ARS | Publication request: X Chromosome SNPs Were Heavily Involved In Epistasis Effects Of Net Merit Component Traits In Contemporary U.S. Holstein Cows

Submitted to: Plant and Animal Genome Conference Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: December 31, 2009
Publication Date: January 9, 2010
Citation: Ma, L., Sonstegard, T.S., Cole, J.B., Wiggans, G.R., Crooker, B.A., Van Tassell, C.P., Yang, J., Matukumalli, L., Da, Y. 2010. X Chromosome SNPs Were Heavily Involved In Epistasis Effects Of Net Merit Component Traits In Contemporary U.S. Holstein Cows . Plant and Animal Genome Conference Proceedings. San Diego, Ca, Jan. 9-13, abstr. P542.

Technical Abstract: Pairwise epistasis effects of net merit and its eight component traits were tested in 1654 contemporary U.S. Holstein cows using the BovineSNP50 (45,878 SNPs). A large number of epistasis effects exceeded the genome-wide significance of 5% type-I error with the Bonferroni correction and a QTL map of 374 SNPs (top 50 epistasis effects/trait) was constructed. The top 50 epistasis effects of each trait explained 30-50% of the phenotypic variation. The 374 SNPs were distributed across all 29 bovine autosomes and the X-chromosome. However, the X chromosome had the highest concentration of epistasis effects although it had the smallest number of SNP markers for analysis among all chromosomes. The X chromosome had 25% of the epistasis effects for milk yield (MY), 37% for fat yield (FY), 32% for protein yield (PY), 61% for fat percent (FPC), 54% for protein percent (PPC), 54% for somatic cell score (SCS), 70% for productive life (PL), and 54% for net merit (NM$). X chromosome genes with or near most significant epistasis effects include:LOC520057 and FLNA for FY, FPC, PPC; IL1RAPL2 for PY; MAOB and FLNA for PPC and PL; LOC786985 and FLNA for SCS; LOC786155, LOC786185, GRPR, LOC537655 and FLNA for DPR; and MAOB for NM$. Autosome genes with or near most significant epistasis effects include: HINT3 of BTA9 for MY; PDE4B and ROR1 of BTA3 for FY, PY and NM$; SORL1 of BTA15 for FPC and PPC; DACH1 and PCDH9 of BTA12 for SCS; and ALDH5A1 of BTA23 for PL and PPC.