本文選題：水稻　切入點：MAGIC群體　出處：《華中農業(yè)大學》2017年碩士論文　論文類型：學位論文

【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藝性狀的遺傳解析一直是育種家們研究的重點內容,定位更多的與粒形、株型相關聯(lián)的QTLs,挖掘其優(yōu)良等位基因型,為分子設計育種提供技術指導服務。傳統(tǒng)的雙親本群體已經廣泛應用于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、較小的群體結構以及可以直接或間接的應用于育種進程等優(yōu)點,開始新興于各種植物研究中。本研究基于一個包含248個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序,獲取了1231431個高質量的SNP,對該群體進行了遺傳多樣性分析、主成分分析以及連鎖不平衡分析(LD),并結合表型數(shù)據對粒形、株型進行了全基因組關聯(lián)分析(GWAS)。同時,利用本實驗室韓忠民博士基于SNP數(shù)據構建的高密度的bin map對粒形以及株型數(shù)據進行bin水平的關聯(lián)分析,并進行了兩種關聯(lián)分析方法的比較。在bin水平基礎上進行了等位基因間的多重比較,確定優(yōu)良等位基因型。主要研究結果如下:1.利用Hiseq-3000對群體家系進行了平均深度為2X的測序,對四個親本材料進行了平均測序深度為10X的測序。利用bwa、samtools、vcftools等生物學工具共獲取1231431個高質量的SNP,并用Mendel_Impute軟件基于家系親緣關系進行了數(shù)據的補缺工作,獲取完整的群體基因型。2.對群體進行了系統(tǒng)發(fā)生樹分析,表明群體存在較低的群體結構。PCA分析結果顯示前10個成分僅解釋25%的樣本方差,群體沒有出現(xiàn)分層現(xiàn)象,即群體內不存在明顯的群體結構。并比較了雙親本和本試驗四親本MAGIC群體的LD衰減圖,結果得出: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,我們分別采用SNP水平以及bin水平對兩年三個重復的粒長、粒寬數(shù)據進行關聯(lián)分析。粒長表型中,兩種方法分別檢測到5個和4個QTLs,其中已克隆基因GS3以及GL3.2在兩種方法三個重復中均檢測到。bin水平關聯(lián)分析將GS3限定在10 kb的bin內,該bin內僅含有一個基因,即GS3。SNP水平單獨關聯(lián)到了已知基因GL7,bin水平并沒有顯著檢測到。SNP水平三個重復均檢測到兩個新的SNP位點chr03_19636931和chr03_22449318,均位于3號染色體上。bin水平也檢測到兩個新的QTLs,一個是位于2號染色體上的B2_275,另外一個是位于8號染色體的B8_350,在該區(qū)間內沒有報道的粒長基因。粒寬表型中,兩種方法分別檢測到7個和6個QTLs,其中GW5以及GL7被兩種方法均檢測到。其中GW5被限定在大小為10 kb的bin區(qū)間內,在SNP水平也是將GW5鎖定在單基因水平。SNP水平上新關聯(lián)的5個QTLs均只在單個重復中檢測得到,bin水平共關聯(lián)到4個新的位點,至少在兩個重復中檢測到。有趣的是SNP水平關聯(lián)到的新的位點chr10_10645936和bin水平關聯(lián)到的B10_93相距很近,我們認為是一個新的QTL位點。4.利用株型中的株高、分蘗角以及劍葉葉夾角數(shù)據,同時采用SNP水平和bin水平進行相對應的關聯(lián)分析。株高表型中,SNP水平關聯(lián)到4個QTLs,對應的bin水平也關聯(lián)到4個QTLs。其中TAD1兩種方法均有檢測到,SNP水平還關聯(lián)到已知QTL Psd1。SNP水平關聯(lián)到的新的SNP位點chr07_24813588與bin水平關聯(lián)到的B7_247共定位,該區(qū)間大小為230kb。對應的在分蘗角表型中兩種方法分別檢測到2個和3個QTLs,均為已克隆QTL/基因,其中ONAC106以及TAC1為兩種方法所共有,bin水平額外還檢測到ta9。劍葉葉夾角表型在兩種方法分別檢測到9個和2個QTLs,新的SNP位點chr07_21605018與bin所檢測到的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.我們利用本室構建的bin map,在bin水平對已知QTL GS3、GW5、TAC1、ONAC106和新的候選區(qū)間B10_93、B7_247進行多重比較。確定優(yōu)良等位基因型以及親本來源,為分子標記輔助選擇育種提供技術指導。
[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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