Identification of plant based potential antifungal compounds against BMK-1 protein of Bipolaris oryzae using molecular docking approach.

Rice brown spot is an important disease of rice worldwide that inflicts substantial yield losses. The antimicrobial potential of methanol, acetone and dimethyl sulfoxide (DMSO) extracts of different medicinal plants, viz., Syzygium aromaticum, Saussurea costus, Acorus calamus, Bergenia ciliate, Geranium pratense, Mentha longifolia, Inula racemosa, Podophyllum hexandrum, Heracleum candicans and Picrorhiza kurroa, against the brown spot pathogen Bipolaris oryzae in vitro was evaluated via mycelial growth inhibition and spore germination inhibition assays. Among the plant extracts tested, 100% mycelial inhibition was observed for the methanol extract of Syzygium aromaticum at all three concentrations (2000 ppm, 3000 ppm and 4000 ppm), followed by the methanol extract of Inula racemosa (90.33%) at 4000 ppm. A maximum conidial germination inhibition of 83.54% was exhibited by the Heracleum candicans leaf extract. Phytochemical profiling of Syzygium aromaticum and Inula racemosa through liquid chromatography and mass spectrometry (HR-LCMS) revealed the presence of several compounds, such as eugenol, ursolic acid, quercetin, chlorogenic acid, and noscapine. A molecular docking approach was used to identify key inhibitory molecules against B. oryzae. Among the compounds detected in S. aromaticum and Inula racemosa, ursolic acid and noscapine were found to have the greatest binding affinity for the Big Mitogen Activated Protein Kinase (BMK-1) enzyme present in B. oryzae. In conclusion, S. aromaticum and Inula racemosa are potent compounds that could serve as lead compounds for drug discovery in the future.

Multi-location evaluation of field pea in Indian climates: eco-phenological dynamics, crop-environment relationships, and identification of mega-environments.

Characterization of crop-growing environments in relation to crop's genotypic performance is crucial to harness positive genotype-by-environment interactions (GEI) in systematic breeding programs. Given that, the study aimed to delineate the impact of diverse environments on crop phenology and yield traits of dwarf-statured field pea, pinpointing location(s) favoring higher yield and distinctiveness within breeding lines. We tested twelve field pea breeding lines across twenty locations in India, covering Central Zone (CZ), North Western Plain Zone (NWPZ), North Eastern Plain Zone (NEPZ), and Northern Hill Zone (NHZ). Across these locations, maximum and minimum temperatures during flowering (TMAXF, TMINF) and reproductive period (TMAXRP, TMINRP) ranged 18.9-28.3, 3.3-18.0, 15.0-30.8, and 7.9-22.1oC, respectively. Meanwhile, notable variations in phenological and agronomic traits (coefficient of variation) were observed: flowering (31%), days to maturity (21%), reproductive period (18%), grain yield (48%), and 100-seed weight (18%). Combined ANOVA demonstrated an oversized impact of environment (81%) on yield, while genotype and GEI effects were 2% and 14%, respectively. The variables TMINF, TMINRP, and cumulative growing degree-day showed positive correlations with yield, while extended vegetative and maturity durations negatively influenced yield (p < 0.05). Additionally, linear mixed-models and PCA results explained that instability in crop phenology had significant influence on field pea yield. Seed weight was markedly varied within the locations (9.9-20.8 g) and both higher and lower seed weights were associated with lower yields (Optimal = 17.1 g). HA-GGE biplot-based on environment focus-scaling demonstrated three mega-environments and specific locations viz. Kota (CZ), SK Nagar (CZ), Raipur (CZ), Sehore (CZ), and Pantnagar (NWPZ) as the ideal testing-environments with high efficiency in selecting new genotypes with wider adaptability. The study findings highlight distinct impact of environments on crop phenology and agronomic traits of field pea (dwarf-type), hold substantial value in designing efficient field pea (dwarf-type) breeding program at mega-environment scale.

Unravelling effects of phytochemicals from buckwheat on cholesterol metabolism and lipid accumulation in HepG2 cells and its validation through gene expression analysis.

BACKGROUND: The objective of this research was to elucidate the hypocholesterolemic effects of a bioactive compound extracted from buckwheat, and to delineate its influence on the regulatory mechanisms of cholesterol metabolism. The compound under investigation was identified as quercetin. MATERIAL AND RESULTS: In vitro experiments conducted on HepG2 cells treated with quercetin revealed a significant reduction in intracellular cholesterol accumulation. This phenomenon was rigorously quantified by assessing the transcriptional activity of key genes involved in the biosynthesis and metabolism of cholesterol. A statistically significant reduction in the expression of HMG-CoA reductase (HMGCR) was observed, indicating a decrease in endogenous cholesterol synthesis. Conversely, an upregulation in the expression of cholesterol 7 alpha-hydroxylase (CYP7A1) was also observed, suggesting an enhanced catabolism of cholesterol to bile acids. Furthermore, the study explored the combinatory effects of quercetin and simvastatin, a clinically utilized statin, revealing a synergistic action in modulating cholesterol levels at various dosages. CONCLUSIONS: The findings from this research provide a comprehensive insight into the mechanistic pathways through which quercetin, a phytochemical derived from buckwheat, exerts its hypocholesterolemic effects. Additionally, the observed synergistic interaction between quercetin and simvastatin opens up new avenues for the development of combined therapeutic strategies to manage hyperlipidemia.

Genome-wide SNP discovery and genotyping delineates potential QTLs underlying major yield-attributing traits in buckwheat.

Buckwheat (Fagopyrum spp.) is an important nutritional and nutraceutical-rich pseudo-cereal crop. Despite its obvious potential as a functional food, buckwheat has not been fully harnessed due to its low yield, self-incompatibility, increased seed cracking, limited seed set, lodging, and frost susceptibility. The inadequate availability of genomics resources in buckwheat is one of the major reasons for this. In the present study, genome-wide association mapping (GWAS) was conducted to identify loci associated with various morphological and yield-related traits in buckwheat. High throughput genotyping by sequencing led to the identification of 34,978 single nucleotide polymorphisms that were distributed across eight chromosomes. Population structure analysis grouped the genotypes into three sub-populations. The genotypes were also characterized for various qualitative and quantitative traits at two diverse locations, the analysis of which revealed a significant difference in the mean values. The association analysis revealed a total of 71 significant marker-trait associations across eight chromosomes. The candidate genes were identified near 100 Kb of quantitative trait loci (QTLs), providing insights into several metabolic and biosynthetic pathways. The integration of phenology and GWAS in the present study is useful to uncover the consistent genomic regions, related markers associated with various yield-related traits, and potential candidate genes having implications for being utilized in molecular breeding for the improvement of economically important traits in buckwheat. Moreover, the identified QTLs will assist in tracking the desirable alleles of target genes within the buckwheat breeding populations/germplasm.

Explicating genetic architecture governing nutritional quality in pigmented rice.

Rice is one of the most important staple plant foods that provide a major source of calories and nutrients for tackling the global hunger index especially in developing countries. In terms of nutritional profile, pigmented rice grains are favoured for their nutritional and health benefits. The pigmented rice varieties are rich sources of flavonoids, anthocyanin and proanthocyanidin that can be readily incorporated into diets to help address various lifestyle diseases. However, the cultivation of pigmented rice is limited due to low productivity and unfavourable cooking qualities. With the advances in genome sequencing, molecular breeding, gene expression analysis and multi-omics approaches, various attempts have been made to explore the genetic architecture of rice grain pigmentation. In this review, we have compiled the current state of knowledge of the genetic architecture and nutritional value of pigmentation in rice based upon the available experimental evidence. Future research areas that can help to deepen our understanding and help in harnessing the economic and health benefits of pigmented rice are also explored.

Buckwheat OMICS: present status and future prospects.

Buckwheat (Fagopyrum spp.) is an underutilized resilient crop of North Western Himalayas belonging to the family Polygonaceae and is a source of essential nutrients and therapeutics. Common Buckwheat and Tatary Buckwheat are the two main cultivated species used as food. It is the only grain crop possessing rutin, an important metabolite with high nutraceutical potential. Due to its inherent tolerance to various biotic and abiotic stresses and a short life cycle, Buckwheat has been proposed as a model crop plant. Nutritional security is one of the major concerns, breeding for a nutrient-dense crop such as Buckwheat will provide a sustainable solution. Efforts toward improving Buckwheat for nutrition and yield are limited due to the lack of available: genetic resources, genomics, transcriptomics and metabolomics. In order to harness the agricultural importance of Buckwheat, an integrated breeding and OMICS platforms needs to be established that can pave the way for a better understanding of crop biology and developing commercial varieties. This, coupled with the availability of the genome sequences of both Buckwheat species in the public domain, should facilitate the identification of alleles/QTLs and candidate genes. There is a need to further our understanding of the molecular basis of the genetic regulation that controls various economically important traits. The present review focuses on: the food and nutritional importance of Buckwheat, its various omics resources, utilization of omics approaches in understanding Buckwheat biology and, finally, how an integrated platform of breeding and omics will help in developing commercially high yielding nutrient rich cultivars in Buckwheat.

Metabolic-GWAS provides insights into genetic architecture of seed metabolome in buckwheat.

BACKGROUND: Buckwheat (Fagopyrum spp.), belonging to the Polygonaceae family, is an ancient pseudo-cereal with high nutritional and nutraceutical properties. Buckwheat proteins are gluten-free and show balanced amino acid and micronutrient profiles, with higher content of health-promoting bioactive flavonoids that make it a golden crop of the future. Plant metabolome is increasingly gaining importance as a crucial component to understand the connection between plant physiology and environment and as a potential link between the genome and phenome. However, the genetic architecture governing the metabolome and thus, the phenome is not well understood. Here, we aim to obtain a deeper insight into the genetic architecture of seed metabolome in buckwheat by integrating high throughput metabolomics and genotyping-by-sequencing applying an array of bioinformatics tools for data analysis. RESULTS: High throughput metabolomic analysis identified 24 metabolites in seed endosperm of 130 diverse buckwheat genotypes. The genotyping-by-sequencing (GBS) of these genotypes revealed 3,728,028 SNPs. The Genome Association and Prediction Integrated Tool (GAPIT) assisted in the identification of 27 SNPs/QTLs linked to 18 metabolites. Candidate genes were identified near 100 Kb of QTLs, providing insights into several metabolic and biosynthetic pathways. CONCLUSIONS: We established the metabolome inventory of 130 germplasm lines of buckwheat, identified QTLs through marker trait association and positions of potential candidate genes. This will pave the way for future dissection of complex economic traits in buckwheat.

Delineating Marker-Trait Associations for Fusarium Wilt in Chickpea Using the Axiom® CicerSNP Array.

Fusarium wilt (FW) caused by Fusarium oxysporum f. sp. ciceri is a devastating disease of chickpea (Cicer arietinum). To identify promising resistant genotypes and genomic loci for FW resistance, a core set of 179 genotypes of chickpea was tested for FW reactions at the seedling and reproductive stages under field conditions and controlled conditions in the greenhouse. Our results revealed that at the seedling stage, most of the genotypes were resistant, whereas at the reproductive stage, most of the genotypes were susceptible. Genotyping using a 50K Axiom® CicerSNP Array and trait data of FW together led to the identification of 26 significant (P ≤ E-05) marker-trait associations (MTAs) for FW resistance. Among the 26 MTAs, 12 were identified using trait data recorded in the field (three at the seedling and nine at the reproductive stage), and 14 were identified using trait data recorded under controlled conditions in the greenhouse (six at the seedling and eight at the reproductive stage). The phenotypic variation explained by these MTAs varied from 11.75 to 15.86%, with an average of 13.77%. Five MTAs were classified as major, explaining more than 15% of the phenotypic variation for FW, and two were declared stable, being identified in two environments. One of the promising stable and major MTAs (Affx_123280060) detected in field conditions at the reproductive stage was also detected in greenhouse conditions at the seedling and reproductive stages. The stable and major (>15% PVE) MTAs can be used in chickpea breeding programs.

Biochemical and proteomic insights revealed selenium priming induced phosphorus stress tolerance in common bean (Phaseolus vulgaris L.).

BACKGROUND: Mineral stress is one of the dominating abiotic stresses, which leads to decrease in crop production. Selenium (Se) seed priming is a recent approach to mitigate the plant's mineral deficiency stress. Although not an essential element, Se has beneficial effects on the plants in terms of growth, quality, yield and plant defense system thus, enhancing plant tolerance to mineral deficiency. METHODS AND RESULTS: The present research was accomplished to find out the effect of Se priming on common bean plant (SFB-1 variety) under phosphorus (P) stress. The seeds were grown invitro on four different MGRL media which are normal MGRL media as control with non-Se primed seeds (Se- P+), non -Se primed seeds grown on P deficient MGRL media (Se- P-), Se primed seeds grown on normal MGRL media (Se+P+) and Se primed seeds grown on P deficient MGRL media (Se+P -). The various morphological and biochemical parameters such as proline content, total sugar content, polyphenols and expression of proteins were analyzed under P stress. The results showed that Se priming has significantly (p ≤ 0.05) affected the morphological as well as biochemical parameters under normal and P stress conditions. The morphological parameters-length, weight, number of nodes and leaves of Se+P+, Se+P- root and shoot tissue showed significant increase as compared to Se-P+, Se-P-. Similarly various biochemical parameters such as total chlorophyll content, proline, total sugar content and polyphenols of Se+P+, Se+P- increased significantly as compared to Se-P+, Se-P-. The differential protein expression in both Se+P+, Se+P- and Se-P+, Se-P- plants were determined using MALDI-MS/MS. The differentially expressed proteins in Se+P+, Se+P- plants were identified as caffeic acid-3-O-methyltransferase (COMT) and SecA protein (a subunit of Protein Translocan transporter), and are found responsible for lignin synthesis in root cell walls and ATP dependent movement of thylakoid proteins across the membranes in shoot respectively. The differential expression of proteins in plant tissues, validated morphological and biochemical responses such as maintaining membrane integrity, enhanced modifications in cellular metabolism, improved polyphenol activities and expression of defensive proteins against mineral deficiency. CONCLUSIONS: The study provided an understanding of Se application as a potential approach increasing tolerance and yield in crop plants against mineral deficiency.

SSR markers in revealing extent of genetic diversity and phylogenetic relationships among chickpea core collection accessions for Western Himalayas.

BACKGROUND: The exploration of genetic diversity is the key source of germplasm conservation and potential to broaden its genetic base. The globally growing demand for chickpea suggests superior/climate-resilient varieties, which in turn necessitates the germplasm characterization to unravel underlying genetic variation. METHODOLOGY AND RESULTS: A chickpea core collection comprising of diverse 192 accessions which include cultivated Cicer arietinum, and wild C. reticulatum, C. echinospermum, and C. microphyllum species were investigated to analyze their genetic diversity and relationship, by assaying 33 unlinked simple sequence repeat (SSR) markers. The results amplified a total of 323 alleles (Na), ranging from 2 to 8 with an average of 4.25 alleles per locus. Expected heterozygosity (He) differed from 0.46 to 0.86 with an average of 0.68. Polymorphic information content (PIC) ranged from 0.73 to 0.98 with an average of 0.89. Analysis of molecular variance (AMOVA) showed that most of the variation was among individuals (87%). Cluster analysis resulted in the formation of four distinct clusters. Cluster I represented all cultivated and clusters II, III, and IV comprised a heterogeneous group of cultivated and wild chickpea accessions. CONCLUSION: We report considerable diversity and greater resolving power of SSR markers for assessing variability and interrelationship among the chickpea accessions. The chickpea core is expected to be an efficient resource for breeders for broadening the chickpea genetic base and could be useful for selective breeding of desirable traits and in the identification of target genes for genomics-assisted breeding.

Morpho-Cultural and Pathogenic Variability of Sclerotinia sclerotiorum Causing White Mold of Common Beans in Temperate Climate.

The present systematic research on cultural, morphological, and pathogenic variability was carried out on eighty isolates of Sclerotinia sclerotiorum collected from major common bean production belts of North Kashmir. The isolates were found to vary in both cultural and morphological characteristics such as colony color and type, colony diameter, number of days for sclerotia initiation, sclerotia number per plate, sclerotial weight, and size. The colony color ranged between white and off-white with the majority. The colony was of three types, in majority smooth, some fluffy, and a few fluffy-at-center-only. Colony diameter ranged between 15.33 mm and 29 mm after 24 h of incubation. The isolates took 4 to 7 days for initiation of sclerotia and varied in size, weight, and number per plate ranging between 14 and 51.3. The sclerotial arrangement pattern on plates was peripheral, sub peripheral, peripheral, and subperipheral, arranged at the rim and scattered. A total of 22 Mycelial compatibility groups (MCGs) were formed with seven groups constituted by a single isolate. The isolates within MCGs were mostly at par with each other. The six isolates representing six MCGs showed variability in pathogenicity with isolate G04 as the most and B01 as the least virulent. The colony diameter and disease scores were positively correlated. Sclerotia were observed to germinate both myceliogenically and carpogenically under natural temperate conditions of Kashmir. Germplasm screening revealed a single resistant line and eleven partially resistant lines against most virulent isolates.

Low Temperature Stress Tolerance: An Insight Into the Omics Approaches for Legume Crops.

The change in climatic conditions is the major cause for decline in crop production worldwide. Decreasing crop productivity will further lead to increase in global hunger rate. Climate change results in environmental stress which has negative impact on plant-like deficiencies in growth, crop yield, permanent damage, or death if the plant remains in the stress conditions for prolonged period. Cold stress is one of the main abiotic stresses which have already affected the global crop production. Cold stress adversely affects the plants leading to necrosis, chlorosis, and growth retardation. Various physiological, biochemical, and molecular responses under cold stress have revealed that the cold resistance is more complex than perceived which involves multiple pathways. Like other crops, legumes are also affected by cold stress and therefore, an effective technique to mitigate cold-mediated damage is critical for long-term legume production. Earlier, crop improvement for any stress was challenging for scientific community as conventional breeding approaches like inter-specific or inter-generic hybridization had limited success in crop improvement. The availability of genome sequence, transcriptome, and proteome data provides in-depth sight into different complex mechanisms under cold stress. Identification of QTLs, genes, and proteins responsible for cold stress tolerance will help in improving or developing stress-tolerant legume crop. Cold stress can alter gene expression which further leads to increases in stress protecting metabolites to cope up the plant against the temperature fluctuations. Moreover, genetic engineering can help in development of new cold stress-tolerant varieties of legume crop. This paper provides a general insight into the "omics" approaches for cold stress in legume crops.

Multidimensional Role of Silicon to Activate Resilient Plant Growth and to Mitigate Abiotic Stress.

Sustainable agricultural production is critically antagonistic by fluctuating unfavorable environmental conditions. The introduction of mineral elements emerged as the most exciting and magical aspect, apart from the novel intervention of traditional and applied strategies to defend the abiotic stress conditions. The silicon (Si) has ameliorating impacts by regulating diverse functionalities on enhancing the growth and development of crop plants. Si is categorized as a non-essential element since crop plants accumulate less during normal environmental conditions. Studies on the application of Si in plants highlight the beneficial role of Si during extreme stressful conditions through modulation of several metabolites during abiotic stress conditions. Phytohormones are primary plant metabolites positively regulated by Si during abiotic stress conditions. Phytohormones play a pivotal role in crop plants' broad-spectrum biochemical and physiological aspects during normal and extreme environmental conditions. Frontline phytohormones include auxin, cytokinin, ethylene, gibberellin, salicylic acid, abscisic acid, brassinosteroids, and jasmonic acid. These phytohormones are internally correlated with Si in regulating abiotic stress tolerance mechanisms. This review explores insights into the role of Si in enhancing the phytohormone metabolism and its role in maintaining the physiological and biochemical well-being of crop plants during diverse abiotic stresses. Moreover, in-depth information about Si's pivotal role in inducing abiotic stress tolerance in crop plants through metabolic and molecular modulations is elaborated. Furthermore, the potential of various high throughput technologies has also been discussed in improving Si-induced multiple stress tolerance. In addition, a special emphasis is engrossed in the role of Si in achieving sustainable agricultural growth and global food security.

Identification of QTLs/ Candidate Genes for Seed Mineral Contents in Common Bean (Phaseolus vulgaris L.) Through Genotyping-by-Sequencing.

Throughout the ages, the common bean has been consumed by humanity as an important food staple crop and source of nutrition on a global scale. Since its domestication, a wide spectrum of phenotypic and genotypic investigations have been carried out to unravel the potential of this crop and to understand the process of nutrient accumulation along with other desirable characteristics. The common bean is one of the essential legume crops due to its high protein and micronutrient content. The balance in micronutrients is critical for the growth and development of plants as well as humans. Iron (Fe), Zinc (Zn), Copper (Cu), Manganese (Mn), Magnesium (Mg), Calcium (Ca), and Molybdenum (Mo) are some of the important micronutrients present in legumes. Thus, we aimed to investigate the quantitative trait loci's (QTLs)/single nucleotide polymorphisms (SNPs) to identify the candidate genes associated with micronutrients through genotyping by sequencing (GBS). In our investigation, through GBS we identified SNPs linked with traits and assessed seven micronutrients in 96 selected common bean genotypes for screening nutritionally rich genotypes. Among 96399 SNPs total identified through GBS, 113 SNPs showed significant phenotypic variance, ranging from 13.50 to 21.74%. SNPs associated with most of the seed micronutrients (Mg, Mn, Fe, Ca, Cu) were found on chr3 & chr11 (Mg, Mn, Mo, Ca, Zn). The findings from this study could be used for haplotype-based selection of nutritionally rich genotypes and for marker-assisted genetic enhancement of the common bean. Further, the identified SNPs for candidate genes/transporters associated with micronutrient content may pave the way for the enrichment of seeds by employing genomics-assisted breeding programs.

Assessment of cold tolerance in chickpea (Cicer spp.) grown under cold/freezing weather conditions of North-Western Himalayas of Jammu and Kashmir, India.

Chickpea is one of the most important grain legume crops in the world. India is the largest producer, consumer as well as importer of chickpea. Cold stress (temperature < 15 °C) is one of the important abiotic stresses limiting chickpea production by hampering its growth and vigor at all phenological stages. This study was aimed to characterize a diverse set of 366 chickpea genotypes for cold tolerance and identify most promising cold tolerant chickpea genotypes in the Western-Himalayas of Jammu and Kashmir, India. The 366 genotypes used during the present study including genotypes belonging to cultivated, primary and secondary gene pools of chickpea. Two important approaches were used including visual screening under field conditions and screening under controlled conditions by measuring cell membrane stability through electrolyte leakage tests. The analysis of trait data collected through both the approaches led to the identification of five most promising/candidate cold tolerant chickpea genotypes including one wild genotype "Ortan-066" from secondary gene pool species (C. echinospermum), one wild genotype "Cudi 1-022" from primary gene pool species (C. reticulatum) and three genotypes (IC 116783, ICC 15200 and AGBLG 170004) from the cultivated species (Cicer arietinum). Wild genotype "Ortan-066" was found best cold tolerance source with the mean Cold Tolerance Rating (CTR) of 2 and Electrolyte Leakage Index (ELI) of 10.82%, followed by wild genotype "Cudi 1-022" (CTR = 3, ELI = 18.89%), and three cultivated genotypes viz., IC 116783, ICC 15200 and AGBL-G-170004, with the mean CTR of 3 and an estimated mean ELI of 21.26%, 21.58% and 21.94%, respectively. The promising, candidate cold tolerant genotypes identified during the present study could be used in chickpea breeding programs aimed at improving cold tolerance of cultivated chickpea worldwide. The candidate lines can be also used for developing bi-parental mapping populations, wild × cultivated introgression lines, transcriptomics and for differential expression analysis of cold tolerant genes in chickpea. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12298-021-00997-1.

North-Western Himalayan Common Beans: Population Structure and Mapping of Quantitative Anthracnose Resistance Through Genome Wide Association Study.

Common bean (Phaseolus vulgaris L.) is an important legume crop of north-western (NW) Himalayan region and the major disease that causes catastrophic loss to the crop is anthracnose, which is caused by Colletotrichum lindemuthianum. The pathogen is highly diverse and most of the commercial cultivars are susceptible to different races prevalent in the region. The lack of information on the genomic regions associated with anthracnose resistance in NW Himalayan common bean population prompted us to dissect Quantitative Resistance Loci (QRLs) against major anthracnose races. In this study, 188 common bean landraces collected from NW region were screened against five important anthracnose races and 113 bean genotypes showed resistance to one or multiple races. Genotyping by sequencing (GBS) was performed on a panel of 192 bean lines (4 controls plus 188 Indian beans) and 22,589 SNPs were obtained that are evenly distributed. Population structure analysis of 192 bean genotypes categorized 188 Indian beans into two major clusters representing Andean and Mesoamerican gene pools with obvious admixtures. Many QRLs associated with anthracnose resistance to Indian C. lindemuthianum virulences (race 3, 87, and 503) are located at Pv04 within the gene models that encode typical resistance gene signatures. The QRLs associated with race 73 are located on Pv08 and overlaps with Co-4 anthracnose resistance gene. A SNP located at distal end of Pv11 in a gene model Phvul.011G202300 which encodes a LRR with a typical NB-ARC domain showed association with race 73 resistance. Common bean genomic regions located at Pv03, Pv09, and Pv11 showed association with resistance to anthracnose race 2047. The present study showed presence of many novel bean genomic regions associated with anthracnose resistance. The presence of Co-4 and Co-2 genes in our material is encouraging for breeding durable anthracnose resistant cultivars for the region.

Gene/QTL discovery for Anthracnose in common bean (Phaseolus vulgaris L.) from North-western Himalayas.

Common bean (Phaseolus vulgaris L.) is one of the most important grain legume crops in the world. The beans grown in north-western Himalayas possess huge diversity for seed color, shape and size but are mostly susceptible to Anthracnose disease caused by seed born fungus Colletotrichum lindemuthianum. Dozens of QTLs/genes have been already identified for this disease in common bean world-wide. However, this is the first report of gene/QTL discovery for Anthracnose using bean germplasm from north-western Himalayas of state Jammu & Kashmir, India. A core set of 96 bean lines comprising 54 indigenous local landraces from 11 hot-spots and 42 exotic lines from 10 different countries were phenotyped at two locations (SKUAST-Jammu and Bhaderwah, Jammu) for Anthracnose resistance. The core set was also genotyped with genome-wide (91) random and trait linked SSR markers. The study of marker-trait associations (MTAs) led to the identification of 10 QTLs/genes for Anthracnose resistance. Among the 10 QTLs/genes identified, two MTAs are stable (BM45 & BM211), two MTAs (PVctt1 & BM211) are major explaining more than 20% phenotypic variation for Anthracnose and one MTA (BM211) is both stable and major. Six (06) genomic regions are reported for the first time, while as four (04) genomic regions validated the already known QTL/gene regions/clusters for Anthracnose. The major, stable and validated markers reported during the present study associated with Anthracnose resistance will prove useful in common bean molecular breeding programs aimed at enhancing Anthracnose resistance of local bean landraces grown in north-western Himalayas of state Jammu and Kashmir.

Linkage disequilibrium based association mapping of micronutrients in common bean (Phaseolus vulgaris L.): a collection of Jammu & Kashmir, India.

Micronutrient deficiencies are of major concern in human health and plant metabolism. Iron (Fe), zinc (Zn), iodine (I), selenium (Se) are regarded as micronutrients having major impact on human health. More than 50% of populations mainly from developing countries are suffering from one or the other micronutrient malnutrition. Ensuring adequate supply of these micronutrients through diet consisting of staple foods, such as common bean (Phaseolus vulgaris L.) is must. Here, we evaluated common bean genotypes that were collected from various regions of Jammu and Kashmir, India for Fe, Zn and protein contents and used SSRs to identify the markers associated with these traits. We found significant variation among genotypes for Fe, Zn and protein contents. Genotype R2 was having 7.22 mg 100 g-1 of Fe content, genotype K15 with 1.93 mg 100 g-1 of Zn content and genotype KS6 with 31.6% of protein content. Diversity study was done using both cluster and structure based approach. Further, association mapping analysis using General Linear Method (GLM) approach was done to identify SSRs associated with accumulation of Fe, Zn and protein. 13 SSRs were identified that significantly (p < 0.05) showed association with Fe, Zn and protein contents in common bean. The markers associated with Fe were located on chromosome no. 2, 5, 6, 7, 9 and 10, markers associated with Zn were located on chromosome no. 1, 3, 5, 7 and 10 whereas only one marker located on chromosome no. 4 was found associated with protein content. These findings will provide potential opportunity to improve Fe and Zn concentrations in common bean, through molecular breeding.