Late Leaf Spot Resistance Research Articles

Identification of new sources of resistance against late leaf spot disease of groundnut using molecular and field screenings

ABSTRACT Late leaf spot (LLS), caused by the fungus Nothopassalora personata, is an important foliar disease in groundnut (Arachis hypogaea L.) production. The present study used previously reported three single nucleotide polymorphism (SNP) markers to screen a set of groundnut germplasm and compared them with phenotypic values of three hotspot locations. The results indicated that marker-identified genotypes had LLS-resistant or moderately resistant phenotypes. About 56% of the phenotypically confirmed genotypes were confirmed with the SNP genotype. Some of the phenotypically resistant genotypes were not confirmed with marker genotypes, indicating some other quantitative trait locus (QTL) responsible for the LLS resistance might have been involved. The findings in this study are relevant to future LLS resistance breeding programs.

Linkage Mapping and Genome-Wide Association Study Identified Two Peanut Late Leaf Spot Resistance Loci, PLLSR-1 and PLLSR-2, Using Nested Association Mapping.

Identification of candidate genes and molecular markers for late leaf spot (LLS) disease resistance in peanut (Arachis hypogaea) has been a focus of molecular breeding for the U.S. industry-funded peanut genome project. Efforts have been hindered by limited mapping resolution due to low levels of genetic recombination and marker density available in traditional biparental mapping populations. To address this, a multi-parental nested association mapping population has been genotyped with the peanut 58K single-nucleotide polymorphism (SNP) array and phenotyped for LLS severity in the field for 3 years. Joint linkage-based quantitative trait locus (QTL) mapping identified nine QTLs for LLS resistance with significant phenotypic variance explained up to 47.7%. A genome-wide association study identified 13 SNPs consistently associated with LLS resistance. Two genomic regions harboring the consistent QTLs and SNPs were identified from 1,336 to 1,520 kb (184 kb) on chromosome B02 and from 1,026.9 to 1,793.2 kb (767 kb) on chromosome B03, designated as peanut LLS resistance loci, PLLSR-1 and PLLSR-2, respectively. PLLSR-1 contains 10 nucleotide-binding site leucine-rich repeat disease resistance genes. A nucleotide-binding site leucine-rich repeat disease resistance gene, Arahy.VKVT6A, was also identified on homoeologous chromosome A02. PLLSR-2 contains five significant SNPs associated with five different genes encoding callose synthase, pollen defective in guidance protein, pentatricopeptide repeat, acyl-activating enzyme, and C2 GRAM domains-containing protein. This study highlights the power of multi-parent populations such as nested association mapping for genetic mapping and marker-trait association studies in peanuts. Validation of these two LLS resistance loci will be needed for marker-assisted breeding.

Validation of SNP markers associated with late leaf spot resistance in groundnut

Validation of SNP markers associated with late leaf spot resistance in groundnut

Validation and identification of promising gene specific markers governing foliar disease resistance in groundnut (Arachis hypogaea L.).

Groundnut is vulnerable to the major foliar fungal disease viz., late leaf spot (LLS) and rust in kharif season, which results in severe yield losses. Until now, LLS and rust resistance linked markers were developed based on GPBD 4 as a major donor source and were validated in its derivatives only, which restricted their use in marker assisted selection (MAS) involving other donors. The current study focused to validate LLS and rust resistance linked markers employing advanced breeding lines of F6 generation, derived from nine different crosses involving nine diverse parents, to identify potential markers for marker-assisted breeding of LLS and rust resistance in groundnut. Out of 28-trait linked markers used for validation, 8 were polymorphic (28.57%). Marker-trait association (MTA) and Single Marker Analysis (SMA) revealed that the SSR marker pPGPseq5D05 is significantly associated with both LLS (15.8% PVE) and rust (17.5% PVE) resistance, whereas, the marker IPAHM103 is tightly linked with rust resistance (26.8% PVE) alone. In silico analysis revealed that the marker gene for IPAHM103 is a zinc finger protein and the marker gene for pPGPseq5D05 is an ADP-ribosylation factor GTPase-activating protein. Both these protein products impart resistance or tolerance to biotic stress in crop plants. Two other markers namely, GMLQ975 and pPGPseq13A10 were also found to be associated with LLS resistance explaining MTA up to 60%. These gene specific markers will enable us to screen more number of germplasm lines or newly developed lines in MAS schemes for LLS and rust resistance using a wide range of resistant sources.

Comparing Regression and Classification Models to Estimate Leaf Spot Disease in Peanut (Arachis hypogaea L.) for Implementation in Breeding Selection

Late leaf spot (LLS) is an important disease of peanut, causing global yield losses. Developing resistant varieties through breeding is crucial for yield stability, especially for smallholder farmers. However, traditional phenotyping methods used for resistance selection are laborious and subjective. Remote sensing offers an accurate, objective, and efficient alternative for phenotyping for resistance. The objectives of this study were to compare between regression and classification for breeding, and to identify the best models and indices to be used for selection. We evaluated 223 genotypes in three environments: Serere in 2020, and Nakabango and Nyankpala in 2021. Phenotypic data were collected using visual scores and two handheld sensors: a red–green–blue (RGB) camera and GreenSeeker. RGB indices derived from the images, along with the normalized difference vegetation index (NDVI), were used to model LLS resistance using statistical and machine learning methods. Both regression and classification methods were also evaluated for selection. Random Forest (RF), the artificial neural network (ANN), and k-nearest neighbors (KNNs) were the top-performing algorithms for both regression and classification. The ANN (R2: 0.81, RMSE: 22%) was the best regression algorithm, while the RF was the best classification algorithm for both binary (90%) and multiclass (78% and 73% accuracy) classification. The classification accuracy of the models decreased with the increase in classification classes. NDVI, crop senescence index (CSI), hue, and greenness index were strongly associated with LLS and useful for selection. Our study demonstrates that the integration of remote sensing and machine learning can enhance selection for LLS-resistant genotypes, aiding plant breeders in managing large populations effectively.

High-throughput diagnostic markers for foliar fungal disease resistance and high oleic acid content in groundnut

BackgroundFoliar diseases namely late leaf spot (LLS) and leaf rust (LR) reduce yield and deteriorate fodder quality in groundnut. Also the high oleic acid content has emerged as one of the most important traits for industries and consumers due to its increased shelf life and health benefits.ResultsGenetic mapping combined with pooled sequencing approaches identified candidate resistance genes (LLSR1 and LLSR2 for LLS and LR1 for LR) for both foliar fungal diseases. The LLS-A02 locus housed LLSR1 gene for LLS resistance, while, LLS-A03 housed LLSR2 and LR1 genes for LLS and LR resistance, respectively. A total of 49 KASPs markers were developed from the genomic regions of important disease resistance genes, such as NBS-LRR, purple acid phosphatase, pentatricopeptide repeat-containing protein, and serine/threonine-protein phosphatase. Among the 49 KASP markers, 41 KASPs were validated successfully on a validation panel of contrasting germplasm and breeding lines. Of the 41 validated KASPs, 39 KASPs were designed for rust and LLS resistance, while two KASPs were developed using fatty acid desaturase (FAD) genes to control high oleic acid levels. These validated KASP markers have been extensively used by various groundnut breeding programs across the world which led to development of thousands of advanced breeding lines and few of them also released for commercial cultivation.ConclusionIn this study, high-throughput and cost-effective KASP assays were developed, validated and successfully deployed to improve the resistance against foliar fungal diseases and oleic acid in groundnut. So far deployment of allele-specific and KASP diagnostic markers facilitated development and release of two rust- and LLS-resistant varieties and five high-oleic acid groundnut varieties in India. These validated markers provide opportunities for routine deployment in groundnut breeding programs.

Validation of Groundnut (Arachis hypogaea L.) Mini-core Genotypes for Phenotypic Extremities along with LLS Resistance Through Genetic and Molecular Intervention

Background: The present investigation was conducted at Agricultural College and Research Institute, Killikulam, Tamil Nadu during the year 2022-2023 involving 220 groundnut genotypes along with a resistant and susceptible check towards validation of phenotypic extremities on yield and its contributing traits besides screening against late leaf spot resistance. Methods: The data collected from two hundred and twenty germplasm along with check varieties for thirteen quantitative traits. The collected data were subjected to statistical analysis (Mahalanobis, 1936) besides interpreted by various genetic tools such as PCV, GCV, heritability and GAM. Further, ten plants were selected at random from each genotype and observation on late leaf spot disease was recorded based on modified 9 point scale. Result: Molecular analysis for LLS resistance among the groundnut germplasm had shown the concurrent superiority in terms of yield and resistance to late leaf spot disease among the genotypesICG 15233, ICG 8760, ICG 76, ICG 111, ICG 297, ICG 405, ICG 238, ICG 4598, ICG 5051, ICG 6057, ICG 8253, ICG 8285, ICG 10701 and ICG 15234. Hence, these genotypes can be exploited to develop a disease resistance and high yielding groundnut culture.

High-density bin-based genetic map reveals a 530-kb chromosome segment derived from wild peanut contributing to late leaf spot resistance.

Twenty-eight QTLs for LLS disease resistance were identified using an amphidiploid constructed mapping population, a favorable 530-kb chromosome segment derived from wild species contributes to the LLS resistance. Late leaf spot (LLS) is one of the major foliar diseases of peanut, causing serious yield loss and affecting the quality of kernel and forage. Some wild Arachis species possess higher resistance to LLS as compared with cultivated peanut; however, ploidy level differences restrict utilization of wild species. In this study, a synthetic amphidiploid (Ipadur) of wild peanuts with high LLS resistance was used to cross with Tifrunner to construct TI population. In total, 200 recombinant inbred lines were collected for whole-genome resequencing. A high-density bin-based genetic linkage map was constructed, which includes 4,809 bin markers with an average inter-bin distance of 0.43cM. The recombination across cultivated and wild species was unevenly distributed, providing a novel recombination landscape for cultivated-wild Arachis species. Using phenotyping data collected across three environments, 28 QTLs for LLS disease resistance were identified, explaining 4.35-20.42% of phenotypic variation. The major QTL located on chromosome 14, qLLS14.1, could be consistently detected in 2021 Jiyang and 2022 Henan with 20.42% and 12.12% PVE, respectively. A favorable 530-kb chromosome segment derived from Ipadur was identified in the region of qLLS14.1, in which 23 disease resistance proteins were located and six of them showed significant sequence variations between Tifrunner and Ipadur. Allelic variation analysis indicating the 530-kb segment of wild species might contribute to the disease resistance of LLS. These associate genomic regions and candidate resistance genes are of great significance for peanut breeding programs for bringing durable resistance through pyramiding such multiple LLS resistance loci into peanut cultivars.

Identification of novel QTLs for resistance to late leaf spot in peanut by SNP array and QTL-seq

Late leaf spot (LLS) is one of important diseases that causes severe yield losses in peanut. Peanut has various sources of resistance to LLS, and the identification of resistant QTLs and the development of related molecular markers are of great importance for breeding of LLS-resistant peanut. In this study, 173 individual lines of a recombinant inbred line (RIL) population and 48K SNP array for genotyping were used to construct a high-density genetic map with 1475 SNP marker and 20 linkage groups. A total of 11 QTLs were obtained through QTL analysis using the constructed genetic map. Among them, a stable major QTL qLLS.LG02 was identified on linkage group 2 in all six environments, with a phenotypic variation explained (PVE) ranging from 15.57 to 31.09%. Additionally, QTL-seq technology was also employed for QTL analysis of LLS resistance. As a result, 14 QTL loci related to LLS resistance were identified using the G prime algorithm. Notably, physical position of qLLS02 and qLLS03 are coincided with that of qLLS.LG02 and qLLS.LG03 respectively. Gene annotation analysis within the 14 QTL intervals by QTL-seq revealed that there were a total of 163 NBS-LRR disease resistance genes, accounting for 22.86% of all R genes in peanut genome and showing a 4.26-fold enrichment with a p-value of 5.19e-57. Within the QTL region qLLS02 of the resistant parent Mi-2, there was a 5 Mb structural variation interval (SV) containing 81 NBS-LRR genes. A PCR diagnostic marker was developed, and validation data suggest that this SV might lead to gene deletion or replacement with other genes. This SV has the potential to enhance peanut resistance to late leaf spot disease. This study holds significant implications for improving peanut breeding for LLS resistance through development of associated molecular markers.

Marker-assisted introgression of wild chromosome segments conferring resistance to fungal foliar diseases into peanut (Arachis hypogaea L.).

Fungal foliar diseases can severely affect the productivity of the peanut crop worldwide. Late leaf spot is the most frequent disease and a major problem of the crop in Brazil and many other tropical countries. Only partial resistance to fungal diseases has been found in cultivated peanut, but high resistances have been described on the secondary gene pool. To overcome the known compatibility barriers for the use of wild species in peanut breeding programs, we used an induced allotetraploid (Arachis stenosperma × A. magna)4x, as a donor parent, in a successive backcrossing scheme with the high-yielding Brazilian cultivar IAC OL 4. We used microsatellite markers associated with late leaf spot and rust resistance for foreground selection and high-throughput SNP genotyping for background selection. With these tools, we developed agronomically adapted lines with high cultivated genome recovery, high-yield potential, and wild chromosome segments from both A. stenosperma and A. magna conferring high resistance to late leaf spot and rust. These segments include the four previously identified as having QTLs (quantitative trait loci) for resistance to both diseases, which could be confirmed here, and at least four additional QTLs identified by using mapping populations on four generations. The introgression germplasm developed here will extend the useful genetic diversity of the primary gene pool by providing novel wild resistance genes against these two destructive peanut diseases.

Marker assisted backcross to introgress late leaf spot and rust resistance in groundnut (Arachis hypogaea L.).

Groundnut is affected by a variety of abiotic and biotic stressors, including late leaf spot and rust, which cause significant economic loss. In this study, QTL for resistance to late leaf spot and rust from donor variety GPBD 4 were incorporated into a popular groundnut variety (ICGV 00350) through marker assisted backcross (MABC) breeding. Eight foreground SSR markers [AhXII (GM1009, GM1573 and Seq8D09) and AhXV (GM1536, GM2009, GM2079, GM2301 and IPAHM103)] linked with disease resistant QTLs were utilized in this study. A set of 217 SSR markers spanning the whole groundnut genome were employed for background analysis. Three backcrosses with recurrent parent and selfing were followed in the cross ICGV 00350 × GPBD 4. Background analysis was carried out in BC3F2; while, phenotypic confirmation for resistance was carried out in BC3F3 generation. Five advanced backcross lines in BC3F2 were found, with more than 90% recurrent parent genome. The phenotyping of the eight ILs recorded disease scores ranging from 2.0 to 3.0 for LLS and from 1.0 to 3.0 for rust disease scores. All these lines had superior characteristics compared to the recurrent parent ICGV 00350 in terms of late leaf spot and rust resistance. The enhanced ILs will be evaluated further for commercial release.

Registration of ‘Naronut 1R’ groundnut

Abstract‘Naronut 1R’ (Reg. no. CV‐150, PI 693985) is a high‐yielding, Spanish‐type groundnut (Arachis hypogaea L. subsp. fastigiata var. vulgaris) cultivar with a red seed coat and two seeds per pod. The cultivar was selected from a cross between International Crops Research Institute for the Semi‐arid Tropics advanced lines ‘ICGV‐SM 90704’ and ‘ICGV‐SM 86715’. Naronut 1R was developed for groundnut rosette disease resistance, late leafspot resistance, yield, red seed coat, and early maturity. Naronut 1R matures in 75–80 d after planting, compared with 90 d for the widely grown and popular landrace Erudu red (Spanish‐type groundnut). Naronut 1R has much higher yields (1,473 kg ha−1) than Erudu red (554 kg ha−1). The overall groundnut rosette disease rating was 44% lower in Naronut 1R (2.8 disease rating) compared with Erudu red (5.0 disease rating). Similarly, the overall late leafspot disease rating was 28% lower in Naronut 1R (3.6 disease rating) compared with Erudu red (5.0 disease rating). Similar to Erudu red, Naronut 1R seed testa is red, but the seed is larger. The sound mature kernel weight was 9.42% higher for Naronut 1R than for Erudu red. The shelling percentage for Naronut 1 was 49.3%, whereas Erudu red was 60%. Naronut 1R has lower protein (18.1 vs. 21.3%) and oil content (36.0 vs. 44.3%) than Erudu red. Naronut 1R will allow for broad adoption of a high yielding, early maturing, red seed coat cultivar that carries resistance to groundnut rosette disease and late leaf spot disease.

Exploration of Alternative Approaches to Phenotyping of Late Leaf Spot and Groundnut Rosette Virus Disease for Groundnut Breeding

Late leaf spot (LLS), caused by Nothopassalora personata (Berk. & M.A Curt.), and groundnut rosette disease (GRD), [caused by groundnut rosette virus (GRV)], represent the most important biotic constraints to groundnut production in Uganda. Application of visual scores in selection for disease resistance presents a challenge especially when breeding experiments are large because it is resource-intensive, subjective, and error-prone. High-throughput phenotyping (HTP) can alleviate these constraints. The objective of this study is to determine if HTP derived indices can replace visual scores in a groundnut breeding program in Uganda. Fifty genotypes were planted under rain-fed conditions at two locations, Nakabango (GRD hotspot) and NaSARRI (LLS hotspot). Three handheld sensors (RGB camera, GreenSeeker, and Thermal camera) were used to collect HTP data on the dates visual scores were taken. Pearson correlation was made between the indices and visual scores, and logistic models for predicting visual scores were developed. Normalized difference vegetation index (NDVI) (r = –0.89) and red-green-blue (RGB) color space indices CSI (r = 0.76), v* (r = –0.80), and b* (r = –0.75) were highly correlated with LLS visual scores. NDVI (r = –0.72), v* (r = –0.71), b* (r = –0.64), and GA (r = –0.67) were best related to the GRD visual symptoms. Heritability estimates indicated NDVI, green area (GA), greener area (GGA), a*, and hue angle having the highest heritability (H2 > 0.75). Logistic models developed using these indices were 68% accurate for LLS and 45% accurate for GRD. The accuracy of the models improved to 91 and 84% when the nearest score method was used for LLS and GRD, respectively. Results presented in this study indicated that use of handheld remote sensing tools can improve screening for GRD and LLS resistance, and the best associated indices can be used for indirect selection for resistance and improve genetic gain in groundnut breeding.

Variability and Trait Association Studies for Late Leaf Spot Resistance in a Groundnut MAGIC Population

Globally, late leaf spot (LLS), a foliar fungal disease is one of the most important biotic constraint in groundnut production. Multi-Parent Advanced Generation Inter Cross (MAGIC) groundnut population was developed in a convergent crossing scheme using eight founder parents to develop a mapping population for multiple traits includes LLS. The experiments conducted in light chamber using detached leaf assay, and disease field screening nurseries at two locations (ICRISAT and ARS, Kasbe Digraj) showed significant variability for LLS resistance and component of resistance traits. Total 10 MAGIC lines with longer incubation (>11.0 days) and two MAGIC lines with longer latent period (>27 days) than the resistant parent, GPBD 4 were identified. The MAGIC lines, ICGR 171413, and ICGR 171443 with a lesion diameter of <1 mm and 4.10–5.67% of leaf area damage can be valuable sources for the alleles limiting the pathogen severity. A total of 20 MAGIC lines recorded significantly superior for disease score at 105 DAP_I (5.60–6.89) compared to resistant check, GPDB 4 (6.89). Further studies to determine the type and number of genes controlling the LLS component traits in groundnut will be useful for improvement of resistance to LLS. Genomic selection approach can be valuable in groundnut breeding to harness the minor alleles contributing to the component traits of LLS resistance.

Identification of major consensus and epistatic QTLs for late leaf spot resistance in a cultivated groundnut breeding line VG 9514

A late leaf spot resistant breeding line VG 9514 was bred through interspecific hybridization between Arachis hypogaea L. and Arachis cardenasii. Genetic study involving segregation for late leaf spot resistance in 164 F2 and recombinant inbred line populations derived from a cross between VG 9514 X TAG 24 revealed duplicate recessive resistance for the disease. Integration of newly developed SSR markers from A02 chromosome with existing linkage map generated a new genetic linkage map with 278 markers and 2679.1 cM map distances. QTL mapping involving this genetic linkage map and phenotypic field score of late leaf spot identified two major consensus additive QTLs in the A02 chromosome of cultivated groundnut. Epistatic interaction between these two major QTLs was also noticed through an epistatic QTL analysis in Ici-Mapping 4.1. In all the fourteen epistatic QTLs, a common component locus was remained within the major additive QTL at 90 cM in chromosome A02. Sequence analysis within the major additive QTL peaks revealed open reading frame of genes that code LRR domain containing proteins which are involved in disease resistance of crop plants.

Comparative Transcriptome Analysis Identified Candidate Genes for Late Leaf Spot Resistance and Cause of Defoliation in Groundnut.

Late leaf spot (LLS) caused by fungus Nothopassalora personata in groundnut is responsible for up to 50% yield loss. To dissect the complex nature of LLS resistance, comparative transcriptome analysis was performed using resistant (GPBD 4), susceptible (TAG 24) and a resistant introgression line (ICGV 13208) and identified a total of 12,164 and 9954 DEGs (differentially expressed genes) respectively in A- and B-subgenomes of tetraploid groundnut. There were 135 and 136 unique pathways triggered in A- and B-subgenomes, respectively, upon N. personata infection. Highly upregulated putative disease resistance genes, an RPP-13 like (Aradu.P20JR) and a NBS-LRR (Aradu.Z87JB) were identified on chromosome A02 and A03, respectively, for LLS resistance. Mildew resistance Locus (MLOs)-like proteins, heavy metal transport proteins, and ubiquitin protein ligase showed trend of upregulation in susceptible genotypes, while tetratricopeptide repeats (TPR), pentatricopeptide repeat (PPR), chitinases, glutathione S-transferases, purple acid phosphatases showed upregulation in resistant genotypes. However, the highly expressed ethylene responsive factor (ERF) and ethylene responsive nuclear protein (ERF2), and early responsive dehydration gene (ERD) might be related to the possible causes of defoliation in susceptible genotypes. The identified disease resistance genes can be deployed in genomics-assisted breeding for development of LLS resistant cultivars to reduce the yield loss in groundnut.

Characterization of peanut lines with interspecific introgressions conferring late leaf spot resistance

AbstractLate leaf spot (LLS) disease caused by Nothopassalora personata (Berk. & M.A. Curtis) U. Braun, C. Nakash, Videira & Crous is prevalent among pathogens encountered in peanut (Arachis hypogaea L.) growing regions. Chemical control is expensive, sometimes inaccessible, and can be difficult to apply. One effective solution to control this disease is the deployment of resistant cultivars. IAC 322 is a breeding line resistant to foliar fungal disease and harbors alien introgressions from A. cardenasii Krapov. & W.C. Gregory, a wild diploid relative of peanut. The objective of this study was to determine the level of LLS resistance conferred by introgressed segments in families derived from TifNV‐High O/L × IAC 322. Phenotyping for LLS resistance was performed under both in vitro and field conditions, which provided sufficient disease pressure to separate the means of susceptible and resistant checks, although there was no statistically significant separation of LLS resistance among the families with introgressions. However, consistent levels of LLS resistance observed in the family with A02‐top/A03‐bottom segments makes it a valuable resource for peanut breeding. In addition, late‐season field disease ratings were found to correlate with the entire LLS infection progression under both field and in vitro conditions. Among the parameters collected for in vitro experiments, numbers of LLS lesions and sporulating LLS lesions at late stages of LLS infection and incubation period can be used to predict LLS resistance under field conditions.

Improving late leaf spot resistance of peanut by molecular breeding

Improving late leaf spot resistance of peanut by molecular breeding

Identification of novel QTLs for late leaf spot resistance and validation of a major rust QTL in peanut (Arachis hypogaea L.).

Co-occurrence of two devastating foliar-fungal diseases of peanut, viz., late leaf spot (LLS), and rust may cause heavy yield loss besides adversely affecting the quality of kernel and fodder. This study reports the mapping of seven novel stress-related candidate EST-SSRs in a region having major QTLs for LLS and rust diseases using an F2 mapping population (GJG17 × GPBD4) consisting of 328 individuals. The parental polymorphism using 1311 SSRs revealed 84 SSRs (6.4%) as polymorphic and of these 70 SSRs could be mapped on 14 linkage groups (LG). QTL analysis has identified a common QTL (LLSQTL1/RustQTL) for LLS and rust diseases in the map interval of 1.41cM on A03 chromosome, explaining 47.45% and 70.52% phenotypic variations, respectively. Another major QTL for LLS (LLSQTL1), explaining a 29.06% phenotypic variation was also found on LG_A03. A major rust QTL has been validated which was found harboring R-gene and resistance-related genes having a role in inducing hypersensitive response (HR). Further, 23 linked SSRs including seven novel EST-SSRs were also validated in 177 diverse Indian groundnut genotypes. Twelve genotypes resistant to both LLS and rust were found carrying the common (rust and LLS) QTL region, LLS QTL region, and surrounding regions. These identified and validated candidate EST-SSR markers would be of great use for the peanut breeding groups working for the improvement of foliar-fungal disease resistance.

Molecular and phenotypic diversity of groundnut (Arachis hypogaea L.) cultivars in Togo.

Diversity assessment of 94 groundnut accessions from Togo and Senegal, using agro-morphological and SNP markers, revealed high variability for many quantitative traits such as late leaf spot (LLS) incidence, number of pods per plant and yield per plant. For qualitative traits, the Simpson Index showed high diversity for primary seed colour (0.75), stem pigmentation (0.60), and Growth habit (0.59). Principal component analysis underscored quantitative traits such as hundred seed weight, days to maturity, and LLS incidence, as the main traits contributing to the divergence. Correlation and path coefficient analysis showed that the number of pods per plant was the main yield-related trait positively affecting yield (r = 0.95, PC = 0.84; p = 0.01). Overall, 990 SNP markers revealed moderate genetic variability in the genotypes and the percentage of heterozygous genotypes varied from 0 to 50% for all loci. Analysis of molecular variance revealed that only 1.1% of the total molecular variance accounted for geographical contribution to the diversity. Co-analysis of phenotypic and SNP data delineated three clusters harbouring useful alleles and interesting phenotypic features such as LLS resistance, large number of pods per plant and early maturity indicating that differences observed at the phenotypic level are underlined by genotypic differences. The phenotypic and genotypic diversity observed could be exploited for the identification of parents with preferred traits for use in the breeding program. However, the low population structure highlights the necessity to improve groundnut diversity in Togo through introduction from various sources.