本文選題：水稻　切入點(diǎn)：MAGIC群體　出處：《華中農(nóng)業(yè)大學(xué)》2017年碩士論文　論文類型：學(xué)位論文

【摘要】：水稻是重要的糧食作物,其較小的基因組大小,豐富的遺傳多樣性等優(yōu)點(diǎn)使其成為遺傳和基因組研究的單子葉模式植物。水稻粒形以及株型等重要農(nóng)藝性狀的遺傳解析一直是育種家們研究的重點(diǎn)內(nèi)容,定位更多的與粒形、株型相關(guān)聯(lián)的QTLs,挖掘其優(yōu)良等位基因型,為分子設(shè)計(jì)育種提供技術(shù)指導(dǎo)服務(wù)。傳統(tǒng)的雙親本群體已經(jīng)廣泛應(yīng)用于QTL定位,但受其遺傳組成狹窄、重組發(fā)生有限、作圖分辨率不高等影響,很難滿足當(dāng)前的需求。MAGIC群體作為新一代作圖群體,憑借其豐富的遺傳組成、較小的群體結(jié)構(gòu)以及可以直接或間接的應(yīng)用于育種進(jìn)程等優(yōu)點(diǎn),開(kāi)始新興于各種植物研究中。本研究基于一個(gè)包含248個(gè)株系的四親本水稻多親本高世代回交MAGIC群體的低豐度的全基因組重測(cè)序,獲取了1231431個(gè)高質(zhì)量的SNP,對(duì)該群體進(jìn)行了遺傳多樣性分析、主成分分析以及連鎖不平衡分析(LD),并結(jié)合表型數(shù)據(jù)對(duì)粒形、株型進(jìn)行了全基因組關(guān)聯(lián)分析(GWAS)。同時(shí),利用本實(shí)驗(yàn)室韓忠民博士基于SNP數(shù)據(jù)構(gòu)建的高密度的bin map對(duì)粒形以及株型數(shù)據(jù)進(jìn)行bin水平的關(guān)聯(lián)分析,并進(jìn)行了兩種關(guān)聯(lián)分析方法的比較。在bin水平基礎(chǔ)上進(jìn)行了等位基因間的多重比較,確定優(yōu)良等位基因型。主要研究結(jié)果如下:1.利用Hiseq-3000對(duì)群體家系進(jìn)行了平均深度為2X的測(cè)序,對(duì)四個(gè)親本材料進(jìn)行了平均測(cè)序深度為10X的測(cè)序。利用bwa、samtools、vcftools等生物學(xué)工具共獲取1231431個(gè)高質(zhì)量的SNP,并用Mendel_Impute軟件基于家系親緣關(guān)系進(jìn)行了數(shù)據(jù)的補(bǔ)缺工作,獲取完整的群體基因型。2.對(duì)群體進(jìn)行了系統(tǒng)發(fā)生樹(shù)分析,表明群體存在較低的群體結(jié)構(gòu)。PCA分析結(jié)果顯示前10個(gè)成分僅解釋25%的樣本方差,群體沒(méi)有出現(xiàn)分層現(xiàn)象,即群體內(nèi)不存在明顯的群體結(jié)構(gòu)。并比較了雙親本和本試驗(yàn)四親本MAGIC群體的LD衰減圖,結(jié)果得出:四親本MAGIC群體LD衰減速度明顯低于雙親本材料。3.利用粒形數(shù)據(jù),我們分別采用SNP水平以及bin水平對(duì)兩年三個(gè)重復(fù)的粒長(zhǎng)、粒寬數(shù)據(jù)進(jìn)行關(guān)聯(lián)分析。粒長(zhǎng)表型中,兩種方法分別檢測(cè)到5個(gè)和4個(gè)QTLs,其中已克隆基因GS3以及GL3.2在兩種方法三個(gè)重復(fù)中均檢測(cè)到。bin水平關(guān)聯(lián)分析將GS3限定在10 kb的bin內(nèi),該bin內(nèi)僅含有一個(gè)基因,即GS3。SNP水平單獨(dú)關(guān)聯(lián)到了已知基因GL7,bin水平并沒(méi)有顯著檢測(cè)到。SNP水平三個(gè)重復(fù)均檢測(cè)到兩個(gè)新的SNP位點(diǎn)chr03_19636931和chr03_22449318,均位于3號(hào)染色體上。bin水平也檢測(cè)到兩個(gè)新的QTLs,一個(gè)是位于2號(hào)染色體上的B2_275,另外一個(gè)是位于8號(hào)染色體的B8_350,在該區(qū)間內(nèi)沒(méi)有報(bào)道的粒長(zhǎng)基因。粒寬表型中,兩種方法分別檢測(cè)到7個(gè)和6個(gè)QTLs,其中GW5以及GL7被兩種方法均檢測(cè)到。其中GW5被限定在大小為10 kb的bin區(qū)間內(nèi),在SNP水平也是將GW5鎖定在單基因水平。SNP水平上新關(guān)聯(lián)的5個(gè)QTLs均只在單個(gè)重復(fù)中檢測(cè)得到,bin水平共關(guān)聯(lián)到4個(gè)新的位點(diǎn),至少在兩個(gè)重復(fù)中檢測(cè)到。有趣的是SNP水平關(guān)聯(lián)到的新的位點(diǎn)chr10_10645936和bin水平關(guān)聯(lián)到的B10_93相距很近,我們認(rèn)為是一個(gè)新的QTL位點(diǎn)。4.利用株型中的株高、分蘗角以及劍葉葉夾角數(shù)據(jù),同時(shí)采用SNP水平和bin水平進(jìn)行相對(duì)應(yīng)的關(guān)聯(lián)分析。株高表型中,SNP水平關(guān)聯(lián)到4個(gè)QTLs,對(duì)應(yīng)的bin水平也關(guān)聯(lián)到4個(gè)QTLs。其中TAD1兩種方法均有檢測(cè)到,SNP水平還關(guān)聯(lián)到已知QTL Psd1。SNP水平關(guān)聯(lián)到的新的SNP位點(diǎn)chr07_24813588與bin水平關(guān)聯(lián)到的B7_247共定位,該區(qū)間大小為230kb。對(duì)應(yīng)的在分蘗角表型中兩種方法分別檢測(cè)到2個(gè)和3個(gè)QTLs,均為已克隆QTL/基因,其中ONAC106以及TAC1為兩種方法所共有,bin水平額外還檢測(cè)到ta9。劍葉葉夾角表型在兩種方法分別檢測(cè)到9個(gè)和2個(gè)QTLs,新的SNP位點(diǎn)chr07_21605018與bin所檢測(cè)到的B7_210距離較近,該區(qū)間可能含有控制劍葉葉夾角的基因。5.我們利用本室構(gòu)建的bin map,在bin水平對(duì)已知QTL GS3、GW5、TAC1、ONAC106和新的候選區(qū)間B10_93、B7_247進(jìn)行多重比較。確定優(yōu)良等位基因型以及親本來(lái)源,為分子標(biāo)記輔助選擇育種提供技術(shù)指導(dǎo)。
[Abstract]:Rice is an important food crop, its small genome size, genetic diversity and other advantages make it become rich monocot plant patterns of genetic and genomic studies. Genetic analysis of important agronomic traits of rice grain shape and the plant has been the focus of the content of the breeders, positioning more with grain shape, plant related with QTLs, the advantageous allele, provide technical guidance services for molecular design breeding. The traditional parents this group has been widely used in QTL, but the genetic composition of narrow recombination Co., mapping resolution is not high, it is difficult to meet the current needs of.MAGIC group as a new generation of mapping population, with its rich genetic composition, population structure of small and can be used directly or indirectly in the breeding process and other advantages, began to study various emerging plants. This research is based on a Whole genome sequencing of low abundance containing 248 clones of four parental rice multi parent Advanced Backcross MAGIC populations, obtained 1231431 high quality SNP, the population genetic diversity was analyzed, principal component analysis and linkage disequilibrium analysis (LD), and the particle shape phenotype the data type, conducted a genome-wide association study (GWAS). At the same time, correlation analysis of SNP data to build a high density bin map based on grain shape and plant type data bin level in the laboratory by Dr. Han Zhongmin, and compares the two kinds of correlation analysis method. The comparison between multiple alleles in the bin level, determine the best genotype. The main results are as follows: 1. using Hiseq-3000 average depth of the population, 2X sequencing, the average depth of sequencing four parent materials for 10X sequencing. The use of BWA, samtools, vcftools and other biological tool has obtained 1231431 high quality SNP, and use Mendel_Impute software related families were carried out based on the data acquisition by working population genotype.2. complete the groups for the analysis of phylogenetic tree showed that.PCA groups exist population structure analysis results show the first 10 low a component account for only 25% of the sample variance, the group did not appear stratified phenomenon, which does not exist in group structure obviously. And compared the two parents and the test of four parent MAGIC groups of LD attenuation maps, the result showed: four parent MAGIC group LD attenuation rate was significantly lower than the parent material.3. using double grain shape data, we the SNP level and bin level for two years three repeated grain length respectively, grain width data correlation analysis. The grain length phenotype, two methods were detected in 5 and 4 QTLs, which has been G Long gene GS3 and GL3.2 in two kinds of methods three repeats were detected in.Bin level correlation analysis we define GS3 at 10 KB bin, the bin contains only one gene, namely GS3.SNP levels alone related to the known genes GL7, bin levels did not significantly detected.SNP levels were detected in three replicates two new SNP loci chr03_19636931 and chr03_22449318 were located on chromosome 3.Bin level was also detected two new QTLs, one is located at B2_275 on chromosome 2, the other one is located at B8_350 on chromosome 8, in the range not reported the grain length grain width phenotype gene. In the two kinds of methods were detected in 7 and 6 QTLs, in which GW5 and GL7 are two kinds of methods were detected. The GW5 is limited in the size of 10 kb in the bin range, at the level of SNP GW5 is locked in a single gene level of.SNP 5 new QTLs link 鍧囧彧鍦ㄥ崟涓噸澶嶄腑媯，

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