Detection of genomic regions affecting reproductive traits in Baluchi sheep using high density markers

Document Type : Research Paper

Authors

1 Ph.D Graduated Student of Genetics and Animal Breeding Department, Sari Agriculture Science and Natural Resources University (SANRU), Iran

2 Professor, Genetics and Animal Breeding Department, Sari Agriculture Science and Natural Resources University (SANRU), Iran

3 Assistant Professor, Genetics and Animal Breeding Department, Sari Agriculture Science and Natural Resources University (SANRU), Iran

4 Faculty member of Genetics and Animal Breeding Department, ALMA MATER STUDIORUM- University of Bologna, Italy

Abstract

Genetic improvement in reproductive and growth traits is major goal in sheep breeding. In this study, we performed a genome wide association study for detection of quantitative trait loci affecting reproductive traits in Baluchi sheep. For this purpose, blood samples were collected from a total of 96 ewes and data on their reproductive traits including total litter weight at birth (TLWB), litter mean weight per lamb born (LMWLB), total litter weight at weaning (TLWW), litter mean weight of lambs at weaned (LMWLW) and number of lambs alive at six months (NLA6m) in four parity. After DNA extraction, samples were genotyped using the Illumina Ovine SNP 50K BeadChip assay. Using PLINK software, a GWA study was performed in linear (GLM) and logistic regression analyses with a model included SNPs effect and sex and number of parities as fixed effects. A total of eight SNPs were found on chromosomes 1, 4, 10, 15 and 17 at the 5% chromosome-wise significance level (P<0.05) for studied reproductive traits. Also, study of genes and QTLs in these regions showed genes and QTLs affecting growth and reproductive traits. The results of this study could be used for discovery of causative variants for reproductive traits in sheep breeding programs.

Keywords

Main Subjects

References

ضمیری م. ج. 1385. فیزیولوژی تولید مثل، انتشارات حق شناس.
Al- Mamun H. A., Kwan P., Clark S. A., Ferdosi M. H., Tellam R. and Gondro C. 2015. Genome-wide association study of body weight in Australian Merino sheep reveals an orthologous region on OAR6 to human and bovine genomic regions affecting height and weight. Genetics Selection Evolution, 47: 66.
Andersson L. and Georges M. 2004. Domestic-animal genomics: deciphering the genetics of complex traits. Nature Reviews Genetics, 5: 202-212.
Ayllon F., Kjærner-Semb E., Furmanek T., Wennevik V., Solberg M. F., Dahle G., Taranger G. L., Glover K. A., Almén M. S. and Rubin C. J. 2015. The vgll3 locus controls age at maturity in wild and domesticated Atlantic salmon (Salmo salar L.) males. PLoS Genetics, 11: 1-15.
Barrett J. C., Fry B., Maller J. and Daly M. J. 2004. Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics, 21: 263-265.
Boichard D., Grohs C., Bourgeois F., Cerqueira F., Faugeras R., Neau A., Rupp R., Amigues Y., Boscher M. Y. and Levéziel H. 2003. Detection of genes influencing economic traits in three French dairy cattle breeds. Genetics Selection Evolution, 35: 77-102.
Cousminer D. L., Berry D. J., Timpson N. J., Ang W., Thiering E., Byrne E., Taal H. R., Huikari V., Bradfield J. P. and Kerkhof M. 2013. Genome-wide association and longitudinal analyses reveal genetic loci linking pubertal height growth, pubertal timing, and childhood adiposity. Human Molecular Genetics, 22: 2735–2747.             
Devlin B. and Roeder K. 1999. Genomic control for association studies. Biometrics, 55: 997-1004.     
Dolan J., Walshe K., Alsbury S., Hokamp K., O'keeffe S., Okafuji T., Miller S. F., Tear G. and Mitchell K. J. 2007. The extracellular leucine-rich repeat superfamily; a comparative survey and analysis of evolutionary relationships and expression patterns. BMC Genomics, 8: 1-24.  
Duguma G., Schoeman S., Cloete S. and Jordaan G. 2002. Genetic parameter estimates of early growth traits in the Tygerhoek Merino flock. South African Journal of Animal Science, 32: 66-75.        
Ekiz B., Özcan M., Yilmaz A. and Ceyhan A. 2005. Estimates of phenotypic and genetic parameters for ewe productivity traits of Turkish Merino (Karacabey Merino) sheep. Turkish Journal of Veterinary and Animal Sciences, 29: 557-564.
Falconer D. S. and Mackay T. F. C. 1996. Introduction to Quantitative Genetics, Ed 4. Longmans Green, Harlow, Essex, UK.
Fogarty N. 1995. Genetic parameters for live weight, fat and muscle measurements, wool production and reproduction in sheep: a review. Animal Breeding Abstracts. 
Gholizadeh M., Rahimi-Mianji G., Nejati-Javaremi A., De Koning D. J. and Jonas E. 2014. Genomewide association study to detect QTL for twinning rate in Baluchi sheep. Journal of Genetics, 93: 489-493.          
Halperin D. S., Pan C., Lusis A. J. and Tontonoz P. 2013. Vestigial-like 3 is an inhibitor of adipocyte differentiation. Journal of Lipid Research, 54: 473-481.         
Hayashi T., Ogawa T., Sato M., Tsuchida N., Fotovati A., Iwamoto H., Ikeuchi Y., Cassens R. G. and Ito T. 2001. S-myotrophin promotes the hypertrophy of myotube as insulin-like growth factor-I does. The International Journal of Biochemistry and Cell Biology, 33: 831-838.        
Hayashi T., Takeshita K., Tsuchida N., Kitano K., Kawabata S.-I., Iwanaga S. and Ito T. 1998. Purification of a novel muscle cell growth factor S-myotrophin from porcine skeletal muscle. The International Journal of Biochemistry and Cell Biology, 30: 897-908.
Hirschhorn J. N. and Daly M. J. 2005. Genome-wide association studies for common diseases and complex traits. Nature Reviews Genetics, 6: 95-108.
Höglund J. K., Buitenhuis A., Guldbrandtsen B., Su G., Thomsen B. and Lund M. 2009. Overlapping chromosomal regions for fertility traits and production traits in the Danish Holstein population. Journal of Dairy Science, 92: 5712-5719.    
Höglund J. K., Guldbrandtsen B., Lund M. S. and Sahana G. 2012. Analyzes of genome-wide association follow-up study for calving traits in dairy cattle. BMC Genetics, 13: 1-9.          
Kogo H., Tsutsumi M., Inagaki H., Ohye T., Kiyonari H. and Kurahashi H. 2012. HORMAD2 is essential for synapsis surveillance during meiotic prophase via the recruitment of ATR activity. Genes to Cells, 17: 897-912.
Lopes M. S., Bastiaansen J. W., Harlizius B., Knol E. F. and Bovenhuis H. 2014. A genome-wide association study reveals dominance effects on number of teats in pigs. PloS one, 9: e105867.  
Mcclure M., Morsci N., Schnabel R., Kim J., Yao P., Rolf M., Mckay S., Gregg S., Chapple R. and Northcutt S. 2010. A genome scan for quantitative trait loci influencing carcass, post‐natal growth and reproductive traits in commercial Angus cattle. Animal Genetics, 41: 597-607.       
Mcdowell E. N., Kisielewski A. E., Pike J. W., Franco H. L., Yao H. H. and Johnson K. J. 2012. A transcriptome-wide screen for mRNAs enriched in fetal Leydig cells: CRHR1 agonism stimulates rat and mouse fetal testis steroidogenesis. PloS one, 7: e47359.            
Meyer K. 2006. WOMBAT–A program for mixed model analyses by restricted maximum likelihood. User notes.’(Animal Genetic and Breeding Unit. University of New England: Armidale) Meyer K, Graser HU, Citeseer.         
Miller S., Dykes D. and Polesky H. 1988. A simple salting out procedure for extracting DNA from human nucleated cells. Nucleic Acids Research, 16: 1215.
Nishio M. and Satoh M. 2014. Including dominance effects in the genomic BLUP method for genomic evaluation. PloS one, 9: 1-6.             
Purcell S., Neale B., Todd-Brown K., Thomas L., Ferreira M. A., Bender D., Maller J., Sklar P., De Bakker P. I. and Daly M. J. 2007. PLINK: a tool set for whole-genome association and population-based linkage analyses. The American Journal of Human Genetics, 81: 559-575.       
Rosati A., Mousa E., Van Vleck L. and Young L. 2002. Genetic parameters of reproductive traits in sheep. Small Ruminant Research, 43: 65-74.
Sas S. and Guide S. U. S. 2003. Version 9.1. SAS Institute Inc., Cary, NC.       
Schreiweis M. A., Hester P. Y. and Moody D. E. 2005. Identification of quantitative trait loci associated with bone traits and body weight in an F2 resource population of chickens. Genetics Selection Evolution, 37: 1-22.            
Sen S., Kundu G., Mekhail N., Castel J., Misono K. and Healy B. 1990. Myotrophin: purification of a novel peptide from spontaneously hypertensive rat heart that influences myocardial growth. Journal of Biological Chemistry, 265: 16635-16643.
Shabir M., Ganai T., Misra S., Shah R. and Ahmad T. 2013. Polymorphism study of growth differentiation factor 9B (GDF9B) gene and its association with reproductive traits in sheep. Gene, 515: 432-438.  
Shiraishi S., Nakamura Y.-N., Iwamoto H., Haruno A., Sato Y., Mori S., Ikeuchi Y., Chikushi J., Hayashi T. and Sato M. 2006. S-myotrophin promotes the hypertrophy of skeletal muscle of mice in vivo. The International Journal of Biochemistry and Cell Biology, 38: 1114-1122.           
Snyman M., Olivier J., Erasmus G. and Van Wyk J. 1997. Genetic parameter estimates for total weight of lamb weaned in Afrino and Merino sheep. Livestock Production Science, 48: 111-116.
Speliotes E. K., Willer C. J., Berndt S. I., Monda K. L., Thorleifsson G., Jackson A. U., Allen H. L., Lindgren C. M., Luan J. A. and Mägi R. 2010. Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index. Nature Genetics, 42: 937-948.
Su G., Christensen O. F., Ostersen T., Henryon M. and Lund M. S. 2012. Estimating additive and non-additive genetic variances and predicting genetic merits using genome-wide dense single nucleotide polymorphism markers. PloS one, 7: 1-7. 
Thomas L. A., Akins M. R. and Biederer T. 2008. Expression and adhesion profiles of SynCAM molecules indicate distinct neuronal functions. Journal of Comparative Neurology, 510: 47-67.   
Vatankhah M., Talebi M. and Edriss M. 2008. Estimation of genetic parameters for reproductive traits in Lori-Bakhtiari sheep. Small Ruminant Research, 74: 216-220.             
Verardo L. L., Silva F. F., Lopes M. S., Madsen O., Bastiaansen J. W., Knol E. F., Kelly M., Varona L., Lopes P. S. and Guimarães S. E. 2016. Revealing new candidate genes for reproductive traits in pigs: combining Bayesian GWAS and functional pathways. Genetics Selection Evolution, 48: 1-9.  
Veugelers M., De Cat B., Ceulemans H., Bruystens A.-M., Coomans C., Dürr J., Vermeesch J., Marynen P. and David G. 1999. Glypican-6, a new member of the glypican family of cell surface heparan sulfate proteoglycans. Journal of Biological Chemistry, 274: 26968-26977.     
Vitezica Z., Moreno C., Bodin L., François D., Barillet F., Brunel J. and Elsen J. 2006. No associations between PrP genotypes and reproduction traits in INRA 401 sheep. Journal of Animal Science, 84: 1317-1322.            
Wang L. and Wang Y. 2012. Molecular characterization, expression patterns and subcellular localization of Myotrophin (MTPN) gene in porcine skeletal muscle. Molecular Biology Reports, 39: 2733-2738.       
Wojtasz L., Daniel K., Roig I., Bolcun-Filas E., Xu H., Boonsanay V., Eckmann C. R., Cooke H. J., Jasin M. and Keeney S. 2009. Mouse HORMAD1 and HORMAD2, two conserved meiotic chromosomal proteins, are depleted from synapsed chromosome axes with the help of TRIP13 AAA-ATPase. PLoS Genetics, 5: e1000702.
Zhang H., Wang Z., Wang S. and Li H. 2012. Progress of genome wide association study in domestic animals. Journal of Animal Science and Biotechnology, 3: 1-26.          
Zhao X., Zhao K., Ren J., Zhang F., Jiang C., Hong Y., Jiang K., Yang Q., Wang C. and Ding N. 2015. An imputation‐based genome‐wide association study on traits related to male reproduction in a White Duroc× Erhualian F2 population. Animal Science Journal, 87: 646-654.
Animal Production Research
Volume 6, Issue 3
December 2017
Pages 29-41

Files

Share

How to cite

Statistics