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首页> 外文期刊>Acta Horticulturae >Data mining for apple 5-RNase alleles in resequencing datasets
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Data mining for apple 5-RNase alleles in resequencing datasets

机译：RESERERENCATED数据集中Apple 5-RNase等位基因的数据挖掘

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摘要

The sequence of the apple {Malus x domestica Borkh.) genome was obtained from the cultivar 'Golden Delicious' and released in 2010; the availability of this draft reference genome opened up the possibility to explore the genetic variation within thisspecies on a genome scale, using high-throughput strategies such as high-density SNP arrays or resequencing of different cultivars. However, while these techniques are immediately effective and highly informative on most genomic loci, the S-locus has some uncommon features, derived from its mechanism of inheritance and evolutionary dynamics, that require different approaches. The extremely high level of allelic polymorphism, the lack of co-linearity between different -haplotypes, the massive presence oftransposable elements and the evidence of extensive gene duplication as one of the main forces driving its evolution, are factors that make the 5-locus an unsuitable target for common genomic procedures, such as SNP-based high-throughput assays and alignment of resequencing data on the reference genome. The aim of this work was to define a strategy for obtaining information on the S-locus from the high-depth resequencing of 6X apple cultivars. We focused on the 5-RNase gene and developed a strategy initially aimed at identifying the 5-genotype of resequenced cultivars; the short sequence reads obtained from each cultivar were then used to check and to expand the available sequence data for each identified allele. Our preliminary results suggest that the huge amount of information that derives from resequencing cultivars can be of great help to resolve incomplete, fragmentary or inconsistent data in the current database of apple 5-RNase alleles.
机译：苹果{Malus X Diverienta Borkh。）基因组是从2010年的品种“金色美味”中发布的基因组;该草案参考基因组的可用性开辟了在基因组规模上探讨该遗传变异的可能性，使用高密度SNP阵列（如不同品种的Resequecing）的高通量策略。然而，虽然这些技术在大多数基因组基因座上立即有效且高度信息丰富，但S-Locus具有一些不常见的特征，从而产生了需要不同方法的遗传和进化动态的机制。等位基因多态性的极高水平，缺乏不同的-haplotypes之间的联合性，巨大的存在元素的巨大存在和广泛的基因重复作为驱动其演变的主要力量之一，是制造5-ocus的因素常见基因组程序的不适合靶标，例如基于SNP的高通量测定和在参考基因组上重新排序数据的对准。这项工作的目的是定义从6倍苹果品种的高深重置的高深重试，了解获取关于S-LOCU的信息的策略。我们专注于5-RNase基因，并开发出最初旨在鉴定重组品种的5基因型的策略;然后使用从每个品种获得的短序列读取检查并扩展每个鉴定的等位基因的可用序列数据。我们的初步结果表明，源于重新排列品种的大量信息可能有很大的帮助，可以有助于解决当前苹果5-RNase等位基因数据库中的不完整，零碎或不一致的数据。

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  • 来源
    《Acta Horticulturae》 |2019年第1231期|共8页
  • 作者

    P. De Franceschi; L. Bianco; A. Cestaro; L. Dondini; R. Velasco;

  • 作者单位

    Dipartimento di Scienze Agrarie Universita degli Studi di Bologna Italy;

    Dipartimento di Scienze Agrarie Universita degli Studi di Bologna Italy;

    Research and Innovation Centre Fondazione Edmund Mach San Michele allAdige Trento Italy;

    Dipartimento di Scienze Agrarie Universita degli Studi di Bologna Italy;

    Research and Innovation Centre Fondazione Edmund Mach San Michele allAdige Trento Italy;

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  • 原文格式 PDF
  • 正文语种 eng
  • 中图分类 园艺;
  • 关键词

    S-locus; Malus; S-haplotypes; NGS; genotyping;

    机译：s-locus;malus;s-haplotypes;ngs;基因分型;

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