Copy number variations and quantitative trait loci in South African Brahman cattle

Transcription

1 Copy number variations and quantitative trait loci in South African Brahman cattle M.D. Wang 1, F.C. Muchadeyi 2, M. Makgahela 1,3, S. Mdyogolo 1 & A. Maiwashe 1,3 1 Agriculture Research Council-Animal Production Campus, Private Bag X2, Irene, 0062, South Africa. 2 Agriculture Research Council- Biotechnology Platform, Private Bag X1, Onderstepoort, 0110, South Africa. 3 University of the Free State, 205 Nelson Mandela Drive, Park West, Bloemfontein, South Africa

2 Background

3 Genetic variation Single base pair Large chromosomal events

4 structural variation

5 Copy number variation

6 Copy number variation CNVs Cattle Disease Adaptation Production Breed formation

7 Brahman Cattle In South Africa bulls 10 cows

8 Brahman Cattle In South Africa bulls 10 cows

9 Brahman Cattle In South Africa Adaptation

10 Brahman Cattle In South Africa Adaptation Maternal line

11 Materials & Methods

12 40 RSA Brahman Bulls Extract DNA Bovine HD GenomeStudio

13 40 RSA Brahman Bulls Extract DNA Bovine HD GenomeStudio Plink SNP QC LogR ratio B Allele frequency PennCNV

14 40 RSA Brahman Bulls Extract DNA Bovine HD GenomeStudio Plink LogR ratio B Allele frequency SNP QC CNVRs CNVs PennCNV

15 40 RSA Brahman Bulls Extract DNA Bovine HD GenomeStudio Genes Plink Gene representation QTLs LogR ratio B Allele frequency Gene ontology Simple Repeats SNP QC CNVRs CNVs PennCNV

16 Results

17 Genome wide CNVR detection CN CNVR MinL AvL MaxL SumL DEL DEL/DUP DUP Total

18 Genome wide CNVR detection CN CNVR MinL AvL MaxL SumL DEL DEL/DUP DUP Total

19 Genome wide CNVR detection CN CNVR MinL AvL MaxL SumL DEL DEL/DUP DUP Total

20 Genome wide CNVR detection CN CNVR MinL AvL MaxL SumL DEL DEL/DUP DUP Total

21 Chr Start(bp) End(bp) Wang Jiang et al.(2012) Hou et al.(2012) Zhang et al.(2015) Del Dup Dup Del/Dup Del Del Dup Dup Dup Del/Dup Dup Del Del Del Dup Dup Dup Del/Dup Dup Del/Dup Del Del/Dup Del Del/Dup Del/Dup Del Del Del/Dup Del/Dup Del/Dup Del/Dup Del/Dup Del/Dup Del Del/Dup Del/Dup Del Del/Dup Del/Dup Dup Del Del Del Dup Del/Dup Dup Del/Dup Del Del/Dup Del Del Dup Del/Dup Del

22 Chr Start(bp) End(bp) Wang Jiang et al.(2012) Hou et al.(2012) Zhang et al.(2015) Del Dup Dup Del/Dup Del Del Dup Dup Dup Del/Dup Dup Del Del Del Dup Dup Dup Del/Dup Dup Del/Dup Del Del/Dup Del Del/Dup Del/Dup Del Del Del/Dup Del/Dup Del/Dup Del/Dup Del/Dup Del/Dup Del Del/Dup Del/Dup Del Del/Dup Del/Dup Dup Del Del Del Dup Del/Dup Dup Del/Dup Del Del/Dup Del Del Dup Del/Dup Del

23 Chr Start(bp) End(bp) Wang Jiang et al.(2012) Hou et al.(2012) Zhang et al.(2015) Del Dup Dup Del/Dup Del Del Dup Dup Dup Del/Dup Dup Del Del Del Dup Dup Dup Del/Dup Dup Del/Dup Del Del/Dup Del Del/Dup Del/Dup Del Del Del/Dup Del/Dup Del/Dup Del/Dup Del/Dup Del/Dup Del Del/Dup Del/Dup Del Del/Dup Del/Dup Dup Del Del Del Dup Del/Dup Dup Del/Dup Del Del/Dup Del Del Dup Del/Dup Del

24 Chr Start(bp) End(bp) Wang Jiang et al.(2012) Hou et al.(2012) Zhang et al.(2015) Del Dup Dup Del/Dup Del Del Dup Dup Dup Del/Dup Dup Del Del Del Dup Dup Dup Del/Dup Dup Del/Dup Del Del/Dup Del Del/Dup Del/Dup Del Del Del/Dup Del/Dup Del/Dup Del/Dup Del/Dup Del/Dup Del Del/Dup Del/Dup Del Del/Dup Del/Dup Dup Del Del Del Dup Del/Dup Dup Del/Dup Del Del/Dup Del Del Dup Del/Dup Del

25 Chr Start(bp) End(bp) Wang Jiang et al.(2012) Hou et al.(2012) Zhang et al.(2015) Del Dup Dup Del/Dup Del Del Dup Dup Dup Del/Dup Dup Del Del Del Dup Dup Dup Del/Dup Dup Del/Dup Del Del/Dup Del Del/Dup Del/Dup Del Del Del/Dup Del/Dup Del/Dup Del/Dup Del/Dup Del/Dup Del Del/Dup Del/Dup Del Del/Dup Del/Dup Dup Del Del Del Dup Del/Dup Dup Del/Dup Del Del/Dup Del Del Dup Del/Dup Del

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31 Conclusions & Recommendations

32 Conclusions & Recommendations 40 RSA Brahman Bulls

33 Conclusions & Recommendations 40 RSA Brahman Bulls 51 common CNVRs using Bovine HD beadchip 29 = Jiang et al., (2012), Hou et al.., (2012) and/or Zhang et al., (2015) Simple repeats, genes and QTLs CNVR genes primarily involved in 7 biological processess Future studies Formation Inheritance Effect

34 Conclusions & Recommendations 40 RSA Brahman Bulls 51 common CNVRs using Bovine HD beadchip 29 = Jiang et al., (2012), Hou et al.., (2012) and/or Zhang et al., (2015) Simple repeats, genes and QTLs CNVR genes primarily involved in 7 biological processess Future studies Formation Inheritance Effect

35 Conclusions & Recommendations 40 RSA Brahman Bulls 51 common CNVRs using Bovine HD beadchip 29 = Jiang et al., (2012), Hou et al.., (2012) and/or Zhang et al., (2015) Simple repeats, genes and QTLs CNVR genes primarily involved in 7 biological processess Future studies Formation Inheritance Effect

36 Thank you!!

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