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Genetics of candidate genes for developmental and domestication-related traits in lettuce.

机译：生菜发育和驯化相关性状候选基因的遗传学。

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摘要

Many crop species, such as lettuce, have been genetically manipulated over hundreds of years of domestication. Favorable traits have been introduced from wild species and unfavorable traits have been reduced through selection. In the past, these efforts were accomplished without knowledge of which genes were responsible for traits such as flowering time, leaf shape, spininess, shattering, etc., that distinguish the domesticated Lactuca sativa from its wild, weedy progenitor, L. serriola. The advent of functional genomics of model species and molecular marker technologies provide the opportunity for developing high density genetic maps of Lactuca spp. that incorporate both Quantitative Trait Locus (QTL) determining phenotypic traits and molecular markers based on transcribed sequences of known function.;ESTs from the Compositae Genomics Project were chosen that either displayed polymorphism between the parents of a recombinant inbred line (RIL) F 7:8 mapping population derived from cultivated L. sativa and a wild L. serriola or contained sequence similarity to genes in Arabidopsis for a variety of developmental processes. I focused on genes affecting leaf development and the vegetative to floral transition. A total of 91 polymorphic EST-based markers were mapped on the reference L. sativa x L. serriola RIL map; 24 of these co-localized with QTL at P0.05 for traits such as flowering time and leaf shape. One hundred and forty-eight candidate lettuce genes with similarity to Arabidopsis genes (most of which have functionally been well characterized) were identified in the EST database from searches of databases and the literature. A total of 114 candidate genes were mapped that represent 93 Arabidopsis genes; 35 of these candidate gene markers were coincident with QTL at P0.05 for 8 phenotypic traits. These two complementary approaches provided mapped genes that will be useful for multiple purposes including functional studies of candidate genes involved in domestication, comparative mapping within the Compositae, and studies of synteny between Lactuca and other plant species as well as molecular markers for efficient introgression of beneficial alleles from wild Lactuca species.;In this thesis, I used two approaches to map agriculturally important and domestication-related genes. The first approach assumed no a priori knowledge of function but relied on sequence polymorphism within the coding region of expressed genes. The second approach relied on functional information from other species, particularly Arabidopsis, to identify candidate genes. In both cases, sequences were mapped relative to QTL determining phenotypic traits to identify correlations between traits and genes. Several methods for genotyping molecular markers based on expressed sequence tag (EST) sequences were evaluated and refined as different marker technologies became available. PCR amplicons were designed to detect insertion/deletion and single nucleotide polymorphisms and analyzed using several technologies. Ultimately, the highly parallel GoldenGateRTM SNP assay (Illumina) provided the lowest cost and fastest generation of high quality data.
机译：在数百年的驯化过程中，对许多农作物物种（例如生菜）进行了基因改造。从野生物种中引入了有利性状，通过选择减少了不利性状。过去，这些努力是在不知道哪个基因导致开花时间，叶片形状，多刺性，破碎等性状发生的情况下完成的，这些基因使驯化的紫苜蓿与其野生的杂草祖先L. serriola区别开来。模型物种的功能基因组学和分子标记技术的出现为开发Lactuca spp的高密度遗传图谱提供了机会。结合定量性状基因座（QTL）确定表型性状和基于已知功能转录序列的分子标记。;选择了Compositae Genomics Project的EST，它们在重组自交系（RIL）F 7的亲本之间表现出多态性：来自栽培的苜蓿和野生L. serriola的8个作图种群，或与拟南芥中的基因在各种发育过程中的序列相似。我专注于影响叶片发育和从植物生长到花卉过渡的基因。在参考L. sativa x L. serriola RIL图谱上共绘制了91个基于EST的多态性标记。其中24个与QTL共同定位于P <0.05，以表现出开花时间和叶片形状等性状。通过搜索数据库和文献，在EST数据库中鉴定了与拟南芥基因相似的148个候选生菜基因（其中大多数在功能上已得到很好的表征）。共绘制了114个代表93个拟南芥基因的候选基因。这些候选基因标记中的35个与8个表型性状的QTL一致（P <0.05）。这两种互补的方法提供了可用于多种目的的定位基因，包括参与驯化的候选基因的功能研究，菊科内部的比较定位以及莴苣和其他植物物种之间的同构关系以及有效导入有益分子标记的分子标记。野生Lactuca物种的等位基因。在本文中，我使用了两种方法来绘制农业重要和驯化相关基因的图谱。第一种方法假设没有先验的功能知识，而是依靠表达基因编码区内的序列多态性。第二种方法依赖于其他物种（尤其是拟南芥）的功能信息来鉴定候选基因。在这两种情况下，都相对于QTL定位了确定表型性状的序列，以鉴定性状和基因之间的相关性。评估和完善了基于表达的序列标签（EST）序列的分子标记基因分型的几种方法，因为有了不同的标记技术。 PCR扩增子设计用于检测插入/缺失和单核苷酸多态性，并使用多种技术进行分析。最终，高度并行的GoldenGateRTM SNP分析（Illumina）提供了成本最低，生成速度最快的高质量数据。

著录项

  • 作者

    Lavelle, Dean Odin.;

  • 作者单位

    University of California, Davis.;

  • 授予单位 University of California, Davis.;
  • 学科 Biology Genetics.;Agriculture Plant Culture.
  • 学位 Ph.D.
  • 年度 2009
  • 页码 327 p.
  • 总页数 327
  • 原文格式 PDF
  • 正文语种 eng
  • 中图分类
  • 关键词

  • 入库时间 2022-08-17 11:38:19

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