利用水稻4亲本MAGIC群体进行粒形和株型的遗传分析

发布时间：2018-03-13 21:43

  本文选题：水稻　切入点：MAGIC群体　出处：《华中农业大学》2017年硕士论文　论文类型：学位论文

【摘要】：水稻是重要的粮食作物,其较小的基因组大小,丰富的遗传多样性等优点使其成为遗传和基因组研究的单子叶模式植物。水稻粒形以及株型等重要农艺性状的遗传解析一直是育种家们研究的重点内容,定位更多的与粒形、株型相关联的QTLs,挖掘其优良等位基因型,为分子设计育种提供技术指导服务。传统的双亲本群体已经广泛应用于QTL定位,但受其遗传组成狭窄、重组发生有限、作图分辨率不高等影响,很难满足当前的需求。MAGIC群体作为新一代作图群体,凭借其丰富的遗传组成、较小的群体结构以及可以直接或间接的应用于育种进程等优点,开始新兴于各种植物研究中。本研究基于一个包含248个株系的四亲本水稻多亲本高世代回交MAGIC群体的低丰度的全基因组重测序,获取了1231431个高质量的SNP,对该群体进行了遗传多样性分析、主成分分析以及连锁不平衡分析(LD),并结合表型数据对粒形、株型进行了全基因组关联分析(GWAS)。同时,利用本实验室韩忠民博士基于SNP数据构建的高密度的bin map对粒形以及株型数据进行bin水平的关联分析,并进行了两种关联分析方法的比较。在bin水平基础上进行了等位基因间的多重比较,确定优良等位基因型。主要研究结果如下:1.利用Hiseq-3000对群体家系进行了平均深度为2X的测序,对四个亲本材料进行了平均测序深度为10X的测序。利用bwa、samtools、vcftools等生物学工具共获取1231431个高质量的SNP,并用Mendel_Impute软件基于家系亲缘关系进行了数据的补缺工作,获取完整的群体基因型。2.对群体进行了系统发生树分析,表明群体存在较低的群体结构。PCA分析结果显示前10个成分仅解释25%的样本方差,群体没有出现分层现象,即群体内不存在明显的群体结构。并比较了双亲本和本试验四亲本MAGIC群体的LD衰减图,结果得出:四亲本MAGIC群体LD衰减速度明显低于双亲本材料。3.利用粒形数据,我们分别采用SNP水平以及bin水平对两年三个重复的粒长、粒宽数据进行关联分析。粒长表型中,两种方法分别检测到5个和4个QTLs,其中已克隆基因GS3以及GL3.2在两种方法三个重复中均检测到。bin水平关联分析将GS3限定在10 kb的bin内,该bin内仅含有一个基因,即GS3。SNP水平单独关联到了已知基因GL7,bin水平并没有显著检测到。SNP水平三个重复均检测到两个新的SNP位点chr03_19636931和chr03_22449318,均位于3号染色体上。bin水平也检测到两个新的QTLs,一个是位于2号染色体上的B2_275,另外一个是位于8号染色体的B8_350,在该区间内没有报道的粒长基因。粒宽表型中,两种方法分别检测到7个和6个QTLs,其中GW5以及GL7被两种方法均检测到。其中GW5被限定在大小为10 kb的bin区间内,在SNP水平也是将GW5锁定在单基因水平。SNP水平上新关联的5个QTLs均只在单个重复中检测得到,bin水平共关联到4个新的位点,至少在两个重复中检测到。有趣的是SNP水平关联到的新的位点chr10_10645936和bin水平关联到的B10_93相距很近,我们认为是一个新的QTL位点。4.利用株型中的株高、分蘖角以及剑叶叶夹角数据,同时采用SNP水平和bin水平进行相对应的关联分析。株高表型中,SNP水平关联到4个QTLs,对应的bin水平也关联到4个QTLs。其中TAD1两种方法均有检测到,SNP水平还关联到已知QTL Psd1。SNP水平关联到的新的SNP位点chr07_24813588与bin水平关联到的B7_247共定位,该区间大小为230kb。对应的在分蘖角表型中两种方法分别检测到2个和3个QTLs,均为已克隆QTL/基因,其中ONAC106以及TAC1为两种方法所共有,bin水平额外还检测到ta9。剑叶叶夹角表型在两种方法分别检测到9个和2个QTLs,新的SNP位点chr07_21605018与bin所检测到的B7_210距离较近,该区间可能含有控制剑叶叶夹角的基因。5.我们利用本室构建的bin map,在bin水平对已知QTL GS3、GW5、TAC1、ONAC106和新的候选区间B10_93、B7_247进行多重比较。确定优良等位基因型以及亲本来源,为分子标记辅助选择育种提供技术指导。
[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�閲嶅�嶄腑妫，

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