Co-segregation analysis and mapping of the anthracnose Co-10 and angular leaf spot Phg-ON disease-resistance genes in the common bean cultivar Ouro Negro

Anthracnose (ANT) and angular leaf spot (ALS) are devastating diseases of common bean (Phaseolus vulgaris L.). Ouro Negro is a highly productive common bean cultivar, which contains the Co-10 and Phg-ON genes for resistance to ANT and ALS, respectively. In this study, we performed a genetic co-segregation analysis of resistance to ANT and ALS using an F₂ population from the Rudá × Ouro Negro cross and the F_2:3 families from the AND 277 × Ouro Negro cross. Ouro Negro is resistant to races 7 and 73 of the ANT and race 63-39 of the ALS pathogens. Conversely, cultivars AND 277 and Rudá are susceptible to races 7 and 73 of ANT, respectively. Both cultivars are susceptible to race 63-39 of ALS. Co-segregation analysis revealed that Co-10 and Phg-ON were inherited together, conferring resistance to races 7 and 73 of ANT and race 63-39 of ALS. The Co-10 and Phg-ON genes were co-segregated and were tightly linked at a distance of 0.0 cM on chromosome Pv04. The molecular marker g2303 was linked to Co-10 and Phg-ON at a distance of 0.0 cM. Because of their physical linkage in a cis configuration, the Co-10 and Phg-ON resistance alleles are inherited together and can be monitored with great efficiency using g2303. The close linkage between the Co-10 and Phg-ON genes and prior evidence are consistent with the existence of a resistance gene cluster at one end of chromosome Pv04, which also contains the Co-3 locus and ANT resistance quantitative trait loci. These results will be very useful for breeding programs aimed at developing bean cultivars with ANT and ALS resistance using marker-assisted selection.     

High-resolution mapping reveals linkage between genes in common bean cultivar Ouro Negro conferring resistance to the rust,anthracnose, and angular leaf spot diseases

Key message

Co-segregation analysis and high-throughput genotyping using SNP, SSR, and KASP markers demonstrated genetic linkage between Ur-14 and Co-3 ⁴ /Phg-3 loci conferring resistance to the rust, anthracnose and angular leaf spot diseases of common bean.

Abstract

Rust, anthracnose, and angular leaf spot are major diseases of common bean in the Americas and Africa. The cultivar Ouro Negro has the Ur-14 gene that confers broad spectrum resistance to rust and the gene cluster Co-3 ⁴ /Phg-3 containing two tightly linked genes conferring resistance to anthracnose and angular leaf spot, respectively. We used co-segregation analysis and high-throughput genotyping of 179 F_2:3 families from the Rudá (susceptible) × Ouro Negro (resistant) cross-phenotyped separately with races of the rust and anthracnose pathogens. The results confirmed that Ur-14 and Co-3 ⁴ /Phg-3 cluster in Ouro Negro conferred resistance to rust and anthracnose, respectively, and that Ur-14 and the Co-3 ⁴ /Phg-3 cluster were closely linked. Genotyping the F_2:3 families, first with 5398 SNPs on the Illumina BeadChip BARCBEAN6K_3 and with 15 SSR, and eight KASP markers, specifically designed for the candidate region containing Ur-14 and Co-3 ⁴ /Phg-3, permitted the creation of a high-resolution genetic linkage map which revealed that Ur-14 was positioned at 2.2 cM from Co-3 ⁴ /Phg-3 on the short arm of chromosome Pv04 of the common bean genome. Five flanking SSR markers were tightly linked at 0.1 and 0.2 cM from Ur-14, and two flanking KASP markers were tightly linked at 0.1 and 0.3 cM from Co-3 ⁴ /Phg-3. Many other SSR, SNP, and KASP markers were also linked to these genes. These markers will be useful for the development of common bean cultivars combining the important Ur-14 and Co-3 ⁴ /Phg-3 genes conferring resistance to three of the most destructive diseases of common bean.

     

Allelism Tests between the Rust Resistance Gene Present in Common Bean Cultivar Ouro Negro and Genes Ur-5 and Ur-11

The pathogenic variability of the fungus Uromyces appendiculatus is an obstacle for the creation of rust‐resistant common bean (Phaseolus vulgaris L.) varieties. Gene pyramiding is an alternative strategy for the development of varieties with durable resistance. However, to reach this goal it is important to identify different genes with ample resistance spectra. Cultivars Ouro Negro, Mexico 309 and Belmidak RR‐3 have been shown to be resistant to several rust races identified in the state of Minas Gerais, Brazil. Ouro Negro is the only rust resistance source being used in the BIOAGRO/Universidade Federal de Viçosa (UFV) breeding programme, which aims at pyramiding resistance genes in the ‘carioca‐type’ cultivar Rudá. It would be also interesting to use Mexico 309 (Ur‐5) and Belmidak RR‐3 (Ur‐11) in the breeding programme. However, there is no available information on the possible allelic relationships between the Ouro Negro resistance gene and Ur‐5 and Ur‐11. This work aimed at: (1) determining the allelic relationship between the Ouro Negro resistance gene and Ur‐5 and Ur‐11; and (2) evaluating a random amplified polymorphic DNA (RAPD) marker previously reported as being linked to Ur‐11, in populations from crosses between Belmidak RR‐3 and Rudá. The allelism tests confirmed that the Ouro Negro rust resistance gene is distinct from Ur‐5 and Ur‐11 and the molecular analyses confirmed that the RAPD marker can be used in our breeding programme to develop ‘carioca‐type’ cultivars with the Ur‐11 gene.     

Introgression and pyramiding into common bean market class fabada of genes conferring resistance to anthracnose and potyvirus

Anthracnose and bean common mosaic (BCM) are considered major diseases in common bean crop causing severe yield losses worldwide. This work describes the introgression and pyramiding of genes conferring genetic resistance to BCM and anthracnose local races into line A25, a bean genotype classified as market class fabada. Resistant plants were selected using resistance tests or combining resistance tests and marker-assisted selection. Lines A252, A321, A493, Sanilac BC6-Are, and BRB130 were used as resistance sources. Resistance genes to anthracnose (Co-2 ^C , Co-2 ^A252 and Co-3/9) and/or BCM (I and bc-3) were introgressed in line A25 through six parallel backcrossing programs, and six breeding lines showing a fabada seed phenotype were obtained after six backcross generations: line A1258 from A252; A1231 from A321; A1220 from A493; A1183 and A1878 from Sanilac BC6-Are; and line A2418 from BRB130. Pyramiding of different genes were developed using the pedigree method from a single cross between lines obtained in the introgression step: line A1699 (derived from cross A1258 × A1220), A2438 (A1220 × A1183), A2806 (A1878 × A2418), and A3308 (A1699 × A2806). A characterization based on eight morpho-agronomic traits revealed a limited differentiation among the obtained breeding lines and the recurrent line A25. However, using a set of seven molecular markers linked to the loci used in the breeding programs it was possible to differentiate the 11 fabada lines. Considering the genetic control of the resistance in resistant donor lines, the observed segregations in the last backcrossing generation, the reaction against the pathogens, and the expression of the molecular markers it was also possible to infer the genotype conferring resistance in the ten fabada breeding lines obtained. As a result of these breeding programs, genetic resistance to three anthracnose races controlled by genes included in clusters Co-2 and Co-3/9, and genetic resistance to BCM controlled by genotype I + bc-3 was combined in the fabada line A3308.     

Inheritance and development of molecular markers linked to angular leaf spot resistance genes in the common bean accession G10909

Angular leaf spot (ALS) is one of the major diseases of the common bean (Phaseolus vulgaris L.). Different sources of resistance have been identified but few have been characterized. Studies were conducted to elucidate the inheritance of ALS resistance in the bean accession G10909 and to identify molecular markers linked to these genes. Evaluation of parental genotypes, F₁, F₂ and backcross to susceptible parent (Sprite) populations revealed that two dominant and complementary genes conditioned ALS resistance. Allelism tests showed that the ALS resistance genes in G10909 were different from those in the Mesoamerican cultivars Mexico 54, MAR 2, G10474 and Cornell 49-242. Three sequence-characterized amplified region (SCAR) markers, PF13₃₁₀, PF9₂₆₀ and OPE04₇₀₉, and a microsatellite, Pv-gaat001, segregated in coupling with the resistance genes in G10909. Pairwise segregation analysis revealed that markers PF13₃₁₀, PF9₂₆₀ and OPE04₇₀₉ were linked, while Pv-gaat001 segregated in a 9:3:3:1 ratio from all markers. Markers PF13₃₁₀, PF9₂₆₀ and OPE04₇₀₉ were mapped to linkage group B08, and segregated with resistance gene Phg _G10909B at 4.9, 7.4 and 9.9 cM, respectively. Pv-gaat001, previously mapped to linkage group B04, segregated with resistance gene Phg _G10909A at 13 cM. The potential utility of these markers to aid breeding for ALS resistance is discussed.     

Identification of novel genomic regions associated with resistance to <Emphasis Type="Italic">Pyrenophora tritici</Emphasis>-<Emphasis Type="Italic">repentis</Emphasis> races 1 and 5 in spring wheat landraces using association analysis

Tan spot, caused by Pyrenophora tritici-repentis, is a major foliar disease of wheat worldwide. Host plant resistance is the best strategy to manage this disease. Traditionally, bi-parental mapping populations have been used to identify and map quantitative trait loci (QTL) affecting tan spot resistance in wheat. The association mapping (AM) could be an alternative approach to identify QTL based on linkage disequilibrium (LD) within a diverse germplasm set. In this study, we assessed resistance to P. tritici-repentis races 1 and 5 in 567 spring wheat landraces from the USDA-ARS National Small Grains Collection (NSGC). Using 832 diversity array technology (DArT) markers, QTL for resistance to P. tritici-repentis races 1 and 5 were identified. A linear model with principal components suggests that at least seven and three DArT markers were significantly associated with resistance to P. tritici-repentis races 1 and 5, respectively. The DArT markers associated with resistance to race 1 were detected on chromosomes 1D, 2A, 2B, 2D, 4A, 5B, and 7D and explained 1.3–3.1% of the phenotypic variance, while markers associated with resistance to race 5 were distributed on 2D, 6A and 7D, and explained 2.2–5.9% of the phenotypic variance. Some of the genomic regions identified in this study correspond to previously identified loci responsible for resistance to P. tritici-repentis, offering validation for our AM approach. Other regions identified were novel and could possess genes useful for resistance breeding. Some DArT markers associated with resistance to race 1 also were localized in the same regions of wheat chromosomes where QTL for resistance to yellow rust, leaf rust and powdery mildew, have been mapped previously. This study demonstrates that AM can be a useful approach to identify and map novel genomic regions involved in resistance to P. tritici-repentis.     

Genetic dissection of the resistance to nine anthracnose races in the common bean differential cultivars MDRK and TU

Resistance to nine races of the pathogenic fungus Colletotrichum lindemuthianum, causal agent of anthracnose, was evaluated in F₃ families derived from the cross between the anthracnose differential bean cultivars TU (resistant to races, 3, 6, 7, 31, 38, 39, 102, and 449) and MDRK (resistant to races, 449, and 1545). Molecular marker analyses were carried out in the F₂ individuals in order to map and characterize the anthracnose resistance genes or gene clusters present in these two differential cultivars. The results of the combined segregation indicate that at least three independent loci conferring resistance to anthracnose are present in TU. One of them, corresponding to the previously described anthracnose resistance locus Co-5, is located in linkage group B7, and is formed by a cluster of different genes conferring specific resistance to races, 3, 6, 7, 31, 38, 39, 102, and 449. Evidence of intra-cluster recombination between these specific resistance genes was found. The second locus present in TU confers specific resistance to races 31 and 102, and the third locus confers specific resistance to race 102, the location of these two loci remains unknown. The resistance to race 1545 present in MDRK is due to two independent dominant genes. The results of the combined segregation of two F₄ families showing monogenic segregation for resistance to race 1545 indicates that one of these two genes is linked to marker OF10₅₃₀, located in linkage group B1, and corresponds to the previously described anthracnose resistance locus Co-1. The second gene conferring resistance to race 1545 in MDRK is linked to marker Pv-ctt001, located in linkage group B4, and corresponds to the Co-3/Co-9 cluster. The resistance to race 449 present in MDRK is conferred by a single gene, located in linkage group B4, probably included in the same Co-3/Co-9 cluster. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Genome-Wide Association Studies of Anthracnose and Angular Leaf Spot Resistance in Common Bean (Phaseolus vulgaris L.)

The common bean (Phaseolus vulgaris L.) is the world’s most important legume for human consumption. Anthracnose (ANT; Colletotrichum lindemuthianum) and angular leaf spot (ALS; Pseudocercospora griseola) are complex diseases that cause major yield losses in common bean. Depending on the cultivar and environmental conditions, anthracnose and angular leaf spot infections can reduce crop yield drastically. This study aimed to estimate linkage disequilibrium levels and identify quantitative resistance loci (QRL) controlling resistance to both ANT and ALS diseases of 180 accessions of common bean using genome-wide association analysis. A randomized complete block design with four replicates was performed for the ANT and ALS experiments, with four plants per genotype in each replicate. Association mapping analyses were performed for ANT and ALS using a mixed linear model approach implemented in TASSEL. A total of 17 and 11 significant statistically associations involving SSRs were detected for ANT and ALS resistance loci, respectively. Using SNPs, 21 and 17 significant statistically associations were obtained for ANT and angular ALS, respectively, providing more associations with this marker. The SSR-IAC167 and PvM95 markers, both located on chromosome Pv03, and the SNP scaffold00021_89379, were associated with both diseases. The other markers were distributed across the entire common bean genome, with chromosomes Pv03 and Pv08 showing the greatest number of loci associated with ANT resistance. The chromosome Pv04 was the most saturated one, with six markers associated with ALS resistance. The telomeric region of this chromosome showed four markers located between approximately 2.5 Mb and 4.4 Mb. Our results demonstrate the great potential of genome-wide association studies to identify QRLs related to ANT and ALS in common bean. The results indicate a quantitative and complex inheritance pattern for both diseases in common bean. Our findings will contribute to more effective screening of elite germplasm to find resistance alleles for marker-assisted selection in breeding programs.     

Codominant PCR-based markers and candidate genes for powdery mildew resistance in melon (<Emphasis Type="Italic">Cucumis melo</Emphasis> L.)

Powdery mildew caused by Podosphaera xanthii is a major disease in melon crops, and races 1, 2, and 5 of this fungus are those that occur most frequently in southern Europe. The genotype TGR-1551 bears a dominant gene that provides resistance to these three races of P. xanthii. By combining bulked segregant analysis and amplified fragment length polymorphisms (AFLP), we identified eight markers linked to this dominant gene. Cloning and sequencing of the selected AFLP fragments allowed the development of six codominant PCR-based markers which mapped on the linkage group (LG) V. Sequence analysis of these markers led to the identification of two resistance-like genes, MRGH5 and MRGH63, belonging to the nucleotide binding site (NBS)-leucine-rich repeat (LRR) gene family. Quantitative trait loci (QTL) analysis detected two QTLs, Pm-R1-2 and Pm-R5, the former significantly associated with the resistance to races 1 and 2 (LOD score of 26.5 and 33.3; 53.6 and 61.9% of phenotypic variation, respectively), and the latter with resistance to race 5 (LOD score of 36.8; 65.5% of phenotypic variation), which have been found to be colocalized with the MRGH5 and MRGH63 genes, respectively. The results suggest that the cluster of NBS-LRR genes identified in LG V harbours candidate genes for resistance to races 1, 2, and 5 of P. xanthii. The evaluation of other resistant germplasm showed that the codominant markers here reported are also linked to the Pm-w resistance gene carried by the accession ‘WMR-29’ proving their usefulness as genotyping tools in melon breeding programmes.     

Genetic linkage map of melon (<Emphasis Type="Italic">Cucumis melo</Emphasis> L.) and localization of a major QTL for powdery mildew resistance

Powdery mildew caused by Podosphaera xanthii has become a major problem in melon since it occurs all year round irrespective of the growing system. The TGR-1551 melon genotype was found to be resistant to several melon diseases, among them powdery mildew. However, the corresponding resistance genes have been never mapped. We constructed an integrated genetic linkage map using an F2 population derived from a cross between the multi-resistant genotype TGR-1551 and the susceptible Spanish cultivar ‘Bola de Oro’. The map spans 1,284.9 cM, with an average distance of 3.6 cM among markers, and consists of 354 loci (188 AFLP, 39 RAPD, 111 SSR, 14 SCAR/CAPS/dCAPS, and two phenotypic traits) distributed in 14 linkage groups. QTL analysis identified one major QTL (Pm-R) on LG V for resistance to races 1, 2, and 5 of powdery mildew. The PM4-CAPS marker is closely linked to the Pm-R QTL at a genetic distance of 1.9 cM, and the PM3-CAPS marker is located within the support interval of this QTL. These codominant markers, together with the map information reported here, could be used for melon breeding, and particularly for genotyping selection of resistance to powdery mildew in this vegetable crop species.     

Genetic analysis of Soil-Borne Cereal Mosaic Virus response in durum wheat: evidence for the role of the major quantitative trait locus QSbm.ubo-2BS and of minor quantitative trait loci

Genetic analysis of Soil-Borne Cereal Mosaic Virus (SBCMV) resistance in durum wheat was carried out using a population of 180 recombinant inbred lines (RILs) obtained from Simeto (susceptible) × Levante (resistant). The RILs were characterized for SBCMV response in the field under severe and uniform SBCMV infection in two growing seasons and genotyped with simple sequence repeat (SSR) and Diversity Arrays Technology^? markers. Transgressive segregation was observed for disease reaction as estimated by symptom severity scores and virus concentration in leaves. Heritability of the disease response was high, with h ² values consistently above 80%. A major quantitative trait locus (QTL) (QSbm.ubo-2BS) in the distal telomeric region of chromosome 2BS accounted for 60–70% of the phenotypic variation for symptom severity, 40–55% for virus concentration and 15–30% for grain yield. The favorable allele was contributed by Levante. Seven additional QTL influenced SBCMV resistance, with the low-susceptibility allele contributed by Levante at five QTL and by Simeto at the remaining two. The meta-QTL analysis carried out using the data from two mapping populations (Simeto × Levante and Meridiano × Claudio) suggests that in both populations SBCMV resistance is likely controlled by QSbm.ubo-2BS. Our results confine QSbm.ubo-2BS to a c. 2-cM-wide interval flanked by SSR markers that are already being used for marker-assisted selection.     

Rpg1, a soybean gene effective against races of bacterial blight, maps to a cluster of previously identified disease resistance genes

 Alleles, or tightly linked genes, at the soybean (Glycine max L. Merr.) Rpg1 locus confer resistance to races of Pseudomonas syringae pv. glycinea that express the avirulence genes avrB or avrRpm1. In this study we demonstrate that Rpg1 maps to a cluster of previously identified resistance genes, including those effective against fungal, viral and nematode pathogens. Rpg1 is in molecular linkage group (MLG) F, flanked by the markers K644 and B212. The RFLP markers R45, php2265 and php2385 cosegregated with Rpg1, as did the marker nbs61, which encodes a protein related to previously isolated resistance genes. Received: 7 July 1997 / Accepted: 6 October 1997     

Mapping Fusarium wilt race 1 resistance genes in cotton by inheritance,QTL and sequencing composition

Knowledge of the inheritance of disease resistance and genomic regions housing resistance (R) genes is essential to prevent expanding pathogen threats such as Fusarium wilt [Fusarium oxysporum f.sp. vasinfectum (FOV) Atk. Sny & Hans] in cotton (Gossypium spp.). We conducted a comprehensive study combining conventional inheritance, genetic and quantitative trait loci (QTL) mapping, QTL marker-sequence composition, and genome sequencing to examine the distribution, structure and organization of disease R genes to race 1 of FOV in the cotton genome. Molecular markers were applied to F₂ and recombinant inbred line (RIL) interspecific mapping populations from the crosses Pima-S7 (G. barbadense L.) × ‘Acala NemX’ (G. hirsutum L.) and Upland TM-1 (G. hirsutum) × Pima 3-79 (G. barbadense), respectively. Three greenhouse tests and one field test were used to obtain sequential estimates of severity index (DSI) of leaves, and vascular stem and root staining (VRS). A single resistance gene model was observed for the F₂ population based on inheritance of phenotypes. However, additional inheritance analyses and QTL mapping indicated gene interactions and inheritance from nine cotton chromosomes, with major QTLs detected on five chromosomes [Fov1-C06, Fov1-C08, (Fov1-C11 ₁ and Fov1-C11 ₂₎ , Fov1-C16 and Fov1-C19 loci], explaining 8–31% of the DSI or VRS variation. The Fov1-C16 QTL locus identified in the F₂ and in the RIL populations had a significant role in conferring FOV race 1 resistance in different cotton backgrounds. Identified molecular markers may have important potential for breeding effective FOV race 1 resistance into elite cultivars by marker-assisted selection. Reconciliation between genetic and physical mapping of gene annotations from marker-DNA and new DNA sequences of BAC clones tagged with the resistance-associated QTLs revealed defenses genes induced upon pathogen infection and gene regions rich in disease-response elements, respectively. These offer candidate gene targets for Fusarium wilt resistance response in cotton and other host plants.     

<Emphasis Type="Italic">ATXN</Emphasis>-<Emphasis Type="Italic">2</Emphasis> CAG repeat expansions are interrupted in ALS patients

It has recently been suggested that short expansions of CAG repeat in the gene ATXN-2 causing SCA2 (spinocerebellar ataxia type 2) are associated with an increased risk of amyotrophic lateral sclerosis (ALS) in the populations of the USA and northern Europe. In this study, we investigated the role of ATXN-2 in Italian patients clinically diagnosed with ALS and characterized the molecular structure of ATXN-2 expansions. We assessed the size of the CAG repeat in ATXN-2 exon 1 in 232 Italian ALS patients and 395 matched controls. ATXN-2 expanded alleles containing >30 repeats have been observed in seven sporadic ALS patients (3.0%), while being absent in the controls (p = 0.00089). Four out of the seven patients had an ATXN-2 allele in the intermediate-fully pathological range: one with 32 repeats, 2 with 33 repeats and 1 with 37 repeats, accounting for 1.7% of the ALS cohort. Sequencing of expanded (>32) alleles showed that they were all interrupted with at least one CAA triplet. ATXN-2 alleles with the same length and structure have been reported in SCA2 patients with parkinsonism or in familial and sporadic Parkinson. Conversely, the phenotype of the present patients was typically ALS with no signs or symptoms of ataxia or parkinsonism. In conclusion, the findings of ATXN-2 expansions in pure ALS cases suggest that ALS may be a third phenotype (alongside ataxia/parkinsonism and pure Parkinson) associated with ATXN-2 interrupted alleles.     

Identification and mapping of the leaf stripe resistance gene Rdg1a in Hordeum spontaneum

Leaf stripe of barley, caused by Pyrenophora graminea, is an important seed-borne disease in organically grown as well as in conventionally grown Nordic and Mediterranean barley districts. Two barley segregating populations represented by 103 recombinant inbred lines (RILs) of the cross L94 (susceptible) × Vada (resistant) and 194 RILs of the cross Arta (susceptible) × Hordeum spontaneum 41-1 (resistant) were analysed with two highly virulent leaf stripe isolates, Dg2 and Dg5, to identify loci for P. graminea resistance. A major gene with its positive allele contributed by Vada and H. spontaneum 41-1 was detected in both populations and for both pathogen isolates on chromosome 2HL explaining 44.1 and 91.8% R ², respectively for Dg2 and Dg5 in L94 × Vada and 97.8 and 96.1% R ², respectively for Dg2 and Dg5 in Arta × H. spontaneum 41-1. Common markers in the gene region of the two populations enabled map comparison and highlighted an overlapping for the region of the resistance locus. Since the map position of the resistance locus identified in this report is the same as that for the leaf stripe resistance gene Rdg1a, mapped earlier in Alf and derived from the ‘botanical’ barley line H. laevigatum, we propose that leaf stripe resistance in Vada and H. spontaneum 41-1 is governed by the same gene, namely by Rdg1a, and that Rdg1a resistance could be traced back to H. spontaneum, the progenitor of cultivated barley. PCR-based molecular markers that can be used for marker-assisted selection (MAS) of Rdg1a were identified. An Rdg1a syntenic interval with the rice chromosome arm 4L was identified on the basis of rice orthologs of EST-based barley markers. Analysis of the rice genes annotated into the syntenic interval did not reveal sequences strictly belonging to the major class (nucleotide-binding site plus leucine-rich repeat) of the resistance genes. Nonetheless, four genes coding for domains that are present in the major disease-resistance genes, namely receptor-like protein kinase and ATP/GTP-binding proteins, were identified together with a homolog of the barley powdery mildew resistance gene mlo. Three (out of five) homologs of these genes were mapped in the Rdg1a region in barley and the mlo homolog map position was tightly associated with the LOD score peak in both populations.     

Quantitative analysis of race-specific resistance to Colletotrichum lindemuthianum in common bean

Molecular genetic maps continue to play a major role in breeding of crop species. The common bean genetic map of the recombinant inbred line population IAC-UNA × CAL 143 (UC) has been used to detect loci controlling important agronomic traits in common bean. In the current study, new microsatellite markers were added to the UC map and the linkage analysis was refined using current genomic resources of common bean, in order to identify quantitative resistance loci (QRL) associated with different races of the anthracnose pathogen. A single race inoculation was conducted in greenhouse using four plants per plot. Both race-specific and joint-adjusted disease severity means, obtained from linear-mixed model, were used to perform multiple interval mapping (MIM) and multi-trait MIM (MTMIM). In total, 13 and 11 QRL were identified by MIM and MTMIM analyses, respectively; with nine being observed in both analyses. ANT02.1^UC and ANT07.1^UC showed major effects on resistance both for MIM and MTMIM. Common major QRL for resistance to the three anthracnose races were expected, since high genetic pairwise-correlation was observed between the race-specific and joint-adjusted disease severity means. Therewith, both ANT02.1 and ANT07.1 can be regarded as valuable targets for marker-assisted selection; and so, putative genes potentially involved in the resistance response were identified in these QRL regions. Minor effect QRL were also observed, showing differential affects either on race-specific or multi-trait analyses and may play a role on durable horizontal resistance. These results contribute to a better understanding of the host-pathogen interaction and to breeding for enhancing resistance to Colletotrichum lindemuthianum in common bean.     

Molecular mapping of wilt resistance genes in chickpea

Fusarium wilt is a widespread and serious chickpea disease caused by the soil-borne fungus Fusarium oxysporum f.sp. ciceri (Foc). We evaluated an F₉ recombinant inbred line population of chickpea for resistance to three Foc races (1, 2 and 3) in pot culture experiments and identified flanking and tightly linked DNA markers for the resistance genes. The simple sequence repeat markers H3A12 and TA110 flanked the Foc1 locus at 3.9 and 2.1 cM, respectively, while Foc2 was mapped 0.2 cM from TA96 and 2.7 cM from H3A12. The H1B06y and TA194 markers flanked the Foc3 locus at 0.2 and 0.7 cM, respectively. These markers were also validated using 16 diverse chickpea genotypes. Identification of tightly linked flanking markers for wilt resistance genes will be useful for their exploitation in breeding programs and to understand the mechanism of resistance and evolution of the genes. S. J. M. Gowda and P. Radhika contributed equally to this study.     

Identification and genomic location of a reniform nematode (Rotylenchulus reniformis) resistance locus (Renari) introgressed from Gossypium aridum into upland cotton (G. hirsutum)

In this association mapping study, a tri-species hybrid, [Gossypium arboreum × (G. hirsutum × G. aridum)²], was crossed with MD51ne (G. hirsutum) and progeny from the cross were used to identify and map SSR markers associated with reniform nematode (Rotylenchulus reniformis) resistance. Seventy-six progeny (the 50 most resistant and 26 most susceptible) plants were genotyped with 104 markers. Twenty-five markers were associated with a resistance locus that we designated Ren ^ari and two markers, BNL3279_132 and BNL2662_090, mapped within 1 cM of Ren ^ari . Because the SSR fragments associated with resistance were found in G. aridum and the bridging line G 371, G. aridum is the likely source of this resistance. The resistance is simply inherited, possibly controlled by a single dominant gene. The markers identified in this project are a valuable resource to breeders and geneticists in the quest to produce cotton cultivars with a high level of resistance to reniform nematode.     

Inheritance and molecular mapping of a downy mildew resistance gene, Pl 13 in cultivated sunflower (Helianthus annuus L.)

The inheritance of resistance to sunflower downy mildew (SDM) derived from HA-R5 conferring resistance to nine races of the pathogen has been determined and the new source has been designated as Pl ₁₃ . The F₂ individuals and F₃ families of the cross HA-R5 (resistant) × HA 821 (susceptible) were screened against the four predominant SDM races 300, 700, 730, and 770 in separate tests which indicated dominant control by a single locus or a cluster of tightly linked genes. Bulked segregant analysis (BSA) was carried out on 116 F₂ individuals with 500 SSR primer pairs that resulted in the identification of 10 SSR markers of linkage groups 1 (9 markers) and 10 (1 marker) of the genetic map (Tang et al. in Theor Appl Genet 105:1124–1136, 2002) that distinguished the bulks. Of these, the SSR marker ORS 1008 of linkage group 10 was tightly linked (0.9 cM) to the Pl ₁₃ gene. Genotyping the F₂ population and linkage analysis with 20 polymorphic primer pairs located on linkage group 10 failed to show linkage of the markers with downy mildew resistance and the ORS 1008 marker. Nevertheless, validation of polymorphic SSR markers of linkage group 1 along with six RFLP-based STS markers of linkage group 12 of the RFLP map of Jan et al. (Theor Appl Genet 96:15–22, 1998) corresponding to linkage group 1 of the SSR map, mapped seven SSR markers (ORS 965-1, ORS 965-2, ORS 959, ORS 371, ORS 716, and ORS 605) including ORS 1008 and one STS marker (STS10D6) to linkage group 1 covering a genetic distance of 65.0 cM. The Pl ₁₃ gene, as a different source with its location on linkage group 1, was flanked by ORS 1008 on one side at a distance of 0.9 cM and ORS 965-1 on another side at a distance of 5.8 cM. These closely linked markers to the Pl ₁₃ gene provide a valuable basis for marker-assisted selection in sunflower breeding programs.