This study describes the identification of a quantitative trait locus (QTL) in the recombinant inbred line population of ILL2024xILL6788 and subsequent validation of associated molecular markers. A high-quality genetic linkage map was constructed with 758 markers that cover 1,057cM, with an average intermarker distance of 2cM. QTL analysis revealed a single genomic region on Lc2 to be associated with B tolerance and accounted for up to 76% of phenotypic variation (Vp). The best markers for B tolerance were assessed for their utility in routine breeding applications using validation panels of diverse lentil germplasm and breeding material derived from ILL2024. A marker generated from the dense genetic map of this study was found to be the most accurate of all markers available for B tolerance in lentil, with a success rate of 93% within a large breeding pool derived from ILL2024. However, given the number of the unrelated lines for which the marker-trait association was not conserved, B tolerance screening is still required at later stages to confirm predicted phenotypes.

Stemphylium blight is an important fungal disease of lentil caused by Stemphylium botryosum. It occurs in all major lentil growing regions of the world, including Bangladesh, India, Nepal, Syria, USA and Canada. As lentil production in Australia is increasing, stemphylium blight is considered a potential threat to the industry. However, information on this pathogen and resistance levels in Australian lentil germplasm is limited. Five fungicides were tested for efficacy against seven isolates of Stemphylium botryosum. Mancozeb and thiram were the most effective in inhibiting the growth of the pathogen under in-vitro conditions. To prevent a disease outbreak, it is prudent to screen germplasm to eliminate stemphylium blight susceptible lines from the breeding program prior to release. Therefore, a screening method for evaluating stemphylium blight resistance in lentil was developed for use under controlled environment conditions. Using this method, stemphylium blight disease ratings were provided on all current Australian lentil varieties. In addition, screening of advanced breeding lines showed variation in resistance/susceptibility for this disease and allowed selection of resistant lines for stemphylium blight resistance breeding. Seven International lentil varieties were tested against Australian isolates of S. botryosum and showed varying levels of resistance. Three hundred lentil accessions obtained from the International Centre for Agricultural Research in the Dry Areas (ICARDA) were evaluated and six accessions were identified with higher resistance than the resistant check ILL6002 that could be used in lentil breeding for stemphylium blight resistance.

Lentil (Lens culinaris Medik.) is a diploid (2n = 2x = 14), self-pollinating, cool-season, grain legume that is cultivated worldwide and is highly valuable due to its high protein content. However, lentil production is constrained by many factors including biotic stresses, majority of which are fungal diseases such as ascochyta blight (AB), fusarium wilt, rust, stemphylium blight, anthracnose, and botrytis gray mold. Among various diseases, AB is a major -problem in many lentil-producing countries and can significantly reduce crop production. Breeding for AB resistance has been a priority for breeding programs across the globe and consequently, a number of resistance sources have been identified and extensively exploited. In order to increase the efficiency of combining genes from different genetic backgrounds, molecular genetic tools can be integrated with conventional breeding methods. A range of genetic linkage maps have been generated based on DNA-based markers, and quantitative trait loci (QTLs) for AB resistance have been identified. Molecular markers linked to these QTLs may potentially be used for efficient pyramiding of the AB disease resistance genes. Significant genomic resources have been established to identify and characterize resistance genes, including an integrated genetic map, expressed sequence tag libraries, gene based markers, and draft genome sequences. These resources are already being utilized for lentil crop improvement, to more effectively select for disease resistance, as a case study of the Australian breeding program will show. The combination of genomic resources, effective molecular genetic tools and high resolution phenotyping tools will improve the efficiency of selection for ascochyta blight resistance and accelerate varietal development of global lentil breeding programs.

Anecdotal evidence identified a change in the reaction of the resistant lentil cv Nipper to ascochyta blight in South Australia in 2010 and subsequent seasons, leading to infection. This study investigated field reactions of lentil cultivars against Ascochyta lentis and the pathogenic variability of the A. lentis population in southern Australia on commonly grown cultivars and on parental germplasm used in the Australian lentil breeding program. Disease data recorded in agronomic and plant breeder field trials from 2005 to 2014 in southern Australia confirmed the change in reaction on the foliage of the previously resistant cvs Nipper and Northfield. Cultivar responses to seed staining from A. lentis did not change. The change in foliar response was confirmed in a series of controlled environment experiments using single, conidium-derived, isolates of A. lentis collected over different years and inoculated onto differential host sets. Specific isolate/cultivar interactions produced a significant range of disease reactions from high to low aggressiveness with a greater percentage of isolates more aggressive on cvs Nipper, Northfield and PBA Flash than previously detected. Specific isolates were tested against Australian lentil cultivars and breeding lines in controlled conditions, again verifying the aggressiveness on cv Nipper. A small percentage of isolates collected prior to the commercial release of cv Nipper were also able to infect this cultivar indicating a natural variability of the A. lentis population which subsequently may have been selected in response to high cropping intensity of cv Nipper. Spore release studies from naturally infested lentil stubbles collected from commercial crops also resulted in a high percentage of infection on the previously resistant cvs Nipper and Northfield. Less than 10% of the lesions developed on the resistant differentials ILL7537 and cv Indianhead. Pathogenic variation within the seasonal populations was not affected by the cultivar from which the stubble was sourced, further indicating a natural variability in aggressiveness. The impact of dominant cultivars in cropping systems and loss of effective disease resistance is discussed. Future studies are needed to determine if levels of aggressiveness among A. lentis isolates are increasing against a range of elite cultivars.

Lentil (Lens culinaris Medik.) is a self-pollinating, diploid, annual, cool-season, food legume crop that is cultivated throughout the world. Ascochyta blight (AB), caused by Ascochyta lentis Vassilievsky, is an economically important and widespread disease of lentil. Development of cultivars with high levels of durable resistance provides an environmentally acceptable and economically feasible method for AB control. A detailed understanding of the genetic basis of AB resistance is hence highly desirable, in order to obtain insight into the number and influence of resistance genes. Genetic linkage maps based on single nucleotide polymorphisms (SNP) and simple sequence repeat (SSR) markers have been developed from three recombinant inbred line (RIL) populations. The IH × NF map contained 460 loci across 1461.6 cM, while the IH × DIG map contained 329 loci across 1302.5 cM and the third map, NF × DIG contained 330 loci across 1914.1 cM. Data from these maps were combined with a map from a previously published study through use of bridging markers to generate a consensus linkage map containing 689 loci distributed across seven linkage groups (LGs), with a cumulative length of 2429.61 cM at an average density of one marker per 3.5 cM. Trait dissection of AB resistance was performed for the RIL populations, identifying totals of two and three quantitative trait loci (QTLs) explaining 52 and 69% of phenotypic variation for resistance to infection in the IH × DIG and IH × NF populations, respectively. Presence of common markers in the vicinity of the AB_IH1- and AB_IH2.1/AB_IH2.2-containing regions on both maps supports the inference that a common genomic region is responsible for conferring resistance and is associated with the resistant parent, Indianhead. The third QTL was derived from Northfield. Evaluation of markers associated with AB resistance across a diverse lentil germplasm panel revealed that the identity of alleles associated with AB_IH1 predicted the phenotypic responses with high levels of accuracy (~86%), and therefore have the potential to be widely adopted in lentil breeding programs. The availability of RIL-based maps, a consensus map, and validated markers linked to AB resistance provide important resources for lentil improvement.

Field pea (Pisum sativum L.) is a grain legume crop that is cultivated for either human or livestock consumption. Development of varieties adapted to damaging abiotic and biotic stresses is a major objective for field pea breeding. Bacterial blight is a serious disease caused by the pathogenic agents Pseudomonas syringae pv. syringae and Pseudomonas syringae pv. pisi. A recombinant inbred line (RIL) genetic mapping population was generated by crossing the susceptible genotype Kaspa to the resistant genotype PBA Oura. Previously described sets of single-nucleotide polymorphism and simple sequence repeat markers were assigned to a genetic linkage map of the Kaspa × PBA Oura population, which contained 358 markers spanning 1070 cM with an average marker density of 1 locus per 3.0 cM. Combination with multiple previously published maps (including that of Kaspa × Parafield) subsequently generated an integrated structure with much higher marker density of 1 locus per 0.85 cM. The Kaspa × PBA Oura and Kaspa × Parafield RILs were screened at the seedling stage for resistance to both pathovars. Totals of four and two QTLs for resistance to infection by P. syringae pv. syringae were detected in the Kaspa × Parafield and Kaspa × PBA Oura populations, respectively. A single common genomic region associated with P. syringae pv. pisi resistance was identified in both mapping populations. To integrate information on bacterial blight resistance from various QTL mapping studies, the relevant regions were extrapolated on to the integrated map through use of common flanking markers. The resources generated in this study will support map enhancement, identification of marker-trait associations, genomics-assisted breeding, map-based gene isolation and comparative genetics.

Chickpea (Cicer arietinum L.) is the third most economically important food legume in the world. Its yield potential is often limited by various biotic stresses, including fungal and viral diseases, insects, nematodes and parasitic weeds. Incorporating genetic resistance into cultivars is the most effective and economical way of controlling biotic stresses and this is a major objective in many breeding programs. Extensive searches for resistances have been conducted by screening commercial varieties, landraces and closely related species. Resistances to disease such as Ascochyta blight and Fusarium wilt have been identified and molecular tools are being used to increase the efficiency of gene transfer from wild species into chickpea elite genotypes. Quantitative trait loci for resistance genes have been located on linkage maps and molecular markers associated with these loci can potentially be used for efficient pyramiding of the traits. Significant chickpea genomic resources have been developed in order to investigate resistance genes. Such resources include an integrated genetic map, expressed sequence tag libraries, bacterial artificial chromosome libraries, microarrays and draft genome sequences. Although these resources have yet to be used to improve chickpea cultivars in the field, this is likely to change in the near future. These genomic resources, as well as high-resolution phenotyping tools and cutting-edge technologies such as next-generation sequencing, promise to increase efficiency as work to identify valuable candidate genes continues.

BACKGROUND:Lentil is a self-pollinated annual diploid (2n = 2× = 14) crop with a restricted history of genetic improvement through breeding, particularly when compared to cereal crops. This limited breeding has probably contributed to the narrow genetic base of local cultivars, and a corresponding potential to continue yield increases and stability. Therefore, knowledge of genetic variation and relationships between populations is important for understanding of available genetic variability and its potential for use in breeding programs. Single nucleotide polymorphism (SNP) markers provide a method for rapid automated genotyping and subsequent data analysis over large numbers of samples, allowing assessment of genetic relationships between genotypes.RESULTS:In order to investigate levels of genetic diversity within lentil germplasm, 505 cultivars and landraces were genotyped with 384 genome-wide distributed SNP markers, of which 266 (69.2%) obtained successful amplification and detected polymorphisms. Gene diversity and PIC values varied between 0.108-0.5 and 0.102-0.375, with averages of 0.419 and 0.328, respectively. On the basis of clarity and interest to lentil breeders, the genetic structure of the germplasm collection was analysed separately for cultivars and landraces. A neighbour-joining (NJ) dendrogram was constructed for commercial cultivars, in which lentil cultivars were sorted into three major groups (G-I, G-II and G-III). These results were further supported by principal coordinate analysis (PCoA) and STRUCTURE, from which three clear clusters were defined based on differences in geographical location. In the case of landraces, a weak correlation between geographical origin and genetic relationships was observed. The landraces from the Mediterranean region, predominantly Greece and Turkey, revealed very high levels of genetic diversity.CONCLUSIONS:Lentil cultivars revealed clear clustering based on geographical origin, but much more limited correlation between geographic origin and genetic diversity was observed for landraces. These results suggest that selection of divergent parental genotypes for breeding should be made actively on the basis of systematic assessment of genetic distance between genotypes, rather than passively based on geographical distance.