| Maize rough dwarf disease which is generally caused by maize rough dwarf virus (MRDV) is one of the main diseases in parts of maize production area for nearly10years. Mining MRDV resistant germplasm and then breeding resistant variety is an economical and effective approach to control the disease. At the same time, when considering the molecular marker assistant breeding project, the process of cultivating a new resistant variety could be accelerated if we found some makers linked to the genes which control the maize rough dwarf disease resistance pathway. In this research184inbred lines including111common maize and73waxy maize were screened for reaction to MRDV under field conditions during2009and2010at Nantong, Jiangsu Province, China. The genetic diversity of the test materials was investigated based on115polymorphic SSR markers. To mining resistant subpopulations, cluster analysis of184inbred lines was conducted based on genetic similarities from SSR data by using Powermarker3.0software with UPGMA method. On the other hand, base on the analysis of linkage disequilibrium and population structure, association analysis were used to map the maize rough dwarf disease gene and mine the resistance alleles. The results were as follows:(1) Though2years identification in area that has rampant maize rough dwarf virus. The disease evaluation resulted in identification of2(T877, YJ7) and14inbred lines offering high resistance and resistance to MRDV, among them3waxy inbred lines were identified. With the joint variance analysis of infected plant rate and disease index across2009and2010, very significant differences were found among the tested maize inbred lines. While at the same time, the different level between two years was very significant, which indicated that the different environment of these2years especially the change of striatellus population and poisoned rate had affected the identification of maize rough dwarf disease of all tested inbred lines. The relation analysis of2years disease index indicated that the evaluation result between2years had a well consistency, the correlation efficient was0.717.(2)115polymorphic SSR markers evenly distributed on10maize chromosomes were chose to analysis the genetic diversity of tested materials. The results showed that644specific DNA bands were detected.2-15polymorphic fragments were amplified stably by each primer with an average of5.6fragments. The value of polymorphism information content (PIC) for each SSR locus varied from0.18to0.91with an average of0.59. Marker umc1226had the least PIC value while bnlg1621b had the biggest PIC value. The gene diversity value of each SSR locus varied from0.19to0.92with an average of0.64.(3) All644specific DNA bands stably amplified by115SSR markers on184maize inbred lines were used to perform the cluster analysis. UPGMA analysis indicated that184inbred lines could be classified into9sub-groups, which were generally consistent to their known pedigree information and breeder’s experiences. Two sub-groups which separately derived from4S and US hybrid78599had better resistance to MRDV than other seven sub-groups and could be used as core germplasm in genetic improvement of maize rough dwarf disease resistance in Jiangsu province.(4) The linkage disequilibrium analysis of tested materials indicated that LD could be detected in both syntenic and un-syntenic marker pairs. Compare with all marker pairs, the proportion of linkage disequilibrium pairs which probability value below0.01was64.04%. Among them the linkage disequilibrium significant level of49.55%marker pairs were smaller than0.0001. The loci pairs with D’>0.5was1.14%of the total. The LD loci pair number of common maize was a little bigger than that of waxy corn. However, when consider the distribution and average value of D’, the LD level of waxy maize inbred lines was a bit higher than that of common maize. We used the model based method in STRUCTURE software to analysis the population structure of tested materials. The result showed that when subpopulation number value K=4, well consistency could be found among the result of population structure, cluster analysis and pedigree information of all tested materials. So all inbred lines was divided into4subpopulations.(5) We used3kind phenotypic values to perform association mapping of maize rough dwarf gene. Two of the phenotypic values are the disease index and average disease degree of2009and2010respectively. The third phenotypic value is estimate value, we used the quantitative genetic model and disease index value in2009and2010to separate the genetic effect value of every inbred line. Association mapping result of the disease index and average disease degree in2009was almost identical. When significant level was0.01,8SSR loci was detected associated with maize rough dwarf disease. These loci were located on chromosome1,2,3,5and9, and there were4SSR loci on chromosome2. Association mapping result of the disease index and average disease degree in2010was also identical. When significant level was0.01,8SSR loci was detected associated with maize rough dwarf disease. These loci were located on chromosome1,2,4,5,6and10. On chromosome2and4, we each detected2SSR loci separately. With the quantitative genetic model, we evaluate the genetic effect of disease index of inbred lines. The association mapping result of estimated value showed that7SSR loci could be detected with significant level P<0.05.5of these loci were on chromosome2, the rest2were on chromosome7. The interpretation rate of genetic variability of maker bmcl267was19.91%, the interpretation rate of rest marker were almost below10%. The analysis result of3kind association mapping showed that umc1553and umc1026which located on chromosome1and2separately, could be detected in both2009and2010. Maker umc1026was also detected when the phenotypic value was the genetic effect value of every inbred line. We also mined the resistant allele of marker umc1026on this association mapping population. The result showed that umcl026-A130was the resistant allele of maize rough dwarf disease. Based on the phenotypic value of2009and2010, we found the resistant allele could reduce5-10disease index and0.2-0.4average disease degree. |
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