栽培大豆和野生大豆在很多表型上存在比較大的差異，這些差異包括種子大小，豆莢的個數，含油量和蛋白含量以及光合作用能力等。在本研究中，我們利用之前發表的31 株大豆重測序鑒定出的在栽培或者野生群體中固定的單核苷酸多態性位元點（SNP）資料進行分析，目的在於找出潛在的受選擇區域以及鑒定出受到固定SNP 位點影響的與我們關心的性狀相關的基因。我們的研究結果表明，人工選擇的強度要比自然選擇的強度大很多，同時我們利用這些SNP資料鑒定出了幾個可能受選擇的區域。我們結合已經發表的一些數量性狀（豆莢數目，種子酪氨酸含量）的QTL 的資訊，找到了一些在這些QTL 裡面可能起到主要作用的主效基因。結合KEGG 通路，我們發現了一些在植物激素信號轉导通路，植物體與病原相互作用通路，週期節律性通路，澱粉和蔗糖合成相關的通路，碳固定通路上面栽培和野生大豆差異比較大的基因，這些基因可能是人工選擇和自然選擇的產物。我們從中可以看到人工選擇和自然選擇的印記。根據在野生大豆裡面固定而在家養大豆裡面是中頻的那些SNP 的分佈情況，我們推測第四號染色體在自然選中可能具有比較大的作用。另外我們還發現第八號染色體在家養和野生之間的分化程度比較大。在所有的受SNP 位點影響的基因中，有三分之一的基因都在這條染色體上。我們進一步分析這些基因發現，很多重要農藝性狀比如矮化，根的生長，抗除草劑，抗病，抗旱等相關的基因都在這裡面。我們的這些發現對於將來高產大豆的遺傳和分子育種會有比較大的幫助。 / Cultivated and wild soybeans exhibit morphological differences in many traits, such as seed size, pod number, protein and oil content, photosynthesis capacity, etc. Here, we analyzed the fixed SNPs in both cultivated and wild soybeans reported previously by our lab for two aims: one is to search the candidate regions under selection; the other is to identify traits-related genes possessing fixed SNPs leading to non-synonymous changes. Our results indicated that artificial selection is much stronger than natural selection. We identified candidate genomic regions and genes under artificial selection, which play a vital role in several traits of interests including pod number and seed tyrosine content. By searching the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, we further discovered those important genes impacted by domestication and natural selection were enriched in several pathways including plant hormone transduction, plant-pathogen interaction, circadian rhythm, starch and sucrose metabolism, and carbon fixation pathway. Our analysis also suggested that Chromosome04 (Chr04) is important for fitness of wild accessions because that most of the residual SNPs fixed in wild soybeans showed intermediate frequency in cultivated accessions. Significantly, we observed considerable divergence between wild and cultivated accessions on Chr08. Detailed analysis indicated that nearly 30% of the genes located on Chr08 with SNPs fixed either in cultivated or wild soybeans. These genes were associated with many important agronomic traits including dwarfing, root growth, herbicide resistance, pathogen resistance, drought/salt tolerance. Our modeling results would be beneficial for genetic modification and molecule breeding in soybean in the near future. / Detailed summary in vernacular field only. / Pan, Shengkai. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2013. / Includes bibliographical references (leaves 85-101). / Abstracts also in Chinese. / ABSTRACT --- p.i / 摘要 --- p.Iii / Acknowledgements --- p.iv / Table of Contents --- p.v / List of Tables --- p.viii / List of Fignres --- p.ix / Chapter CHAPTER 1 --- LITERATURE REVIEW --- p.1 / Chapter 1.1 --- Morphology differences --- p.2 / Chapter 1.2 --- Herbicide --- p.4 / Chapter 1.2.1 --- Sulfonylureas herbicides --- p.4 / Chapter 1.2.2 --- Herbicide resistance --- p.5 / Chapter CHSPTER 2 --- METHODS --- p.8 / Chapter 2.1 --- SNP detection --- p.9 / Chapter Fignre 2.1. --- SOAPsnp flow chart --- p.10 / Chapter 2.2 --- Fixed SNPs detection --- p.10 / Chapter 2.2.1 --- Fixed SNPs in the wild population at low frequency (FWLC) or at intermediate frequency (FWIC) in the cultivated population --- p.11 / Chapter 2.2.2 --- Fixed SNPs in the cultivated population at low frequency (FCLW) or at intermediate frequency (FCIW) in the wild population --- p.11 / Chapter 2.3 --- InDel detection --- p.12 / Chapter 2.3.1 --- Statistics of conserved InDels in the wild population at low frequency (CWLC), intermediate (CWIC), or high frequency (CWHC) in the cultivated population --- p.13 / Chapter 2.3.2 --- Identification of conserved InDels in the cultivated population at low frequency (CCLW), intermediate (CCIW), or high frequency (CCHW) in the wild population --- p.13 / Chapter 2.4 --- Result visualization --- p.14 / Chapter CHAPTER 3 --- RESULTS --- p.15 / Chapter 3.1 --- Number of fixed SNPs and conserved InDels in cultivated accessions is much more than in wild accessions --- p.16 / Chapter 3.2 --- Candidate regions under selection --- p.24 / Chapter 3.2.1 --- Analysis of wild-unique distribution on Chromosome 04 --- p.24 / Chapter 3.2.2 --- Analysis of distribution on Chromosome 08 --- p.25 / Chapter 3.3 --- Other analysis on fixed SNPs --- p.35 / Chapter 3.3.1 --- Genes with amino acid code changes caused by SNPs fixed in the cultivated population at low frequency in wild population --- p.35 / Chapter 3.3.2 --- Genes with amino acid code changes caused by SNPs fixed in the wild population at low frequency in the cultivated population --- p.44 / Chapter 3.3.3 --- Genes with non-synonymous caused by SNPs fixed in both cultivated and wild populations --- p.56 / Chapter 3.3.4 --- Analysis combining KEGG pathway with genes containing amino acid code change sites resulted from fixed SNPs --- p.60 / Chapter CHAPTER 4 --- DISCUSSION --- p.75 / Chapter 4.1 --- Differences between cultivated and wild soybeans --- p.76 / Chapter 4.2 --- Roles of fixed SNPs in the wild and cultivated populations study --- p.76 / Chapter 4.3 --- The possible reason for number of fixed SNPs and conserved InDels in cultivated soybeans is much more than that in wild soybeans --- p.77 / Chapter 4.3.1 --- Artificial selection is much stronger than natural selection --- p.77 / Chapter 4.3.2 --- Bottleneck in domestication process of cultivated soy bean --- p.78 / Chapter 4.4 --- Notes about fixed SNPs in the gene regions --- p.79 / Chapter 4.5 --- Possible reason for divergence in Chromosome 08 --- p.79 / Chapter 4.6 --- Possible reason for unique pattern of SNPs fixed in wild accessions on Chromosome 04 --- p.80 / Chapter CHAPTER 5 --- PROSPECTIVE --- p.81 / REFERENCES --- p.84
| Identifer | oai:union.ndltd.org:cuhk.edu.hk/oai:cuhk-dr:cuhk_328478 |
| Date | January 2013 |
| Contributors | Pan, Shengkai., Chinese University of Hong Kong Graduate School. Division of Life Sciences. |
| Source Sets | The Chinese University of Hong Kong |
| Language | English, Chinese |
| Detected Language | English |
| Type | Text, bibliography |
| Format | electronic resource, electronic resource, remote, 1 online resource (ix, 101 leaves) : ill. (some col.) |
| Rights | Use of this resource is governed by the terms and conditions of the Creative Commons “Attribution-NonCommercial-NoDerivatives 4.0 International” License (http://creativecommons.org/licenses/by-nc-nd/4.0/) |
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