| Rice(Oryza sativa L.) is one of the most important crops, and it is the staple food for more than half of the people worldwide. During the domestication of rice, two subspecies indica and japonica formed under natural and artificial selection. Crosses between indica rice and japonica rice often lead to inter-species hybrid sterility. Because rice is a monocot with 12 pairs of chromosomes(~430 Mb), it has been widely used as model plant in research and breeding. Construction of linkage maps, mapping and cloning of genes or quantitative trait loci(QTLs) related to important agronomic traits are meaningful to the breeding of rice varieties with good traits.To estimate the influences of segregation distorted markers on the building of linkage map and QTL identification, we designed a GoldenGate SNP array harboring 384 evenly distributed SNPs along chromosomes that selected and experimentally validated based on the SNPs between 9311(indica) and Nipponbare(japonica) to genotype the 298 stably inherited recombination inbred lines(RILs) derived from 9311(paternal) and Nipponbare(maternal), of which, 259 are from F5 generation, and 39 are from F6 generation. Moreover, we have also collected 14 agronomic traits in total for 152 randomly selected RILs, including one-thousand-grain weight(TGW), the ratio of grain length to grain width(L/W), panicle length(PL), arista length(AL), arista color(AC), grain color(GC), plant height(PH), flag leaf length(FLL), flag leaf width(FLW), the ratio of the length of the flag leaf to its width(FLL/FLW), tiller number(TN), growth period(GP), seed setting rate(SR), and lodging rate(LR). After bioinformatic analysis, 323 SNPs in total were found to be polymorphic among RILs. Ultimately, 294 SNPs were selected to build the linkage map with distance of 1,583.2 cM, of which, 78.57% SNPs are segregation distortedmarkers. The linkage map constructed here is highly consistent with the map built without segregation distorted markers in previous study(R2=0.6924, p<0.01). Based the linkage map, 85 QTLs that can explain the phenotypes larger than 5% were identified to be significantly related to the collected agronomic traits. Of the QTLs identified in this study, 34 QTLs are identical to known genes and QTLs responsible for corresponding traits, and 17 QTLs are found to be related to fertility. Interestingly, individuals with genotypes derived from 9311 or Nipponbare show quite different phenotypes within the QTLs harboring segregation distorted markers.In summary, the results in this study indicate that the segregation distorted markers can be sufficiently used in the construction of linkage maps, as well as mapping important agronomic trait related QTLs. The segregation distorted markers may be induced by the inter-species hybrid incompatibility between indica rice and japonica rice. The quite different phenotypes between samples derived from different parents at QTLs that harboring segregation distorted markers indicate that the segregation distortion may be the reason for these QTLs. Through this study, we provided sufficient evidences for the formation of inter-species hybrid incompatibility and the correlation between segregation distorted markers and QTLs. |
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