VOL. 41-42 (2022-23): THE INDIAN JOURNAL OF ANIMAL GENETICS AND BREEDING

  • Journal ISSN:

    0971-8494

  • Issue DOI:

    https://doi.org/10.59317/VOL41422023IJAGB

  • Editor:

    Dr Manishi Mukesh

Keywords

Animal Genetics, Animal Breeding, Animal Sciences

 Transforming Indian cattle industry for building sustainable future
Sheikh Firdous Ahmad, Amod Kumar, K. Tamilarasan, Munish Gangwar and Gyanendra Kumar Gaur

India is one of the 17 global mega-biodiversity hotspots and harbours a rich diversity of flora and fauna with more than 212 breeds of various livestock species registered at the national level. Livestock sector contributes immensely to the national GDP of India with appreciable annual growth in dairying sector. The cattle population in India is mainly concentrated in its northern and western regions. Raising cattle is deeply ingrained into the social, cultural, and traditional fabric of many communities in India. It forms an important source of livelihood for rural masses. India faces a twin challenge of sustainable management of its huge cattle inventory while improving the productivity of animals and profitability of farmers within the minimum possible time. It is coupled with other challenges in terms of the limited resource base and changing agro-climatic trends along with the ever-looming threat of climate change. The profitability of rearing cattle has increased gradually since independence mainly due to staunch efforts made during the White Revolution and subsequently its carry-over effect. The adult female cattle population of India has increased 1.67 times from 54.4 million in 1951 to 145.12 million in 2019. There is an utmost need for improvement of productivity of cows using modern genetic approaches coupled with improvement in different facets of breeding, feeding and healthcare management. Streamlining the marketing channels, expanding the market network, and establishing a suitable farmers’ co-operative system across the country for dairy products offer opportunities for improved income of the dairy farmers besides providing nutritional security to rural masses. The present policy paper attempts to traverse through the important milestones and programmes in the cattle sector that led India to the stage of self-sustenance, besides analyzing the current threats and challenges faced by the industry along with possible solutions

 Genetic improvement and conservation of goats in tropic
P K Rout

Goats indeed have a significant historical and contemporary importance in human civilization, particularly in the realm of agriculture and food production. Their adaptability and widespread distribution have made them crucial for various societies across the world. Goats have played a central role in the Neolithic agricultural revolution, aiding in the spread of human civilization globally. Their adaptability allowed them to thrive in diverse environments, contributing to the sustenance and expansion of human settlements. Goats are highly adaptable and are found in a wide range of geographical regions. Their presence spans across continents, from tropical to temperate climates, showcasing their ability to thrive in various environmental conditions. There is diversity in the production performance of goats based on the region of the world and the specific breeds. Genetic improvement programs aim to enhance economically important traits such as milk production, growth rates and fiber production, thereby increasing productivity and income for goat farmers. Understanding the genetic parameters such as heritabilities and repeatabilities for various traits is crucial for designing effective breeding programs. These parameters provide insights into the genetic potential of goats for traits like milk production, growth and fiber quality. Heritability estimates for reproductive traits, body weight, daily gain and direct and maternal heritability are important for implementing selective breeding strategies aimed at improving overall productivity and efficiency in goat farming. Genetic improvement programs have been implemented in tropical environments to enhance milk production traits in goats. Genetic improvements have also targeted fiber production in goats, with a focus on traits such as grease fleece weight and average fiber diameter. These efforts aim to enhance the quality and quantity of fiber produced by goats for various commercial purposes. Despite the importance of conserving goat breeds with unique characteristics, planned conservation programs in tropical regions are often neglected. It’s emphasized that preserving indigenous goat breeds in their native habitats is essential for maintaining genetic diversity and ensuring future resilience in goat farming.

 Recent advances on strategies and technologies for isolation of bovine milk-derived exosomes: An overview
Vidhi Garg, Manishi Mukesh, Amarjeet, Parvesh Kumari, Ritu Mahajan and Monika Sodhi

Exosomes are small extracellular vesicles that play an important role in intercellular communication by facilitating the transfer of cell-specific constituents of the source cell to the recipient cell. They are secreted by various cell types and are available in all body fluids. Milk has been a part of the human diet since ages and is known to contain diverse bioactive components, including exosomes. Milk-derived exosomes (MDE) contain specific cargo with proteins, lipids, nucleic acids and other bioactive molecules that help in cell-to-cell communication and can alter the biological and physical processes of the recipient cells. These MDE can act as excellent nanocarriers for the delivery of drugs due to their stability and low immunogenicity. In this comprehensive review, the conventional isolation strategies based on ultracentrifugation, immunocapture, polymer-based precipitation, and chromatography and also the emerging technologies like microfluidic chips are discussed in detail. These provide functionally intact exosomes with high recovery rate. The available methods have one or the other limitations which pose challenges for the downstream analysis. Hence, integration of different methods is the most effective way to isolate exosomes with high recovery rate, purity and intact biological functions that open new avenues for exploring the therapeutic potential of MDE improving health and developing innovative medical interventions.

 Application of nutrigenomics and metagenomics in livestock
Ojal Singh, Neha Sahu, Amrish Kumar Tyagi And Sachin Kumar

Nutrigenomics tools, such as transcriptomics referring to RNA, proteomics referring to protein molecules and metabolomics referring to metabolites, can be used to effectively explore the events at molecular level occurring in a genome that receives signals from various nutrients and responds to them through different metabolic processes in the living organism. Nutrigenomics has the potential to identify personalized diets, elucidate diet-related diseases, pinpoint genes associated with diet-gene interactions, and detect gene polymorphisms influenced by significant nutritional and environmental factors affecting genetic expression. Limited information is available on the dietary impact on gene expression associated with reproductive and productive traits in livestock. However, this might be feasible to initiate an understanding of the significance of the connection between specific nutrients or dietary ingredients and the gene expression regulation. Utilizing nutrigenomic approaches will augment researchers’ capacities to uphold animal health, optimize animal performance, and enhance the milk quality and meat quality. Despite being rapidly advancing science, nutrigenomics is still in its early phase. Metagenomics is emerging as a robust and efficient approach for the metagenome sequencing derived from environmental samples. Investigating the gut microflora of various livestock and poultry species holds the potential to identify probiotic communities possessing both immunity-boosting properties and growth-promoting. Analyzing the diversity of gut microbes’ aids in identifying strains that contribute to animals’ adaptability to their native conditions. This approach is optimal for unveiling the phylogenetic and evolutionary connections between contemporary species and the ancestors of livestock and poultry

 Identification of transcription factor binding sites of HSP60 and HSP90B1 Genes’ promoter in Bubalus bubalis
Ravinder Singh, Ankita Gurao, Karpenahalli Ranganatha Sriranga, Meenakshi Chitkara, Monika Sodhi, Changanamkandath Rajesh and Ranjit Singh Kataria

The gene expression determines cellular homeostasis while spatio-temporal nature of gene expression is regulated by several cis regulatory elements, such as promoter regions which bind to transcription factors. The ever-changing global climatic conditions have raised a necessity to scan heat tolerant livestock especially the riverine buffalo in tropics. The study focuses on characterization of the promoter region of HSP60 and HSP90B1 and looking for the binding sites of transcription factors in Bubalus bubalis and comparison with the nearest relative Bos taurus to gauge the interspecies variations. The results indicated no transcription binding factors in HSP90B1 promoter (550 nucleotides) within the region analyzed except for the Elk-1 and COMP1 in the cattle while promoter region of HSP60 gene (971 nucleotides) varied highly. Nine and seven transcription factor binding sites were specifically unique in Bubalus bubalis and in Bos taurus respectively. Occurrence of 1-Oct, BR-C Z4, Hairy, and HSF was higher in buffalo. Overall, this study provided the framework to explore cis regulatory elements and contributes to decipher the transcriptional regulatory elements of HSP60 and HSP90B1 genes in Bubalus bubalis.

 Genetic variations in HsP90AA1 chaperone gene across diverse Indian native cattle (Bos indicus) breeds adapted to varied agroclimatic regions
Nampher Masharing, Monika Sodhi, Parvesh Kumari, Prince Vivek, Manish Tiwari and Manishi Mukesh

Indian zebu cattle during their separate evolution from Bos taurus, have acquired certain changes in a set of genes that regulate the body temperature in response to heat stress. Heat shock proteins (HSPs), the abundant and ubiquitous molecular chaperones play essential role in many cellular biological processes, and are preferentially transcribed in response to heat stress. The objective of this study was to comparatively screen variants/ single nucleotide polymorphisms (SNPs) in the HSP90AA1 gene in cattle breeds, viz., Gir, Kankrej, Ladakhi, Nagori, Nimari, Ongole, Rathi and Sahiwal, adapted to different agroclimatic regions of India including the exotic breed Holstein Friesian and yak (Bos grunniens). Sanger sequencing was carried out in all the translatable exons of the gene. The analysis revealed 6 SNPs – 3 were located in exon 3, 1 SNP each in exon 4 and 6, and another SNP in exon 9. We also identified a novel SNP 2937 (G>T) nucleotide position of exon 9. Interestingly, 2 variants detected at position 1924 (A>G) of exon 3 and 2343 (T>C) of exon 6 with a frequency of 0.9 and 0.73, respectively, were found to be almost fixed in nearly all of the Indian native cattle breeds. These SNPs could potentially be utilized to undertake genotype-phenotype association studies for superior heat stress tolerance trait in Indian native cattle.

 Delineating marker genotypes for higher reproduction performance to aid in selection of Murrah bulls
Ramendra Das, Vikas Vohra and Supriya Chhotaray

Unraveling the genetic variability of performance traits is the key basis of selection in farm animals. Murrah is a predominant milch breed of India, efforts were being made in the past to select them for higher production, which is negatively related with the fertility. Keeping this fact in mind and to select the animals having optimum production and fertility performance, present study was conducted to validate suitable markers and the association of their allelic variation with the fertility traits in Murrah buffaloes. Study was conducted on 280 Murrah buffaloes to explore SNPs in SPEF2 gene and their association with sire conception rate (SCR), conception rate (CR) and weight at birth of Murrah bulls. Results revealed that SNP C168T of SPEF2 gene with genotype CC was found to have non-significant but higher CR and SCR in comparison to CT and TT genotype. Although no significant association of the identified SNPs could be established with bull fertility traits, a further study with a large number of samples could make the differences due to genotypes a significant effect and can be used as an aid for early selection of high fertile Murrah bulls

 Deciphering genomic signatures in different Indian milch cattle breeds
Divya Rajawat, Manjit Panigrahi, Sonali Sonejita Nayak, Karan Jain, Anurodh Sharma, Nishu Bharia, Bharat Bhushan and Triveni Dutt

In the present study, the population genomic data of different cattle breeds were explored to decipher the genomic regions affected due to selective events and reflected in the productive, reproductive, thermo-tolerance, and health-related traits. To find out these genomic deviations due to selective sweeps, four statistical tools (Tajima’s D, CLR, ROH, and iHS) were used on four indigenous cattle breeds. Several candidate genes were found to be related to milk production (ADARB, WDR70, and CA8), reproductive (PARN, FAM134B2, and ZBTB20), and health-related traits (SP110, CXCL2, CLXCL3, CXCL5, IRF8, and MYOM1). Our findings serve as a foundation for identifying selective sweeps responsible for the genetic variation of traits. These sweeps could hold functional significance for multiple cattle breeds across various subcontinents. However, to enhance the robustness of the results, further studies with high-density arrays or whole-genome sequencing, employing greater resolution and larger sample sizes, are warranted.

 A comprehensive guide to bioinformatics tools and databases: from SNPs to haplotypes
Dapinder Singh, Bhawanpreet Kaur, Sehajpal Dhillon, Chandra Sekhar Mukhopadhyay

The interest in the functional aspects of the genome has increased eventually with the expansion of genomic databases. In this review, various genetic alterations within the genome, such as Single Nucleotide Polymorphisms (SNPs), disease-associated mutations, neutral polymorphisms, and small insertions or deletions (INDELs), have been identified and characterized. These polymorphisms, particularly SNPs, have become widely employed in genetic analyses, serving as valuable molecular markers. They are applied across diverse genetic studies, including the reconstruction of haplotypes. In addition to experimental methods for investigating specific genetic variants, there has been a significant surge in bioinformatics research over the past decade, aimed at the molecular consequences of these genetic alterations. Haplotypes, which represent various alleles of a gene, can be reconstructed not only for entire chromosomes but also for specific genes, utilizing the information derived from SNPs. The computational approach to SNP and haplotype discovery has gained prominence due to the continuous expansion of sequence data within public databases. This growth enables more precise identification of SNPs. This article aims to introduce easily accessible and practical online tools for researchers. In summary, SNP and haplotype identification tools are indispensable in bioinformatics for studying genetic variation, population genetics, disease associations, and personalized medicine. They provide valuable insights into the genetic underpinnings of various traits and diseases, helping advance our understanding of genetics and its applications in healthcare.

 Characterization, Registration and Gazette Notification: New Initiatives for Recognizing Native Dog Breeds
Raja K N, A K Mishra, S K Niranjan, B P Mishra

The first animal to be domesticated by the man was dog which probably occurred at least 14,000 years ago- the animals being used for hunting and as watchdogs. In India many exotic dog breeds (mainly German Shepherd, Labrador, Doberman, Pomeranian etc) are kept as pet but little emphasis has been given to the native dog breeds. Some Indian breeds of dogs reported in India are Caravan Hound, Combai, Chippiparai, Rajapalayam, Rampur Hound, Kanni, Mudhol Hound, Indian Mastiff (Bulli), Himalayan sheep dog, Bhutia dogs, Bhakarwal dogs etc. ICAR-NBAGR has developed methodology for characterization of dog breeds of Indian through systematic survey in the area of its distribution along with Breed Descriptors format for dog breeds. Phenotypic characterization of two indigenous dog breeds viz Rajapalayam and Chippiparai were completed by ICAR-NBAGR. Rajapalayam and Chippiparai dogs are exclusively reared for guarding the farm and farm houses. Chippiparai dogs are even given to brides during marriage. There is huge demand for the pups of these dog breeds. State of Karnataka has also completed the characterization of Mudhol hound breed. All three dog have been registered by ICAR & Gazette notified by Govt. of India

 Phenotypic characterization of the native yaks of Sikkim
R A K Aggarwal, Aneet Kour, R S Gandhi, Tenzing Lobsang Bhutia, Karma Doma Bhutia

Native yaks of Sikkim are reared in a pastoral production system by the tribal Dokpa community for their economic and socio-religious significance. Sikkimese yaks are phenotypically distinguishable from the yaks found in the neighbouring state of Arunachal Pradesh. Animals are generally black, broad and convex forehead, horizontal ears, curved upward pointing horns and docile temperament. Females have round udder and cylindrical teats. Also, Sikkimese yaks have comparatively shorter body length, lesser heart girth and greater height at withers as compared to Arunachali yaks. Animals are reared in a pastoral production system with characteristic features like seasonal migration, temporary shelters, highland forage grazing and ethno-veterinary practices. However, there are certain threats, which must be countered to ensure the continual existence and sustainability of this valuable germplasm.

This journal caters to a wide clientele comprising veterinarians, researchers and students. Articles are included on animal breeding and genetics, biotechnology from India and internationally. 

CHIEF EDITOR 

Dr Manishi Mukesh, Principal Scientist (Animal Biotechnology), ICAR-NBAGR, Karnal 132 001, Haryana, India, manishi.mukesh@icar.gov.in; mmukesh_26@hotmail.com

 

EXECUTIVE EDITOR

Dr Aruna T Kumar, Former Editor, Indian Journal of Animal Sciences, (ICAR-DKMA), arunatkumar11@gmail.com

 

EDITOR

Dr Anil Kumar, Professor, College of Veterinary and Animal Sciences, KVASU, Mannuthy, Kerala, India, anilkumar@kvasu.ac.in

 

EDITORIAL COMMITTEE

Dr Reena Arora , Principal Scientist (Animal Biotechnology), ICAR-NBAGR, Karnal 132 001, Haryana, India; Renna.Arora@icar.gov.in

Dr Sonika Ahlawat, Scientist SS (Animal Biotechnology), ICAR-NBAGR, Karnal 132 001, Haryana, India; Sonika.hlawat@icar.gov.in

Dr Manjit Panigrahi, Senior Scientist (Animal Genetics and Breeding), ICAR-Indian Veterinary Research Institute, Izatnagar, Uttar Pradesh, India; aanjit707@gmail.com

Dr K.P. Ramesha, Principal Scientist & Head, Southern Campus of NDRI, Bengaluru, Karnataka; kpragb@gmail.com

Dr R. Jayashree, Associate Professor & Head, Veterinary College, Karnataka Veterinary, Animal and Fisheries Sciences University, Karnataka, India; jayavet@gmail.com

Dr S. Banik, Head & Principal Scientist (Animal Genetics and Breeding),  Eastern Campus of NDRI, Kayani, West Bengal, India; sbanik2000@gmail.com

Dr A.K. Patel, Principal Scientist (Animal Genetics and Breeding), ICAR-CAZRI, Jodhpur, Rajasthan; abi.cazri@icar.gov.in

Dr C.S. Mukopadhyay, Senior Scientist (Animal Genetics and Breeding), College of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana 141 001, Punjab, India; csmukopadhyay@gadvasu.in

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