| Rice is the most important food crop in China.Its breakthrough in yield and disease resistance depends on the discovery and utilization of favorable genes.Therefore,it will makes important sense to widen the genetic basis,increase rice yield of new rice varieties in the future by clarifying the genetic status of existing rice varieties and exploring the elite alleles of agronomic and yield-related traits through asociation analysis.Rice blast disease has been an important disease in rice production especially the neck blast is the most serious.Identifying the combination of dominant resistance genes and exploring new resistance loci will be favorable to cultivate new disease-resistant varieties.In this study,83 findica rice varieties and 181 japonica riee varieties from home and abroad were used as test materials.Genetic variation and population structure were analyzed based on 210 SSR/lndel markers.Then the association analysis of 13 agronomic and yield related traits,such as plant height,plant seed setting rate,grain length and so on,and neck blast resistance were executed.At the same time,to state the region distribution of Pi-tat Pi-5,Pi-km,Pi-b genes and their relationship with neck blast resistance,238 japonica rice varieties(lines)were genotyped using the functional markers of the four genes and their disease reactions were detected to evaluate the effects of these genes on the resistance of neck blast.The main results were as follows:1.In 83 indica rice varieties,a total of 727 alleles were detected by 210 SSR/Indel markers,ranging from 2 to 9 with an average value of 3.46 alleles per marker.Genetic diversity index ranged from 0.02 to 0.81 with an average value of 0.41.The polymorphism information content(PIC)ranged from 0.02 to 0.79 with an average value of 0.36.91 moderately polymorphic loci(0.25<PIC<0.5)and 56 highly polymorphic locus(PIC>0.5)were detected.In japonica rice varieties,a total of 639 alleles were detected,with an average value of 3.04 alleles per marker.Genetic diversity index ranged from 0.01 to 0.75 with an average value of 0.26.The polymorphism information content(PIC)ranged from 0.01 to 0.71 with an average value of 0.23.70 moderately polymorphic loci(0.25<PIC<0.5)and 18 highly polymorphic locus(PIC>0.5)were detected,indicating that the genetic diversity of japonica rice varieties was not enough than indica rice.2.Population structure analysis and UPGMA cluster analysis based on Nei's genetic distance indicated that there was a strong subpopulation didfferentiation bwteen indica andjaponica rice populations(Fst=0.67).83 indica rice varieties were divided into 3 main subpopulations and 1 mixed subpopulation.Only 0.62%of the genetic relationship coefficient among the varieties was greater than 0.5,showing that the source of the test materials was extensive and the genetic relationship of varieties between groups was far.181 japonica rice varieties could be divided into 3 main subpopulations and 4 clusters.The analysis result of cluster was consistent with population genetic structure showing a clear geographical orientation.There was large genetic differentiation for most of the varieties among groups,and a small number of varieties that come from the same area or geographic proximity had close genetic relationship.The kinship coefficient among the varieties of the same breeding institutes was much higher.3.Analysis were performed on 13 agronomic and yield-related traits such as plant height,plant seed setting rate,thousand-grain weight and so on.Agronomic and yield-related traits were mutually restricted and closely related.Among these traits,panicle exertion showed the greatest variation in indica and japonica rice populations with the coefficient of variation were 100.97%and 72.45%,respectively.However,the variations of grain thickness was the smallest with the coefficient variation of 5.01%and 4.85%,respectively.4.Based on the results of association analysis between markers and traits,for agronomic and yield related traits,14 and 37 significant loci were detected in 83 indica and 181 japonica rice varieties,respectively,and 1 locus were identified across two groups.RM440,RM470,etc.,was associated with several traits.There were 12 loci significantly associated with grain length which was much higher than other traits,while only one locus was significantly associated with plant seed setting rate.Among these loci,19 loci appeared to be similar to previous studies by comparing with the reported associated loci,QTL mapping or cloning loci.The remaining loci were newly discovered in this study.Further analysis of positive elite alles and nagetive elite alles of these associated loci showed that there were 15 typical cultivars carried elite alleles in indica rice.For example,Luchang 3,Kasalath carryed the positive-alleles of RM255 and RM292 increasing secondary branch number and grain nunber per Plants and 43 typical japonica cultivars,such as Wuyunjing 29,Chugoku 91,etc.,carryed the positive alleles of RM430,RM470 and RM6313 controlling panicle number per plant,seed yield per plant and grain length.X023,41583,Chugoku 91,Changnongjing 5,etc.,carryed multiple excellent allelic variations of panicle number per plant,grain number per plant,seed yield per plant and grain thickness.5.Functional markers of blast resistance genes were used to detect 238 japonica rice varieties(lines).The results showed that 33,30,29 and 38 varieties(lines)were detected to carry the single gene of Pi-ta,Pi-5,Pi-km and Pi-b,respectively.66 varieties(lines)carried two resistance genes and there were 28 varieties(lines)harboring Pi-ta/Pi-b which was much higher than other gene combinations.12 varieties(lines)carried three resistance genes Pi-tat Pi-5 and Pi-km.No variety carried four resistance genes.30 varieties(lines)were detected with no resistance gene.Pi-ta gene had the best effects to neck blast resistance with a prevalence of 0 and a disease index of 22.73,followed by Pi-5 and Pi-km genes with a disease index of 59.17 and 70.69,respectively.The resistance of Pi-b gene was the lowest among them with a prevalence of 86.84 and a disease index of 83.55.The effects of double genes to neck blast resistance showed that Pi-ta/Pi-5>Pi-ta/Pi-km>Pi-ta/Pi-->Pi-5/Pi-kmn.Three varieties containing Pi-ta/Pi-5/Pi-km genes were detected and showed the strongest effOeects to neck blast resistance.9 loci significantly associated with neck blast reasistance in 181 japonica rice varieties were identified,with 1 known cloned gene(Pi-ta),and 1 known QTL(qBLASTads-6).In addition to the known loci,RM4472,RM440,RM7119,RM348,RM136,RM318 and RM515 might be new resistance locus. |
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