Qtl Analysis For The Traits Associated With Plant Architecture And Silique In Brassica Napus1

At present, the breeding of rapeseed varieties with improved plant type and suitable for the mechanised production is one of the major directions of rapeseed breeding in China. The work on the genetic basis and QTL mapping of the traits associated with plant type could provide a basis for molecular marker assisted breeding of the new B. napus varieties with specific plant type. In this study, a population consisting of181DH lines, which was derived from F1microspore culture of a cross of the B. napus lines8008(normal plant type, high seed-yield per plant) and94942C-5(compact plant type, low seed-yield per plant), was used as the field test materials. Sixteen plant type-or yield-associated traits were analyzed, and the QTLs for these traits were mapped. The major results are as following:1. The genetic map construction and comparative genomics information of B. napusUsing the double haploid population, a linkage map containing1904markers, including160AFLPs,254SSRs,79IPs,3SCARs and1048SNPs, was constructed. The resulting map consisted of20linkage groups (the C1was divided into two linkage groups), covering2328.97cM with an average of1.46cM between markers, with a considerable consistence to the previously published linkage maps. Moreover, the BLASTN analysis showed that456,549and421homologous genes from A. thaliana, B. rapa and B. oleracea respectively, could be mapped on A genome of B. napus. And212,209and250homologous genes from A. thaliana, B. rapa and B. oleracea respectively, could be mapped on C genome of B. napus. Based on the24identified conserved regions in A. thaliana,63sythenic blocks and82insertion fragments were identified by using the A. thaliana genes mapped on the genetic map of B. napus.2. Synteny analysisThe results indicated that the synteny in A genome was better than that in C genome. Alignments of linkage groups in B. napus to pseudochromosomes in B. napus, linkage group in B. napus to the pseudochromosomes in B. rapa and B. oleracea, and the pseudochromosomes in B. napus to pseudochromosomes in B. rapa and B. oleracea showed that the synteny extents in the first two alignments were equivalent and the synteny extent in the third alignment was mostly better than that in in the first two alignments. These results suggested that though the linkage relationship between some loci on the genetic map constructed in this study maybe needs further confirmation, or it is possible that chromosomal rearrangement really exits in these regions, the results from synteny analysis still fully confirmed the fact that B. napus is derived from B. rapa and B. oleracea. Considering the arrangement directions in the linkage groups in B. napus (BnA1-BnA10, BnC1-BnC9), the pseudochromosomes in B. napus (Bnl-Bnl9), B. rapa (BrA1-BrA10) and B. oleracea (BoC1-BoC9), the consistent direction was found in each element of the trisomes of BnAl-Bnl-BrAl, BnA2-Bn2-BrA2, BnA4-Bn4-BrA4, BnA6-Bn6-BrA6, BnA7-Bn7-BrA7, BnC3-Bn13-BoC3, BnC4-Bn14-BoC4, BnC8-Bnl8-BoC8, BnC9-Bnl9-BoC9. The information on direction and synteny extent could provide a basis for the revolution of the practical problem in B. napus by utilizing the genome sequence information from other crops.3. Frequency distribution in DH populationThe frequency distribution of the16traits in the DH population was analyzed in three environments. The results indicated that most traits showed a multimodal continuous distribution, deviating from the standard normal distribution. Using the composite interval mapping (MCIM), a genome-wide scan for QTLs was conducted. A total of337QTLs for the16traits were detected in three environments (117QTLs in11WH,122QTLs in12WH,98QTLs in11EZ). After meta-analysis was conducted for each trait, the337QTLs were consolidated into234QTLs covering20LGs. Seventeen QTLs controlling average length of primary branches (ALPB) were identified on6LGs:A1, A3, A5, A6, A7and Cla, with the individual QTL explaining3.9-25.9%of the phenotypic variation. For length of main inflorescence (LMI),10QTLs were detected on LGs Al, A3, A5, A6, A7, C8and C9, with the individual QTL explaining4.7-25.5%of the phenotypic variation. For the length of silique layer (LSL),10QTLs were detected on LGs A1, A3, A6, A9, C3and C8, with the individual QTL explaining5.1-11.8%of the phenotypic variation. Nine QTLs for number of siliques on branches (NSB) were assigned on four LGs: A1, A3, A9and C3, with the individual QTL accounting for4.4-20.1%of the phenotypic variation. For the number of primary branches (PB),15QTLs were detected on LGs Al, A4, A7, Cla, Clb, C2, C3and C4, with the individual QTL explaining4.7-15.1%of the phenotypic variation. Fifteen QTLs controlling plant height (PH) were detected on6LGs:A1, A3, A6, A7, Clb and C9, with the individual QTL explaining0.7-32.2%of the phenotypic variation. Twenty-four QTLs for silique density of branches (SDB) were assigned on11LGs:A1, A3, A5, A6, A7, A9, Cla, Clb, C6, C7and C9, with the individual QTL accounting for4.4-16.0%of the phenotypic variation. For silique density on main inflorescence (SDMI), 10QTLs were detected on LGs A3, A6, A7, Cla, and C7, with the individual QTL explaining5.3-12.9%of the phenotypic variation. For silique length (SL),11QTLs were detected on LGs Al, A7, A9and A10, with the individual QTL explaining2.4-60.0%of the phenotypic variation. Seventeen QTLs controlling number of siliques on main inflorescence (SMI) were detected on6LGs:Al, A2, A3, A5, A9and Cla, with the individual QTL explaining4.7-14.8%of the phenotypic variation. For number of seeds per silique (SN),15QTLs were detected on8LGs:Al, A6, A7, A8, Cla, Clb, C3and C5, with the individual QTL explaining4.9-26.6%of the phenotypic variation. Nine QTLs for silique number per plant (SNPP) were assigned on3LGs:Al, A9and C3, with the individual QTL accounting for4.8-24.3%of the phenotypic variation. For seeds yield per plant (SY),10QTLs were identified on5LGs: A1, A3, A9, C3and C8, with the individual QTL explaining4.4-35.7%of the phenotypic variation. Thirteen QTLs for total length of primary branches (TLPB) were assigned on6LGs:A1, A3, A6, A9, Cla and C3, with the individual QTL accounting for5.3-17.9%of the phenotypic variation. For and thousand seed weight (TSW),16QTLs were detected on7LGs:Al, A7, A9, Cla, Clb, C8and C9, with the individual QTL explaining3.4-38.8%of the phenotypic variation. Twenty QTLs for silique the width of silique layer (WSL) were assigned on6LGs:Al, A2, A3, A7and A9, with the individual QTL accounting for4.2-31.3%of the phenotypic variation.4. QTLs and homologous QTLs mapped in paralogous conserved blocks in B. napus.One hundred and sixty-eight of the234QTLs identified by the first round meta-analysis could be mapped in silico in the14conserved crucifer blocks (U, H, F, W, E, R, J, C, X, M, N, B, I and A). Eight pairs of homologous QTLs for PB, SL, WSL, SN, TSW, PH, LMI and SY were found in paralogous conserved blocks E, U, X and R in B. napus.5. Pleiotropic QTLs and indicator-QTLs for yieldThe integrated results from the second round meta-analysis showed that there were59pleiotropic QTLs, and each of them was associated with2to8traits for designing ideal plant architecture. For example, mqA1.14integrated the traits on plant architecture traits, plant architecture and silique-traits, silique traits and seed yield together. Seven of ten QTLs detected in this study for seed yield were identified as pleiotropic QTLs. Among these pleiotropic QTLs, indicator traits of mqA1.14, mqA9.4and mqC8.1were length of main inflorescence, number of siliques on main inflorescence and thousand seeds weight, respectively, but no a QTL could be regarded as yield-indicator QTL in mqA1.5, mqA1.9, mqC3.2and mqC3.4.6. The mapping of candidate genes governing plant type and yield traits on the genetic mapLinkage analysis showed that26markers, which derived from21primer pairs designed by the A. thaliana genes governing plant type and seed traits (TCP24, Sepl, API, STM, LFY, ANT, AXR6, PIN1, AP3, REV, TTG2and TT5), could be mapped at the different locations on this genetic map. Nearby some genic-markers, QTLs could be detected. However, the correlation between these QTLs and the candidate genes needs further confirmation. Using the A. thaliana genes mapped on the genetic map in this study as a bridge, some important genes governing plant type and yield component traits in rice and corn were roughly mapped on the genetic map in this study. The results showed that6candidate genes(GS5, ARGOS, MINI3, CLAVATA1, DEP2and IPAl/OsSPL14) could be mapped at eight locations. Among these candidate genes, GS5, ARGOS and MINI3which controlling seed component traits were mapped at the locations neighboring QTLs for thousand seeds weight (TSW), the number of seeds per silique (SN), silique length (SL) and seed yield (SY). The A. thaliana gene CLAVATA1, which governs flower/inflorescence traits, was mapped in the E conserved blocks neighboring a QTL for number of siliques on main inflorescence (SMI) on LG A2. The dense and erect panicle gene DEP2was mapped in the F conserved blocks neighboring QTLs for average length of primary branches (ALPB) and total length of primary branches (TLPB) on LG A5. The rice ideal plant architecture gene IPA1/OsSPL14was mapped in the N conserved blocks neighboring two QTLs for silique density of branches (SDB) on LG A9.