本文選題：大豆 + 分子標(biāo)記�。� 參考：《山東師范大學(xué)》2016年博士論文

【摘要】：大豆[Glycine max L.Merr.]屬于豆科、蝶形花亞科、大豆屬,是世界范圍內(nèi)重要的經(jīng)濟作物,為人類提供了大量的植物蛋白以及油料。大豆是古四倍體,基因組大小為1.1 Gb,編碼蛋白質(zhì)的基因超過46430個,其中大約有75%的基因是以同源基因的形式出現(xiàn)的。由于大豆基因組復(fù)雜,遺傳轉(zhuǎn)化較為困難,一直以來對大豆基因功能的研究進展較為緩慢。隨著大豆基因組序列的公布,大豆遺傳學(xué)研究邁入了新的時代。本文通過篩選菏豆12突變體庫,獲得葉皺縮表型的突變體。通過重測序技術(shù)獲得菏豆12基因組序列信息,并與參考基因組Williams 82進行序列比對得到數(shù)量眾多的插入缺失片段的物理位置信息,并以此開發(fā)新的插入/缺失(INsertion/DELetion,INDEL)分子標(biāo)記。與此同時構(gòu)建突變體與Williams82的雜交群體,并通過正向遺傳學(xué)的手段,對造突變的基因進行圖位克隆,利用表型相同的突變體株系之間雜交進行等位鑒定,以及突變體轉(zhuǎn)基因恢復(fù)表型等手段確認(rèn)了該突變體的突變基因。進一步研究發(fā)現(xiàn),該基因參與了大豆葉表皮角質(zhì)層的發(fā)育過程,并進一步影響了突變體應(yīng)對干旱以及病原菌脅迫。所以該基因?qū)ξ磥砼嘤购狄约翱共【拇蠖剐缕贩N具有重要的意義。具體實驗結(jié)果如下:1.大豆品種之間分子標(biāo)記的篩選1)大豆擴增片段長度多態(tài)性(AFLP)的設(shè)計以及多態(tài)性的篩選對菏豆12,Williams 82,吉林35進行AFLP分析,經(jīng)過統(tǒng)計這三個大豆品種利用27對不同的選擇性擴增引物組合分別獲得625條,619條,622條條帶,三個品種兩兩之間共產(chǎn)生了410個差異片段,其中菏豆12與吉林35之間有138個差異性位點,菏豆12與Williams 82之間有145個差異性位點,吉林35與Williams 82之間有127個差異位點。2)大豆SSR分子標(biāo)記的設(shè)計與篩選從BARCSOYSSR Potential SSRs中選取了98個潛在的具有SSR多態(tài)性的位點,對菏豆12,Williams 82,吉林35進行了SSR多態(tài)性分析。結(jié)果表明:菏豆12與Williams 82之間多態(tài)性位點有41個,占總數(shù)的42%;菏豆12與吉林35之間多態(tài)性位點26個,占總數(shù)的27%;吉林35與williams82之間多態(tài)性位點16個,占總數(shù)的16%。菏豆12與williams82之間ssr分子標(biāo)記設(shè)計成功率較高,反映出兩者之間的遺傳多樣性更高,使得兩者成為較合適的構(gòu)建群體組合。3)大豆indel分子標(biāo)記的設(shè)計以及篩選本實驗篩選了在染色體上均勻分布的248個indel位點以獲得足夠數(shù)量的錨定分子標(biāo)記。經(jīng)pcr驗證確定共有169個分子標(biāo)記具有多態(tài)性,預(yù)測成功率為69%。169個indel分子標(biāo)記分布于所有二十條染色體中,其中分布最多的是gm01染色體,共分布有24個,最少的也有4個,平均每條染色體上有8個。indel分子標(biāo)記的分布基本均勻,很少成簇出現(xiàn),基本能夠滿足圖位克隆粗定位的要求。運用這些分子標(biāo)記對其他12個大豆品種進行多態(tài)性鑒定發(fā)現(xiàn):這些分子標(biāo)記在中國和美國品種之間有著良好的多態(tài)性。進一步分析實驗結(jié)果發(fā)現(xiàn):具有多態(tài)性的分子標(biāo)記中有77%pcr產(chǎn)物是單產(chǎn)物,遠遠高于假陽性indel的41%,這可能表明位于具有同源序列的indel位點可信度較低。生物信息學(xué)分析得到近五萬個indel位點當(dāng)中可能會有相當(dāng)一部分是不真實的,造成這個問題的原因可能是重測序片段錯誤地比對上了參考基因組相應(yīng)位置的同源序列,造成了一小段沒有比對上的片段被分析成為indel位點。2.大豆皺葉突變體的鑒定在菏豆12伽馬射線誘變突變體庫中篩選出一個株系的皺葉突變體。皺葉突變體的第一三出復(fù)葉葉尖在種植18天之后開始壞死,導(dǎo)致小葉遠軸端無法伸長,葉細胞在葉片發(fā)育過程中不斷堆積,形成皺葉的表型。在純化突變體遺傳背景過程中發(fā)現(xiàn)突變體與菏豆12野生型雜交f1代為野生型表型,f2代群體中突變體與野生型的比例為1:3,符合孟德爾遺傳定律,證明該突變位點為隱性單位點突變。3.大豆皺葉突變體的圖位克隆首先構(gòu)建了皺葉突變體與williams82的雜交群體。在f2代中選取突變體表型植株做圖位克隆。通過粗定位,將突變位點定位于7號染色體1.371mb和2.417mb之間,但再繼續(xù)向內(nèi)設(shè)計分子標(biāo)記的時候發(fā)現(xiàn)一段區(qū)間內(nèi)擴增不出條帶,故懷疑可能存在片段缺失。在缺失邊界附近設(shè)計inversepcr引物,最終確定缺失范圍是7號染色體2118557到2371744bp。內(nèi)共包含有27個基因涉及脂肪酸代謝,甘油代謝,生長素極性運輸?shù)认嚓P(guān)功能。4.突變基因的確定隨后又在williams82伽馬射線誘變,ems誘變突變體庫中篩選到表型一致的突變體株系4個,編號分別為:msn7442,sc5591,sc5962,sc7321。菏豆12與msn7442雜交后發(fā)現(xiàn)f1代為突變體表型,證明兩個株系的突變位點是等位關(guān)系。提取msn7442株系突變體的基因組dna,將菏豆12突變體缺失的27個基因進行pcr擴增并測序,發(fā)現(xiàn)在glyma.07g028600(soybasev1.1版本的該基因編號為glyma07g03230)基因外顯子出存在g到t的堿基顛換,導(dǎo)致編碼的氨基酸由天冬氨酸變?yōu)槔野彼帷ζ溆嗳齻�株系的glyma.07g028600基因pcr擴增并測序之后發(fā)現(xiàn):sc7321在外顯子處缺失tcttttatcc十個堿基并加入a;sc5591在第三個外顯子前2個堿基的內(nèi)含子處存在一個由a到t的堿基顛換,推測可能導(dǎo)致了mrna的錯誤剪切;sc5962在外顯子處有一個g到a的堿基替換,導(dǎo)致編碼的氨基酸由甘氨酸變?yōu)榫彼�。綜上測序的結(jié)果表明:這四個株系的突變體在glyma.07g028600基因上存在非同義突變,并且菏豆12皺葉突變與msn7442為等位突變體。構(gòu)建glyma.07g028600過表載體,并遺傳轉(zhuǎn)化msn7442,突變體表型恢復(fù)為野生型。以上實驗證明glyma.07g028600基因的突變造成了皺葉的表型。5.glyma.07g028600基因的表達模式glyma.07g028600基因編碼甘油三磷酸激酶,其在擬南芥中的直系同源基因是nho1/gli1。擬南芥nho1突變體的非寄主性抗性降低導(dǎo)致突變體對病原菌的侵染不耐受。大豆glyma.07g028600基因在全身各組織器官中均有表達,其中果莢中的表達豐度最高,葉片次之。構(gòu)建glyma.07g028600融合egfp過表載體,轉(zhuǎn)化擬南芥原生質(zhì)體,結(jié)果表明融合蛋白主要定位于細胞膜上。莖尖原位雜交的結(jié)果表明該基因在大豆莖尖分生組織,葉原基等處均有表達。6.glyma.07g028600基因的功能分析菏豆12背景的皺葉突變體較其野生型,williams82背景下的4個株系的皺葉突變體較其野生型的離體葉片失水速率均快一倍以上。由此推測突變體葉表皮的角質(zhì)層可能存在問題。掃描電鏡結(jié)果顯示:突變體葉表面的蠟質(zhì)晶體堆積不正常。突變體及野生型葉片橫切切片的透射電鏡結(jié)果表明:突變體的表皮層變薄;真角質(zhì)層親鋨性降低,表明突變體角質(zhì)的密度變低。對突變體及野生型表層蠟質(zhì)進行的質(zhì)譜分析表明:突變體和野生型的蠟質(zhì)總量沒有顯著區(qū)別,但不同成分含量差別很大。突變體和野生型接種大豆細菌斑點病菌4天后,突變體葉子內(nèi)的細菌數(shù)量是野生型的6倍多,證明突變體應(yīng)對病原菌侵染的能力變低。7.角質(zhì)層發(fā)育相關(guān)基因的表達豐度受Glyma.07G028600基因影響結(jié)合掃描電鏡,透射電鏡,以及蠟質(zhì)成分質(zhì)譜分析的結(jié)果,對涉及植物蠟質(zhì),角質(zhì)合成,轉(zhuǎn)運,組裝,調(diào)控的20多個基因在野生型和突變體葉片中的表達豐度進行了分析,結(jié)果表明:轉(zhuǎn)運相關(guān)基因表達豐度差異不顯著。角質(zhì)合成酶基因(GmLTL1)等合成相關(guān)基因在野生型和突變體中表達豐度差異很大,一些轉(zhuǎn)錄因子表達豐度差異也很大。推測Glyma.07G028600基因?qū)χ参锝琴|(zhì)層的發(fā)育起著重要的作用。本論文的主要創(chuàng)新點:1.開發(fā)了一定數(shù)量的INDEL分子標(biāo)記,這些標(biāo)記在其他大豆品種之間也具有較好的多態(tài)性。生物信息學(xué)比對得到的近五萬個INDEL位點能夠為大豆遺傳以及分子輔助育種提供豐富的信息。這些數(shù)據(jù)已經(jīng)上傳至Soybase,并填補了大豆公共數(shù)據(jù)庫中沒有INDEL分子標(biāo)記的空白。2.通過圖位克隆,定位到一個參與大豆角質(zhì)層發(fā)育的基因Glyma.07G028600。該基因在擬南芥中的同源基因的研究中發(fā)現(xiàn)參與了植物的非寄主性抗性,但沒有該基因參與角質(zhì)層發(fā)育的報道。3.進一步揭示了大豆角質(zhì)層發(fā)育的分子調(diào)控機制,為下一步培育抗旱,抗病蟲的大豆新品種打下基礎(chǔ)。
[Abstract]:Soybean [Glycine Max L.Merr.] belongs to leguminous, spoenoy and soybean, which is an important economic crop in the world. It provides a large amount of plant protein and oil for mankind. The soybean is an ancient tetraploid, the genome size is 1.1 Gb, and the gene encoding protein is more than 46430, of which about 75% of the genes are in the form of homologous genes. Because of the complexity of the soybean genome and the difficulty of genetic transformation, the research of soybean gene function has been progressing slowly. With the publication of the soybean genome sequence, the research of soybean genetics has entered a new era. In this paper, the mutant library of the 12 mutants of hedou was screened and the mutant of the leaf shrinkage phenotype was obtained. The genomic sequence information of hedou 12 was obtained, and the sequence alignment of the reference genome Williams 82 was compared to obtain the physical location information of a large number of inserted deletion fragments, and to develop a new insertion / deletion (INsertion/DELetion, INDEL) molecular marker. At the same time, the hybrid population of the mutant and Williams82 was constructed and passed through forward inheritance. By means of the study, the mutant gene was cloned, the mutant gene was identified by the allele identification of the mutant lines with the same phenotype, and the mutant transgenic recovery phenotype. The further study found that the gene was involved in the development of the cuticle of the soybean leaf and further shadow The mutants respond to drought and pathogen stress. Therefore, the gene is of great significance to the future cultivation of drought resistant and anti pathogenic soybean varieties. The specific results are as follows: 1. the screening of molecular markers between soybean varieties 1) the design of the amplified fragment length polymorphism of Soybean (AFLP) and the selection of polymorphism in hedou 12, William S 82, Jilin 35 performed AFLP analysis. After statistics, the three soybean varieties obtained 625, 619, 622 bands using 27 different selective amplification primers, and 410 differences were produced between three varieties and 22, of which there were 138 difference sites between hedou and Jilin 35. Difference loci, Jilin 35 and Williams 82 have 127 difference sites.2) the design and screening of soybean SSR molecular markers, 98 potential SSR polymorphic loci were selected from BARCSOYSSR Potential SSRs, and SSR polymorphism analysis was carried out on hedou 12, Williams 82, and 35. The results showed that the polymorphism between hedou 12 and Williams 82 was polymorphic. There were 41 loci, accounting for 42% of the total, 26 polymorphic loci between hedou 12 and Jilin 35, 27% of the total, and 16 polymorphic loci between Jilin 35 and williams82, which accounted for a higher success rate of SSR molecular markers between the total and williams82, reflecting the higher genetic diversity between the two and making the two more appropriate. Construction of group combination.3) the design of soybean indel molecular markers and screening the 248 indel loci evenly distributed on the chromosome to obtain a sufficient number of anchoring molecular markers. A total of 169 molecular markers were identified by PCR, and the prediction success rate was 69%.169 indel molecular markers distributed in all twenty. Among the chromosomes, the most distributed is the gm01 chromosome, with a total distribution of 24, the least and 4. The average distribution of 8.Indel markers on each chromosome is basically uniform and rarely appears in clusters. It can basically meet the requirements of the rough location of the clones. These molecular markers are used for the polymorphism of the other 12 soybean varieties. It is found that these molecular markers have good polymorphism between Chinese and American varieties. Further analysis of the experimental results found that 77%pcr products with polymorphic molecular markers are single products, far higher than 41% of false positive indel, which may indicate that the indel loci with homologous sequence are lower in reliability. A considerable portion of the nearly fifty thousand indel loci may be untrue, and the cause of this problem may be that the sequenced fragment is wrongly compared to the homologous sequence on the corresponding position of the reference genome, causing a small segment to be identified as the identification of the indel site.2. soybean wrinkle mutant. A leaf mutant of a plant line was screened in the 12 gamma ray mutants Library of hedou. The first three leaves of the mutant leaf mutant began to die after 18 days of planting, causing the apex of the lobule far axis to grow, the leaf cells accumulated during the leaf development and formed the phenotypes of the leaves, and the genetic background process of the mutant was purified. The mutant and hedou 12 wild type hybrid F1 generation is a wild type, and the proportion of the mutant and the wild type in the F2 generation group is 1:3, which conforms to the Mendel's law of inheritance. It is proved that the mutation site is a recessive unit point mutation of the.3. soybean leaf mutant and first constructs a hybrid population of the wrinkled leaf mutant and williams82. In the F2 generation. The mutant phenotypic plants were cloned. The mutant loci were located between 1.371mb and 2.417mb on chromosome 7 by rough location, but the deletion bands were found in a section of the interval when the molecular markers were continuously designed. Therefore, the deletion of fragments might exist. The design of inversepcr primers near the missing boundary was finally determined. The deletion range is 2118557 to 2371744bp. of chromosome 7, including 27 genes involved in fatty acid metabolism, glycerol metabolism, auxin polar transport and other related.4. mutation genes, followed by williams82 gamma ray mutagenesis, and EMS mutants library screening 4 phenotypic mutant lines, respectively, msn74 42, sc5591, sc5962, and sc7321. hedou 12 were hybridized with msn7442 and found that the F1 generation was the mutant phenotype. It was proved that the mutation site of the two strains was allele. The genomic DNA of the mutant msn7442 strain was extracted and 27 genes missing from the 12 mutant of hedou were amplified and sequenced by PCR, and now the glyma.07g028600 (soybasev1.1 version number) was issued. The exons of glyma07g03230) exon exon from G to t, causing the encoded amino acid to change from aspartic acid to tyrosine. After amplification and sequencing of the glyma.07g028600 gene PCR of the remaining three lines, it was found that sc7321 was missing the ten bases of tcttttatcc at exon and added to a; sc5591 was within the 2 bases of the third exons. There is a base change from a to t in the subregion, which may lead to the wrong shear of mRNA; sc5962 has a base substitution of G to a at exons, causing the encoded amino acid to be transformed from glycine to arginine. The results of the sequencing show that the mutants of these four strains have a non synonymous mutation on the glyma.07g028600 gene, and The mutation of 12 leaf of hedou and msn7442 was a allelic mutant. The glyma.07g028600 overtable vector was constructed and msn7442 was transformed into the wild type. The mutation of the mutant body surface was in the wild type. The above experiment proved that the mutation of the glyma.07g028600 gene resulted in the expression pattern of the.5.glyma.07g028600 gene of the phenotypic.5.glyma.07g028600 gene of the wrinkle, which encodes the glycerol three phosphate kinase. The direct homologous gene in Arabidopsis thaliana is the non host resistance of nho1/gli1. Arabidopsis nho1 mutant, which leads to the infection intolerance of the mutant to the pathogen. The soybean glyma.07g028600 gene is expressed in all tissues and organs of the whole body, among which the expression in the fruit pods is the highest and the leaves are the second. The glyma.07g028600 fusion EGFP has been constructed. The results showed that the fusion protein was mainly located on the cell membrane. The results of the stem tip in situ hybridization showed that the gene expressed.6.glyma.07g028600 gene in the shoot apex meristem, leaf primordium and other parts of the leaf primordium. The leaf mutants of the 12 background were compared with the wild type and 4 in the background of williams82. The leaf epidermis of the mutant leaf mutant was more than twice as fast as that of the wild type. Therefore, it is suggested that the cuticle of the mutant leaf epidermis may have problems. The scanning electron microscope shows that the wax crystal accumulation in the mutant leaf surface is not normal. The transmission electron microscope results of the mutant and the wild type leaf cross section show that the mutant is a mutant. The epidermis of the epidermis was thinner, the true osmium in the true stratum corneum decreased, indicating the low density of the mutant horniness. The mass spectrometric analysis of the mutants and wild type surface wax showed that there was no significant difference between the mutants and the wild type, but the content of different components was very different. The mutant and the wild type inoculated with soybean bacterial speckles were 4 days after the mutant and wild type inoculation. The number of bacteria in the variant leaves is more than 6 times that of the wild type. It is proved that the ability of the mutant to cope with the infection of the pathogen is less than that of the pathogen. The expression abundance of the.7. cuticle related genes is affected by the Glyma.07G028600 gene combined with scanning electron microscopy, transmission electron microscopy, and the fruit of the wax composition mass spectrometry analysis, which involves plant wax, horniness synthesis, transport and assembly. The expression abundance of more than 20 genes regulated in the wild and mutant leaves was analyzed. The results showed that there was no significant difference in the expression abundance of the transporter related genes. The expression abundance difference between the horny synthase gene (GmLTL1) and other genes in the wild type and mutant was very large, and the expression abundance difference of some transcription factors was also great. The Glyma.07G028600 gene plays an important role in the development of the plant cuticle. The main innovation of this paper is: 1. a certain number of INDEL markers have been developed, and these markers also have good polymorphism among other soybean varieties. The nearly fifty thousand INDEL loci obtained by bioinformatics comparison can be genetic and molecular for soybeans. Auxiliary breeding provides rich information. These data have been uploaded to Soybase and fill the blank.2. without INDEL molecular markers in the soybean public database by mapping the gene to a gene involved in the development of the soybean cuticle, which is found to be involved in the plant's homologous gene in Arabidopsis. Non host resistance, but no part of the gene involved in the development of cuticle,.3. further revealed the molecular regulation mechanism of the development of soybean cuticle, which lays the foundation for the next breeding of drought resistant and disease resistant soybean varieties.

【學(xué)位授予單位】：山東師范大學(xué)
【學(xué)位級別】：博士
【學(xué)位授予年份】：2016
【分類號】：S565.1

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