Genome‐wide association analysis of residual feed intake in Junmu No. 1 White pigs

Abstract

Residual feed intake (RFI) is a measure of feed efficiency. Pigs with low RFI have reduced feed costs without compromising their growth. For marker-assisted selection, it is helpful to identify genes or genetic markers associated with RFI in animals with improved feed efficiency at an early age. Using Illumina's PorcineSNP60 BeadChip, we performed a pilot genome-wide association study of 217 Junmu No. 1 white male pigs phenotyped for RFI. Two-step and one-step methods were used separately to identify associated SNPs. Both methods obtained similar results. Twelve SNPs were identified as significantly associated with RFI at a Bonferroni adjusted P-level < 9.7 × 10 , and 204 were found to have suggestive (moderately significant) association with RFI at P < 5 × 10 . NMBR, KCTD16, ASGR1, PRKCQ, PITRM1, TIAM1 and RND3 were identified as candidate genes for RFI.

Genomic measures of inbreeding coefficients and genome-wide scan for runs of homozygosity islands in Iranian river buffalo, Bubalus bubalis

“…INHBC and INHBE (inhibin beta C and E subunits, on BTA5) have been reported as candidate genes associated with reproductive performance in tropical young bulls [55], and composite reproductive traits in Lori-Bakhtiari sheep [56]. KCTD16 (potassium channel tetramerization domain containing 16, on BTA7) was reported as a candidate gene for meat quality in Simmental beef cattle [57], for residual feed intake in Junmu White pigs [58], and for fat yield in Nordic Holstein cattle [59]. PMEL (premelanosome protein) and MYO1A (myosin IA) on BTA5 have been reported as putative candidate genes related to coat colour phenotypes in cattle [60,61].…”

New Insights From Imputed Whole-Genome Sequence-Based Genome-Wide Association Analysis and Transcriptome Analysis: The Genetic Mechanisms Underlying Residual Feed Intake in Chickens

“…Over the past decade, the genome-wide association analysis (GWAS), based on single nucleotide polymorphism (SNP) chip data to identify the genetic mechanisms of FE, has been widely implemented in livestock, especially in cattle (Seabury et al, 2017;Higgins et al, 2018;Schweer et al, 2018) and pig (Do et al, 2014;Bai et al, 2017;Horodyska et al, 2017). These GWAS studies revealed many candidate genes and provided useful information for genomic breeding programs to select more efficient animals in livestock.…”

Inbreeding estimations based on runs of homozygosity revealed genes associated with local adaptation and dairy traits in Iranian water buffaloes, Bubalus bubalis

“…KCTD16 gene on BTA7 were reported as candidate gene for fat yield in Nordic Holstein cattle [52], with meat quality in Simmental beef cattle [53]. And with residual feed intake in Junmu White pigs [54]. The PMEL (premelanosome protein) and MYO1A (myosin IA) on BTA 5 are two genes within this category that have been reported as putative candidate genes related to coat color phenotypes in cattle by [55] and [56], respectively.…”