An intraspecific genetic map of water yam (<Emphasis Type="Italic">Dioscorea alata</Emphasis> L.) based on AFLP markers and QTL analysis for anthracnose resistance

Water yam (Dioscorea alata L.) is the most widely cultivated food yams. Despite its importance, its production is limited by anthracnose disease caused by Colletotrichum gloeosporioides (Penz.). The use of resistant yam varieties is the most reliable approach of management of this disease. The speed and precision of breeding can be improved by the development of genetic linkage maps which would provide the basis for locating and hence manipulating quantitative traits such as anthracnose resistance in breeding programmes. An F1 diploid population was developed by crossing ‘Boutou’ a female clone (with field resistance to anthracnose) with ‘Pyramide’ (susceptible). A linkage map was generated with 523 polymorphic markers from 26 AFLP primer combinations. The resulting map covered a total length of 1538 cM and included 20 linkage groups. It is the most saturated of all genetic linkage maps of yam to date. QTL analysis of anthracnose resistance was performed based on response to two isolates of C. gloeosporioides. Resistance to anthracnose appeared to be inherited quantitatively. Using a LOD significance threshold of 2.6 we identified a total of nine QTLs for anthracnose resistance. The phenotypic variance explained by each QTL ranged from 7.0 to 32.9% whereas the total amount of phenotypic variation for anthracnose resistance explained by all significant QTLs varied from 26.4 to 73.7% depending on the isolate and the variable considered. These QTLs displayed isolate-specific resistance as well as broad spectrum resistance. The availability of molecular markers linked to the QTLs of anthracnose resistance will facilitate marker-assisted selection in breeding programmes.     

Mapping of a gene for leaf scald resistance in barley line 'B87/14' and validation of microsatellite and RFLP markers for marker-assisted selection

Seedlings of the barley line ‘B87/14’ were resistant to 22 out of 23 Australian isolates of Rhynchosporium secalis, the causal agent of leaf scald.‘B87/14’‐based populations were developed to determine the location of the resistance locus. Scald resistance segregated as a single dominant trait in BC₁F₂ and BC₁F₃ populations. Bulked segregant analysis identified amplified fragment length polymorphisms (AFLPs) with close linkage to the resistance locus. Fully mapped populations not segregating for scald resistance located these AFLP markers on chromosome 3H, possibly within the complex Rrs1 scald locus. Microsatellite and restriction fragment length polymorphism markers adjacent to the AFLP markers were identified and validated for their linkage to scald resistance in a second segregating population, with the closest marker 2.2 cM from the resistance locus. These markers can be used for selection of the Rrs.B87 scald‐resistance locus, and other genes at the chromosome 3H Rrs1 locus.     

Molecular mapping and identification of QTL's associated to oat crown rust partial resistance

Summary Molecular mapping is a promising strategy for studying and understanding traits with complex genetic control, such as partial resistance to oat crown rust. The objectives of this research were to develop molecular maps from the progenies of the cross UFRGS7 (susceptible) × UFRGS910906 (partially resistant) and to identify QTLs (quantitative trait loci) associated to partial resistance to oat crown rust in two generations of that population.DNA of 86 genotypes of the F₂ and 90 genotypes of the F₆ UFRGS7 × UFRGS910906 population were used to generate AFLP markers. Molecular maps were constructed using Mapmaker Exp. 3.0 and QTLs for partial resistance to oat crown rust were identified with Mapmaker/QTL software. Five hundred and fifty seven markers in the F₂ and 243 markers in the F₆ generations were identified. The F₂ map integrated 250 markers in 37 linkage groups. The F₆ map integrated 86 markers in 17 linkage groups.Five QTLs were identified for partial resistance to oat crown rust in the F₂ generation and three QTLs in the F₆. The QTL identified on F₆ through the PaaaMctt340 AFLP marker showed consistency across two environments and two generations (F₄ and F₆), and appear to have potential for marker-assisted selection in oat.     

Mapping of quantitative trait loci controlling partial resistance against rust incited by <Emphasis Type="Italic">Uromyces pisi</Emphasis> (Pers.) Wint. in a <Emphasis Type="Italic">Pisum fulvum</Emphasis> L. intraspecific cross

A quantitative trait loci (QTL) associated with resistance to pea rust, caused by the fungus Uromyces pisi (Pers.) Wint., has been identified in a F₂ population derived from an intraspecific cross between two wild pea (Pisum fulvum L.) accessions, IFPI3260 (resistant) and IFPI3251 (susceptible). Both parental lines and all the segregating population displayed a fully compatible interaction (high infection type), which indicates absence of hypersensitive response. Nevertheless, differences on the percentage of symptomatic area of the whole plant (disease severity) were observed. A genetic map was developed covering 1283.3 cM and including 146 markers (144 random amplified polymorphic DNA (RAPDs) and two sequence tagged sites (STSs) markers) distributed in 9 linkage groups. A QTL explaining 63% of the total phenotypic variation was located in linkage group 3. RAPDs markers (OPY11₁₃₁₆ and OPV17₁₀₇₈) flanking this QTL should allow, after their conversion in SCARs, a reliable marker-assisted selection for rust resistance.     

Genetic mapping provides evidence for the role of additive and non-additive QTLs in the response of inter-specific hybrids of <Emphasis Type="Italic">Eucalyptus</Emphasis> to <Emphasis Type="Italic">Puccinia psidii</Emphasis> rust infection

Eucalypts are susceptible to a wide range of diseases. One of the most important diseases that affect Eucalyptus plantations worldwide is caused by the rust fungus Puccinia psidii. Here, we provide evidence on the complex genetic control of rust resistance in Eucalyptus inter-specific hybrids, by analyzing a number of full-sib families that display different patterns of segregation for rust resistance. These families are totally unrelated to those previously used in other inheritance studies of rust resistance. By using a full genome scan with 114 genetic markers (microsatellites and expressed sequence tag derived microsatellites) we also corroborated the existence and segregation of a resistance locus, explaining 11.5% of the phenotypic variation, on linkage group 3, corresponding to Ppr1. This find represents an additional validation of this locus in totally unrelated pedigree. We have also detected significant additive × additive digenic interactions with LOD >10.0 on several linkage groups. The additive and epistatic QTLs identified explain between 29.8 and 44.8% of the phenotypic variability for rust resistance. The recognition that both additive and non-additive genetic variation (epistasis) are important contributors to rust resistance in eucalypts reveals the complexity of this host-pathogen interaction and helps explain the success that breeding has achieved by selecting rust-resistant clones, where all the additive and non-additive effects are readily captured. The positioning of epistatic QTLs also provides starting points to look for the underlying genes or genomic regions controlling this phenotype on the upcoming E. grandis genome sequence.     

Developing new markers and QTL mapping for greenbug resistance in sorghum [Sorghum bicolor (L.) Moench]

Greenbug is a major damaging insect to sorghum production in the United States. Among various virulent greenbug biotypes, biotype I is the most predominant and severe for sorghum. To combat with the damaging pest, greenbug resistant sources were obtained from screening sorghum germplasm collection. This experiment was conducted to identify the genomic regions contributing resistance to greenbug biotype I in a sorghum accession, PI 607900. An F₂ mapping population consisting of 371 individuals developed from a cross of the resistant line with an elite cultivar, BTx623 (susceptible) were tested and scored for their response to greenbug feeding in the greenhouse. Significant differences in resistance were observed between the two parental lines and among their F₂ progeny in response to greenbug feeding at 7, 10, 14 and 21 days after infestation. A linkage map spanning a total length of 729.5 cM across the genome was constructed with 102 polymorphic SSR markers (69 genomic and 33 EST SSRs). Of those microsatellite markers, 48 were newly developed during this study, which are a useful addition for sorghum genotyping and genome mapping. Single marker analysis revealed 29 markers to be significantly associated with the plant response to greenbug feeding damage. The results from interval mapping, composite interval mapping and multiple interval mapping analyses identified four major QTLs for greenbug resistance on chromosome 9. These QTLs collectively accounted for 34–82 % of the phenotypic variance in greenbug resistance. Minor QTLs located on chromosome 3 explained 1 % of the phenotypic variance in greenbug resistance. The major allele for greenbug resistance was on chromosome 9 close to receptor-like kinase Xa21-binding protein 3. These markers are useful to screen more resistant genotypes. Furthermore, the markers tagged to QTL regions can be used to enhance the sorghum breeding program for greenbug resistance through marker-assisted selection and map-based cloning.     

SCAR and CAPS markers flanking the Brassica oleracea L. Pp523 downy mildew resistance locus demarcate a genomic region syntenic to the top arm end of Arabidopsis thaliana L. chromosome 1

We recently mapped the Pp523 locus that includes a single, dominant gene conferring resistance to downy mildew expressed in adult plants to a 75.1 cm long linkage group on a genetic linkage map of Brassica oleracea L. More recently, we identified a new AFLP marker 2.8 cm downstream from the resistance gene. The five DNA markers within an 8.5 cm region encompassing the Pp523 gene were cloned and sequenced. Three of these markers were transformed into SCARs (sequence characterised amplified regions), however, two among them were monomorphic and were analysed as CAPS (cleaved amplified polymorphic sequence) markers among the mapping population. Searched against genomic databases, the five B. oleracea DNA-marker sequences matched Arabidopsis thaliana L. gene sequences that delimit a conserved syntenic region in the top arm end of chromosome 1 of this last species. Considering the close genetic relatedness between both species, the information on this specific genomic region in A. thaliana is particularly useful for the construction of a fine-scale map of the corresponding genomic region in B. oleracea. The identified SCAR and CAPS markers can be used for marker assisted selection (MAS) in breeding programs aimed at the introgression of the Pp523 resistance locus, allowing the reliable indirect identification of plants harbouring the resistance gene with a margin of error of approximately six in ten-thousand selected plants.     

New molecular markers linked to qualitative and quantitative powdery mildew and scald resistance genes in barley for dry areas

A partial genetic linkage map was constructed on 71 doubled-haploid lines derived from a cross between the barley lines Tadmor and WI2291 with 181 molecular markers. The segregating population was used to detect markers linked to the gene Mlg conferring resistance to powdery mildew (Erysiphe graminis f. sp. hordei) and to genes for quantitative resistance to scald (Rhynchosporium secalis). The gene Mlg on chromosome 4H was flanked by two AFLP markers at a distance of 2.0 and 2.4 cM, respectively. QTLs for resistance to scald were detected on chromosomes 2H and 3H. This association of molecular markers with qualitative and quantitative disease resistance loci represents a valuable starting-point for marker-assisted selection. This revised version was published online in July 2006 with corrections to the Cover Date.     

Identification of genomic regions for rust resistance in sorghum

The location and effects of genomic regions for rust resistance in sorghum were determined. One hundred and sixty recombinant inbreds, which derived from a cross between QL39 and QL41, were used as a segregating population for genome mapping and rust resistance evaluation. Phenotypic data were collected in replicated field trials in two years. Interval mapping and non-parametric mapping identified four regions, each in a separate linkage group, associated with rust resistance. The region with the largest effect on rust resistance is on linkage group 10; it accounted for 40% of the total phenotypic variation. This revised version was published online in July 2006 with corrections to the Cover Date.     

AFLP-based STS markers closely linked to a fertility restoration locus (Rfm1) for cytoplasmic male sterility in barley

The Rfm1 gene restores the fertility of the msm1 and msm² male‐sterile cytoplasms in barley. Rfm1 is located on the short arm of chromosome 6H. To develop molecular markers tightly linked to Rfm1 for use in sophisticated marker‐assisted selection and map‐based cloning, an amplified fragment‐length polymorphism (AFLP) marker system with isogenic lines and a segregating BC₁F₁ population was used. Nine hundred primer combinations were screened and a linkage map was constructed around the Rfm1 locus by using 25 recombinant plants selected from 214 BC₁F₁ plants. Three AFLP markers were identified, e34m2, e46m19 and e48m17, linked to the locus. The most closely linked markers were e34m2, at 1.0 cM distally and e46m19, at 1.1 cM proximally. The two AFLP markers were converted to dominant STS markers. These markers should accelerate programmes for breeding restorer lines and will be useful for map‐based cloning.     

Genetic analysis of partial resistance to coffee leaf rust ( Hemileia vastatrix Berk & Br.) introgressed into the cultivated Coffea arabica L. from the diploid C. canephora species

The objective of this study was to identify polymorphic molecular markers associated with partial resistance to coffee leaf rust, Hemileia vastarix. A segregating F ₂ population derived from a cross between the susceptible Coffea arabica cv. Caturra and a C. canephora-introgressed Arabica line exhibiting high partial resistance was analyzed. Rust resistance measured as rust incidence (RI) and defoliation (DEF) was evaluated in field conditions in three consecutive years (2003–2005). During the 2003 season, which was characterized by favorable conditions for a rust epidemic, the F ₂ plants exhibited different levels of resistance ranging from very susceptible (50.1% for DEF and 49.5% for RI) to highly partial resistance (9.1% for DEF and 3.7% for RI). Molecular analysis enabled identification of seven polymorphic markers (5 AFLP and 2 SSR) exhibiting significant association with partial resistance. Coexistence of resistance homozygous alleles (RR) at codominant SSR loci was correlated with high resistance. This study is the first attempt to develop PCR-based sequence specific markers linked to partial rust resistance in coffee.     

Targeted BSA mapping of Scmv1 and Scmv2 conferring resistance to SCMV using PstI/MseI compared with EcoRI/MseI AFLP markers

In a previous study, two chromosome regions (Scmv1 and Scmv2), conferring sugarcane mosaic virus (SCMV) resistance in maize, were enriched with EcoRI/MseI AFLP (Eco‐AFLP) markers (methylation insensitive) by targeted bulked segregant analysis (tBSA). The objective of the present study was to further saturate these two regions with PstI/MseI AFLP (Pst‐AFLP) markers (methylation sensitive) using the same tBSA approach, and to compare the genomic distribution of both Pst‐AFLP and Eco‐AFLP markers. Out of 470 PstI/MseI primer combinations screened, four Pst‐AFLP markers were identified in the Scmv1 region (chromosome 6), and none in the Scmv2 region (chromosome 3). These Pst‐AFLP markers were more closely linked to the Scmv1a gene than any of the Eco‐AFLP markers, and could be useful for marker‐assisted selection and even map‐based cloning. In addition, Pst‐AFLP and Eco‐AFLP markers were dissimilarly distributed in both target regions. Pst‐AFLP markers were equally distributed across both regions, while Eco‐AFLPs were clustered in the Scmv2 region.     

Mapping of powdery mildew and leaf rust resistance genes on the wheat-rye translocated chromosome T1BL·1RS using molecular and biochemical markers

Powdery mildew and leaf rust resistance genes on the 1RS arm of the T1BL·1RS translocated chromosome were mapped in relation to the Sec‐1 locus and AFLP and restriction fragment length polymorphism markers, respectively, employing segregating F₃ populations. Integration of molecular markers indicated that Pm17 lies between the Lr26 and Sec‐1 loci, with both resistance genes allocated distally to the Sec‐1 locus in the satellite of the 1RS arm.     

Association of RFLP markers with trait loci affecting clubroot resistance and morphological characters in Brassica oleracea L.

Summary Resistance to Plasmodiophora brassicae Wor. race 7, the causal agent of the disease clubroot, was examined in an F₂ population of a cross between a clubroot resistant broccoli (Brassica oleracea var. italica) and a susceptible cauliflower (B. oleracea var. botrytis). A genetic linkage map was constructed in the same population based on the segregation of 58 dispersed restriction fragment length polymorphism (RFLP) markers. Associations between the inheritance of RFLP marker genotypes and segregation for disease resistance, morphological and maturity characteristics were examined. For each triat examined, several chromosomal regions marked by RFLP probes appeared to contain trait loci, suggesting that each trait was under polygenic control. RFLP marker linkage to a major factor imparting dominance for clubroot resistance from the broccoli parent was observed in this population. Additionally, RFLP marker linkage to an independently segregating factor contributing clubroot resistance from the cauliflower parent was observed, indicating that it should be possible to use RFLP markers to facilitate selection of transgressive segregants having the combined resistance from both parental sources. In some instances, RFLP markers from the same or closely linked chromosomal regions were associated with both clubroot resistance and morphological traits. Analysis of RFLP marker genotypes at linked loci should facilitate the selection of desired disease resistant morphotypes.     

QTL mapping of resistance in lentil (Lens culinaris ssp. culinaris) to ascochyta blight (Ascochyta lentis)

Quantitative trait locus (QTL) analysis of ascochyta blight resistance in lentil was conducted using genomic maps developed from two F₂ populations, viz. ILL5588/ILL7537 and ILL7537/ILL6002. Five QTLs for ascochyta blight resistance were identified by composite interval mapping (CIM) across four linkage groups (LG) in population ILL5588/ILL7537. Three QTLs were identified by CIM in population ILL7537/ILL6002 (two in close proximity on LGI and one on LGII). Two of these coincided with regions identified using multiple interval mapping (MIM) and were shown to be conditioned by dominant and partial dominant gene action. Together, they accounted for approximately 50% of the phenotypic variance of disease severity. Comparison between the two populations revealed a potentially common QTL and several common regions that contained markers significantly associated with resistance. This study demonstrated the transferability of QTLs among populations and identified markers closely linked to the major QTL that may be useful for future marker‐assisted selection for disease resistance.     

Quantitative trait analysis in Theobroma cacao using molecular markers

The aim of this study was to determine the genetic components controlling yield in an F₁ cacao cross between Catongo and Pound 12 clones. Genetic maps were constructed for the two parents using molecular markers which detected 158 polymorphic loci covering 772 cM for the heterozygous genotype Pound 12 and only 4 loci representing 16.9 cM of a linkage group which indicated a high level of homozygosity of Catongo. Yield was recorded twice a month during 15 years on 55 individuals from this segregating population. Ten yield QTL were detected on eight linkage groups. Some of these QTL were frequently detected over 15 years of production, while others were specific for a given year. Total yield genetic variance, on a yearly basis, ranged from 0 to 56%. Two major QTL (E and I) each explained approximately 20% of the total variance of the average yield over 15 years. The analysis of potential cacao yield components, such as pod index and trunk diameter, suggested that some regions of the genome exert effects on more than one trait, providing a possible genetic explanation for the correlations detected between some of title traits studied. Data showed that correlation between successive annual yield decreased when the lag between corresponding seasons increased. When separated by more than 10 years, annual yields were no longer correlated. The utilisation of molecular markers alone or in combination with phenotypic selection showed an advantage in the early selection of the best cacao producer trees. Further use of molecular markers in breeding programs is discussed with a view to reducing the generation time of a selection procedure. This revised version was published online in July 2006 with corrections to the Cover Date.     

Molecular mapping of <Emphasis Type="Italic">Pc68</Emphasis>, a crown rust resistance gene in <Emphasis Type="Italic">Avena</Emphasis><Emphasis Type="Italic">sativa</Emphasis>

Crown rust, which is caused by Puccinia coronata f. sp. avenae, P. Syd. & Syd., is the most destructive disease of cultivated oats (Avena sativa L.) throughout the world. Resistance to the disease that is based on a single gene is often short-lived because of the extremely great genetic diversity of P. coronata, which suggests that there is a need to develop oat cultivars with several resistance genes. This study aimed to identify amplified fragment length polymorphism AFLP markers that are linked to the major resistance gene, Pc68, and to amplify the F₆ genetic map from Pc68/5*Starter × UFRGS8. Seventy-eight markers with normal segregation were discovered and distributed in 12 linkage groups. The map covered 409.4 cM of the Avena sativa genome. Two AFLP markers were linked in repulsion to Pc68: U8PM22 and U8PM25, which flank the gene at 18.60 and 18.83 centiMorgans (cM), respectively. The marker U8PM25 is located in the linkage group 4_12 in the Kanota × Ogle reference oat population. These markers should be useful for transferring Pc68 to genotypes with good agronomic characteristics and for pyramiding crown rust resistance genes.     

Mapping QTLs for Witches' Broom (Crinipellis Perniciosa) Resistance in Cacao (Theobroma Cacao L.)

Molecular markers (RAPD, AFLP and microsatellites) were used to generate a linkage map and to identify QTLs associated to witches' broom (Crinipellis perniciosa) resistance in cacao (Theobroma cacao), using 82 individuals of an F₂ population derived from the clones ICS-1 (susceptible) and Scavina-6 (resistant). Fifteen evaluations of the number of brooms have been carried out in six years (1997–2002). In order to increase the precision and accuracy in the measures of resistance, each F₂ plant was cloned in three replications in a randomized block design with single-tree plots and evaluated over 2 years. Three hundred and forty-two markers were obtained, being 33 microsatellites, 77 AFLPs and 232 RAPDs. The distribution of the number of brooms in the F₂ population was skewed to resistance, suggesting the involvement of major genes controlling resistance and the repeatability estimated for resistance was 44%. A strong putative QTL was detected as being related to witches' broom resistance. Associated to this QTL, the microsatellite mTcCIR35 explained 35.5% of the phenotypic variation in resistance. This marker is being used for marker-assisted selection in Scavina-6 progenies, including those selected in private plantations, as an auxiliary tool to the phenotypic selection.     

Development of genic molecular markers linked to a rust resistance gene in cultivated groundnut (Arachis hypogaea L.)

Development of molecular markers for different economically important traits in cultivated groundnut has progressed at slow pace. Although many genomic SSR markers were developed in both the wild and cultivated groundnut, the genetic linkage map in the species is still not saturated. Availability of a large number of ESTs in GenBank opened up the possibility of integrating new markers and to identify markers closely linked to agronomic traits. EST-SSR markers are also considered as genic molecular markers. In this study, 259 EST-SSR markers were developed by mining 5,184 Arachis hypogaea ESTs from NCBI database. These EST-SSRs and 34 resistance gene candidate markers were used for association and genetic mapping of rust resistance in cultivated groundnut. From these, Cer2, SSR_GO340445, SSR_HO115759, SSR_GO341324 and RGC 2 had a significant association with rust resistance based on locus-by-locus AMOVA and/or Kruskal?CWallis ANOVA. Some of these associated markers also had protein activity related to biotic stress responses. Through genetic mapping, EST-SSR markers SSR_GO340445 and SSR_HO115759 were found closely linked to a rust resistance gene at 1.9 and 3.8?cM distances, respectively. These markers are thus suitable candidates for marker assisted selection in groundnut. The tight linkage of SSR_GO340445 would be helpful to screen BAC clones and to isolate rust resistance gene in groundnut.     

Molecular characterization of <Emphasis Type="Italic">Fusarium</Emphasis> head blight resistance from wheat variety Wangshuibai

Fusarium head blight (FHB) is a destructive disease of wheat worldwide. FHB resistance genes from Sumai 3 and its derivatives such as Ning 7840 have been well characterized through molecular mapping. In this study, resistance genes in Wangshuibai, a Chinese landrace with high and stable FHB resistance, were analyzed through molecular mapping. A population of 104 F₂-derived F₇ recombinant inbred lines (RILs) was developed from the cross between resistant landrace Wangshuibai and susceptible variety Alondras. A total of 32 informative amplified fragment length polymorphism (AFLP) primer pairs (EcoRI/MseI) amplified 410 AFLP markers segregating among the RILs. Among them, 250 markers were mapped in 23 linkage groups covering a genetic distance of 2,430 cM. In addition, 90 simple sequence repeat (SSR) markers were integrated into the AFLP map. Fifteen markers associated with three quantitative trait loci (QTL) for FHB resistance (P < 0.01) were located on two chromosomes. One QTL was mapped on 1B and two others were mapped on 3B. One QTL on 3BS showed a major effect and explained up to 23.8% of the phenotypic variation for type II FHB resistance.