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"X 83ffff̙̙3f3fff3f3f33333f33333ьPUBQTL_EXPERIMENTJMAP_COLLECTION*MAPSaQTL0MAP_POSITION G#publink_citationspeciesref_typeyeartitleauthorsjournalvolumeissuepagesdoipmidabstractBurow, Starr et al., 2014aarachisJournalIntrogression of homeologous quantitative trait loci (QTLs) for resistance to the rootknot nematode [Meloidogyne arenaria (Neal) Chitwood] in an advanced backcrossQTL population of peanut (Arachis hypogaea L.)4Burow MD, Starr JL, Park CH, Simpson CE, Paterson AHMolecular Breeding39340610.1007/s1103201400422Resistance to rootknot nematodes [Meloidogyne arenaria (Neal) Chitwood] is needed for cultivation of peanut in major peanutgrowing areas, but significant resistance is lacking in the cultivated species (Arachis hypogaea L.). Markers to two closelylinked genes introgressed from wild relatives of peanut have been identified previously, but phenotypic evidence for the presence of additional genes in wild species and introgression lines has eluded quantitative trait locus (QTL) identification. Here, to improve sensitivity to smalleffect QTLs, an advanced backcross population from a cross between a Florunner component line and the synthetic amphidiploid TxAG6 [Arachis batizocoi x (A. cardenasii x A. diogoi)]4x was screened for response to rootknot nematode infection. Composite interval mapping results suggested a total of seven QTLs plus three putative QTLs. These included the known major resistance gene plus a second QTL on LG1, and a potentially homeologous Bgenome QTL on LG11. Additional potential homeologs were identified on linkage group (LG) 8 and LG18, plus a QTL on LG9.2 and putative QTLs on LG9.1 and 19. A QTL on LG15 had no inferred resistanceassociated homeolog. Contrary to expectation, two introgressed QTLs were associated with susceptibility, and QTLs at some homeologous loci were found to confer opposite phenotypic responses. Longterm functional conservation accompanied by rapid generation of functionally divergent alleles may be a singular feature of NBSLRR resistance gene clusters, contributing to the richness of resistance alleles available in wild relatives of crops. The significance for peanut evolution and breeding is discussed.#specieslink_abvpublink_citationnamedescriptiongeolocationmap_namecommentBurow, Starr et al., 2014a exp1Texas, USA (Greenhouse)2TT_Florunner_x_A.batizocoiA.cardenasiiA.diogoi_aB'As part of an effort to detect smalleffect QTLs for rootknot nematode resistance within introgression lines, an advanced backcross population was developed by crossing the cultivated tetraploid peanut line ''Florunner'' (component line UF439161032) with the synthetic amphidiploid TxAG6 [(A. batizocoi K9484_x_(A. cardenasii GKP10017_x_ A. diogoi GKP10602))4x]. This BC3 population was derived from a 78 member BC1 population that provided the genetic map (Burow, Simpson et al., 2001a) upon which the authors placed the QTLs revealed by the advanced backcrossQTL analysis. The BC1 genetic map (Burow, Simpson et al., 2001a) is thus the source of the RFLP markers used to genotype the BC3 population and established the cM distances between markers. These BC1 progeny were then backcrossed to ''Florunner'' to form a BC2 population; each resulting BC2 line was again backcrossed to ''Florunner'' to produce up to 10 BC3 plants per BC2 line (mean of 5.7 BC3 progeny per BC2 line). Out of the original 78 BC1 families described in Burow, Simpson et al. (2001a), the descendents of 41 of them were tested for nematode resistance. All BC3 linkage groups in this study showed evidence of genetic introgression from the TxAG6 amphidiploid. The 233 BC3 plants were grown in a greenhouse and inoculated with eggs of Meloidogyne arenaria.'publication_map_nameparent1parent2pop_sizepop_typeanalysis_methodunitFlorunner_x_TxAG6This RFLPbased genetic map was constructed using a BC1 population derived from the cross of a cultivated tetraploid peanut 'Florunner' with a fertile synthetic amphidiploid TxAG6. The amphidiploid was itself developed using the diploid accessions A. batizocoi K9484, A. cardenasii GKP10017, and A. diogoi GKP10602. The map is composed of 23 linkage groups that include 9 pairs of homeologous linkage groups (LG1 and LG11,< LG2 and LG12, LG3 and LG13, LG4 and LG14, LG5 and LG15, LG6 and LG16, LG7 and LG17, LG8 and LG18, LG10 and LG20) and one homeologue (LG19) paired with two partial homeologues (LG9.1 and LG9.2). The map includes 370 RFLP loci (discovered using 220 cDNA probes) and covers a total distance of 2210 cM. FlorunnerG(A. batizocoi K9484_x_(A. cardenasii GKP10017_x_ A. diogoi GKP10602))4xBC1MapMaker EXP (v. 3.0)Burow, Simpson et al., 2001acM map_startmap_end7TT_Florunner_x_A.batizocoiA.cardenasiiA.diogoi_aLG017TT_Florunner_x_A.batizocoiA.cardenasiiA.diogoi_aLG027TT_Florunner_x_A.batizocoiA.cardenasiiA.diogoi_aLG037TT_Florunner_x_A.batizocoiA.cardenasiiA.diogoi_aLG047TT_Florunner_x_A.batizocoiA.cardenasiiA.diogoi_aLG057TT_Florunner_x_A.batizocoiA.cardenasiiA.diogoi_aLG067TT_Florunner_x_A.batizocoiA.cardenasiiA.diogoi_aLG077TT_Florunner_x_A.batizocoiA.cardenasiiA.diogoi_aLG089TT_Florunner_x_A.batizocoiA.cardenasiiA.diogoi_aLG09.19TT_Florunner_x_A.batizocoiA.cardenasiiA.diogoi_aLG09.27TT_Florunner_x_A.batizocoiA.cardenasiiA.diogoi_aLG107TT_Florunner_x_A.batizocoiA.cardenasiiA.diogoi_aLG117TT_Florunner_x_A.batizocoiA.cardenasiiA.diogoi_aLG127TT_Florunner_x_A.batizocoiA.cardenasiiA.diogoi_aLG137TT_Florunner_x_A.batizocoiA.cardenasiiA.diogoi_aLG147TT_Florunner_x_A.batizocoiA.cardenasiiA.diogoi_aLG157TT_Florunner_x_A.batizocoiA.cardenasiiA.diogoi_aLG167TT_Florunner_x_A.batizocoiA.cardenasiiA.diogoi_aLG177TT_Florunner_x_A.batizocoiA.cardenasiiA.diogoi_aLG187TT_Florunner_x_A.batizocoiA.cardenasiiA.diogoi_aLG197TT_Florunner_x_A.batizocoiA.cardenasiiA.diogoi_aLG207TT_Florunner_x_A.batizocoiA.cardenasiiA.diogoi_aLG217TT_Florunner_x_A.batizocoiA.cardenasiiA.diogoi_aLG22qtl_experimentlink_nameexpt_trait_nameexpt_trait_description
trait_unit
qtl_symbolqtl_identifierexpt_qtl_symbolfavorable_allele_source treatmentlodlikelihood_ratio marker_r2total_r2
additivitynearest_markerflanking_marker_lowflanking_marker_highRootknot nematode resistanceOResistance to colonization by the rootknot nematode (Meloidogyne arenaria race 1) was estimated using the number of nematode eggs per gram of fresh root weight. Nematode resistance was assessed in the greenhouse on a per plant basis, and the eggs were counted at 8 weeks following an initial inoculation with 10,000 M. arenaria eggs.log of count/gPeanut rootknot nematode21 Nematode egg count (LG01, 36 cM)CIM S1118HbCDR2612EbCThis QTL on LG01 was detected using both composite interval mapping (CIM) and interval mapping (IM); the CIM QTL is the one we have chosen to represent the locus. The locus LOD value exceeds a threshold of 3.3 and it was judged to represent a 'definitive' QTL. There is another definitive QTL for nematode resistance on LG01 and one other on the homeologous linkage group LG11; in all three cases the increased resistance was derived from TxAG6 wild species alleles. The nematode egg count data were approximately normalized using a logarithmic (base10) transformation. The publication presented two different conservative estimates of phenotypic variance (partial variance effects); partial regression (0.145) and sequential regression in twomarker ANOVA (0.027). Please see Burow, Starr et al., 2014a for further details on the variances and how they were used to calculate additivities.211"Nematode egg count (LG09.1, 13 cM)S1176HaDS1118HaDThis QTL on LG09.1 was detected only when using composite interval mapping (CIM). The locus LOD value exceeds a threshold of 2.3 and it was judged to represent a 'putative' QTL. There is a definitive QTL for nematode resistance on LG09.2 and one other putative QTL on the homeologous linkage group LG19; on LG09.1 the enhanced resistance comes from TxAG6 wild species alleles, for LG09.2 the increased resistance is derived from Florunner alleles, and on LG19 only very weak resistance was inherited from TxAG6 wild species alleles. The nematode egg count data were approximately normalized using a logarithmic (base10) transformation. The publication presented two different conservative estimates of phenotypic variance (partial variance effects); partial reg< ression (0.068) and sequential regression in twomarker ANOVA (0.061). Please see Burow, Starr et al., 2014a for further details on the variances and how they were used to calculate additivities.212"Nematode egg count (LG09.2, 39 cM)R2469HbCR2496HaCThis QTL on LG09.2 was detected only when using composite interval mapping (CIM). The locus LOD value exceeds a threshold of 3.3 and it was judged to represent a 'definitive' QTL. There is a putative QTL for nematode resistance on LG09.1 and another putative QTL on the homeologous linkage group LG19; on LG09.1 the enhanced resistance comes from TxAG6 wild species alleles, for LG09.2 the increased resistance is derived from Florunner alleles, and on LG19 only very weak resistance was inherited from TxAG6 wild species alleles. The nematode egg count data were approximately normalized using a logarithmic (base10) transformation. The publication presented two different conservative estimates of phenotypic variance (partial variance effects); partial regression (0.221) and sequential regression in twomarker ANOVA (0.068). Please see Burow, Starr et al., 2014a for further details on the variances and how they were used to calculate additivities.215 Nematode egg count (LG11, 23 cM)
R0193EcBCDR2005HaBnThis QTL on LG11 was detected using both composite interval mapping (CIM) and interval mapping (IM); the CIM QTL is the one we have chosen to represent the locus. The locus LOD value exceeds a threshold of 3.3 and it was judged to represent a 'definitive' QTL. There are two other definitive QTLs for nematode resistance on the homeologous linkage group LG01; in all three cases the increased resistance was derived from TxAG6 wild species alleles. The nematode egg count data were approximately normalized using a logarithmic (base10) transformation. The publication presented two different conservative estimates of phenotypic variance (partial variance effects); partial regression (0.15) and sequential regression in twomarker ANOVA (0.063). Please see Burow, Starr et al., 2014a for further details on the variances and how they were used to calculate additivities.217 Nematode egg count (LG15, 19 cM)R2410EaBS1103HbB\This QTL on LG15 was detected only when using composite interval mapping (CIM). The locus LOD value exceeds a threshold of 2.3 and it was judged to represent a 'putative' QTL. The nematode egg count data were approximately normalized using a logarithmic (base10) transformation. The publication presented two different conservative estimates of phenotypic variance (partial variance effects); partial regression (0.048) and sequential regression in twomarker ANOVA (0.035). Please see Burow, Starr et al., 2014a for further details on the variances and how they were used to calculate additivities.218 Nematode egg count (LG15, 75 cM)S1075EbBR2494HaB^This QTL on LG15 was detected only when using composite interval mapping (CIM). The locus LOD value exceeds a threshold of 3.3 and it was judged to represent a 'definitive' QTL. The nematode egg count data were approximately normalized using a logarithmic (base10) transformation. The publication presented two different conservative estimates of phenotypic variance (partial variance effects); partial regression (0.144) and sequential regression in twomarker ANOVA (0.064). Please see Burow, Starr et al., 2014a for further details on the variances and how they were used to calculate additivities.219 Nematode egg count (LG18, 11 cM)R2060HeBS1166HaBThis QTL on LG18 was detected using both composite interval mapping (CIM) and interval mapping (IM); the CIM QTL is the one we have chosen to represent the locus. The locus LOD value exceeds a threshold of 3.3 and it was judged to represent a 'definitive' QTL. There is another definitive QTL for nematode resistance on LG18 and one other on the homeologous linkage group LG08; on LG08 the increased resistance was derived from Florunner alleles whereas on LG18 the enhanced resistance comes from TxAG6 wild species alleles. The nematode egg count data< were approximately normalized using a logarithmic (base10) transformation. The publication presented two different conservative estimates of phenotypic variance (partial variance effects); partial regression (0.153) and sequential regression in twomarker ANOVA (0.066). Please see Burow, Starr et al., 2014a for further details on the variances and how they were used to calculate additivities.221 Nematode egg count (LG18, 34 cM)R2039EaB R2060HbBC4This QTL on LG18 was detected using both composite interval mapping (CIM) and interval mapping (IM); the CIM QTL is the one we have chosen to represent the locus. The locus LOD value exceeds a threshold of 3.3 and it was judged to represent a 'definitive' QTL. There is another definitive QTL for nematode resistance on LG18 and one other on the homeologous linkage group LG08; on LG08 the increased resistance was derived from Florunner alleles whereas on LG18 the enhanced resistance comes from TxAG6 wild species alleles. The nematode egg count data were approximately normalized using a logarithmic (base10) transformation. The publication presented two different conservative estimates of phenotypic variance (partial variance effects); partial regression (0.013) and sequential regression in twomarker ANOVA (0.39). The variance estimate for the twomarker ANOVA is less reliable because it is based on the egg counts of only 12 plants. Please see Burow, Starr et al., 2014a for further details on the variances and how they were used to calculate additivities.223 Nematode egg count (LG19, 41 cM)S1176HbBS1044EaBThis QTL on LG19 was detected only when using composite interval mapping (CIM). The locus LOD value exceeds a threshold of 2.3 and it was judged to represent a 'putative' QTL. There is a putative QTL for nematode resistance on the partial homeologue LG09.1 and a definitive QTL for resistance on the partial homeologue LG09.2; on LG09.1 the enhanced resistance comes from TxAG6 wild species alleles, for LG09.2 the increased resistance is derived from Florunner alleles, and on LG19 only very weak resistance was inherited from TxAG6 wild species alleles. The nematode egg count data were approximately normalized using a logarithmic (base10) transformation. The publication presented two different conservative estimates of phenotypic variance (partial variance effects); partial regression (0.086) and sequential regression in twomarker ANOVA (0.056). Please see Burow, Starr et al., 2014a for further details on the variances and how they were used to calculate additivities.23 Nematode egg count (LG01, 82 cM)Vmc3HaC S1018EbCDSThis QTL on LG01 was detected using composite interval mapping (CIM), interval mapping (IM), and singlemarker analysis (SMA); the CIM QTL is the one we have chosen to represent the locus. The locus LOD value exceeds a threshold of 3.3 and it was judged to represent a 'definitive' QTL. There is another definitive QTL for nematode resistance on LG01 and one other on the homeologous linkage group LG11; in all three cases the increased resistance was derived from TxAG6 wild species alleles. The nematode egg count data were approximately normalized using a logarithmic (base10) transformation. The publication presented two different estimates of phenotypic variance for this major QTL; CIM (0.154) and ANOVA (0.174). Please see Burow, Starr et al., 2014a for further details on the variances and how they were used to calculate additivities.29 Nematode egg count (LG08, 42 cM)R2409EbDR2015EaDThis QTL on LG08 was detected using both composite interval mapping (CIM) and interval mapping (IM); the CIM QTL is the one we have chosen to represent the locus. The locus LOD value exceeds a threshold of 3.3 and it was judged to represent a 'definitive' QTL. There are two other definitive QTLs for nematode resistance on the homeologous linkage group LG18; on LG08 the increased resistance was derived from Florunner alleles whereas on LG18 the enhanced resistance comes from TxAG6 wild species alleles. The nematode egg count data were approxima<tely normalized using a logarithmic (base10) transformation. The publication presented two different conservative estimates of phenotypic variance (partial variance effects); partial regression (0.119) and sequential regression in twomarker ANOVA (0.02). Please see Burow, Starr et al., 2014a for further details on the variances and how they were used to calculate additivities. #map_namelgleft_end right_endQTL_peakinterval_calc_methodPeanut rootknot nematode 21LG01cM from ImageJPeanut rootknot nematode 211LG09.1plus one minus one cMPeanut rootknot nematode 212LG09.2Peanut rootknot nematode 215LG11Peanut rootknot nematode 217LG15Peanut rootknot nematode 218Peanut rootknot nematode 219LG18Peanut rootknot nematode 221Peanut rootknot nematode 223LG19Peanut rootknot nematode 23Peanut rootknot nematode 29LG08qa!(}e+9. }2Q
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