玉米抗粗缩病全基因组关联与连锁分析
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摘要
玉米(Zea mays L.)是重要的粮食和饲料作物，在农业生产和经济发展中占有重要地位，但玉米生产面临多重逆境影响。玉米粗缩病（Maize Rough Dwarf Disease, MRDD）是全球玉米种植区广泛发生的病毒性病害，主要由灰飞虱（Laodelphax striatellus Fallen）以持久性方式传播的玉米粗缩病毒或者水稻黑条矮缩病毒引起。20世纪70年代中期，曾导致河北、北京大面积的玉米减产或绝产。目前，该病害已成为我国黄淮海玉米主产区的主要病害之一。玉米生产上采取的农业防治措施存在易造成环境污染且防治效果差等缺点，因此，培育和种植抗病品种是防控粗缩病的有效途径。本文采用全基因组关联分析与连锁定位研究玉米抗粗缩病遗传，发掘主效抗病QTL或者基因，为玉米抗粗缩病种质改良和品种选育提供基础。具体研究内容和结果如下：
1.以遗传基础丰富的236份玉米自交系为材料，通过2010年和2011年2个环境的抗粗缩病鉴定，采用41101个稀有等位基因频率大于5%的高质量SNP，结合群体结构、亲缘关系通过TASSEL软件进行全基因组关联分析。2个环境下共检测到73个SNP与抗粗缩病显著相关（P <0.0001值），单个SNP可以解释2.68%-6.18%的表型变异。2个环境下同时检测到14个SNP，分布于玉米染色体bin5.03、bin7.02、bin8.03、bin10.02和bin10.03，其中SNP PZE-108052072和PZE-108057211位于bin8.03。在连锁不平衡（LinkageDisequilibrium, LD）r2大于0.1的范围，48个SNP的LD区域内筛选到41个候选基因，其中32个SNP位于基因内部，包括GRMZM2G413544、GRMZM2G405760等。
2.利用来源于美国杂交种P78599的5份高抗粗缩病自交系（R18，P138，X178，金黄59和齐318）和全基因组41101个SNP，筛选到9个包含与抗病性显著相关SNP的衍生片段，9个衍生片段的基因型都不同于感病对照掖478的基因型，其中，最小片段长48.84Kb，最大片段长81.57Mb，平均长9351.03Kb。位于bin8.03长81.57Mb的片段包括6个与抗病性显著相关的SNP和2个前人定位到的抗玉米粗缩病主效QTL。
3.以来源于X178×B73杂交组合的重组自交系NL203与B73构建的3个F2群体（表示为F2-1，F2-2和F2-5）为材料，通过玉米粗缩病人工接种和自然发病鉴定，在第8染色体发掘抗粗缩病QTL。基于3个F2群体的分析结果如下：（1）采用F2-1群体构建第8染色体的区段连锁图谱，包括9个标记，全长35.28cM，平均间距4.41cM。结合人工接种表型鉴定，在bin8.03标记umc1617和phi121之间定位到1个来自于NL203的主效QTL，LOD值为5.1，加性效应0.73，解释11%的表型变异；（2）利用F2-2群体构建第8染色体区段连锁图谱，包括10个标记，全长38.36cM，平均间距3.8cM，全部标记与IBM2008neighbor图谱的顺序一致。结合人工接种表型鉴定，在bin8.03标记umc1617和phi121之间定位到1个来自于NL203的主效QTL，LOD值6.18，解释11%的表型变异；（3）利用F2-5群体构建第8染色体的连锁图谱，包括18个标记，全长153.81cM，平均间距9.01cM，除SSR标记bnlg2037，其余标记与IBM2008neighbor图谱的顺序一致。结合自然发病表型鉴定，分别在标记umc1139-bnlg1194与umc1735-phi121之间各检测到1个QTL，2个QTL都来自于NL203，LOD值分别为3.30、18.80，分别解释3.99%、25.71%的表型变异。综合以上结果，在bin8.03标记umc1617和phi121之间存在1个来自于NL203的主效抗病QTL，可以解释25.71%的表型变异。
Maize (Zea mays L.) is an important crop which serves as food and forage. It plays ansignificant role in agricultural and economic development. However, the production of maize wasdisturbed by a lot of biotic stress. Maize rough dwarf disease (MRDD) is a kind of viral disease allover the world, which is caused by maize rough dwarf virus (MRDV), or rice black-streakeddwarf virus (RBSDV), and is transmitted by the insect vector Laodelphax striatellus Fallen. In the1970s, MRDD caused serious loss in maize production in beijing and hebei province. Now, it isone of the most serious diseases in the Yellow-Huai river region which is very important for maizeproduction. The currently agricultural measures protecting maize production are inclined to causeenvironmental pollution, and have little effects. So the most effective measures to conquer MRDDare to breed and plant resistant varieties. In this study, genome wide association and linkageanalysis were used to explore the genetic architecture of resistance to MRDD，and to find themajor resistant quantitative trait loci (QTL) or genes. The main results were as fellows：
1A total of236maize inbred lines with rich diversity were evaluated for resistance to MRDD in2010and2011, respectively. Using41101high quality SNP with minor allele frequencies(MAF) greater than5%, a genome wide association analysis (GWAS) was conducted toinvestigate the genetic architecture underlying this viral disease. As a result, a total of73SNPwere found to be associated with resistance to MRDD at a significant threshold of-log10(P)>4controlling false discovery rate (FDR) at α=0.1, single SNP could explain phenotypicvariance from2.68%to6.18%. Fourteen out of these SNP were detected in both environments.They distributed across chromosome bin5.03, bin7.02, bin8.03, bin10.02, and bin10.03, andSNP PZE-108052072and PZE-108057211were located in bin8.03. A total of48SNP wereidentified in LD blocks (r2>0.1) with candidate resistance genes, and32were included bycandidate genes, including GRMZM2G413544and GRMZM2G405760.
2Using41101SNP to analysis5highly resistant inbred lines derived from the hybrid ‘P78599’,nine derivative fragments harboring SNP associated with MRDD resistance were detected,which were not harbored by the susceptible line ‘Ye478’. The r2within these fragments weregreater than0.1. The length of these fragments varied from48.84Kb to81.57Mb with anaverage of9351.03Kb. The fragment with a length of81.57Mb, which was located in bin8.03and contained6SNP associated with MRDD resistance, included the major resistant QTL thathad been identified in previous studies.
3Three F2populations (assigned as F2-1, F2-2, and F2-5) were constructed with a cross betweenthe susceptible line 'B73' and the resistant line ‘NL203’ which was selected from therecombinant inbred line population developed from the line ‘X178’ crossed with the line ‘B73’.(1) Based on F2-1, the linkage map of chromosome8was constructed, which contained9SSRmarkers with a length of35.28cM. After evaluation for resistance to MRDD through artificial inoculation, one QTL was detected between the marker umc1617and phi121in bin8.03with apeak LOD of5.1, which could explain11%phenotypic variance;(2) Based on F2-2, the linkagemap of chromosome8was constructed, which contained10markers with a length of38.36cM.The order of markers was consistant with that in IBM2008neighbor map. After evaluationthrough artificial inoculation, one QTL was identified between the marker umc1617and phi121with a peak LOD of6.18, which could explain11%phenotypic variance;(3) Based on F2-5, thelinkage map of chromosome8was constructed containing18markers with a length of153.81cM. After evaluation for resistance to MRDD through natural infection, two QTL were detectedwithin the interval of umc1139-bnlg1194and umc1735-phi121, respectively. The QTL in thefirst interval could explain3.99%phenotypic variance, and another could explain25.71%phenotypic variance.
1.以遗传基础丰富的236份玉米自交系为材料，通过2010年和2011年2个环境的抗粗缩病鉴定，采用41101个稀有等位基因频率大于5%的高质量SNP，结合群体结构、亲缘关系通过TASSEL软件进行全基因组关联分析。2个环境下共检测到73个SNP与抗粗缩病显著相关（P <0.0001值），单个SNP可以解释2.68%-6.18%的表型变异。2个环境下同时检测到14个SNP，分布于玉米染色体bin5.03、bin7.02、bin8.03、bin10.02和bin10.03，其中SNP PZE-108052072和PZE-108057211位于bin8.03。在连锁不平衡（LinkageDisequilibrium, LD）r2大于0.1的范围，48个SNP的LD区域内筛选到41个候选基因，其中32个SNP位于基因内部，包括GRMZM2G413544、GRMZM2G405760等。
2.利用来源于美国杂交种P78599的5份高抗粗缩病自交系（R18，P138，X178，金黄59和齐318）和全基因组41101个SNP，筛选到9个包含与抗病性显著相关SNP的衍生片段，9个衍生片段的基因型都不同于感病对照掖478的基因型，其中，最小片段长48.84Kb，最大片段长81.57Mb，平均长9351.03Kb。位于bin8.03长81.57Mb的片段包括6个与抗病性显著相关的SNP和2个前人定位到的抗玉米粗缩病主效QTL。
3.以来源于X178×B73杂交组合的重组自交系NL203与B73构建的3个F2群体（表示为F2-1，F2-2和F2-5）为材料，通过玉米粗缩病人工接种和自然发病鉴定，在第8染色体发掘抗粗缩病QTL。基于3个F2群体的分析结果如下：（1）采用F2-1群体构建第8染色体的区段连锁图谱，包括9个标记，全长35.28cM，平均间距4.41cM。结合人工接种表型鉴定，在bin8.03标记umc1617和phi121之间定位到1个来自于NL203的主效QTL，LOD值为5.1，加性效应0.73，解释11%的表型变异；（2）利用F2-2群体构建第8染色体区段连锁图谱，包括10个标记，全长38.36cM，平均间距3.8cM，全部标记与IBM2008neighbor图谱的顺序一致。结合人工接种表型鉴定，在bin8.03标记umc1617和phi121之间定位到1个来自于NL203的主效QTL，LOD值6.18，解释11%的表型变异；（3）利用F2-5群体构建第8染色体的连锁图谱，包括18个标记，全长153.81cM，平均间距9.01cM，除SSR标记bnlg2037，其余标记与IBM2008neighbor图谱的顺序一致。结合自然发病表型鉴定，分别在标记umc1139-bnlg1194与umc1735-phi121之间各检测到1个QTL，2个QTL都来自于NL203，LOD值分别为3.30、18.80，分别解释3.99%、25.71%的表型变异。综合以上结果，在bin8.03标记umc1617和phi121之间存在1个来自于NL203的主效抗病QTL，可以解释25.71%的表型变异。
Maize (Zea mays L.) is an important crop which serves as food and forage. It plays ansignificant role in agricultural and economic development. However, the production of maize wasdisturbed by a lot of biotic stress. Maize rough dwarf disease (MRDD) is a kind of viral disease allover the world, which is caused by maize rough dwarf virus (MRDV), or rice black-streakeddwarf virus (RBSDV), and is transmitted by the insect vector Laodelphax striatellus Fallen. In the1970s, MRDD caused serious loss in maize production in beijing and hebei province. Now, it isone of the most serious diseases in the Yellow-Huai river region which is very important for maizeproduction. The currently agricultural measures protecting maize production are inclined to causeenvironmental pollution, and have little effects. So the most effective measures to conquer MRDDare to breed and plant resistant varieties. In this study, genome wide association and linkageanalysis were used to explore the genetic architecture of resistance to MRDD，and to find themajor resistant quantitative trait loci (QTL) or genes. The main results were as fellows：
1A total of236maize inbred lines with rich diversity were evaluated for resistance to MRDD in2010and2011, respectively. Using41101high quality SNP with minor allele frequencies(MAF) greater than5%, a genome wide association analysis (GWAS) was conducted toinvestigate the genetic architecture underlying this viral disease. As a result, a total of73SNPwere found to be associated with resistance to MRDD at a significant threshold of-log10(P)>4controlling false discovery rate (FDR) at α=0.1, single SNP could explain phenotypicvariance from2.68%to6.18%. Fourteen out of these SNP were detected in both environments.They distributed across chromosome bin5.03, bin7.02, bin8.03, bin10.02, and bin10.03, andSNP PZE-108052072and PZE-108057211were located in bin8.03. A total of48SNP wereidentified in LD blocks (r2>0.1) with candidate resistance genes, and32were included bycandidate genes, including GRMZM2G413544and GRMZM2G405760.
2Using41101SNP to analysis5highly resistant inbred lines derived from the hybrid ‘P78599’,nine derivative fragments harboring SNP associated with MRDD resistance were detected,which were not harbored by the susceptible line ‘Ye478’. The r2within these fragments weregreater than0.1. The length of these fragments varied from48.84Kb to81.57Mb with anaverage of9351.03Kb. The fragment with a length of81.57Mb, which was located in bin8.03and contained6SNP associated with MRDD resistance, included the major resistant QTL thathad been identified in previous studies.
3Three F2populations (assigned as F2-1, F2-2, and F2-5) were constructed with a cross betweenthe susceptible line 'B73' and the resistant line ‘NL203’ which was selected from therecombinant inbred line population developed from the line ‘X178’ crossed with the line ‘B73’.(1) Based on F2-1, the linkage map of chromosome8was constructed, which contained9SSRmarkers with a length of35.28cM. After evaluation for resistance to MRDD through artificial inoculation, one QTL was detected between the marker umc1617and phi121in bin8.03with apeak LOD of5.1, which could explain11%phenotypic variance;(2) Based on F2-2, the linkagemap of chromosome8was constructed, which contained10markers with a length of38.36cM.The order of markers was consistant with that in IBM2008neighbor map. After evaluationthrough artificial inoculation, one QTL was identified between the marker umc1617and phi121with a peak LOD of6.18, which could explain11%phenotypic variance;(3) Based on F2-5, thelinkage map of chromosome8was constructed containing18markers with a length of153.81cM. After evaluation for resistance to MRDD through natural infection, two QTL were detectedwithin the interval of umc1139-bnlg1194and umc1735-phi121, respectively. The QTL in thefirst interval could explain3.99%phenotypic variance, and another could explain25.71%phenotypic variance.
引文
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