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Structural variants exhibit widespread allelic heterogeneity and shape variation in complex traits

Author

Listed:
  • Mahul Chakraborty

    (University of California Irvine)

  • J. J. Emerson

    (University of California Irvine)

  • Stuart J. Macdonald

    (University of Kansas)

  • Anthony D. Long

    (University of California Irvine)

Abstract

It has been hypothesized that individually-rare hidden structural variants (SVs) could account for a significant fraction of variation in complex traits. Here we identified more than 20,000 euchromatic SVs from 14 Drosophila melanogaster genome assemblies, of which ~40% are invisible to high specificity short-read genotyping approaches. SVs are common, with 31.5% of diploid individuals harboring a SV in genes larger than 5kb, and 24% harboring multiple SVs in genes larger than 10kb. SV minor allele frequencies are rarer than amino acid polymorphisms, suggesting that SVs are more deleterious. We show that a number of functionally important genes harbor previously hidden structural variants likely to affect complex phenotypes. Furthermore, SVs are overrepresented in candidate genes associated with quantitative trait loci mapped using the Drosophila Synthetic Population Resource. We conclude that SVs are ubiquitous, frequently constitute a heterogeneous allelic series, and can act as rare alleles of large effect.

Suggested Citation

  • Mahul Chakraborty & J. J. Emerson & Stuart J. Macdonald & Anthony D. Long, 2019. "Structural variants exhibit widespread allelic heterogeneity and shape variation in complex traits," Nature Communications, Nature, vol. 10(1), pages 1-11, December.
  • Handle: RePEc:nat:natcom:v:10:y:2019:i:1:d:10.1038_s41467-019-12884-1
    DOI: 10.1038/s41467-019-12884-1
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    Cited by:

    1. Xiaoling Tong & Min-Jin Han & Kunpeng Lu & Shuaishuai Tai & Shubo Liang & Yucheng Liu & Hai Hu & Jianghong Shen & Anxing Long & Chengyu Zhan & Xin Ding & Shuo Liu & Qiang Gao & Bili Zhang & Linli Zhou, 2022. "High-resolution silkworm pan-genome provides genetic insights into artificial selection and ecological adaptation," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    2. Ting Wang & Shiyao Duan & Chen Xu & Yi Wang & Xinzhong Zhang & Xuefeng Xu & Liyang Chen & Zhenhai Han & Ting Wu, 2023. "Pan-genome analysis of 13 Malus accessions reveals structural and sequence variations associated with fruit traits," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    3. Gabriel E. Rech & Santiago Radío & Sara Guirao-Rico & Laura Aguilera & Vivien Horvath & Llewellyn Green & Hannah Lindstadt & Véronique Jamilloux & Hadi Quesneville & Josefa González, 2022. "Population-scale long-read sequencing uncovers transposable elements associated with gene expression variation and adaptive signatures in Drosophila," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    4. Hangxing Jia & Shengjun Tan & Yingao Cai & Yanyan Guo & Jieyu Shen & Yaqiong Zhang & Huijing Ma & Qingzhu Zhang & Jinfeng Chen & Gexia Qiao & Jue Ruan & Yong E. Zhang, 2024. "Low-input PacBio sequencing generates high-quality individual fly genomes and characterizes mutational processes," Nature Communications, Nature, vol. 15(1), pages 1-19, December.

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