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. 2022 Jun 9;20:136. doi: 10.1186/s12915-022-01322-2

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© The Author(s) 2022

Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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Fig. 5 — Validation of newly-identified candidate functional SNPs. a IGV plot of AGE trait regulated by candidate functional SNP based on multi-omics analysis. b Phenotypic differences of AGE (days to 100 kg) in a population of 182 LW individuals with different genotypes. The number of animals with different genotypes for AGE: n_C/C = 21, n_C/T = 31, and n_T/T = 130. Outliers are shown as individual dots. Statistical significance is determined by single-tailed Mann-Whitney U test. The predicted motif affected by the candidate functional SNP is shown at the bottom, and the locus of this SNP is highlighted by black dotted line. c, d Phenotypic differences of LMP (Lean meat percentage at 100 kg) and LMD (Loin muscle depth at 100 kg) in a population of 2869 Duroc individuals with different genotypes. The number of animals with different genotypes for LMP: n_C/C = 344, n_T/C = 1306, and n_T/T = 1135. The number of animals with different genotypes for LMD: n_C/C = 2456, n_C/T = 328, and n_T/T = 11. Outliers are shown as individual dots. Statistical significance is determined by single-tailed Mann-Whitney U test. The predicted motifs affected by the candidate functional SNPs are shown at the bottom, and the locus of SNPs is highlighted by black dotted line. e The alternative alleles exhibited significantly higher luciferase activity compared to the reference alleles. f Distribution of frequency of target alleles with enhanced phenotypic performance for AGE, LMP, and LMD traits