Cost-effectively dissecting the genetic architecture of complex wool traits in rabbits by low-coverage sequencing.

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  • Additional Information
    • Source:
      Publisher: BioMed Central Country of Publication: France NLM ID: 9114088 Publication Model: Electronic Cited Medium: Internet ISSN: 1297-9686 (Electronic) Linking ISSN: 0999193X NLM ISO Abbreviation: Genet Sel Evol Subsets: MEDLINE
    • Publication Information:
      Publication: London : BioMed Central
      Original Publication: Paris : Elsevier, c1989-
    • Subject Terms:
      Rabbits*/genetics ; Multifactorial Inheritance* ; Wool* ; Animal Fur*; Animals ; Genome-Wide Association Study ; Polymorphism, Single Nucleotide ; Quantitative Trait Loci
    • Abstract:
      Background: Rabbit wool traits are important in fiber production and for model organism research on hair growth, but their genetic architecture remains obscure. In this study, we focused on wool characteristics in Angora rabbits, a breed well-known for the quality of its wool. Considering the cost to generate population-scale sequence data and the biased detection of variants using chip data, developing an effective genotyping strategy using low-coverage whole-genome sequencing (LCS) data is necessary to conduct genetic analyses.
      Results: Different genotype imputation strategies (BaseVar + STITCH, Bcftools + Beagle4, and GATK + Beagle5), sequencing coverages (0.1X, 0.5X, 1.0X, 1.5X, and 2.0X), and sample sizes (100, 200, 300, 400, 500, and 600) were compared. Our results showed that using BaseVar + STITCH at a sequencing depth of 1.0X with a sample size larger than 300 resulted in the highest genotyping accuracy, with a genotype concordance higher than 98.8% and genotype accuracy higher than 0.97. We performed multivariate genome-wide association studies (GWAS), followed by conditional GWAS and estimation of the confidence intervals of quantitative trait loci (QTL) to investigate the genetic architecture of wool traits. Six QTL were detected, which explained 0.4 to 7.5% of the phenotypic variation. Gene-level mapping identified the fibroblast growth factor 10 (FGF10) gene as associated with fiber growth and diameter, which agrees with previous results from functional data analyses on the FGF gene family in other species, and is relevant for wool rabbit breeding.
      Conclusions: We suggest that LCS followed by imputation can be a cost-effective alternative to array and high-depth sequencing for assessing common variants. GWAS combined with LCS can identify new QTL and candidate genes that are associated with quantitative traits. This study provides a cost-effective and powerful method for investigating the genetic architecture of complex traits, which will be useful for genomic breeding applications.
      (© 2022. The Author(s).)
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    • Grant Information:
      SDAIT-21-02 Shandong Province Special Economic Animal Innovation Team; 2021LZGC002 Agricultural Improved Seed Project of Shandong Province; 2020M682217 China Postdoctoral Science Foundation; ZR2020QC175 Shandong Provincial Natural Science Foundation; ZR2020QC176 Shandong Provincial Natural Science Foundation; 32102526 National Natural Science Foundation of China; 32002172 National Natural Science Foundation of China
    • Publication Date:
      Date Created: 20221119 Date Completed: 20221123 Latest Revision: 20221123
    • Publication Date:
      20221213
    • Accession Number:
      PMC9673297
    • Accession Number:
      10.1186/s12711-022-00766-y
    • Accession Number:
      36401180