eChapters

Meta-analyses has been used extensively to combine the results of existing studies and obtain powerful estimates of a parameter. In animal breeding, attempts have been made to obtain meta-analysis estimates for genetic parameters. This tool is more pertinent to animal breeding on account of heterogeneity in terms of location, sample size and other factors in the estimation of genetic parameters. This chapter explains the background, methodology, precautions and implications of meta-analysis with respect to genetic parameters.

A meta-analysis is a powerful tool of statistics that could combine several estimates from different studies for a parameter and the resulting weighted estimate could be used as a representative value for the particular parameter. However, not all the studies are similar with respect to location, sample size, and methodology used and thus various precautions are to be taken right from the selection of studies to incorporating of between-study heterogeneity in the models. In animal breeding, met-analysis is very much useful for obtaining meaningful estimates of genetic parameters and this chapter explains the methodology of meta-analysis in animal breeding.

Animal breeding data is unique in terms of volume, statistical analysis, type of information required etc. The large volume of data extended spatially and temporally warrants additional tools in the form of databases to handle data and enable accuracy, retrieval, efficient utilization and adaptability to software. This chapter explains the nature of animal breeding data and the importance of databases with examples and explanations.

Animals are raised for some utility including meat, milk, hide, wool etc., and efforts are on to continuously improve the quality and quantity of these products. Some of the important economic traits in this regard were already discussed in earlier chapters. Record maintenance is primary for decision-making with respect to the selection of animals. The details of record maintenance including the format of registers are already explained in chapter 2. Apart from the actual information required for economic traits, pedigree information forms an important part of animal breeding data.

Maintaining the required type of information in the form of records is primary for any type of animal breeding analysis and this chapter explains the importance of records and ways to maintain them in the form of registers or computer databases. The formats for different types of registers to be maintained are also given as a template in appendix. Any breeding plan is formulated to improve the economic traits depending on the utility of species reared and the chapter lists important economic traits of livestock and poultry with definitions and formulae, where ever required.

Basic record maintenance is a must for any animal breeding program. Every farm or breeding program is expected to maintain records in the form of registers or computerized databases. The goal of animal breeding is to select mates with the objective to improve economically important traits. In this chapter, the most common economic traits in different species of livestock are described. Even though the list is not exhaustive the basic economic traits that have been worked for improvement are explained. Breeders also explore new composite traits which are a combination of these base traits.

This chapter describes various multivariate techniques which are useful in animal breeding. The genetic correlation with multiple response variables is already explained in the chapters on Correlation and Genetic Parameters. The other techniques including MANOVA, Principal Component Analysis, Factor Analysis, Cluster Analysis and Discriminant Analysis are explained.

Multivariate analysis is referred to a set of data with multiple response variables in general and such data is encountered often in animal breeding analysis. The simplest form of multivariate analysis is the genetic correlation where two or more traits are analysed together as response variables with factors affecting them on the right-hand side (RHS) and details of these are already explained in earlier chapters.

Domestic livestock plays a major role in meeting the food requirement of human beings. Especially with dwindling resources, improvement in production efficiency is primary to meet the ever-increasing demand for animal protein. The role of an animal breeder is to bring about a sustained improvement in the quality and quantity of such products. Over the years, there has been an enormous improvement in the production ability of livestock and statistical analysis has played a predominant role in the application of principles of animal breeding to improve the productivity of animals. The combination of genetics and statistics developed into a separate branch of science called biometry.

The large volume, type and nature of animal breeding data and the complex nature of analytical requirement warrants additional tools for handling, storage, retrieval and solving complex equations. Accuracy, speed, computational requirement, applicability, etc., has resulted in the development of numerous software exclusive for animal breeding data analysis. The database management system is already explained in the chapter on ‘Nature of animal breeding data and database management’. This chapter gives a note on the commonly used animal breeding software.

Q1. Fill in the blanks with appropriate answers.

1. India ranks …first…. position in cattle population in the world.

2. India ranks … first …. position in buffalo population in the world.

3. India ranks … first ……. position in total milk production in the world.

4. …Buffalo…….. species produce the highest amount of milk in India.

5. Frieswal cattle is a cross of …Holstein Friesian….and ……Sahiwal…

6. Mehsana buffalo is a cross of …Murrah….and ……Surti……

7. India ranks … first …. position in goat population in the world.

20th Livestock Census of India

India has highest cattle population (192.49 million), buffalo population (109.85), in the world producing 24% is the highest milk yield (221.1 million tons in the year 2021-2022, and per capita availability was 444 gm/day) in the world (Source NDDB). India produces 43% of world buffalo meat production. Unfortunately, 80% cattle and 70% buffaloes are non-descriptive and yield very low amount of milk.

After independence Indian Council of Agricultural Research (ICAR) has developed serval projects and plans for research and characterization of livestock species all over the country. Our country holds enormous genetic biodiversity in our domestic animals, result in increasing number of registered breeds in every decade. Breed registration Committee on its online meeting held on 5th December, 2023 approved registration of eight new breeds of livestock. This includes Aravali Chicken (Gujarat) Andamani Duck (Andaman and Nicobar Islands), Anjori Goat (Chhattisgarh), Andamani Goat (Andaman and Nicobar Islands), Bhimthadi Horse (Maharashtra), Andamani Pig (Andaman and Nicobar Islands), Macherla Sheep (Andhra Pradesh), Frieswal Cattle (Uttar Pradesh and Uttarakhand). Endangered, critical and vulnerable breeds of livestock also have been identified by ICAR which need more scientific research and multiplication breed.

Using the FAO criteria, Bargur and Siri cattle breeds and Attapadi goat breeds were categorized under vulnerable status of risk; Krishna Valley, Mewati, Pullikulam and Punganur cattle breeds, Chilika and Toda buffalo breeds and Karnah and Poonchi sheep breeds under endangered status of under risk and Vechur cattle under critical status of risk. All these breeds need immediate steps for rescue by using suitable conservation methodology. Breed-wise census should be continued in future so that trends in breed populations may also be estimated for fine tuning of risk assessment of breeds.

Rate of inbreeding in Indian livestock breeds: The rate of inbreeding estimated for different breeds of cattle was well below 0.5% (needed for a breed ‘not at risk’) except for Mewati (1.193%), Pullikulam (0.72%) and Vechur (17.893%). The rate of inbreeding in buffalo breeds was also well below 0.5% except in Chilika buffalo, where it was 0.731%. The rate of inbreeding of these breeds may be reduced by increasing the number of breeding males and in Vechur also the breeding females. The rate of inbreeding in all the breeds of sheep (Indian or exotic), goat and pig were estimated to be less than 0.5%. In these species, a good balance of breeding males and females is always expected.

Some have described Mithun as domesticated Gaur others as a hybrid descent from the crossing of gaur bulls and common cows. Considered to have originated along the Assam and Myanmar border. • Mithun, also known as ‘Cattle of Mountain” is an important bovine species of north-eastern hill region of India and also of China, Myanmar, Bhutan and Bangladesh. This magnificent massive bovine is presently reared under free-range condition in the hill forests at an altitude of 1000 to 3000 m above mean sea level.

• Mithun plays an important role in the socio-economic and cultural life of the local tribal population.

• Presently, this animal is mainly reared for meat, which is considered to be more tender and superior over the meat of any other species.

• Mithun milk, though produced less in quantity, is of high quality and can be used for preparation of various milk products.

• Leather obtained from this species has been found to be superior to cattle.

The yak is a bovine species that provides livelihoods for people in high altitude conditions of extreme harshness and deprivation. Yaks live predominantly on the “roof of the world”, as the Qinghai-Tibetan Plateau is often called, and provide milk, meat, hair and down fibre, hides, draught power and dung (principally used as fuel). The yak has physical and physiological characteristics that allow it to thrive at high altitudes (low oxygen) and in extreme cold (at temperatures as low as -40 °C) and to survive feed shortages in the winter (FAO).

The milk yield of the yak cow is often no more than the amount suckled by the calf and is not comparable to the milk yield of dairy cattle. However, although milk offtake for human consumption may be at the expense of the calf, yak milk is important for households. In economic terms, milk is often the most important yak product. Yak milk is generally produced by small-scale farmers in traditional systems where management is highly influenced by climate and seasons. Lactation is seasonal and yak cows produce between 150 and 500 litres; yields vary by breed and location. Lactation can generally continue into a second year without another calving. During the winter, yak cows do not go dry and continue to produce a small amount of milk, with milk yields as low as 2 to 4 litres/month. During the second year of lactation, milk yields are between half and two-thirds of those in the first year. Currently, there are no specialized dairy yak breeds (FAO).

The full name of an organism technically has eight terms. For the dog it is: Eukarya, Animalia, Chordata, Mammalia, Carnivora, Canidae, Canis, and lupus. Notice that each name is capitalized except for species, and the genus and species names are italicized. Scientists generally refer to an organism only by its genus and species, which is its two-word scientific name, or binomial nomenclature. Therefore, the scientific name of the dog is Canis lupus. The name at each level is also a taxonomy Carnivora is the name of the taxon at the order level; Canidae is the taxon at the family level, and so forth. Organisms also have a common name that people typically use, in this case, dog. Note that the dog is additionally a subspecies: the “familiaris” in Canis lupus familiaris. Subspecies are members of the same species that are capable of mating and reproducing viable offspring, but they are separate subspecies due to geographic or behavioural isolation or other factors. Dogs, which are under the species Canis lupus familiaris, are known to have a total of 78 chromosomes (2n). The diploid genes can be classified into 38 pairs with two sex chromosomes.

Donkeys can also be termed as ass (Equus africanus asinus) and is a domesticated member of the horse family, Equidae with chromosome number 62. The Wild ass of Africa, E. africanus is the wild ancestor of the donkey. For approximately 5000-7000 years, the donkey has been used as a working animal.

An adult male donkey is a jack or jackass, an adult female is a jenny or jennet, and an immature donkey of either sex is a foal. Jacks are often mated with female horses (mares) to produce mules, the less common hybrid of a male horse (stallion) and jenny is called hinny. NBAGR-ICAR has registered three breeds of donkey till date.

1. Kachchhi

• These donkeys are found in Kachchh district of Gujarat.

• Coat colour is mainly grey (dorsal surface grey and ventral surface white) followed by white, brown and black.

• Forehead is convex. Nasal bone is straight.

• Height at wither ranges from 77 to 115 cm.

• Docile in temperament.

• Only donkeys are used for agricultural purposes like inter cultivation for weed removing.

• Also utilized for transportation as donkey cart, as pack animal during pastoralist migration, etc.

In some developing countries, milk from horses (Equus caballus) and donkeys (Equus asinus) is an essential food for poor farmers. Generally, horses are more commonly used for dairy purposes in cool areas and donkeys in dry semi-arid regions. Milking equines is time-consuming and has to be repeated five or six times a day. In addition, an equine will not release milk unless it is stimulated by the presence of its foal. Mare’s milk is commonly consumed in the steppe areas of Central Asia, where a traditional lactic-alcoholic beverage called koumiss is produced through fermentation. Horse milk is also an important source of animal protein for pastoralists in Mongolia. The consumption of donkey milk has become very marginal. In some African communities, donkey milk is consumed for medical purposes.

Equus is a genus of mammals in the family Equidae, which includes horses, asses, and zebras. Within the Equidae, Equus is the only recognized existing genus, comprising seven living species. Like Equidae more broadly, Equus has numerous extinct species recognized only from fossils. Equines are odd-toed ungulates with slender legs, long heads, relatively long necks, manes (erect in most subspecies), and long tails. All species are herbivorous, and mostly grazers, with simpler digestive systems than ruminants but able to subsist on lower-quality vegetation. The chromosome number of a horse is 64 (2n).

Camels could be exploited for augmenting the country’s milk production capacity as a supplementary milk resource in India for the benefit of increasing human population. Since milk production potential of camels in India have remained unexploited and considering its therapeutic utility it can fetch good prices. Camels are raised for milk, meat, fibre (wool and hair), transport and other work; their dung is used as fuel. Milk is often the most important camel product and is the staple food of nomads.

The camel is an important species of the Indian fragile desert ecosystem, a proven icon of adaptation with its unique bio-physiological characteristics and has formidable ways of living in harsh situations of arid and semi-arid regions. The proverbial Ship of Desert earned its epithet on account of its indispensability as a mode of transportation and draught ability in desert. However, its utilities are subject to continuous social and economic changes. The camel has also played a significant role in civil law and order, defence and battles from the ancient times till date. Camels formed an important component of the Mauryan Army (C.322-232 BC) and continued through the Mughal period (1200-1700 AD) to the present times.

Pork production in India is limited, representing only 9% of the country’s animal protein sources. Production is concentrated mainly in the northeastern states of the country and consists primarily of backyard and informal sector producers. The contribution of pork products in terms of value works out to 0.80% of total livestock products and 4.32% of the meat and meat products. The contribution of pigs to Indian exports is very poor.

The chromosomes of the domestic pig (Sus scrofa domesticus) are known to be prone to reciprocal chromosome translocations and other balanced chromosome rearrangements with concomitant fertility impairment of carriers. The domestic pig has diploid chromosome (2n) number 38. The domestic pig karyotype shows a tendency for balanced structural chromosomal rearrangements, such as reciprocal, Robertsonian, and tandem translocations, as well as inversions. There is extensive polymorphism in the heterochromatin, with G-C-rich heterochromatin located in centromere regions of biarmed chromosomes and less G-C-rich heterochromatin in the centromere regions of one-armed chromosomes.

The diploid chromosome number of the pig is 2n = 38, consisting of 18 autosomal chromosome pairs, which vary in length and morphology (12-bi-armed and 6 one-armed pairs), and two sex chromosomes, XX or XY. Robertsonian translocation is known to occur in the acrocentric chromosomes 13, 14, 15, 16, 17, and 18. In these cases, the chromosomes fuse at the centromeric region, resulting in the production of two derivative chromosomes, a large bi-armed chromosome, and a secondary short chromosome often lost in subsequent cell divisions. Thus, the karyotype of a domestic pig carrying Robertsonian translocation has a distinct 2n = 37 diploid chromosome number, with the noticeable addition of a novel large bi-armed chromosome.

Origin of Fowl

Domestication of poultry seems to have been undertaken in south-east Asia. The chickens were brought to India by 1000 BC, and later on they spread north, westwards and reached Greece by 525 BC. By the beginning of Christian era, the birds were already popular in West Asia and East Europe, and then gradually reached South Africa, Australia, Japan, USSR and USA.

Red Jungle fowls are the ancestors of the present-day poultry breeds. There are four known species of wild fowl and they belong to the same genus “Gallus” meaning a cock. The four species are as follows:

The Red Jungle fowl is supposed to be the main contributor for the development of modern-day poultry and is widely distributed throughout Burma, China, India, Philippines, Sumatra and Thailand. The plumage (colour of the feather) of females resembles that of Brown Leghorn, the males have orange red feathers in hackle, wing bow and saddle regions, while the breast is black. Eggs are buff (off-white) in colour. The legs are slate (dark bluish grey) coloured. The comb is all red.

In India, goats are known as “poor man's cow” because they are an important source of income for poor and landless people. They can be reared on cheaper resources easily than other livestock.

Goats come under the genus Capra have evolved from five wild species, including Capra hircus (which includes Bezoar), Capra ibex, Capra caucasica, Capra pyrenaica, and Capra falconeri. This evolutionary pattern contributes to their phenotypic diversity and adaptability to various environments. The chromosome profile of goats (specifically the Capra hircus species) reveals some interesting features which are as follows:

Chromosome Number
The modal chromosome number for goats is 60.
These chromosomes can be categorized into different types based on their centromere position:
Autosomes: These are either acrocentric or telocentric.
X Chromosome: It is acrocentric.
Y Chromosome: It is submetacentric.

Identification

Quinacrine-mustard staining and fluorescence microscopy allow us to identify 28 out of 30 chromosome pairs in goats.

According to the karyotyping the domestic sheep (Ovis aries) has 54 chromosomes. The following is a brief summary of their chromosome composition:

Autosomes: There are one pair of sex chromosomes, 52 autosomes and three pairs of these autosomes are submetacentric (having a centromere slightly off centre), while the rest are acrocentric (with the centromere near one end).

Sex Chromosomes: The X chromosome is acrocentric and the Y chromosome varies from submetacentric to metacentric.

Important features

• According to the Food and Agriculture Organization Corporate Statistical (FAOSTAT) Database (2019) and database of the United Nations Food and Agriculture Organization, the top three countries by the number of heads of sheep were: China (163.48 million heads), India (74.26 million) and Australia (65.75 million). • India has second largest sheep population in the World.

• Sheep milk is an important product in the Near East and North Africa (9% of total milk production) and sub-Saharan Africa (4%).

• The countries with the most dairy sheep are China, Sudan, Turkey and Algeria (FAO).

• Major sheep milk producers are China, Turkey and Greece.

• More than half of the world’s sheep population is found in developing countries. Sheep are more prevalent than goats in cold climatic conditions. The major produce from Sheep production are milk, meat, skin, fibre and manure. However, most of the small-scale producers in developing countries raise sheep for meat or sale.

The buffalo belonged to the Bovidae family, Bovinae subfamily and the scientific name is Bubalus bubalis. This is descended from the Bubalus arnee or wild Indian buffalo, and is widely dispersed throughout Southern Asia. The world population of buffaloes is approximately 204 million head: more than 98% are in Asia; 0.8%are in Africa, particularly in Egypt; 0.9% are in South America; and 0.2% are in Europe (FAO, 2024).

The countries with the largest numbers of dairy buffaloes are India, Pakistan, China, Nepal and Egypt. In Pakistan and Nepal there are more dairy buffaloes than dairy cows. Water buffaloes are the main source of milk in South Asia. India is the largest water buffalo milk producer compared to Pakistan, where buffaloes produce more milk than cattle.

 Scientific classification
 Genus: Bubalus 
 Species: bubalis
 Wild water buffalo: Bubalus arnee
 Domestic water buffalo: Bubalus bubalis
 Lowland anoa: Bubalus depressicornis
 Mountain anoa: Bubalus quarlesi
 Tamaraw: Bubalus mindorensis
 Cebu tamaraw: Bubalus cebuensis