Biotechnological Applications in Buffalo Research

Preface
Contents
About the Editors
Part I: Buffalo, A Black Beauty in Livestock Farming
	1: Buffalo in the World: Situation and Perspectives
		1.1 Buffalo: A Tool for Sustainability?
		1.2 Buffalo Population Trend
		1.3 Buffalo in Central Asia
			1.3.1 India
			1.3.2 Pakistan
			1.3.3 China
			1.3.4 Nepal
			1.3.5 Bangladesh
			1.3.6 Sri Lanka
		1.4 Buffalo in Far East of Asia
			1.4.1 Myanmar
			1.4.2 Philippines
			1.4.3 Vietnam
			1.4.4 Laos
			1.4.5 Indonesia
			1.4.6 Thailand
			1.4.7 Malaysia
		1.5 Buffalo in Near East of Asia
			1.5.1 Iran
			1.5.2 Iraq
			1.5.3 Azerbaijan
			1.5.4 Other Near East Asian Countries
		1.6 Buffalo in Mediterranean Area
			1.6.1 Egypt
			1.6.2 Italy
			1.6.3 Turkey
			1.6.4 Greece
		1.7 Buffalo in Europe
			1.7.1 Bulgaria
			1.7.2 Romania
			1.7.3 Hungary
			1.7.4 Other Balkan Countries
			1.7.5 Rest of Europe
		1.8 Buffalo in America
			1.8.1 Brazil
			1.8.2 Venezuela
			1.8.3 Colombia
			1.8.4 Argentina
			1.8.5 Bolivia
			1.8.6 Center American countries
		1.9 Buffalo Livestock in Oceania
		1.10 Perspectives
		References
	2: Water Buffalo Genomic Diversity
		2.1 The Water Buffalo Genome
		2.2 Reference Genome Sequences
		2.3 Genetic Diversity
			2.3.1 Microsatellite Markers
			2.3.2 SNP (Single-Nucleotide Polymorphism) Diversity
		2.4 Nuclear Genome Diversity
		2.5 Functional Variation
		2.6 Uniparental Genomes Diversity
			2.6.1 Mitochondrial Genome
			2.6.2 Y-Chromosome
		2.7 Conclusions
		References
	3: Advances in Buffalo Breeding: A Journey from Classical Breeding to Genomic Selection
		3.1 Introduction
		3.2 Buffaloes Play a Major Role for Milk Production in India
		3.3 Improving Production Potential of Buffaloes in the World
		3.4 Genetic Improvement in Buffalo Has Seen Tremendous Leap in the Production Status in India
		3.5 Concept of Selection and Classical Problems of Animal Breeding
			3.5.1 Long Generation Interval
			3.5.2 The Intensity of Selection (i)
			3.5.3 The Genetic Variability of the Trait Affects Selection Response
			3.5.4 The Accuracy of Selection Also Affects the Response to Selection Directly
		3.6 Buffalo Breeding Also Faced the Inherent Challenges of Classical Breeding
		3.7 The Paradigm Change: Genomic Selection Has Prospects for Better Genetic Gains in Buffalo Breeding
			3.7.1 Slow Pace of Buffalo Genomic Selection in the World
			3.7.2 How Does the Genomic Selection Actually Work?
			3.7.3 Single Step Can be a Better Solution for Indian Genomic Selection Program
			3.7.4 Where Do We Stand and Can We Benefit from This Technology?
		References
	4: Reproductive Management of Dairy Buffaloes
		4.1 Introduction
		4.2 Breeding Programs in Buffaloes
			4.2.1 Natural Breeding
			4.2.2 Artificial Breeding
		4.3 Synchronization Programs in Buffaloes
			4.3.1 Use of Prostaglandins and Gonadotropin-Releasing Hormones
			4.3.2 Progestin-Based Protocols
				4.3.2.1 New Vs. Used Controlled Internal Drug Release Devices
				4.3.2.2 Progesterone and Estradiol Benzoate-Based protocol
				4.3.2.3 Progesterone and Gonadotropin Releasing Hormone Modified Protocol
				4.3.2.4 Progesterone and Equine Chorionic Gonadotropin-Based Protocol
				4.3.2.5 Progesterone and Human Chorionic Gonadotropin-Based Protocol
		4.4 Resynchronization Programs
		4.5 Conclusion
		References
	5: Behavior and Welfare of Dairy Buffaloes: Calving, Milking, and Weaning
		5.1 Introduction
		5.2 Calving
			5.2.1 Origin and Transmission of Painful Stimuli During Labor
		5.3 Behavior and Welfare of the Dairy Buffalo During Milking
			5.3.1 Factors That Predispose Female Buffaloes to Mastitis
			5.3.2 Perception of Pain During Milking in Female Buffaloes with Mastitis
		5.4 Weaning in Buffaloes
			5.4.1 Widely Used, Routine Approaches
			5.4.2 Novel Weaning Strategies
		5.5 Final Considerations
		References
	6: Buffalo Milk and Its Products: Composition, Nutrition and Benefits
		6.1 Introduction
		6.2 Chemical Composition of Buffalo Milk Vis-a- Vis Bovine Milk
			6.2.1 Milk Fat
			6.2.2 Milk Proteins
			6.2.3 Amino Acids
			6.2.4 Minerals
			6.2.5 Vitamins and Enzymes in Buffalo Milk
		6.3 Important Physico-Chemical and Technological Properties of Buffalo and Bovine Milk
		6.4 Significance of Buffalo Milk in Product Formulation
		6.5 Nutritive Value of Buffalo Milk
			6.5.1 Milk Fat
				6.5.1.1 Gangliosides
				6.5.1.2 Carnitines and Valerobetaine
			6.5.2 Minerals
			6.5.3 Proteins
		6.6 Conclusion
		References
	7: Welfare of Buffaloes at Slaughter: Signs of the Return of Sensibility
		7.1 Introduction
		7.2 Loss of Consciousness and Insensibility
		7.3 Neurophysiology of the Ascendent Transmission of the Painful Impulse from the Reticular Formation to the Cerebral Cortex
		7.4 Signs of the Return to Sensibility to Assess Stunning Quality
		7.5 Why Must the River Buffalo be Stunned Differently than Cattle?
		7.6 Final Considerations
		References
Part II: Omics Approaches to Understand Buffalo´s Genome, Physiology, and Reproduction
	8: Molecular Evolution and Genome Architecture of Water Buffalo (Bubalus Bubalis), the ``Living Bank´´ for Marginal Farmers in...
		8.1 Introduction
		8.2 Different Types of Buffaloes and Their Evolution
		8.3 Migration History of Buffaloes Across the World
		8.4 Chromosomal Organization of Asian and African Buffaloes
		8.5 Similarity in Chromosome Organization Among Ruminants: A Comparative Cytogenetics Approach
			8.5.1 Autosome
			8.5.2 Sex Chromosome
			8.5.3 Nuclear Organizer Region (NOR)
		8.6 Genome Diversity in Buffalo
			8.6.1 Microsatellite Markers
				8.6.1.1 Microsatellite Markers in Indian Buffalo Breeds
			8.6.2 Mitochondrial DNA Variation
			8.6.3 Y-chromosome Variation
			8.6.4 Single Nucleotide Polymorphisms (SNPs) Marker in Buffalo Genome
			8.6.5 Copy Number Variation (CNV) in Buffalo Genome
		8.7 Genotype Meets Phenotype: Buffalo Structural Genome Variations in Determining Economic Traits
			8.7.1 Candidate Gene Approach
				8.7.1.1 Milk Production and Growth
				8.7.1.2 Reproductive Traits
				8.7.1.3 Innate Immunity and Disease Resistance
		8.8 Future of Buffalo Production
		References
	9: Advances in Buffalo Bull Fertility Prediction
		9.1 Introduction
		9.2 Sperm Phenotypic Characteristics and Bull Fertility: What to Assess?
			Box 9.1: Sperm Characteristic Required for Fertilization of an Oocyte
		9.3 Sperm-Oviduct Explants Binding Assay for Fertility Prediction
		9.4 Sperm Molecular Signatures for Fertility and beyond
			9.4.1 Sperm Transcripts
			9.4.2 Types of RNA and their Role in Spermatozoa
			9.4.3 Role of Sperm Transcripts in Oocyte Activation
			9.4.4 Sperm Transcripts and Epigenetic Modification
			9.4.5 Small Non-coding RNAs and Early Embryogenesis
			9.4.6 Transcriptomic Studies of Bull Spermatozoa
		9.5 Sperm Proteins
			9.5.1 Techniques for Semen Proteomic Studies
			9.5.2 Semen Proteomics with Special Reference to Buffaloes
			9.5.3 Proteins Associated with Sperm Functions in Buffaloes
		9.6 Epilogue
		References
	10: Being Sweet Is Being Smart: Lessons Learnt from Buffalo Spermatozoa
		10.1 The Epididymal Sperm-Surface Remodeling (SSR) Events and Acquisition of a Substantial Glycocalyx
		10.2 Diversity and Complexity of Sperm Glycans
		10.3 Localization and Functional Specialization of Sperm-Associated Sugars
		10.4 Changes in Glycan Localization after the Introduction of Perturbations in Sperm Glycocalyx
		10.5 Glycans Affect Sperm Survival: Determination of Self Vs. Non-self
		10.6 Role of Glycans in Inter-and Intra-Cellular Communication
		10.7 Implications in Immune Recognition and Evasion with Special Reference to AI
		10.8 Regulation of Male Fertility
		10.9 Future Perspectives
		References
	11: Protein Signatures of Lactation and Early Pregnancy Diagnosis in Buffalo (Bubalus bubalis)
		11.1 Introduction
		11.2 Protein Signatures Related to Lactation in Buffaloes
		11.3 Gene Expression Studies Related to Lactation in Buffaloes
		11.4 Protein Signatures Related to Pregnancy in Buffaloes
		11.5 Gene Expression Studies Related to Pregnancy in Buffaloes
		11.6 Conclusion
		References
	12: Pluripotent Stem Cells from Buffalo: Basic and Translational Applications
		12.1 Introduction
		12.2 Embryonic Stem Cells from Buffalo
		12.3 Induced Pluripotent Stem Cells from Buffalo
		12.4 Translational Application of Buffalo Pluripotent Stem Cells
		References
	13: Domesticated Buffalo: A Model for Human Biomedical Research
		13.1 Domestication of Buffaloes
		13.2 Farm Animals as Animal Research Model
		13.3 Domesticated Buffalo as Animal Research Model
			13.3.1 Role of Buffalo in Stem Cell Research
				13.3.1.1 Extra-Embryonic Stem Cells
				13.3.1.2 Reprogrammed Stem Cells
			13.3.2 Transgenic Buffaloes and Their Prospects
			13.3.3 Buffalo Milk
			13.3.4 Bubaline Placenta
			13.3.5 Animal Research Model of Vitiligo
		13.4 Challenges
		References
Part III: Reproductive Biotechnologies
	14: Advances in Embryo Production in Buffaloes: In Vivo Versus In Vitro Procedures
		14.1 Introduction
		14.2 In Vivo Embryo Production
			14.2.1 MOET
				14.2.1.1 Selection of Animals (Donors and Recipients)
				14.2.1.2 Superovulation
				14.2.1.3 Artificial Insemination or Natural Mating
				14.2.1.4 Flushing of Embryos and Transfer
				14.2.1.5 Classification or Grading of Embryos
		14.3 In Vitro Embryo Production
			14.3.1 Ovum Pick-Up (OPU)
				14.3.1.1 Grading of Oocytes
			14.3.2 In Vitro Maturation (IVM)
			14.3.3 In Vitro Fertilization (IVF)
			14.3.4 In Vitro Culture (IVC)
		14.4 Conclusion
		References
	15: Application of Fixed-Time Artificial Insemination in Water Buffaloes
		15.1 Introduction
		15.2 Overview of the Water Buffalo´s Estrous Cycle and Reproductive Performance
		15.3 Conventional Artificial Insemination Vs. Fixed-Time Artificial Insemination
		15.4 Fixed-Time Artificial Insemination (TAI) Programs
			15.4.1 Definition
			15.4.2 Advantages
			15.4.3 Disadvantages
		15.5 Fixed-TAI Protocols During the Reproductive Season
			15.5.1 GnRH and PGF2α Based Protocols (Ovsynch)
			15.5.2 Mechanism of Action of Ovsynch-Based Protocols
			15.5.3 Hybrids-Ovsynch Protocols in Water Buffalo
			15.5.4 Cosynch
			15.5.5 Double Ovsynch
			15.5.6 Ovsynch Plus
			15.5.7 Double Synch
			15.5.8 G6G
			15.5.9 Melatonin and Progesterone Supplementation
		15.6 Fixed-TAI Protocols During Both the Reproductive and Non-reproductive Season
			15.6.1 Progesterone (P4)-Based Fixed-TAI Protocols
			15.6.2 Mechanism of Action of P4-Based Protocols
			15.6.3 P4/Estradiol (E2)-Based Fixed-TAI Vs. P4/GnRH/PGF2α-Based Fixed-TAI
			15.6.4 Addition of Equine Chorionic Gonadotropin (eCG)
			15.6.5 Progesterone Concentration and Reuse of Intravaginal Devices
			15.6.6 Protocol Length and Device Permanence
		15.7 Evaluation and Factors Affecting the Efficiency of the Fixed-TAI Programs
		15.8 Conclusions
		References
	16: Semen Sexing in the Buffalo (Bubalus bubalis)
		16.1 Introduction
		16.2 The Technology for Semen Sexing Today
		16.3 The Backbone of Reproductive Physiology in the Buffalo
		16.4 Early Attempts in the Buffalo
		16.5 More Recent Developments
		16.6 Future Expectations
		References
	17: Advances in Cryopreservation of Buffalo Semen
		17.1 Introduction
		17.2 Management of Young Buffalo Aiming Its Use as a Future Semen Donor
		17.3 Pre-breeding Management of Young Buffalo
			17.3.1 Onset of Puberty
			17.3.2 Relationship of Age, Body Size, and Scrotal Circumference to Semen Production
		17.4 The Breeding Soundness Examination (BSE)
		17.5 Libido, Semen Collection, and Evaluation
		17.6 Assessment of Buffalo Semen Characteristics
			17.6.1 Color
			17.6.2 Volume
			17.6.3 Wave Motion
			17.6.4 Concentration
			17.6.5 Sperm Motility
			17.6.6 Vigor
			17.6.7 Live and Dead
			17.6.8 Sperm Morphology
		17.7 The Establishment of Suitable Extenders for Deep Freezing Buffalo Semen
			17.7.1 Semen Extenders
		17.8 Technological Processing for Semen Freezing
			17.8.1 The Phase I
			17.8.2 The Phase II
			17.8.3 The Phase III
			17.8.4 Analysis for Thawing Frozen Semen for Fertility Assessment
		17.9 Effect of Reactive Oxygen Species (ROS) on Buffalo Semen
		17.10 Adverse Effects of Cryopreservation on Sperm Cells
		17.11 Biochemical Characteristics of Semen
		17.12 Climatic Effects on Buffalo Reproduction
		17.13 Conclusion
		References
	18: Advances in Semen Quality Assessments in AI Programs in Buffalo
		18.1 Introduction
		18.2 Seminal Cryopreservation
		18.3 Sperm Quality Assessment
			18.3.1 General Aspects
			18.3.2 Basic Parameters for Assessing Sperm Quality
				18.3.2.1 Colour
				18.3.2.2 Volume
				18.3.2.3 Sperm Concentration
				18.3.2.4 Sperm Motility
					Mass Motility
					Progressive Individual Motility (PIM)
				18.3.2.5 Vitality
				18.3.2.6 Sperm Morphology and Acrosome Integrity
				18.3.2.7 Assessment of the Functional Integrity of Plasma Membrane by the Endosmosis Test (HOST)
				18.3.2.8 DNA Fragmentation
			18.3.3 Reference Values for Buffalo Semen with Special Emphasis on AI
			18.3.4 Sexed Semen
		18.4 Conclusion
		References
	19: Reproductive Ultrasonography in Buffalo: Basic Concepts and Recent Advances
		19.1 Introduction
		19.2 Components of Ultrasound
			19.2.1 Echo Display Modes in Ultrasonography
			19.2.2 Types of Transducer
			19.2.3 Range of Frequencies
		19.3 Assessment of Normal Ovarian Structure
			19.3.1 Ovaries
			19.3.2 Ovarian Stroma
			19.3.3 Follicle
			19.3.4 Corpus Luteum (CL)
		19.4 Detection of Ovarian Pathologies
			19.4.1 Ovarian Cysts
			19.4.2 Parovarian Cysts
			19.4.3 Ovarian Abscess
			19.4.4 Follicular Growth Pattern
			19.4.5 Anoestrus and Silent Oestrus
			19.4.6 Oestrus and Ovulation
			19.4.7 Oestrus Induction and Ovulation Synchronization
		19.5 Ultrasonography in Embryo Transfer (ET) Program
			19.5.1 Ultrasound-Guided Ovum Pick Up and IVF Technique
			19.5.2 Early Pregnancy Diagnosis
			19.5.3 Uterus and Cervix
			19.5.4 Determination of Fetal Age
			19.5.5 Determination of Fetal Sex
		19.6 Ultrasonography in Male Reproduction
			19.6.1 Male Reproductive System
			19.6.2 External Scanning
			19.6.3 Internal Scanning
		19.7 Anatomy of the Reproductive System
			19.7.1 Testis
			19.7.2 Epididymis
			19.7.3 Penis
			19.7.4 Bulbourethral Glands
			19.7.5 Pelvic Urethra
			19.7.6 Prostate
			19.7.7 Seminal Vesicles
			19.7.8 Orchitis
			19.7.9 Testicular Degeneration
			19.7.10 Testicular Neoplasm
			19.7.11 Inguinal Hernia
			19.7.12 Hydrocele
			19.7.13 Vesiculitis
		19.8 Advantages and Clinical Uses of Ultrasound
		References
	20: Spermatogonial Stem Cells and Testis-Tissue Cryopreservation as a Tool for Conservation of Buffalo Germplasm
		20.1 Introduction
		20.2 The Biology of Testes
		20.3 Spermatogonial Stem Cells (SSCs) and Their Biological Markers
		20.4 SSC Transplantation
		20.5 Cryopreservation of SSCs
		20.6 Cryopreservation of Testis
			20.6.1 Testicular Tissue Cryopreservation
			20.6.2 Retrieval of Gametes from Cryopreserved Adult Testis
			20.6.3 Production of Gametes from Immature Testis after Xenotransplantation
			20.6.4 Applications in Assisted Reproduction Technology (ART)
		20.7 Conclusions and Future Prospective
		References
	21: Somatic Cell Nuclear Transfer and its Applications in Buffalo (Bubalus bubalis)
		21.1 Introduction
		21.2 Journey of Buffalo Cloning
		21.3 Attempts to Improve the Cloning Success
		21.4 Growth, Health, and Fertility of Clones
		21.5 Application of Buffalo Cloning, Special Reference to Bull Cloning for India
		21.6 Perspectives and Prospective
		References