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Absolute Copy Number Differences of Y Chromosomal Genes Between Mukherjee et al. Journal of Animal Science and Biotechnology 2013, 4:15 http://www.jasbsci.com/content/4/1/15 JOURNAL OF ANIMAL SCIENCE AND BIOTECHNOLOGY RESEARCH Open Access Absolute copy number differences of Y chromosomal genes between crossbred (Bos taurus × Bos indicus) and Indicine bulls Ayan Mukherjee1*, Gulshan Dass1, Jagan Mohanarao G1,2, Moloya Gohain1, Biswajit Brahma1, Tirtha Kumar Datta1 and Sachinandan De1 Abstract Background: The Y chromosome in mammal is paternally inherited and harbors genes related to male fertility and spermatogenesis. The unique intra-chromosomal recombination pattern of Y chromosome and morphological difference of this chromosome between Bos taurus and Bos indicus make it an ideal model for studying structural variation, especially in crossbred (Bos taurus × Bos indicus) bulls. Copy Number Variation (CNV) is a type of genomic structural variation that gives information complementary to SNP data. The purpose of this study was to find out copy number differences of four Y chromosomal spermatogenesis-related candidate genes in genomic DNA of crossbred and purebred Indicine bulls. Result: Four Y chromosomal candidate genes of spermatogenesis namely, sex determining gene on Y chromosome (SRY), DEAD box polypeptide 3-Y chromosome (DDX3Y), Ubiquitin specific peptidase 9,Y-linked (USP9Y), testis-specific protein on Y chromosome (TSPY) were evaluated. Absolute copy numbers of Y chromosomal genes were determined by standard curve-based quantitative real time PCR. Copy numbers of SRY and TSPY genes per unit amount of genomic DNA are higher in crossbred than Indicine bulls. However, no difference was observed in DDX3Y and USP9Y gene copy numbers between two groups. Conclusion: The present study demonstrates that the structural organization of Y chromosomes differs between crossbred and Indicine bulls which are reproductively healthy as observed from analysis of semen attributes. The absolute copy numbers of SRY and TSPY genes in unit mass of genomic DNA of crossbred bulls are significantly higher than Indicine bulls. No alteration in absolute copies of DDX3Y and USP9Y gene was found between the genome of crossbred and Indicine bulls. This study suggests that the DDX3Y and USP9Y arelikelytobesinglecopygenesinthegenomeofcrossbredandIndicinebullsand variation in Y chromosome length between crossbred and Indicine bulls may be due to the copy number variation of SRY gene and TSPY array. Keywords: Absolute copy, SRY, DDX3Y, USP9Y,TSPY, Crossbred Background recombination pattern of Y chromosome with its X- The Y chromosome plays an essential role in male sex counterpart makes it prone to structural variation [4]. development, spermatogenesis and male fertility [1]. The Changes in DNA content and structure are a significant eutherian Y chromosome has unique characteristic feature source of genetic and phenotypic variation among individ- that most part of this chromosome escapes meiotic recom- uals [5-8]. These types of structural variations ranging from 1 bination process with X chromosome except two regions kilobase (kb) to 5 megabase (Mb) comprised mainly of copy at the tips of the X and Y chromosomes [2,3]. In absence numbervariation(CNVintheform of large-scale insertions of inter-chromosomal recombination the repeated gene and deletions), as well as inversions and translocations. sequences within a chromatid or between sister chromatids Studies on human Y chromosome has indicated act as substrates for recombination. This unique the presence of 78 protein coding genes that encode 27 (18 single copy genes and 9 gene families) distinct pro- * Correspondence: [email protected] teins [3]. SRY gene encodes a protein product containing 1Animal Genomics Lab, Animal Biotechnology Centre, National Dairy Research Institute, Karnal, India HMG box domain. The domain binds to DNA in the Full list of author information is available at the end of the article © 2013 Mukherjee et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Mukherjee et al. Journal of Animal Science and Biotechnology 2013, 4:15 Page 2 of 7 http://www.jasbsci.com/content/4/1/15 minor groove at a 6-base consensus target sequence and Assessment of seminal quality parameters subsequently activates the cascade of testis determining We assessed progressive motility, plasmalemma and acro- pathway [9]. DDX3Y and USP9Y genes are construed as somal integrity of the spermatozoa to evaluate the bulls as ‘fine-tuner’ of normal spermatogenesis process [10-12]. these are the most common semen evaluation tests in The protein product of the TSPY gene probably interacts cattle. The percentage of sperm showing progressive for- with type B cyclins and activates cyclin B-CDK com- ward motility was determined by mixing 100 μLofun- plexes. The activated complex, in turn, impacts on bio- diluted semen into pre-warmed tubes containing 900 μL logical machineries in spermatogonial cell renewal and of Tris buffer (pH 7.2). A thin drop of diluted semen was in prophase I spermatocyte differentiation [13]. placed on a pre-warmed glass slide (37°C) and evaluated Crossbreeding between taurine (Bos taurus) and indi- under microscope. The mean of the three estimations was genous cattle (Bos indicus) is a popular practice in used as the final motility score [17]. 6-carboxyfluorescein Indian dairy industry. Semen of three exotic breeds diacetate (CFDA) and propidium iodide (PI) staining was namely, European Holstein Friesian, Brown Swiss and done to assess the sperm viability as described by Jersey are extensively used for this purpose. The karyo- Selvaraju et al. [18]. Briefly, semen sample was incubated types of two bovine subspecies Bos taurus and Bos with phosphate buffered saline (PBS) based CFDA/PI indicus have a high similarity except for the morphology staining solution at 37°C for 15 min. After incubation, of the Y chromosome [14]. Y chromosome in Bos taurus 0.2% glutaraldehyde was added and stained sample were is submetacentric and acrocentric in Bos indicus. This examined under magnifications of 400× using an Olympus morphological difference between Bos taurus and Bos BX51 microscope (Olympus America, Center Valley, PA, indicus Y chromosome is the consequence of pericentric USA) equipped with CFDA filter set (excitation, 510– inversion [15]. In crossbred animal this difference in Y 560 nm; emission, 505 nm). The sperm showing complete chromosome morphology may lead to small deletions or green fluorescence were considered plasmalemma intact altered position between the synapse region of the X and (live), and the cells showing partial or complete red nuclei Y chromosomes, or change in genes present on sex were classified as dead. The hypo osmotic swelling chromosomes. So far no study has been conducted on Y test was performed for assessment of sperm membrane chromosomal gene copy number determination and integrity based on curled and swollen tails. The assay their comparison between crossbred and Indicine bulls. was performed mixing neat semen with 150 mOsm/L Therefore, present study was designed to investigate ab- hypoosmotic solution (13.51 g fructose + 7.35 g trisodium solute copy number differences of major Y chromosomal citrate per liter of distilled water) and incubating at genes SRY, DDX3Y, USP9Y and TSPY between Karan 38.5°C for 1 h [19]. After incubation, semen sample was Fries (a crossbred) and Sahiwal (purebred Bos indicus). examined under the high power magnification (400×) We included reproductively healthy bulls in this study to of a bright field microscope. Acrosomal integrity of the avoid animals having poor semen quality which could be sperm was assessed by staining air-dried smears with sequelae to the detrimental changes in Y chromosomal fluorescein isothiocyanate-conjugated pisum sativum gene copies. agglutinin (FITC-PSA) staining [20]. Air-dried smear was flooded with the FITC-PSA and kept in darkness for Methods 30 min. Slides were washed in distilled water and Animals and semen collection mounted with glycerol with a cover slip. The fluorescence All the experimental procedures involving animals were pattern of 200 sperm in randomly selected fields was approved by the Institutional Animal Ethics Committee determined under Olympus BX51 microscope (Olympus (IAEC), National Dairy Research Institute, Karnal, India. America, Center Valley, PA, USA) with 1,000× magnifica- The seminal attributes of the bulls under study were tion. The proportions of intact, reacting, and reacted assessed and those consistently producing good quality acrosome were expressed as percentages of the respective semen were included in the study. Semen samples were patterns in the total number of sperm counted [21]. collected from 10 Karan Fries (F1 generation crossbred of Holstein-Friesian sire and Tharparkar or Sahiwal Collection of blood and isolation of genomic DNA dam) and 10 Sahiwal (purebred Bos indicus) bulls by About 10 mL of blood sample was collected from each W artificial vagina (IMV, L’Aigele cedex, France) in the early animal in sterile Vacutainer (Beckton-Dickinson, Franklin morning. The volume of the semen was measured in a Lakes, NJ, USA) containing sodium heparin as an anti- graduated conical tube, mass motility was evaluated by coagulant. The collected samples were stored at 4°C light microscopy and sperm concentration
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