Joint linkage and linkage disequilibrium mapping reveals association of BRMS1L with total teat number in a large intercross between Landrace and Korean native pigs

Abstract

Previously, we reported a quantitative trait locus (QTL) that affects total teat number (TTN) on pig chromosome 7 (SSC7) in a large F2 intercross population between Landrace and Korean native pigs. The aim of this study was to refine the QTL associated with TTN and to identify positional candidate gene(s) within the refined genomic region. TTN was recorded in 1105 F2 progeny. All experimental animals were genotyped using 980 informative single nucleotide polymorphism (SNP) markers located on SSC7. A haplotype-based linkage and association analysis using the PHASEBOOK programme was applied to refine the QTL region. Additionally, linear mixed-effect models were used to assess the effect of a positional candidate gene on TTN and other economically important traits [i.e., thoracic vertebrae number (THO), carcass body length (CBL) and weight (CW), back fat thickness (BFT) and intramuscular fat content (IMF) in loin muscles]. Joint linkage and association analysis refined the critical region to a 4.50 Mb region that included a novel positional candidate gene, BRMS1L that encodes the breast cancer metastasis-suppressor 1-like protein, which could possibly be implicated in normal mammary gland development. Significant association of an SNP marker (g. −1087 G > A) in the 5′-flanking region of BRMS1L with TTN (P = 1.10 × 10−8), THO (P = 5.80 × 10−4), and CBL (P = 0.038) was observed. Based on these data, we propose BRMS1L as a positional candidate gene for TTN in pigs. After validation of the association in other independent populations, these results could be useful in optimizing breeding programmes that improve TTN and other economically important traits in swine.