Refining genomewide association for growth and fat deposition traits in an F2 pig population

BERNAL RUBIO, Y.L.; RANEY, N. E.; GUALDRÓN DUARTE, J. L.; BATES, R. O.; ROGBERG MUÑOZ, A.; CANTET, R. J. C.; ERNST, C. W.; STEIBEL, J. P.

JOURNAL OF ANIMAL SCIENCE

AMER SOC ANIMAL SCIENCE

Lugar: Urbana; Año: 2016 vol. 94 p. 1387 - 1397

0021-8812

The identification of genomic regions that affect additive genetic variation and contain genesinvolved in controlling growth and fat deposition has enormous impact in the farm animal industry (e.g., carcass merit and meat quality). Therefore, a genomewide association study was implemented in an F2 pig population using a 60,000 SNP marker panel for traits related to growth and fat deposition. Estimated genomic EBV were linearly transformed to calculateSNP effects and to identify genomic positions possibly associated with the genetic variability of each trait.  Genomic segments were then defined considering the markers included in a region 1 Mb up- and downstream from the SNP with the smallest P-value anda false discovery rate < 0.05 for each trait. The significance for each 2-Mb segment was tested using the Bonferroni correction. Significant SNP were detected on SSC2, SSC3, SSC5, and SSC6, but 2-Mb segment significant effects were observed on SSC3 for weightat birth (wt_birth) and on SSC6 for 10th-rib backfat and last-rib backfat measured by ultrasound at different ages. Furthermore, a 6-Mb segment on SSC6 was also considered because the 2-Mb segments for 10 different fat deposition traits were overlapped. Althoughthe segment effects for each trait remain significant, the proportion of additive variance explained by this larger segment was slightly smaller in some traits. In general, the results confirm the presence of genetic variability for wt_birth on SSC3 (18.0?20.2 Mb) and for fat deposition traits on SSC6 (133.8?136.0 Mb). Within these regions, fibrosin (FBRS) and myosin light chain, phosphorylatable, fast skeletal muscle (MYLPF) genes could be considered as candidates for the wt_birth signal on SSC3, and the SERPINE1 mRNA binding protein 1 gene (SERBP1) may be a candidate for the fat deposition trait signals on SSC6.