研究揭示結構變異對番茄基因表達和作物改良的影響
作者：
小柯機器人發布時間：2020/6/18 22:07:06
近日，美國冷泉港實驗室Zachary B. Lippman和約翰·霍普金斯大學Michael C. Schatz小組合作，揭示了廣泛結構變異（SV）對番茄基因表達和作物改良的主要影響。 這一研究成果於2020年6月17日在線發表在《細胞》上。
研究人員使用長讀納米孔測序技術對100種不同番茄品系中238,490個SV進行了探究。該panSV基因組連同14個新的參考程序集，揭示了各種基因型的大規模混合以及成千上萬個與基因和順式調控區相交的SV。數百個SV基因對表現出微妙而顯著的表達變化，可能廣泛影響數量性狀的變異。
通過將定量遺傳學與基因組編輯相結合的方法，研究人員揭示了多種SV基因劑量和表達水平的改變是如何改變果實的風味、大小和產量。在最後一個示例中，影響三個相關轉錄因子的四個SV中，具有較高上位性的SV允許在現代番茄中引入重要的產量性狀。該研究揭示了SV在基因型與表型關係中尚未探索的作用，以及它們在作物改良中的重要性和實用性。
據介紹，SV是作物改良和性狀馴化的重要基礎。但是，揭示SV的範圍、多樣性和定量影響一直是一項挑戰。
附：英文原文
Title: Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato
Author: Michael Alonge, Xingang Wang, Matthias Benoit, Sebastian Soyk, Lara Pereira, Lei Zhang, Hamsini Suresh, Srividya Ramakrishnan, Florian Maumus, Danielle Ciren, Yuval Levy, Tom Hai Harel, Gili Shalev-Schlosser, Ziva Amsellem, Hamid Razifard, Ana L. Caicedo, Denise M. Tieman, Harry Klee, Melanie Kirsche, Sergey Aganezov, T. Rhyker Ranallo-Benavidez, Zachary H. Lemmon, Jennifer Kim, Gina Robitaille, Melissa Kramer, Sara Goodwin, W. Richard McCombie, Samuel Hutton, Joyce Van Eck, Jesse Gillis, Yuval Eshed, Fritz J. Sedlazeck, Esther van der Knaap, Michael C. Schatz, Zachary B. Lippman
Issue&Volume: 2020-06-17
Abstract: Structural variants (SVs) underlie important crop improvement and domestication traits.However, resolving the extent, diversity, and quantitative impact of SVs has beenchallenging. We used long-read nanopore sequencing to capture 238,490 SVs in 100 diversetomato lines. This panSV genome, along with 14 new reference assemblies, revealedlarge-scale intermixing of diverse genotypes, as well as thousands of SVs intersectinggenes and cis-regulatory regions. Hundreds of SV-gene pairs exhibit subtle and significant expressionchanges, which could broadly influence quantitative trait variation. By combiningquantitative genetics with genome editing, we show how multiple SVs that changed genedosage and expression levels modified fruit flavor, size, and production. In the lastexample, higher order epistasis among four SVs affecting three related transcriptionfactors allowed introduction of an important harvesting trait in modern tomato. Ourfindings highlight the underexplored role of SVs in genotype-to-phenotype relationshipsand their widespread importance and utility in crop improvement.
DOI: 10.1016/j.cell.2020.05.021
Source: https://www.cell.com/cell/fulltext/S0092-8674(20)30616-4
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