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. 2020 Aug 28;3:472. doi: 10.1038/s42003-020-01199-3

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© The Author(s) 2020

Open Access This 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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 1 — Manhattan plots for associations to body weight at 8 weeks of age (BW8) in the F₂ (a) and F₉ (b) generations of the HQLA-HB deep intercross population. The horizontal red/blue lines indicate the genome-wide 1/5% significance thresholds (P values = 8.1 × 10⁻⁷ in F₂ and 1.8 × 10⁻⁷ in F₉)/(P values = 4.1 × 10⁻⁶ in F₂ and 9.2 × 10⁻⁷ in F₉), respectively. c Scatter plot illustrating all tested SNPs in the QTL region on GGA1 for BW8 in the F₉ generation. The colors of the dots indicate their LD (r²) with the peak SNP (GGA1 at 169,241,142 bp, the highest red dot). d The detailed phenotypic scales (mean ± SD) for the three genotypes (HQLA/HQLA, HQLA/HB, and HB/HB) in the 168.6–171.7 Mb region in 503 individuals carrying unrecombined progenitor chromosomes. **≤0.01 significance level; *≤0.05 significance level. e Seventy-two individuals (144 chromatids) in the F₉ generation carry one or two recombinant F₀ chromosomes in the peak GGA1 region from 168.6–171.7 Mb. Blue/red lines represent chromosome segments inherited from the HQLA/HB and a block-wise association analysis across this region identified a significant association only to block1 and block2 (168.6–169.8 Mb) to BW8 (P = 0.0007/0.011/0.081/0.326/0.429, respectively). Sample sizes are given below the box plots. Numbers in brackets represent corresponding number of recombinant chromatids. f The detailed phenotypic scales for the three genotypes (HQLA/HQLA, HQLA/HB, and HB/HB) for each block in 72 individuals carrying recombined progenitor chromosomes. g Regional association plots for the significance testing to the 76 additionally genotyped SNPs (red) and GBS-SNPs (blue) across the 1.2 Mb window from 168.6–169.8 Mb.