A chromosome region-specific mapping strategy reveals gene-rich telomeric ends in wheat

A strategy is described for rapid chromosome region-specific mapping in hexaploid wheat (Triticum aestivum L. em. Thell., 2n=6x=42, AABBDD). The method involves allocation of markers to specific chromosome regions by deletion mapping and ordering of probes by high resolution genetic mapping in Triticum tauschii, the D-genome progenitor species. The strategy is demonstrated using 26 chromosome deletion lines for wheat homoeologous group-6. Twenty-five DNA probes from the T. tauschii genetic linkage map and six wheat homoeologous group-6 specific probes were mapped on the deletion lines. Twenty-four of the 25 probes from 6D of T. tauschii also mapped on wheat homoeologous group-6 chromosomes, and their linear order in wheat is the same as in T. tauschii. A consensus physical map of wheat group-6 was constructed because the linear order and the relative position of the probe loci was the same among the three group-6 chromosomes. Comparison of the consensus physical map with the genetic map demonstrated that most of the recombination occurs in the distal ends of the wheat chromosomes. Most of the loci mapped in the distal regions of the chromosomes. The probes were mostly either PstI genomic clones or cDNA clones indicating that the undermethylated single-copy sequences are concentrated in the distal ends of the wheat chromosomes. Fifteen loci are uniformly distributed in the distal 11% of the group-6 chromosomes. Physically, the region spans only 0.58 m, which in wheat translates to about 40 Mb of DNA. The average distance between the markers is, therefore, less than 2.7 Mb and is in the range of PFGE (pulsed-field gel electrophoresis) resolution. Any gene present in the region can be genetically ordered with respect to the markers since the average recombination frequency in the region is very high (>90 cM genetic distance).     

High-density genetic and physical bin mapping of wheat chromosome 1D reveals that the powdery mildew resistance gene <Emphasis Type="Italic">Pm24</Emphasis> is located in a highly recombinogenic region

Genetic maps of wheat chromosome 1D consisting of 57 microsatellite marker loci were constructed using Chinese Spring (CS) × Chiyacao F₂ and the International Triticeae Mapping Initiative (ITMI) recombinant inbred lines (RILs) mapping populations. Marker order was consistent, but genetic distances of neighboring markers were different in two populations. Physical bin map of 57 microsatellite marker loci was generated by means of 10 CS 1D deletion lines. The physical bin mapping indicated that microsatellite marker loci were not randomly distributed on chromosome 1D. Nineteen of the 24 (79.2%) microsatellite markers were mapped in the distal 30% genomic region of 1DS, whereas 25 of the 33 (75.8%) markers were assigned to the distal 59% region of 1DL. The powdery mildew resistance gene Pm24, originating from the Chinese wheat landrace Chiyacao, was previously mapped in the vicinity of the centromere on the short arm of chromosome 1D. A high density genetic map of chromosome 1D was constructed, consisting of 36 markers and Pm24, with a total map length of 292.7 cM. Twelve marker loci were found to be closely linked to Pm24. Pm24 was flanked by Xgwm789 (Xgwm603) and Xbarc229 with genetic distances of 2.4 and 3.6 cM, respectively, whereas a microsatellite marker Xgwm1291 co-segregated with Pm24. The microsatellite marker Xgwm1291 was assigned to the bin 1DS5-0.70-1.00 of the chromosome arm 1DS. It could be concluded that Pm24 is located in the ‘1S0.8 gene-rich region’, a highly recombinogenic region of wheat. The results presented here would provide a start point for the map-based cloning of Pm24.     

半矮秆基因brh1在大麦中的精细定位

选用从大麦、小麦和水稻中分离的RFLP标记 ,构建了大麦半矮秆基因brh1精细图谱。以快中子处理六棱大麦品种Steptoe的种子 ,从M2 代中选择出brh1突变体FN5 3。brh1是一个极易鉴别的形态学标记 ,通过对FN5 3×Morex的F2 代群体进行鉴定表明 ,brh1基因为隐性 ,前人通过BSA法将其初步定位在大麦第 1染色体 (7H)短臂上 ,靠近端粒区。这一区间还有一个控制秆锈病抗性的显性基因Rpg1。所以 ,brh1的精细定位不仅对研究其本身具有重要意义 ,同时 ,也为Rpg1的图位克隆和功能研究提供了更大的重组配子群体。定位实验全部以F2 中具有brh1特征的个体为对象完成 ,鉴定工作在苗期进行。在该精细图上 ,brh1区间长15 .2cM ,各标记间的平均距离为 0 .8cM。其中 ,大麦的cDNA克隆MWG2 0 74B与brh1共分离。 2 0 74A在靠近着丝点一侧 ,与brh1相距 0 .8cM。BCD12 9和R3139在定位群体内呈现与MWG2 0 74A共分离。CDO5 4 5位于端粒一侧 ,距离brh1为 0 .8cM。根据禾谷类作物基因组的共线性原理 ,CDO5 4 5成功定位在水稻的同源染色体即第 6染色体短臂brh1区间内。然而 ,由于在定位亲本间缺乏多态性 ,BCD12 9和MWG2 0 74的 2条主带A和B均未能定位在水稻的共线性区段内。推测MWG2 0 74的其他各带可能被定位在水稻的目标区间内 ,从而有     

A genetic map of <Emphasis Type="Italic">Lophopyrum ponticum</Emphasis> chromosome 7E,harboring resistance genes to Fusarium head blight and leaf rust

The leaf rust resistance gene Lr19 and Fusarium head blight (FHB) resistance quantitative trait loci (QTL) derived from the wild wheatgrass Lophopyrum ponticum have been located on chromosome 7E. The main objectives of the present study were to develop a genetic map of chromosome 7E and map the two resistance loci using a population of 237 F_7:8 recombinant inbred lines (RILs) derived from a cross between two Thatcher-L. ponticum substitution lines, K11463 (7el₁(7D)) and K2620 (7el₂(7D)). 532 G-SSR, E-SSR and STS markers from wheat chromosome group 7 were screened in the parent lines. Of these, 118 markers were polymorphic, with a polymorphism frequency of 22.2%. A genetic map of L. ponticum chromosome 7E was constructed with 64 markers, covering 95.76 cM, with an average genetic distance of 1.47 cM between markers. The major FHB resistance locus, temporarily assigned as FhbLoP, was mapped to the very distal region of the long arm of chromosome 7E within a 3.71 cM interval flanked by Xcfa2240 and Xswes19, which accounts for 30.46% of the phenotypic variance. Lr19 was bracketed by Xwmc273 and XBE404744, with a map distance of 1.54 and 1.43 cM from either side, respectively. The closely linked markers identified in this study will be helpful for marker-assisted introgression of the L. ponticum-derived FhbLoP and Lr19 genes into elite cultivars of wheat, and the development of a genetic map will accelerate the map-based cloning of these two genes.     

H22, a major resistance gene to the Hessian fly (Mayetiola destructor), is mapped to the distal region of wheat chromosome 1DS

H22 is a major resistance gene conferring high-level of antibiosis to Hessian fly [Mayetiola destructor (Say)] larvae. It was previously assigned to wheat chromosome 1D through monosomic analysis (Raupp et al. in J Hered 84:142–145, 1993). The objective of this study was to identify molecular markers that can be used for marker-assisted selection for wheat breeding, and to further map this gene toward map-based cloning. Forty-five simple sequence repeat (SSR) and sequence-tagged site (STS) markers specific to chromosome 1D were evaluated for linkage to H22 using a segregating population consisting of 192 F_2:3 families, which were derived from the cross Tugela-Dn1 × KS85WGRC01(H22). The STS Xhor2kv and SSR Xgdm33 are two flanking markers that are tightly linked to H22 at genetic distances of 0.3 and 1.0 cM, respectively. Five other SSR markers including Xgpw7082, Xwmc147, Xcfd15, Xwmc432 and Xwmc336 were also linked to H22 at the distance from 0.8 to 20.8 cM. Analysis of Chinese Spring (CS) deletion lines revealed that all the H22-linked markers are located distal to the breakpoint of del 1DS-5, indicating that the H22 gene is located at the distal 30% region on the short arm of wheat chromosome 1D. Genomic comparison suggested that the H22 gene is located in the same or similar chromosomal region as the leaf rust resistance genes Lr21 and Lr40 on 1DS, and orthologous to the H9 gene cluster of 1AS.     

A molecular genetic map of the long arm of chromosome 6R of rye incorporating the cereal cyst nematode resistance gene, CreR

 A genetic map of the long arm of chromosome 6R of rye was constructed using eight homoeologous group-6 RFLP clones and five PCR markers derived from the rye-specific dispersed repetitive DNA family, R173. The map was developed using a novel test-cross F₁ (TC-F₁) population segregating for resistance to the cereal cyst nematode. Comparisons were made between the map generated with other rye and wheat group-6 chromosome maps by the inclusion of RFLP clones previously mapped in those species. Co-linearity was observed for common loci. This comparison confirmed a dramatic reduction in recombination for chromosome 6R in the TC-F₁ population. The CreR locus was included in the linkage map via progeny testing of informative TC-F₁ individuals. CreR mapped 3.7 cM distal from the RFLP locus, XksuF37. Comparative mapping should allow the identification of additional RFLP markers more closely linked to the CreR locus. Received: 14 April 1998 / Accepted: 29 April 1998     

Genomic targeting and high-resolution mapping of the domestication gene Q in wheat.

The Q locus is largely responsible for the domestication of bread wheat. Q confers the free-threshing character of the spike and influences other important agronomic traits. Using chromosome deletion lines, Q was placed on the physical map within a submicroscopic segment of the long arm of chromosome 5A. We targeted markers to the segment by comparative mapping of anonymous RFLP clones, AFLP, and mRNA differential display analysis of deletion lines 5AL-7 and -23, which have deletion breakpoints that flank the Q locus. Differentially expressed sequences detected fragments at various loci on group 5 chromosomes suggesting that Q may be a regulatory gene. We identified 18 markers within the Q gene deletion interval and used them to construct a genetic linkage map of the region in F2 populations derived from chromosome 5A disomic substitution lines. The genetic map corresponding to the deletion segment was 20-cM long, and we identified markers as close as 0.7 cM to the Q gene. An estimate of base pairs per centimorgan within the region is 250 kb/cM, an 18-fold increase in recombination compared with the genomic average. Genomic targeting and high-density mapping provide a basis for the map-based cloning of the Q gene.     

A High-Density SNP Map of Sunflower Derived from RAD-Sequencing Facilitating Fine-Mapping of the Rust Resistance Gene R12

A high-resolution genetic map of sunflower was constructed by integrating SNP data from three F₂ mapping populations (HA 89/RHA 464, B-line/RHA 464, and CR 29/RHA 468). The consensus map spanned a total length of 1443.84 cM, and consisted of 5,019 SNP markers derived from RAD tag sequencing and 118 publicly available SSR markers distributed in 17 linkage groups, corresponding to the haploid chromosome number of sunflower. The maximum interval between markers in the consensus map is 12.37 cM and the average distance is 0.28 cM between adjacent markers. Despite a few short-distance inversions in marker order, the consensus map showed high levels of collinearity among individual maps with an average Spearman''s rank correlation coefficient of 0.972 across the genome. The order of the SSR markers on the consensus map was also in agreement with the order of the individual map and with previously published sunflower maps. Three individual and one consensus maps revealed the uneven distribution of markers across the genome. Additionally, we performed fine mapping and marker validation of the rust resistance gene R₁₂, providing closely linked SNP markers for marker-assisted selection of this gene in sunflower breeding programs. This high resolution consensus map will serve as a valuable tool to the sunflower community for studying marker-trait association of important agronomic traits, marker assisted breeding, map-based gene cloning, and comparative mapping.     

Identification and mapping of pm2026: a recessive powdery mildew resistance gene in an einkorn (Triticum monococcum L.) accession

Triticum monococcum accession TA2026 showed resistance to wheat powdery mildew. To identify the resistance gene and transfer it to common wheat, genetic analysis and molecular mapping were conducted using an F₂ population and derived F₃ families from the cross of TA2026 × M389. The results indicated that TA2026 possessed a recessive powdery mildew resistance gene. This gene was mapped to the terminal portion of chromosome 5A^mL and flanked by SSR marker loci Xcfd39 and Xgwm126. Eight RFLP markers previously mapped to the terminal chromosome 5A^mL were converted into STS markers. Three loci, detected by MAG1491, MAG1493 and MAG1494, the STS markers derived from RFLP probes CDO1312, PSR164 and PSR1201, respectively, were linked to this resistance gene with Xmag1493 only 0.9 cM apart from it. In addition, the STS marker MAG2170 developed from the tentative consensus wheat cDNA encoding the Mlo-like protein identified a locus co-segregating with Xmag1493. This is the first recessive powdery mildew resistance gene identified on chromosome 5A^m, and is temporarily designated pm2026. We have successfully transferred it to a tetraploid background, and this resistance stock will now be used as the bridge parent for its transfer to common wheat.     

Molecular mapping of the ge s gene controlling the super-giant embryo character in rice (Oryza sativa L.)

The giant-embryo character is useful for quality improvement in rice. Three alleles controlling embryo size have been reported at the ge locus. Based on trisomic analysis, this locus is known to reside on chromosome 7. The objective of the present study was to identify linkage between molecular markers and the ge ^s gene using an existing molecular map of rice and an F₂ population derived from Hwacheongbyeo-ge ^s (super-giant embryo)/Milyang 23. The bulked-segregant method was used to screen 38 RFLPs and two microsatellite markers from rice chromosome 7. RZ395 and CDO497 flanked the ge ^s gene, at 2.4 cM and 3.4 cM, respectively. The two microsatellite markers, RM18 and RM10, were linked with ge ^s at 7.7 cM and 9.6 cM, respectively. The availability of molecular markers will facilitate selection of this grain character in a breeding program and provide the foundation for map-based gene isolation.     

A cytogenetic ladder-map of the wheat homoeologous group-4 chromosomes

We report the results of chromosome maps of wheat homoeologous chromosomes 4A, 4B, and 4D using 40 RFLP markers and 39 homozygous deletion lines. Deletion breakpoints divide the chromosomes into 45 subarm intervals with 32 intervals distinguished by molecular markers. The chromosome maps confirm the homoeology of arms 4AS to 4BL and 4DL, and 4AL to 4BS and 4DS. The chromosome map of 4A reveals novel information concerning the 4AL-5AL-7BS cyclical translocation. The presence of homoeologous group-4 long-arm markers, Xksu G10 and Xpsr 1051, intervening between the translocated 5AL and 7BS chromosome segments in 4AL suggests that the translocation events are more complex than was earlier believed. Chromosome maps confirm a pericentric inversion in Chinese Spring chromosome 4B. The consensus chromosome map is compared to the genetic map of wheat to construct a cytogenetic ladder-map (CLM). The CLM reveals an unequal distribution of recombination along the length of the chromosome arms. Recombination is highest in the distal half, and low in the proximal half, of the chromosome arms.     

A Physical Map of the Short Arm of Wheat Chromosome 1A

Bread wheat (Triticum aestivum) has a large and highly repetitive genome which poses major technical challenges for its study. To aid map-based cloning and future genome sequencing projects, we constructed a BAC-based physical map of the short arm of wheat chromosome 1A (1AS). From the assembly of 25,918 high information content (HICF) fingerprints from a 1AS-specific BAC library, 715 physical contigs were produced that cover almost 99% of the estimated size of the chromosome arm. The 3,414 BAC clones constituting the minimum tiling path were end-sequenced. Using a gene microarray containing ∼40 K NCBI UniGene EST clusters, PCR marker screening and BAC end sequences, we arranged 160 physical contigs (97 Mb or 35.3% of the chromosome arm) in a virtual order based on synteny with Brachypodium, rice and sorghum. BAC end sequences and information from microarray hybridisation was used to anchor 3.8 Mbp of Illumina sequences from flow-sorted chromosome 1AS to BAC contigs. Comparison of genetic and synteny-based physical maps indicated that ∼50% of all genetic recombination is confined to 14% of the physical length of the chromosome arm in the distal region. The 1AS physical map provides a framework for future genetic mapping projects as well as the basis for complete sequencing of chromosome arm 1AS.     

Mapping a resistance gene in wheat cultivar Yangfu 9311 to yellow mosaic virus, using microsatellite markers

Wheat yellow mosaic disease, which is caused by wheat yellow mosaic bymovirus (WYMV) and transmitted by soil-borne fungus, results in severe damage on wheat (Triticum aestivum L.) production in China. For development of resistant cultivars to reduce wheat yield losses due to wheat yellow mosaic disease, resistance test and genetic analysis indicated that a single dominant gene in wheat cultivar Yangfu 9311 contributed to the resistance. Bulk segregant analysis was used to identify microsatellite markers linked to the resistance gene in an F₂ population derived from the cross Yangfu 9311 (resistant) × Yangmai 10 (susceptible). Microsatellite markers Xwmc41, Xwmc181, Xpsp3039, and Xgwm349 were co-dominantly or dominantly linked with the gene responsible for WYMV resistance at a distance of 8.1–11.6 cM. Based on the wheat microsatellite consensus map and the results from amplification of the cultivar Chinese Spring nulli-tetrasomic stocks, the resistance gene to wheat yellow mosaic disease derived from Yangfu 9311, temporarily named as YmYF, was thus mapped on the long arm of chromosome 2D (2DL).     

Pm34: a new powdery mildew resistance gene transferred from Aegilops tauschii Coss. to common wheat (Triticum aestivum L.)

Powdery mildew is a major fungal disease in wheat growing areas worldwide. A novel source of resistance to wheat powdery mildew present in the germplasm line NC97BGTD7 was genetically characterized as a monogenic trait in greenhouse and field trials using F₂ derived lines from a NC97BGTD7 X Saluda cross. Microsatellite markers were used to map and tag this resistance gene, now designated Pm34. Three co-dominant microsatellite markers linked to Pm34 were identified and their most likely order was established as: Xbarc177-5D, 5.4cM, Pm34, 2.6cM, Xbarc144-5D, 14cM, Xgwm272-5D. These microsatellite markers were previously mapped to the long arm of the 5D chromosome and their positions were confirmed using Chinese Spring nullitetrasomic Nulli5D-tetra5A and ditelosomic Dt5DL lines. Pm2, the only other known Pm gene on chromosome 5D, has been mapped to the short arm and its specificity is different from that of Pm34.     

H9, H10, and H11 compose a cluster of Hessian fly-resistance genes in the distal gene-rich region of wheat chromosome 1AS

H9, H10, and H11 are major dominant resistance genes in wheat, expressing antibiosis against Hessian fly [(Hf) Mayetiola destructor (Say)] larvae. Previously, H9 and H10 were assigned to chromosome 5A and H11 to 1A. The objectives of this study were to identify simple-sequence-repeat (SSR) markers for fine mapping of these genes and for marker-assisted selection in wheat breeding. Contrary to previous results, H9 and H10 did not show linkage with SSR markers on chromosome 5A. Instead, H9, H10, and H11 are linked with SSR markers on the short arm of chromosome 1A. Both H9 and H10 are tightly linked to flanking markers Xbarc263 and Xcfa2153 within a genetic distance of 0.3–0.5 cM. H11 is tightly linked to flanking markers Xcfa2153 and Xbarc263 at genetic distances of 0.3 cM and 1.7 cM. Deletion bin mapping assigned these markers and genes to the distal 14% of chromosome arm 1AS, where another Hf-resistance gene, Hdic (derived from emmer wheat), was also mapped previously. Marker polymorphism results indicated that a small terminal segment of chromosome 1AS containing H9 or H10 was transferred from the donor parent to the wheat lines Iris or Joy, and a small intercalary fragment carrying H11 was transferred from the resistant donor to the wheat line Karen. Our results suggest that H9, H10, H11, Hdic, and the previously identified H9- or H11-linked genes (H3, H5, H6, H12, H14, H15, H16, H17, H19, H28, and H29) may compose a cluster (or family) of Hf-resistance genes in the distal gene-rich region of wheat chromosome 1AS; and H10 most likely is the same gene as H9.Mention of commercial or proprietary product does not constitute an endorsement by the USDA.     

Comparative mapping of wheat chromosome 1AS which contains the tiller inhibition gene (<Emphasis Type="Italic">tin</Emphasis>) with rice chromosome 5S

The capacity to tiller is a key factor that determines plant architecture. Using molecular markers, a single major gene reducing tiller number, formally named the tiller inhibition gene (tin), was mapped to the short arm of chromosome 1A in wheat. We identified a tightly linked microsatellite marker (Xgwm136) that may be useful in future marker-assisted selection. The tin gene was mapped to the distal deletion bin of chromosome 1AS (FLM value 0.86) and wheat ESTs which were previously mapped to the same deletion bin were used to identify 18 closely related sequences in the syntenic region of rice chromosome 5. For a subset of wheat ESTs that detected flanking markers for tin, we identified closely related sequences within the most distal 300 kb of rice chromosome 5S. The synteny between the distal chromosome ends of wheat 1AS and rice 5S appeared to be disrupted at the hairy glume locus and seed storage protein loci. We compared map position of tin with other reduced tillering mutants characterised in other cereals to identify possible orthologous genes.     

Detection of quantitative trait loci for heading date based on the doubled haploid progeny of two elite Chinese wheat cultivars

Quantitative trait loci (QTLs) with epistatic and QTL × environment (QE) interaction for heading date were studied using a doubled haploid (DH) population containing 168 progeny lines derived from a cross between two elite Chinese wheat cultivars Huapei 3 × Yumai 57 (Triticum aestivum L.). A genetic map was constructed based on 305 marker loci, consisting of 283 SSR loci and 22 EST-SSR markers, which covered a total length of 2141.7 cM with an average distance of 7.02 cM between adjacent markers in the genome. QTL analyses were performed using a mixed linear model approach. Two main-effect QTLs and two pairs of digenic epistatic effects were detected for heading date on chromosomes 1B, 2B, 5D, 6D, 7A, and 7D at three different environments in 2005 and 2006 cropping seasons. A highly significant QTL with an F-value 148.96, designated as Qhd5D, was observed within the Xbarc320-Xwmc215 interval on chromosome 5DL, accounting for 53.19% of the phenotypic variance and reducing days-to-heading by 2.77 days. The Qhd5D closely links with a PCR marker Xwmc215 with the genetic distance 2.1 cM, which can be used in molecular marker-assisted selection (MAS) in wheat breeding programs. Moreover, the Qhd5D was located on the similar position of well-characterised vernalization sensitivity gene Vrn-D1. We are also spending more efforts to develop near-isogenic lines to finely map the Qhd5D and clone the gene Vrn-D1 through map-based cloning. The Qhd1B with additive effect on heading date has not been reported in previous linkage mapping studies, which might be a photoperiod-sensitive gene homoeologous to the Ppd-H2 gene on chromosome 1B. No main-effect QTLs for heading date were involved in epistatic effects.     

A microcolinearity study at the earliness per se gene Eps-A m 1 region reveals an ancient duplication that preceded the wheat–rice divergence

Wheat flowering is controlled by numerous genes, which respond to environmental signals such as photoperiod and vernalization. Earliness per se (Eps) genes control flowering time independently of these environmental cues and are responsible for the fine tuning of flowering time. We recently mapped the Eps-A ^m 1 gene on the end of Triticum monococcum chromosome arm 1A^mL. As a part of our efforts to clone Eps-A ^m 1 we developed PCR markers flanking this gene within a 2.7 cM interval. We screened more than one thousand gametes with these markers and identified 27 lines with recombination between them. Recombinant lines were used to generate a high-density map and to investigate the microcolinearity between wheat and rice in this region. We mapped ten genes from a 149 kb region located at the distal part of rice chromosome 5 (cdo393 – Ndk3) on a 3.7 cM region on wheat chromosome one. This region is part of an ancient duplication between rice chromosomes 5 and 1. Genes present in both rice chromosomes were less similar to each other than to the closest wheat orthologues, suggesting that this duplication preceded the divergence between wheat and rice. This hypothesis was supported by the presence of 18 loci duplicated both in rice chromosomes 5 and 1 and in the colinear wheat chromosomes from homoeologous groups 1 and 3. Independent gene deletions in wheat and rice lineages explain the alternations of colinearity between rice chromosome 5 and wheat chromosomes 1 and 3. Colinearity between the end of rice chromosome 5 and wheat chromosome 1 was also interrupted by a small inversion, and several non-colinear genes. These results suggest that the distal region of the long arm of wheat chromosome 1 was involved in numerous changes that differentiated wheat and rice genomes. This comparative study provided sufficient markers to saturate the Eps-A ^m 1 gene region and to precisely map this gene within a 0.9 cM interval flanked by the VatpC and Smp loci. Sequences obtained in this study: DQ196178, DQ196179, DQ196180, DQ196181, DQ196182, DQ196183, DQ196184, DQ196185, DQ196186, DQ196187, DQ196488, DQ198537, DQ308530, DQ308531, DQ308532, DQ308533, DQ308534, DQ308535, DQ308536, DQ308537, DQ308538, DQ308539, DQ308540     

Genetic and physical characterization of chromosome 4DL in wheat.

The long arm of chromosome 4D in wheat (Triticum aestivum L.) has been shown in previous studies to harbor genes of agronomic importance. A major dominant gene conferring Aluminum (Al) tolerance (Alt2 in 'Chinese Spring' and AltBH in 'BH 1146'), and the Knal locus controlling the K+/Na+ discrimination in saline environments have been mapped to this chromosome arm. However, accurate information on the genetic and physical location of markers related to any of these genes is not available and would be useful for map-based cloning and marker-assisted plant breeding. In the present study, using a population of 91 recombinant inbred lines segregating for Al tolerance, we provide a more extensive genetic linkage map of the chromosome arm 4DL based on RFLP, SSR, and AFLP markers, delimiting the AltBH gene to a 5.9-cM interval between markers Xgdm125 and Xpsr914. In addition, utilizing a set of wheat deletion lines for chromosome arm 4DL, the AltBH gene was physically mapped to the distal region of the chromosome, between deletion breakpoints 0.70 and 0.86, where the kilobase/centimorgan ratio is assumed to be low, making the map-based cloning of the gene a more realistic goal. The polymorphism rates in chromosome arm 4DL for the different types of markers used were extremely low, as confirmed by the physical mapping of AFLPs. Finally, analysis of 1 Mb of contiguous sequence of Arabidopsis chromosome 5 flanking the gene homologous to the BCD1230 clone (a cosegregating marker in our population coding for a ribulose-5-phosphate-3-epimerase gene), revealed a previously identified region of stress-related and disease-resistance genes. This could explain the collinearity observed in comparative mapping studies among different species and the low level of polymorphism detected in the chromosome arm 4DL in hexaploid wheat.