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Nanopore sequencing reveals diverse structural variations in domestic chickens

2021 CPRF
Modern chickens have undergone intense phenotypic selection for two primary purposes: meat production and egg laying. While the poultry industry has successfully developed specialized lines with much higher productivity than their wild ancestors, the incomplete understanding of the genetic basis of phenotypic variations among chicken breeds has stymied efforts to further improve their production. Among all the genetic differences among chicken breeds, structural variations (SVs, large DNA alterations ≥50 bp) are the least characterized. Our lack of understanding of SVs is due to the limitations of conventional short-read sequencing techniques in detecting SVs comprehensively and accurately across the genome. The recent application of single-molecule long-read sequencing methods in humans has helped overcome such challenges, revealing the prevalence of SVs in human populations and their significance in reproduction. Here, we performed nanopore long-read sequencing on a broiler line (meat-type), a layer line (egg-type), three indigenous village lines, and an undomesticated wild chicken line. We developed a new bioinformatic pipeline that allowed us to detect ~17,000 SVs in each domestic line, including insertions, deletions, duplications, and inversions, which impact 2.5% of the chicken genome. Although the chicken genome is generally believed to be devoid of transposable element (TE) activities, we identified 29 active endogenous retrovirus families and one active LINE family in chickens. These active TEs insert into protein coding genes enriched for neurological functions, likely to contribute to attenuation of behavioral responses to the domesticated environments. Taken together, our results indicate that extensive SVs exist in chickens and are generated via diverse mutational mechanisms. SVs impact a comparable number of base pairs as single nucleotide polymorphisms in domestic chicken breeds, suggesting their biological significance in phenotypic variations.
Tags :
genetic selection,nanopore sequencing
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University of Rochester

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