductive records were collected over five decades from ICAR-National Dairy Research Institute, Karnal, Haryana (1971-2021).

ASIP gene polymorphism associated with black coat and skin color in Murrah buffalo.

The melanogenesis pathway regulates pigmentation through the synergic action of various genes. We are interested in analyzing the genetic variations in the ASIP which determine eumelanin production in the dermis layer. In the present study, the ASIP gene was characterized in buffalo and 268 genetically unrelated buffaloes belonging to 10 different populations were genotyped for the non-synonymous SNP (c.

Genetic improvement of economic traits in Murrah buffalo using significant SNPs from genome-wide association study.

GWAS helps to identify QTL and candidate genes of specific traits. Buffalo breeding has primarily focused on milk production, but its negative correlation with reproduction traits resulted in unfavorable decline of reproductive performance among buffaloes. A genome wide scan was performed on a total of 120 Murrah buffaloes genotyped by ddRAD sequencing for 13 traits related to female fertility, production, and growth.

Comparative analysis of various methods for estimating expected genetic gain of production and reproduction traits in Murrah buffaloes.

The present study was conducted to assess the expected genetic gain for first lactation production and reproduction traits in Murrah buffaloes, in addition to optimization of progenies/sire. Data for period 1971-2020 were used from National Dairy Research Institute. Performance traits considered were 305 days milk yield (305DMY), average daily milk yield (ADMY), peak yield (PY), lactation length (LL), calving to first insemination interval (CFI), days open (DO), and calving interval (CI).

Genomic clues of association between clinical mastitis and SNPs identified by ddRAD sequencing in Murrah buffaloes.

The total milk production of India is 209.96 MT out of which 45% is contributed by the indigenous buffalo and due to their high producing virtue, the prevalence of mastitis is 5-20%. Despite the increasing level of technological advancement, mastitis is still an issue of concern for dairy industry in India as well as across the world.

Identification of differential methylome signatures of white pigmented skin patches in Nili Ravi buffalo of India.

The DNA methylation events mark a major epigenetic change in the genome, reflecting non-genetic disease developments and varied phenotypes. The water buffalo is a dairy production animal with wide agro-climatic distribution in India. Breed-wise the coat color of water buffalo varies from ash-gray to jet black.

Genetic analysis of milk and milk composition traits in Murrah buffaloes using Bayesian inference.

Accurate and unbiased assessment of genetic parameters of milk and milk composition traits play an important role in formulating breeding program for genetic improvement of Murrah buffaloes. In this study, data spread over 28 years were utilized to estimate genetic parameters of traits viz., 305 d milk yield (305MY), 305 d fat yield (305FY), 305 d solid not fat yield (305SNFY), milk fat percentage (fat%) and solid not fat percentage (SNF) percentage (SNF%) in Murrah buffaloes kept at ICAR-National Dairy Research Institute, Karnal.

Impact and utility of shallow pedigree using single-step genomic BLUP for prediction of unbiased genomic breeding values.

In unstructured dairy programs, pedigree is usually shallow, which leads to biased prediction of breeding values using best linear unbiased prediction (BLUP). The objective of this study was to come out with a genomic prediction strategy that can utilize shallow pedigree information and predict unbiased and more accurate GEBV for sex-limited traits in a small population using single-step GBLUP (ssGBLUP). The data and models for a population under selection were simulated.