doctor of philosphy in animal genetics and breeding by tavsief ahmad

211 Pages·2016·4.04 MB·English

GENETIC AND MOLECULAR CYTOGENETIC EVALUATION OF
THARPARKAR AND KARAN FRIES MALES

THESIS SUBMITTED TO THE
NATIONAL DAIRY RESEARCH INSTITUTE, KARNAL
(DEEMED UNIVERSITY)
IN PARTIAL FULFILMENT OF THE REQUIREMENTS
FOR THE DEGREE OF

DOCTOR OF PHILOSPHY
IN
ANIMAL GENETICS AND BREEDING
BY
TAVSIEF AHMAD
M.V.Sc.
(Animal Genetics & Breeding)

DAIRY CATTLE BREEDING DIVISION
NATIONAL DAIRY RESEARCH INSTITUTE
(I.C.A.R.)
KARNAL-132 001 (HARYANA), INDIA
2014

Regn. No. 1071105

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Acknowledgement
All praise is due to Allah (SWT) in profound sense of love, adoration, and awe of the power,
glory and mercy. I have no words to express my immense gratitude to Him for bestowing upon
me the blessings, patience, strength and caliber for successful completion of this work.
I have this honour to confer my sincere appreciation to my respected guide and Chairman of
the Advisory committee Dr. A. K. Gupta, Principal Scientist and Head, Dairy Cattle Breeding
Division, NDRI, Karnal for channelising and focusing my energy to explore the unknown. As
my mentor and as an expert of Animal Genetics & Breeding, his concrete acquaintance on the
subject area and deep scientific temperament has assisted me in every possible way to accomplish
this task. I have deepest appreciation for his constant guidance, thought provoking creativity,
enormous encouragement, continuous valuable suggestions and critical analysis throughout the
study. His passion and patience answered my endless queries and corrected my shortcomings.
Without his deep involvement, care and support at every stage, this PhD work would not have
been accomplished.
At the outset, I consider myself fortunate and greatly privileged in expressing my deep sense
of gratitude and indebtedness to have partly worked under the supervision and guidance of Dr.
B. R. Yadav, Ex-National Fellow and Retd. Principal Scientist, Dairy Cattle Breeding Division,
NDRI, Karnal.
I also owe my sincere thanks to my respected members of the advisory committee Dr. A.
K. Chakravarty, Principal scientist, DCB Division, Dr. I. D. Gupta Principal scientist, DCB
Division, Dr. T. K. Mohanty Principal scientist, LPM Division, Dr. R. Malhotra, Principal
scientist, DESM Division and Dr. A. Kumaresan, Senior scientist LPM Division for their
suggestions, supportive attitude and sustained encouragement during the tenure of my study.
I express my warmest regards to all the faculty members of the DCB Division, NDRI,
Karnal; Dr. Avtar Singh, Principal scientist and Dr. Archana Verma, Principal scientist for
their affection, expert guidance and needful suggestions that helped me in improving the
eminence of my work.
I extend an elite memorandum of thanks to Dr. A. K. Srivastava, Director & Vice
Chancellor, National Dairy Research Institute, Karnal for providing me the opportunity to
pursue higher studies from such a great institute and granting approval for my research topic.
I am fortunate to learn from the knowledge and experience of my master’s degree advisor
Prof. T. A. S. Ganai Registrar, SKUAST-K who has been always the source of inspiration. The
promotion of my experimental skill and maturation of my theoretical knowledge has all been due
to him.
A word of special thanks goes to my NDRIan friends Dr. Ankit Magotra, Dr. Vijay
Sharma, Dr. Sumit Mahajan, Dr. Ajay, Dr. Raghvendra, & Dr. Anil for their persistent
and permanent love & affection, understanding, compassion and positive reciprocity in
everything.
I extend and elite memorandum of thanks and warmest regards to Dr. Zubair Ahsan.
Special thanks to my Navodian friends at my home Babar, Altaf, Khalid, Arshid,
Firdous, Suhail, Imran and Qaiser.
People whose contributions have helped me and have left an everlasting impression of
being the wonderful people who acquainted me with their scholastic ideas, include, Dr. Ovais,
Syed Aftab, Shahid, Nazir, & Zaffar Iqbal
I extend warm personal appreciation to Dr. Shaktikant Das and Dr. Ved Prakash for
their collective spirit that stood by me during this period.
I have been very much enthused by the support and affection shown by my juniors, Dr.
Mohsin, Hujaz, Bilal, Irfan, Shaktivel, Saroj, Pushpendra & Manvender.
The financial support provided by Indian Council of Agricultural Research, New Delhi
is duly acknowledged.
Where I would have been without my parents? There are no words which can grossly
express my feelings towards my loving parents for their eternal and undemanding affection and
ethical support. Without their inspiration and encouragement, I would not have been able to trod
even a single stride. They have supported and stood by me at every point of my subsistence and I
give the entire success of my life to their love and affection. I miss their prayers and wish they
would have been with me! May Allah forgive and grant them paradise (Aameen).
My sincere love and thanks to my sister Sameera and brothers Dr. Javaid and Irfan,
for those lovable moments, which they have given me. It is the warmth of their love and ever
willing care that I could count upon for any kind of challenges of my life. They rendered me
enormous support during the whole tenure of my research and given me the encouragement and
motivation needed. Am sincerely obliged and indebted to whole of my extended family for their
care and support at every step of my life.
I will miss lifelong the great childhood moments of my sweet angels, Iqra, Misbah,
Faiyza, Falak, Nayeem, Faheem and Saadiq.
Finally, I wish to acknowledge the contributions of different people who have left
untraced footprints and who have made this thesis possible in the real sense, which I might have
inadvertently forgotten to mention.

Tavsief Ahmad
CONTENTS
Chapter Title Page
No No.
1 INTRODUCTION 1-4
2. REVIEW OF LITERATURE 5-39
2.1 Growth traits in cattle 5
2.2 General performance and effect of non-genetic 6
factors on different body weights
2.2.1 Birth weight 6
2.2.2 Body weight at six months 6
2.2.3 Effect of non-genetic factors on body 7
weights
2.2.3.1 Period of birth (pob) 7
2.2.3.2 Season of birth 7
2.2.4 Growth curves, bands and rate 12
2.2.4.1 Growth curves 12
2.2.4.2 Growth bands 12
2.2.4.3 Growth rate 12
2.3 Genetic parameters of growth traits 13
2.3.1 Heritability estimates of body weights 14
2.3.2 Genetic and phenotypic correlations 16
2.4 Genetic evaluation of growth traits 17
2.5 Chromosomes of cattle 18
2.5.1 Chromosome anomalies in farm animals 19
2.5.1.1 Translocations 20
2.5.1.2 Fragile sites on chromosomes 21
2.5.1.3 Historical review 24
2.5.1.4 Domestic animal fragile sites 26
2.5.1.5 Bovidea 26
2.5.1.6 Fragile sites and evolutionary 28
breakpoints
2.5.1.7 Mechanisms and molecular 29
characterization
Chapter Title Page
No No.
2.5.1.8 A model for instability at CFSs 31
2.5.1.9 Future efforts 33
2.6 Semen evaluation 35
2.6.1 Ejaculate volume (ml) 35
2.6.2 Mass activity 36
2.6.3 Individual motility (%) 36
2.6.4 Spermatozoa concentration (millions/ml) 37
2.6.5 Hypo-osmotic swelling test (HOST) (%) 37
2.6.6 Percent non eosinophilic (live) sperms 38
3. MATERIALS AND METHODS 40-77
3.1 General appraisal of data 40
3.2 Location of the farm and climate 41
3.3 Brief history of the ndri KF and TP herd 41
3.4 General feeding, breeding and managemental 42
practices
3.5 Recording of information 42
3.6 Standardization of records 43
3.7 Classification of data 43
3.7.1 Classification of seasons 43
3.7.2 Classification of periods 43
3.7.3 Classification of genetic group 44
3.7.4 Classification of order of parity 44
3.8 Statistical analysis 45
3.8.1 Measures of central tendency and 45
dispersion
3.8.2 Least squares analysis 45
3.8.3 Duncan’s multiple range test (DMRT) 46
3.8.4 Estimation of genetic parameter 47
3.8.5 Sire evaluation 51
3.9 Growth curves and growth bands 52
3.9.1 Fitting of growth curve 52
Chapter Title Page
No No.
3.9.2 Construction of growth bands 53
3.10 Conventional cytogenetical examination of fragile 53
chromosomes
3.10.1 Chromosome preparations 53
3.10.2 Conventional staining with giemsa 58
3.10.3 Screening and photomicrography of 59
slides
3.11 Molecular assessment of fragile sites 59
3.11.1 Blood collection 59
3.11.2 Isolation of DNA 59
3.11.3 Evaluation of Quality, Purity and 61
Concentration
3.12 Primers 62
3.12.1 Dissolving the Primers 64
3.12.2 PCR amplification of different fragile site 65
associated genes
3.12.3 Agarose gel electrophoresis of PCR 70
product
3.12.4 Visualization of gel 70
3.13 Assessment of seminal attributes 70
3.13.1 Semen collection 70
3.13.2 Volume 70
3.13.3 Mass activity 70
3.13.4 Individual progressive motility estimate 71
(%)
3.13.5 Sperm concentration 72
3.13.6 Non-eosinophilic (live) Sperm Count 73
3.13.7 Hypo-osmotic swelling Test (HOST) 74
3.13.8 Acrosomal integrity test 75
3.13.9 Libido 76
3.14 Classification of percentage of fragility 77
Chapter Title Page
No No.

4 RESULTS AND DISCUSSION 78-109
4.1 Descriptive statistics of growth traits in KF and TP 79
males
4.1.1 Birth weight and other weights 79
4.2 Least squares analysis of variance for birth weight 79
and other body weights
4.2.1 Least squares analysis of variance for 80
birth weight in KF and TP males
4.2.2 Least squares analysis of variance for 1 82
month body weight in KF and TP males
4.2.3 Least squares analysis of variance for 2 82
month body weight in KF males
4.2.4 Least squares analysis of variance for 3 83
month body weight in KF males
4.2.5 Least squares analysis of variance for 4 83
month body weight in KF males
4.2.6 Least squares analysis of variance for 5 83
month body weight in KF males
4.2.7 Least squares analysis of variance for 6 84
month body weight in KF males
4.2.8 Least squares analysis of variance for 7 85
month body weight in KF males
4.2.9 Least squares analysis of variance for 8 85
month body weight in KF males
4.2.10 Least squares analysis of variance for 9 86
month body weight in KF males
4.2.11 Least squares analysis of variance for 86
10 month body weight in KF males
4.2.12 Least squares analysis of variance for 87
11 month body weight in KF males