Inheritance and molecular mapping of new greenbug resistance genes in wheat germplasms derived from Aegilops tauschii

Molecular mapping of genes for crop resistance to the greenbug, Schizaphis graminum Rondani, will facilitate selection of greenbug resistance in breeding through marker-assisted selection and provide information for map-based gene cloning. In the present study, microsatellite marker and deletion line analyses were used to map greenbug resistance genes in five newly identified wheat germplasms derived from Aegilops tauschii. Our results indicate that the Gb genes in these germplasms are inherited as single dominant traits. Microsatellite markers Xwmc157 and Xgdm150 flank Gbx1 at 2.7 and 3.3 cM, respectively. Xwmc671 is proximately linked to Gba, Gbb, Gbc and Gbd at 34.3, 5.4, 13.7, 7.9 cM, respectively. Xbarc53 is linked distally to Gba and Gbb at 20.7 and 20.2 cM, respectively. Xgdm150 is distal to Gbc at 17.9 cM, and Xwmc157 is distal to Gbd at 1.9 cM. Gbx1, Gba, Gbb, Gbc, Gbd and the previously characterized Gbz are located in the distal 18% region of wheat chromosome 7DL. Gbd appears to be a new greenbug resistance gene different from Gbx1 or Gbz. Gbx1, Gbz Gba, Gbb, Gbc and Gbd are either allelic or linked to Gb3.     

Microsatellite markers linked to six Russian wheat aphid resistance genes in wheat

The Russian wheat aphid (RWA), Diuraphis noxia Mordvilko, is a serious economic pest of wheat and barley in North America, South America, and South Africa. Using aphid-resistant cultivars has proven to be a viable tactic for RWA management. Several dominant resistance genes have been identified in wheat, Triticum aestivum, including Dn1 in PI 137739, Dn2 in PI 262660, and at least three resistance genes (Dn5+) in PI 294994. The identification of RWA-resistant genes and the development of resistant cultivars may be accelerated through the use of molecular markers. DNA of wheat from near-isogenic lines and segregating F₂ populations was amplified with microsatellite primers via PCR. Results revealed that the locus for wheat microsatellite GWM111 (Xgwm111), located on wheat chromosome 7DS (short arm), is tightly linked to Dn1, Dn2 and Dn5, as well as Dnx in PI 220127. Segregation data indicate RWA resistance in wheat PI 220127 is also conferred by a single dominant resistance gene (Dnx). These results confirm that Dn1, Dn2 and Dn5 are tightly linked to each other, and provide new information about their location, being 7DS, near the centromere, instead of as previously reported on 7DL. Xgwm635 (near the distal end of 7DS) clearly marked the location of the previously suggested resistance gene in PI 294994, here designated as Dn8. Xgwm642 (located on 1DL) marked and identified another new gene Dn9, which is located in a defense gene-rich region of wheat chromosome 1DL. The locations of markers and the linked genes were confirmed by di-telosomic and nulli-tetrasomic analyses. Genetic linkage maps of the above RWA resistance genes and markers have been constructed for wheat chromosomes 1D and 7D. These markers will be useful in marker-assisted breeding for RWA-resistant wheat. Received: 17 May 2000 / Accepted: 13 June 2000     

Quantitative trait loci and molecular markers associated with wheat allelopathy

Wheat (Triticum aestivum L.) has been examined for allelopathic potential against annual ryegrass (Lolium rigidum). The bioassay technique, 'equal-compartment-agar-method', was employed to evaluate seedling allelopathy in a doubled-haploid (DH) population derived from cv Sunco (weakly allelopathic) and cv Tasman (strongly allelopathic). A significant difference in allelopathic activity was found among the DH lines, which inhibited the root length of ryegrass across a range from 23.7 to 88.3%. The phenotypic data showed that wheat allelopathic activity was distributed normally within this DH population and a substantial transgressive segregation for seedling allelopathic activity was also found. Analysis of restriction fragment length polymorphism (RFLP), amplified fragment length polymorphism (AFLP) and microsatellite (SSRs) markers identified two major QTLs on chromosome 2B associated with wheat allelopathy. The linkage analysis of genetic markers and the QTLs may improve genetic gains for the allelopathic activity through marker-assisted selection in wheat breeding. The development of wheat allelopathic cultivars could reduce the over-reliance of weed control on synthetic herbicides.Communicated by J. Dvorak     

Categories of resistance to greenbug (Homoptera: Aphididae) biotype K in wheat lines containing Aegilops tauschii genes

The wheat lines (cultivars) 'Largo', 'TAM110', 'KS89WGRC4', and 'KSU97-85-3' conferring resistance to greenbug, Schizaphis graminum (Rondani), biotypes E, I, and K were evaluated to determine the categories of resistance in each line to greenbug biotype K. Our results indicated that Largo, TAM110, KS89WGRC4, and KSU97-85-3 expressed both antibiosis and tolerance to biotype K. Largo, KS89WGRC4, and KSU97-85-3, which express antixenosis to biotype I, did not demonstrate antixenosis to biotype K. The results indicate that the same wheat lines may possess different categories of resistance to different greenbug biotypes. A new cage procedure for measuring greenbug intrinsic rate of increase (r(m)) was developed, by using both drinking straw and petri dish cages, to improve the efficiency and accuracy of r(m)-based antibiosis measurements.     

Biochemical markers associated with two Mv chromosomes from Aegilops ventricosa in wheat-Aegilops addition lines

Summary The distribution of three biochemical markers, U-1, CM-4 and Aph_v-a, -b, among wheat-Aegilops addition lines carrying M^v chromosomes from Aegilops ventricosa (genomes D^vM^v) has been investigated. Addition lines which had been previously grouped together on the basis of common non-biochemical characters carried marker U-1, a protein component from the 2M urea extract. The added chromosome, in the appropriate genetic background, seems to confer a high level of resistance to the eyespot disease, caused by the fungus Cercosporella herpotrichoides. The other two markers were concomitantly associated with another similarly formed group of addition lines. Both CM-4, a protein component from the chloroform:methanol extract, and Aph_v-a, -b, alkaline phosphate isozymes, have been previously shown to be associated with homoeologous chromosome group 4, which suggests that the added chromosome in the second group of addition lines is 4M^v.     

Mapping and validation of quantitative trait loci associated with wheat yellow mosaic bymovirus resistance in bread wheat

Wheat yellow mosaic (WYM) caused by wheat yellow mosaic bymovirus (WYMV) has been growing as one of the most serious diseases affecting wheat production in China. In this study, the association of quantitative trait loci (QTLs) governing WYMV resistance with molecular markers was established using 164 recombinant inbred lines (RILs) derived from 'Xifeng Wheat' (highly resistant)?×?'Zhen 9523' (highly susceptible). Phenotypic data of WYMV resistance of the RILs were collected from 4-year, two-location replicated field trials. A molecular marker-based linkage map, which was comprised of 273 non-redundant loci and represented all the 21 wheat chromosomes, was constructed with the JoinMap 4.0 software. Using the Windows QTL Cartographer V2.5 software, three QTLs associated with WYMV resistance, QYm.njau-3B.1, QYm.njau-5A.1 and QYm.njau-7B.1, were detected on chromosomes 3BS, 5AL, and 7BS, respectively. The favorable allele effects were all contributed by 'Xifeng Wheat'. Among the three QTLs, QYm.njau-3B.1 and QYm.njau-5A.1 were detected in all the four trials and the overall mean, and could explain 3.3-10.2% and 25.9-53.7% of the phenotypic variation, respectively, while QYm.njau-7B.1 was detected in one trial and the overall mean and explained 4.9 and 3.3% of the phenotypic variation, respectively. A large portion of the variability for WYMV response was explained by a major QTL, QYm.njau-5A.1. The relationship of the molecular markers linked with QYm.njau-5A.1 and the WYMV resistance was further validated using a secondary F(2) population. The results showed that three markers, i.e., Xwmc415.1, CINAU152, and CINAU153, were closely linked to QYm.njau-5A.1 with the genetic distances of 0.0, 0.0, and 0.1?cM, respectively, indicating they should be useful in marker-assisted selection (MAS) wheat breeding for WYMV resistance. A panel of germplasm collection consisting of 46 wheat varieties with known WYMV response phenotypes was further used to validate the presence and effects of QYm.njau-5A.1 and the above three markers. It was found that QYm.njau-5A.1 was present in 12 of the 34 WYMV-resistant varieties.     

Detection of quantitative trait loci associated with leaf rust resistance in bread wheat.

Leaf rust, caused by Puccinia recondita Rob. ex Desm., is a common disease in wheat. The objective of this study was to develop molecular markers associated with the quantitative trait loci (QTLs) putatively conferring durable leaf rust resistance in Triticum aestivum L. em. Thell. A population of 77 recombinant inbred lines (RILs) developed from 'Parula' (resistant) and 'Siete Cerros' (moderately susceptible) was used. Bulked segregant analysis was done using random amplified polymorphic DNAs (RAPDs) with DNA enriched for low-copy sequences using hydroxyapatite chromatography. Out of 400 decamer primers screened, 3 RAPD markers were identified between the bulk of the most resistant and the bulk of the most susceptible lines. These were cloned and used as probes on the RILs in Southern hybridizations. Two probes revealed two tightly linked loci. One-way analysis of variance showed that these two loci, and another revealed by the third probe, were linked to QTLs controlling leaf rust resistance based on data taken from 2 years of replicated field trials. Cytogenetic analysis placed the two tightly linked loci on the long arm of chromosome 7B. The third probe detected loci located on the short arms of chromosomes 1B and 1D. It is suggested that the QTL detected on 7BL may well be homoeoallelic to Lr34.     

Conversion of AFLP markers associated with FHB resistance in wheat into STS markers with an extension-AFLP method.

Amplified fragment length polymorphism (AFLP) has proven a powerful tool for tagging genes or quantitative trait loci (QTLs) of interest in plants. However, conversion of AFLP markers into sequence-tagged site (STS) markers is technically challenging in wheat owing to the complicated nature of its genome. In this study, we developed an "extension-AFLP" method to convert AFLP markers associated with Fusarium head blight (FHB) resistance into STS markers. When an AFLP marker of interest was detected with an EcoRI+3-MseI+4-selective primer combination, the PCR product was used as a template for an additional selective amplification with four primer pairs, in which one additional selective base (either A, C, G, or T) was added to the 3' end of one of the two primers. The extended primer pair that produced the targeted band was further extended by adding each of the four selective nucleotide bases for the next round of selective amplification. Extension selective amplification was performed until the target bands became clear enough for subsequent cloning and sequencing. By using the extension-AFLP method, we successfully converted two AFLP markers located on chromosome 3BS and associated with FHB resistance into STS markers. Our results indicated that the extension-AFLP method is an efficient approach for converting AFLP markers into STS markers in wheat. The developed STS markers might be used for marker-assisted selection (MAS) for FHB resistance in wheat breeding programs.     

Categories of resistance to greenbug (Homoptera: Aphididae) biotype I in Aegilops tauschii germplasm

Categories of resistance to greenbug, Schizaphisgraminum (Rondani), biotype I, were determined in goatgrass, Aegilops tauschii (Coss.) Schmal., accession 1675 (resistant donor parent), 'Wichita' wheat, Triticum aestivum L., (susceptible parent), and an Ae. tauschii-derived resistant line, '97-85-3'. Antibiosis was assessed using the intrinsic rate of increase (rm) of greenbugs confined to each of the three genotypes. Neither parent nor the resistant progeny expressed antibiosis. Mean rm values for greenbug I on Wichita (0.0956), and Ae. tauschii (0.10543) were not significantly different. Mean rm values for Wichita and 97-85-3 were also not significantly different. Antixenosis was determined by allowing aphids a choice to feed on plants of each of the three genotypes. Ae. tauschii 1675 exhibited antixenosis, but this resistance was not inherited and expressed in '97-85-3'. In experiments comparing Wichita and Ae. tauschii 1675, greenbug I population distributions were not significantly different on Wichita at 24 h, but were shifted toward Wichita at 48 h. In the second antixenosis experiment, there were no significant differences in greenbug I population distributions on 97-85-3 or Wichita at 24 or 48 h. When all three lines were compared, there were no significant differences in greenbug biotype I populations at 24 or 48 h after infestation. Comparisons of proportional dry plant weight loss (DWT) and SPAD meter readings were used to determine tolerance to greenbug I feeding. Ae. tauschii 1675 and 97-85-3 were highly tolerant compared with Wichita. Infested and uninfested Ae. tauschii 1675 DWT was nonsignificant, and infested Wichita plants weighed significantly less than uninfested plants. When Wichita and 97-85-3 were contrasted, DWT of infested and uninfested Wichita plants were significantly different, but those of 97-85-3 were not. Mean percent leaf chlorophyll losses for the three genotypes, as measured by the SPAD chlorophyll meter, were as follows: Wichita = 65%; Ae. tauschii 1675 = 25%; and 97-85-3 = 39%. Percent leaf chlorophyll losses caused by greenbug feeding was significantly different in comparisons between Wichita and Ae. tauschii 1675, and comparisons between Wichita and 97-85-3, although feeding damage was not significantly different in comparisons between Ae. tauschii 1675 and 97-85-3. These data provided further evidence of the expression of tolerance to greenbug feeding in Ae. tauschii 1675 and 97-85-3.     

Genetic mapping of QTLs associated with greenbug resistance and tolerance in Sorghum bicolor

Ninety three recombinant inbreds of Sorghum bicolor (L. Moench) were derived from a cross between two sorghum lines GBIK and Redlan. This population was used to identify quantitative trait loci (QTLs) for resistance and tolerance to greenbug (Schizaphids graminum Rondani) Biotypes I and K. One hundred and thirteen loci (38 SSRs and 75 RAPDs) were mapped in 12 linkage groups covering 1,530 cM. In general, nine QTLs were detected affecting both resistance and tolerance to greenbug (GB) Biotypes I and K. The phenotypic variance explained by each QTL ranged from 5.6% to 38.4%. Four SSRs and one RAPD marker were associated with the expression of all resistance and tolerance traits. These markers appear to be linked to biotype non-specific resistance and tolerance genes. Four additional markers were associated with biotype-specific resistance or tolerance traits. The detection of more than one locus for each biotype supports the hypothesis that several regions, which represent different genes, control the expression of resistance and tolerance to greenbug in sorghum. The results can be used for marker-assisted selection and the breeding of greenbug-tolerant sorghum cultivars.     

Microsatellite markers associated with quantitative trait loci controlling antibody response to Escherichia coli and Salmonella enteritidis in young broilers

A unique resource population was produced to facilitate detection of microsatellite markers associated with quantitative trait loci controlling antibody (Ab) response in broiler chickens. Three F1 males were produced by mating two lines divergently selected on Ab response to Escherichia coli vaccination. Each F1 male was mated with females from four genetic backgrounds: F1, high-Ab line (HH), low-Ab line and commercial line, producing three resource families, each with four progeny types. About 1700 chicks were immunized with E. coli and Salmonella enteritidis vaccines. Selective genotyping was conducted on the individuals with highest or lowest average Ab to E. coli and S. enteritidis within each progeny type in each sire family. Twelve markers were significantly associated with Ab to E. coli and six of them were also associated with Ab to S. enteritidis, mostly exhibiting a similar low effect (approximately 0.35 phenotypic SD) in all progeny types. Four markers exhibited a highly significant and much larger effect (approximately 1.7 SD), but only in progeny of females from the HH, suggesting that a backcross to the high parental line should be preferred over the commonly used F2 population. Results from two markers suggested a quantitative trait locus on chromosome 2 around 400 cM. The marker MCW0083, significant in two sire families, is closely linked to the bone morphogenetic protein 2 (BMP2) gene, known to be associated with the control of T-cell transformation in humans.     

Broad-spectrum resistance loci for three quantitatively inherited diseases in two winter wheat populations

Septoria tritici blotch (STB), caused by S. tritici, Stagonospora glume blotch (SGB), caused by S. nodorum, and Fusarium head blight (FHB), caused by F. graminearum and F. culmorum, are the most important diseases of wheat (Triticum aestivum L.) in temperate growing areas. The main goals of this study were to detect (1) new quantitative trait loci (QTL) for STB resistance in two adapted European biparental populations (Arina/Forno, History/Rubens) and (2) QTL regions for broad-spectrum resistance (BSR) to the above-mentioned diseases during the adult-plant stage in the field. The three resistances were phenotyped across 4–7 field environments and phenotypic data revealed significant (P < 0.01) genotypic differentiation in all cases. Entry-mean heritabilities (h2) ranged from 0.73 to 0.93. For STB resistance, correlations between disease ratings and heading date were significant (P < 0.01), but moderate (r = −0.23 to −0.30) in both populations. Correlations between STB and plant height were higher in Arina/Forno (r = −0.45) and History/Rubens (r = −0.55), the latter population segregating at the Rht-D1 locus. During the initial QTL analysis, 5 QTL were detected for STB resistance in each of the populations, amounting to an explained genotypic variance of 45–63%, thus, showing the same ranges as FHB and SGB resistances in Arina/Forno and FHB resistance in History/Rubens. In total, 7 BSR QTL were found in the meta-analysis with the raw data, including the QTL on chromosome 4D at the Rht-D1 locus. A BSR QTL for all three diseases was not found but several BSR QTL for combinations with two diseases were detected. Combining the BSR QTL detected in the present breeding material by applying marker-assisted selection seems a promising approach.     

DNA markers for Fusarium head blight resistance QTLs in two wheat populations

Genetic resistance to Fusarium head blight (FHB), caused by Fusarium graminearum, is necessary to reduce the wheat grain yield and quality losses caused by this disease. Development of resistant cultivars has been slowed by poorly adapted and incomplete resistance sources and confounding environmental effects that make screening of germplasm difficult. DNA markers for FHB resistance QTLs have been identified and may be used to speed the introgression of resistance genes into adapted germplasm. This study was conducted to identify and map additional DNA markers linked to genes controlling FHB resistance in two spring wheat recombinant inbred populations, both segregating for genes from the widely used resistance source ’Sumai 3’. The first population was from the cross of Sumai 3/Stoa in which we previously identified five resistance QTLs. The second population was from the cross of ND2603 (Sumai 3/Wheaton) (resistant)/ Butte 86 (moderately susceptible). Both populations were evaluated for reaction to inoculation with F. graminearum in two greenhouse experiments. A combination of 521 RFLP, AFLP, and SSR markers were mapped in the Sumai 3/Stoa population and all DNA markers associated with resistance were screened on the ND2603/Butte 86 population. Two new QTL on chromosomes 3AL and 6AS wer found in the ND2603/Butte 86 population, and AFLP and SSR markers were identified that explained a greater portion of the phenotypic variation compared to the previous RFLP markers. Both of the Sumai 3-derived QTL regions (on chromosomes 3BS, and 6BS) from the Sumai 3/Stoa population were associated with FHB resistance in the ND2603/Butte 86 population. Markers in the 3BS QTL region (Qfhs.ndsu-3BS) alone explain 41.6 and 24.8% of the resistance to FHB in the Sumai 3/Stoa and ND2603/Butte 86 populations, respectively. This region contains a major QTL for resistance to FHB and should be useful in marker-assisted selection. Received: 17 August 2000 / Accepted: 16 October 2000     

Efficacy of pyramiding greenbug (Homoptera: Aphididae) resistance genes in wheat

Durable resistance to greenbug, Schizaphis graminum (Rondani), in wheat is a goal of wheat improvement teams, and one that has been complicated by the regular occurrence of damaging biotypes. Simulation modeling studies suggest that pyramiding resistance genes, i.e., combining more than one resistance gene in a single cultivar or hybrid, may provide more durable resistance than sequential releases of single genes. We examined this theory by pyramiding resistance genes in wheat and testing a series of greenbug biotypes. Resistance genes Gb2, Gb3, and Gb6, and pyramided genes Gb2/Gb3, Gb2/Gb6, and Gb3/Gb6 were tested for effectiveness against biotypes E, F, G, H, and I. By comparing reactions of plants with pyramided genes to those with single resistance genes, we found that pyramiding provided no additional protection over that conferred by the single resistance genes. Based on the results of this test, we concluded that the sequential release of single resistance genes, combined with careful monitoring of greenbug population biotypes, is the most effective gene deployment strategy for greenbug resistance in wheat.     

Mapping and validation of powdery mildew resistance loci from spring wheat cv. Naxos with SNP markers

Powdery mildew, caused by Blumeria graminis f.sp. tritici, is a major wheat disease in maritime and temperate climates. Breeding for race-non-specific or partial resistance is a cost-effective and environmentally friendly disease control strategy. The German spring wheat cultivar Naxos has proven to be a good source for partial resistance to powdery mildew. The objectives of the present study were to map the resistance loci in Naxos with use of high-density SNP markers in the Shanghai3/Catbird x Naxos inbred line population and validate the results in a different genetic background; Soru#1 x Naxos. Both populations were genotyped with the Illumina iSelect 90K wheat chip, and integrated linkage maps developed by inclusion of previously genotyped SSR and DArT markers. With the new linkage maps, we detected a total of 12 QTL for powdery mildew resistance in Shanghai3/Catbird x Naxos, of which eight were derived from Naxos. Previously reported QTL on chromosome arms 1AS and 2BL were more precisely mapped and the SNP markers enabled discovery of new QTL on 1AL, 2AL, 5AS and 5AL. In the Soru#1 x Naxos population, four QTL for powdery mildew resistance were detected, of which three had resistance from Naxos. This mapping verified the 1AS and 2AL QTL detected in Shanghai3/Catbird x Naxos, and identified a new QTL from Naxos on 2BL. In conclusion, the improved linkage maps with SNP markers enabled discovery of new resistance QTL and more precise mapping of previously known QTL. Moreover, the results were validated in an independent genetic background.     

Identification of genetic loci associated with ear-emergence in bread wheat

A doubled haploid population constructed from a cross between the South Australian wheat cultivars ‘Trident’ and ‘Molineux’ was grown under winter field conditions, under field conditions over summer and under artificial light both with and without vernalisation. The duration from planting to ear-emergence was recorded and QTL associated with heading date were detected using a previously constructed genetic linkage map. Associations were shown with chromosomal regions syntenous to previously identified photoperiod (Ppd-B1) and vernalisation (Vrn-A1) sensitive loci. Additional QTL associated with time to heading were also identified on chromosomes 1A, 2A, 2B, 6D, 7A and 7B. Comparisons between the genetic associations observed under the different growing conditions allowed the majority of these loci to be classified as having either photoperiod-sensitive, vernalisation-sensitive or earliness per se actions. The identification of a photoperiod-sensitive QTL on chromosome 1A provides evidence for a wheat gene possibly homoeologous to Ppd-H2 previously identified on chromosome 1H of barley. The occurrence of a putative major gene for photoperiod sensitivity observed on chromosome 7A is presented. The combined additive effects at these loci accounted for more than half the phenotypic variance in the duration from planting to ear-emergence in this population. The possible role of these loci on the adaptation of wheat in Australia is discussed.     

Mapping QTL for resistance to eyespot of wheat in Aegilops longissima

Eyespot is an economically important disease of wheat caused by the soilborne fungi Oculimacula yallundae and O. acuformis. These pathogens infect and colonize the stem base, which results in lodging of diseased plants and reduced grain yield. Disease resistant cultivars are the most desirable control method, but resistance genes are limited in the wheat gene pool. Some accessions of the wheat wild relative Aegilops longissima are resistant to eyespot, but nothing is known about the genetic control of resistance. A recombinant inbred line population was developed from the cross PI 542196 (R) × PI 330486 (S) to map the resistance genes and better understand resistance in Ae. longissima. A genetic linkage map of the S(l) genome was constructed with 169 wheat microsatellite markers covering 1261.3 cM in 7 groups. F(5) lines (189) were tested for reaction to O. yallundae and four QTL were detected in chromosomes 1S(l), 3S(l), 5S(l), and 7S(l). These QTL explained 44 % of the total phenotypic variation in reaction to eyespot based on GUS scores and 63 % for visual disease ratings. These results demonstrate that genetic control of O. yallundae resistance in Ae. longissima is polygenic. This is the first report of multiple QTL conferring resistance to eyespot in Ae. longissima. Markers cfd6, wmc597, wmc415, and cfd2 are tightly linked to Q.Pch.wsu-1S ( l ), Q.Pch.wsu-3S ( l ), Q.Pch.wsu-5S ( l ), and Q.Pch.wsu-7S ( l ), respectively. These markers may be useful in marker-assisted selection for transferring resistance genes to wheat to increase the effectiveness of resistance and broaden the genetic diversity of eyespot resistance.     

Quantitative trait loci for aluminum resistance in wheat

Quantitative trait loci (QTL) for wheat resistance to aluminum (Al) toxicity were analyzed using simple sequence repeats (SSRs) in a population of 192 F₆ recombinant inbred lines (RILs) derived from a cross between an Al-resistant cultivar, Atlas 66 and an Al-sensitive cultivar, Chisholm. Wheat reaction to Al was measured by relative root growth and root response to hematoxylin stain in nutrient-solution culture. After screening 1,028 SSR markers for polymorphisms between the parents and bulks, we identified two QTLs for Al resistance in Atlas 66. One major QTL was mapped on chromosome 4D that co-segregated with the Al-activated malate transporter gene (ALMT1). Another minor QTL was located on chromosome 3BL. Together, these two QTLs accounted for about 57% of the phenotypic variation in hematoxylin staining score and 50% of the variation in net root growth (NRG). Expression of the minor QTL on 3BL was suppressed by the major QTL on 4DL. The two QTLs for Al resistance in Atlas 66 were also verified in an additional RIL population derived from Atlas 66/Century. Several SSR markers closely linked to the QTLs were identified and have potential to be used for marker-assisted selection (MAS) to improve Al-resistance of wheat cultivars in breeding programs.