| Cabbage (Brassica oleracea L. var. capitata) is a major crop with the characteristics of high quality,high yield and resistance storage, which is widely cultivated in the world. It plays an important role invegetables all-year supply in China.This study is based on the B. oleracea Genome Sequence Project which was launched in2009,using next generation sequencing technology. A number of SSR, SNP and InDel markers are developedby using the data from the de novo sequence and re-sequence. A DH population derives from F1crossbetween two advanced homozygous inbred lines,01-88and02-12, by microspore culture. Then asaturated genetic map of B. oleracea genome is constructed. This genetic map could be used to orientatesequence Scaffolds from the B. oleracea genome assembly. Some InDel markers are developed by usingthe information of the Scaffolds with long fragments, which are not anchored to the genome. This studyis aim to the supplement assembly of the genome. Combined with the transcriptome sequence, the geneswhich control the main agronomic traits could be predicted, through the genetic, correlative and QTLanalysis. So this study provides the whole genetic information of these traits. The markers are screenedto identify which linked to the male sterile gene, with the purpose of development an efficient malesterile gene identified method. In summary, this study is facilitated to enhance the breeding technologyand selection efficiency.The main conclusions of this study are as listed follows:(1) Two diverse advanced homozygous inbred lines of cabbage,01-88and02-18, were used as theparents to develop a doubled haploid (DH) mapping population containing189lines. The DHpopulation was derived from F1by microspore culture and contained lines with a wide variety ofmorphological traits.(2) A total of233844putative SSR sequences were identified from the cabbage assembled Scaffoldsequences. Six different SSR repeat types were identified, and of these the HNRs (163621,69.97%)were the most abundant and the MNRs were the least abundant (311,0.13%).3378SSR primerpairs were designed using the Primer3.0program. A total of1026766SNPs were detected between01-88and02-12.2200SNP markers were developed by SNAPER program.(3) To construct the map, a total of8497markers were screened with the DNA from the01-88and02-12parental lines.1274markers (14.99%) were polymorphic. The B. oleracea high-densitygenetic linkage map that was constructed includes1227markers in nine linkage groups spanning1197.9cM with an average of0.98cM and503.3kb between two loci. This genetic map is themost saturated in B. oleracea crops.(4) A total of172InDel markers were developed, using the information of long Scaffolds which werenot anchored to the genome.84InDel markers showed the polymorphism. Using thesepolymorphic markers,43Scaffolds with22.6Mb were supplemented anchored to the genome.Now, the size of assembled B. oleracea genome is562.6Mb. And the assembly rate is from85.0% up to89.3%.(5) Using mixed major gene plus inheritance model,5traits related to leaf head (head weight, lengthof stem in head, vertical diameter of head, primary color of head, length of shortening stem) and6traits related to plants (number of outer leaf, plant breadth, plant height, length of outer leaf, widthof outer leaf, primary color of outer leaf) were investigated. All the11main agronomic traits werequantitative. Except the Wol and Pcl traits, the other9traits inheritances showed the models of twomajor genes plus polygenes. The heritability range was from19.56%(Pb) to79.45%(Hw).(6) Using IBM SPSS Statistics19program Pearson method in partial correlation analysis,11mainagronomic traits were analysed. Pch-Pcl and Vdh-Lsh, etc paired traits were significant positivecorrelation. Hw-Ls and Vdh-Nol, etc were significant negative correlation. Vdh-Lol and Ls-Pb, etcwere with no correlation.(7) MapQTL4.0software and IM&MQM methods were employed in QTL mapping. As a result, atotal39QTLs were mapped for11main agronomic traits in B. oleracea. Among them, Vdh, Ls,Nol and Pb traits mapped the most QTLs (5). Lsh, Pch and Wol traits were the least with2QTLs.All the QTLs distributed on all the9linkage groups. Some QTLs showed coincidence and linkagephenomenons.(8) Using BSA method,2male sterile and fertile bulks were construed. A total of3SSR markers wereidentified and linked with CDMS-399-3gene. Respectively, scaffold38115and scaffold13994wereflanking markers with genetic distances of8.3cM and15.3cM.(9) Two parental lines of DH population were analysied by RNA-seq technology. Combined with theQTLs and differentially expressed genes from transcriptomic results. A total10genes wereidentified as candidate genes. Of these genes,8genes were related to the processes of anabolismand transport in auxin and cytokinin. The other2genes were related to the processes of anabolismin chlorophyll and carotenoid. |
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