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Discovery of Candidate Genes for Stallion Fertility from the Horse Y Chromosome

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Discovery of Candidate Genes for Stallion Fertility from the Horse Y Chromosome DISCOVERY OF CANDIDATE GENES FOR STALLION FERTILITY FROM THE HORSE Y CHROMOSOME A Dissertation by NANDINA PARIA Submitted to the Office of Graduate Studies of Texas A&M University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY August 2009 Major Subject: Biomedical Sciences DISCOVERY OF CANDIDATE GENES FOR STALLION FERTILITY FROM THE HORSE Y CHROMOSOME A Dissertation by NANDINA PARIA Submitted to the Office of Graduate Studies of Texas A&M University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Approved by: Chair of Committee, Terje Raudsepp Committee Members, Bhanu P. Chowdhary William J. Murphy Paul B. Samollow Dickson D. Varner Head of Department, Evelyn Tiffany-Castiglioni August 2009 Major Subject: Biomedical Sciences iii ABSTRACT Discovery of Candidate Genes for Stallion Fertility from the Horse Y Chromosome. (August 2009) Nandina Paria, B.S., University of Calcutta; M.S., University of Calcutta Chair of Advisory Committee: Dr. Terje Raudsepp The genetic component of mammalian male fertility is complex and involves thousands of genes. The majority of these genes are distributed on autosomes and the X chromosome, while a small number are located on the Y chromosome. Human and mouse studies demonstrate that the most critical Y-linked male fertility genes are present in multiple copies, show testis-specific expression and are different between species. In the equine industry, where stallions are selected according to pedigrees and athletic abilities but not for reproductive performance, reduced fertility of many breeding stallions is a recognized problem. Therefore, the aim of the present research was to acquire comprehensive information about the organization of the horse Y chromosome (ECAY), identify Y-linked genes and investigate potential candidate genes regulating stallion fertility. To achieve theses goals, a direct cDNA (complementary DNA) selection procedure was used to isolate Y-linked genes from horse testes and 29 Y-specific genes were identified. All 29 genes were mapped to ECAY and their sequences were used to iv further expand the existing map. Copy number analysis identified 15 multicopy genes of which 9 were novel transcripts. Gene expression analysis on a panel of selected body tissues showed that some ECAY genes are expressed exclusively in testes while others show ubiquitous or intermediate expression. Quantitative Real-Time PCR using primers for 9 testis-specific multicopy genes revealed 5 genes with statistically significant differential expression in testis of normal fertile stallions and stallions with impaired fertility. Gene copy number analysis showed that the average copy number of 4 such genes was decreased in subfertile/infertile stallions compared to normal animals. Taken together, this research generated the first comprehensive physical gene map for the horse Y chromosome and identified a number of candidate genes for stallion fertility. The findings essentially expand our knowledge about Y chromosome genes in horses, open a new avenue for investigating the potential role of ECAY genes in stallion fertility which contribute to the development of molecular tools for the assessment of fertility in stallions. v DEDICATION This work is dedicated to my loving parents, Mrs. Kalpana Paria and Dr. Nandadulal Paria. This research would not have been possible without their blessings, encouragement and constant support. vi ACKNOWLEDGEMENTS The journey of three and half years of my graduate program has been quite eventful and memorable with the help and co-operation of a lot of people to whom I’m really grateful from the bottom of my heart. First and foremost, I would like to express my sincere gratitude to my major advisor Dr. Terje Raudsepp for her valuable guidance, suggestion and assistance throughout my entire project. I cannot remember a single incident when I required her help and she was not available!!! Thanks a lot, Terje, whatever I learnt from you, is going to be a big asset for my future. I’m grateful to all of my committee members for their immense help and co- operation during my research. I’m extremely thankful to Dr. Bhanu Chowdhary, who was more like my unofficial coadvisor. His valuable guidance always kept me on track and on top of things. He played a very significant role in my graduate career and I will always be grateful to him for his constant support. I would like to gratefully acknowledge Dr. William Murphy for patiently teaching me some of the experiments, helping me to troubleshoot and of course for his valuable suggestions. I would like to thank Dr. Paul Samollow for his insightful discussions and suggestions to improve my research. Many thanks go to Dr. Dickson Varner for his immense help in providing tissue samples for my study and valuable suggestions during my research. I’m especially thankful to all of my past and present lab members who helped me in this project as well as made my stay in this lab a wonderful one! I am especially vii grateful to Dr. Ashley Seabury for being a great office-mate, mentor and friend. She helped me in all possible ways whenever I encountered any difficulty. Many thanks go to Dr. Keith Durkin for his endless sequencing and helping me with tissue sample collection. I gratefully acknowledge Dr. Sankar Chaki for technical assistance and his jovial jestures that kept me smiling, Dr. Pranab Das for helping me with tissue collection and sequencing, Dr. Dhruva Mishra and Dr. Monica Vishnoi for being great labmates. I am also thankful to my fellow graduate students Priyanka Kachroo, Jana Caldwell and Jixin Wang who helped me either by providing tissue samples for my experiments or teaching me how to use new software and for being great co-workers! I would also like to thank my past lab members Dr. Christopher Seabury, Dr. Eun-Joon Lee, Dr. Deeann Wallis and Dr. Candice Brinkmeyer-Langford for their assistance during the early phase of my tenure. I would also like to thank Dr. Charle Love and Dr. Caroline Arnold for providing tissue samples, Dr. Loren Skow for letting me use the TAMU equine BAC library. My sincere thanks go to Alison Pearks Wilkerson who patiently taught me some of my experiments and she always had answers for my endless queries with a smiling face. My sincere gratitude goes to Dr. Brian Williams and the members of my support group at SCS who have been a major help during my entire process of disseratation writing. Thank you all. I am especially thankful to my friends Sucharita Bose, Soumya Ganguly, Rangan Gupta and Sharmila Ghosh whose support means a lot to me. Their love and friendship helped me to overcome any hurdle that I faced during my entire stay in USA. viii And finally I would like to acknowledge my parents, grandparents and all other family members who are thousands of miles away from me but still were a constant source of love, encouragement and blessings for me. They gave me the courage and strength to accomplish the goal that I came here for. Love you all. ix NOMENCLATURE BAC Bacterial Artificial Chromosome BES BAC End Sequence cDNA Complementary DNA ECA Equus caballus, horse ECAY Horse Y chromosome EST Expressed Sequence Tag FCA Felis catus, cat HSA Homo sapiens, human MMU Mus musculus, mouse MSY Male-specific region of Y chromosome PCR Polymerase Chain Reaction qRT-PCR Quantitative Real Time PCR RACE Rapid Amplification of cDNA Ends RH Radiation Hybrid RT-PCR Reverse Transcriptase PCR SNP Single Nucleotide Polymorphism STS Sequence Tagged Site x TABLE OF CONTENTS Page ABSTRACT.............................................................................................................. iii DEDICATION .......................................................................................................... v ACKNOWLEDGEMENTS ...................................................................................... vi NOMENCLATURE.................................................................................................. ix TABLE OF CONTENTS .......................................................................................... x LIST OF FIGURES................................................................................................... xii LIST OF TABLES .................................................................................................... xiii CHAPTER I GENERAL INTRODUCTION............................................................ 1 Overview of the Genetics of Male Fertility in Mammals.............. 1 Mammalian Y Chromosome and Its Role in Male Fertility .......... 19 Male Fertility in Horses................................................................. 38 Present Status of the Horse Y Chromosome Research .................. 40 Rationale of the Present Study....................................................... 41 II DISCOVERY OF Y-SPECIFIC GENES FROM HORSE TESTIS AND GENERATION OF A DETAILED MAP FOR THE HORSE Y CHROMOSOME............................................................................. 44 Introduction.................................................................................... 44 Objectives....................................................................................... 46 Materials and Methods................................................................... 46 Results............................................................................................ 60 Discussion...................................................................................... 74 III EVALUATION OF THE Y-LINKED
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