Rapid Communication: High-resolution quantitative trait loci analysis identifies encoding latent transforming growth factor beta binding protein 2 associated with thoracic vertebrae number in a large F intercross between Landrace and Korean native pigs

Abstract

Number of vertebrae is associated with body size and meat productivity in pigs. The aim of this study was to identify QTL and associated positional candidate genes affecting the number of thoracic vertebrae (THO). A genomewide association study was conducted in a large resource population derived from an F intercross between Landrace and Korean native pigs using the Porcine SNP 60K BeadChip and the genomewide complex trait analysis (GCTA) program based on a linear mixed-effects model. A total of 38,385 SNP markers from 1,105 F progeny were analyzed for the THO trait after filtering for quality control. A total of 90 genomewide significant SNP markers ( < 1.30 × 10) on SSC 7 covering a 20-Mb region were identified for THO in this study. Several previous studies also mapped QTL for vertebral numbers in this region. The strongest association signals were detected at ASGA0035500 (-value = 4.46 × 10; 103,574,383 bp) and DIAS0000795 (-value = 4.46 × 10; 103,594,753 bp). The QTL region on SSC 7 for THO encompasses and , which are previously described candidate genes for vertebral number variation. To refine the QTL region, a haplotype-based linkage and linkage disequilibrium (LALD) analysis using the DualPHASE program was applied because subsequent conditional association and haplotype block analyses could not resolve the region that contains the 2 loci. The LALD analysis refined the critical region to a 533.9-kb region including ; was located outside the critical region. The gene encoding latent transforming growth factor beta binding protein 2 is involved in bone metabolisms. Based on these data, we propose as a positional candidate gene for THO in pigs. After further functional studies and verification of the association in other independent populations, these results could be useful for optimizing breeding programs that improve THO and other economically important traits in pigs.

Whole-genome sequence analysis reveals selection signatures for important economic traits in Xiang pigs

“…The first was a c.T485C (p.L162P, rs326780270) substitution in NR6A1 (nuclear receptor subfamily 6 group A member 1), which encodes an orphan nuclear receptor and has been considered a strong candidate for affecting the numbers of vertebrae in swine 42 . The other was a c.T2732C (p.M911T, rs328662847) substitution in LTBP2 (latent transforming growth factor beta binding protein 2) that are associated with thoracic vertebrae numbers in the pig population 43 . Our results indicated that both of the two genes might play important roles in the vertebrae development of Xiang pigs.…”

“…Gdf11 knock-out mice exhibit an increase in the numbers of ribs from 13 (wild type) to 18 68 . SNP (c.4481A > C) in LTBP2 is associated with thoracic vertebrae numbers in an F2 intercross population between Landrace and Korean native pigs 43 . In our study, we observed one nonsynonymous mutation (c.T2732C, rs328662847) in the coding region of exon-17 of LTBP2 gene.…”

Positive selection signatures in Anqing six‐end‐white pig population based on reduced‐representation genome sequencing data

“…The LTBP2 gene encompassed by the QTL region on SSC7 for thoracic vertebrae number was proposed as a positional candidate gene for thoracic vertebrae in pigs (Park et al . 2017). The number of vertebrae is an important economical trait, closely related to carcass traits, such as carcass length (Zhang et al .…”

“…GRM4 was the top significant gene associated with swine facial wrinkles in Erhualian pigs (Chen et al 2017;Huang et al 2019), which explains the clear facial wrinkles and rhombus wrinkle on the head of AQ pig. The LTBP2 gene encompassed by the QTL region on SSC7 for thoracic vertebrae number was proposed as a positional candidate gene for thoracic vertebrae in pigs (Park et al 2017). The number of vertebrae is an important economical trait, closely related to carcass traits, such as carcass length (Zhang et al 2018), and may indirectly affect body size.…”