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ThesisItem Open Access Cyanobacteria Mediated Enhancement of Drought Stress Tolerance in Wheat Genotypes(DIVISION OF MICROBIOLOGY ICAR - INDIAN AGRICULTURAL RESEARCH INSTITUTE NEW DELHI-110012, 2023) SNEHA G R; Dr. Gerard Abraham,; T-11292Drought stress is one of the most serious constraints that limit agricultural productivity worldwide and affect the food security. Management of drought stress is therefore important to sustain the agricultural productivity to feed the population. The cyanobacteria are emerging as potential candidates in this regard. In the present study, experiments were conducted to assess the desiccation tolerance of Anabaena species. Based on physiological parameters and multivariate analysis A. fertilissima and A. variablis were identified as most tolerant. Ten cyanobacterial strains isolated from the desert areas of Pokhran, Rajasthan, India were identified on the basis of morphological and molecular attributes. The cyanobacterial isolates Hapalosiphon sp. (SGR2), Nostoc sp. (SGR3), Anabaena sp. (SGR7), Neowestiellopsis sp. (SGR8) and Fischerella sp. (SGR16) grew optimally at desiccation level (10% w/v polyethylene glycol). They showed higher activity of antioxidant enzymes, exopolysaccharide production and plant growth promoting traits. The isolates Nostoc sp. (SGR3) and Neowestiellopsis sp. (SGR8) were selected for their establishment in liquid and soil microcosm and these studies did not show any antagonism due to combined inoculation. Neowestiellopsis sp. (SGR8) exhibited the highest soil chlorophyll content and nitrogenase activity. A pot experiment was conducted to evaluate the application of Nostoc sp. (SGR3) and Neowestiellopsis sp. (SGR8) on wheat cultivars. Growth and several of the physiological parameters were inhibited due to drought stress (25% FC). However, under drought stress conditions the cyanobacterial inoculation by Neowestiellopsis sp. (SGR8) enhanced the growth as well as physiological characteristics during the tillering and anthesis stages. Cyanobacterial inoculation helped the plants to maintain redox status through efficient modulation of antioxidant enzymes. It was also observed that under drought stress and cyanobacterial inoculation helped in the maintenance of root system architecture and development of roots. The cyanobacterial inoculation also improved the soil chemical and biological properties such as available nitrogen, available phosphorous, dehydrogenase activity and microbial biomass carbon under drought stress. Improvement in the yield parameters were also recorded in wheat plants exposed to drought and cyanobacterial inoculation. Protein profiling through twodimensional gel electrophoresis and nano-LC-MS/MS showed the differential expression of proteins related to drought tolerance due to cyanobacterial inoculation. The overall results show the potential of cyanobacterial inoculation in the effective management of drought stress in wheat.ThesisItem Open Access Genotypic Characterization and population dynamics of Bemisia tabaci (Gennadius) in vegetable crops in Chhattisgarh(DIVISION OF ENTOMOLOGY ICAR- INDIAN AGRICULTURAL RESEARCH INSTITUTE NEW DELHI – 110012, 2023) Archita Das; Dr. Kailash Chander Sharma; T-11291The Whitefly, Bemisia tabaci Gennadius (Family: Aleyrodidae, Order: Hemiptera) has been listed as one among the "100 of the World's Worst Invasive Alien Species" by the International Union for the Conservation of Nature and Natural Resources (IUCN). The whitefly is one of the most significant pests because it transmits more than 100 viruses and causes economic loss in more than 60 crops. India holds the second position globally in vegetable crop production. Unfortunately, vegetable yields are significantly impacted, with an average reduction of 40%, due to the presence of whiteflies and whitefly transmitted begomoviruses. These whiteflies pose a challenge in terms of differentiation through conventional taxonomy due to their morphological similarities within genetic groups and also due to cryptic nature. Therefore, the molecular based diagnostics have come in place to decode the cryptic species. To address this, a total of 79 B. tabaci samples were collected from vegetable crops across 9 districts in Chhattisgarh, covering the north, central, and south zones, using a handheld aspirator. DNA isolation was performed using a Qiagen kit, and PCR was carried out, followed by partial sequencing of the mitochondrial cytochrome oxidase I gene using universal primers. The DNA sequences were aligned using the ClustalW program in MEGA Software, and homology search was conducted using NCBI-BLAST to identify the genetic groups through the construction of a phylogenic tree. Among the crops studied, Tomato (T2) exhibited the highest number of genetic groups, while Okra (T4) had the lowest. The overall genetic distance is 0.10. The diversity of genetic groups increased as we moved towards the southern region of Chhattisgarh. Specifically, six genetic groups namely Asia I, Asia II-1, Asia II-5, Asia I-India, Asia II-8, and Asia IV were found in the southern region, whereas only three genetic groups (Asia I, Asia II-1, and Asia II-5) were observed in the northern and central areas. Notably, Asia I was the most widely distributed genetic group, accounting for 69.62% of the occurrences in Chhattisgarh. Furthermore, Asia IV, which was obtained from brinjal in the Kanker region, represents the first report of its kind in India. In the second experiment, a field trial was conducted at Baronda farm, NIBSM, focusing on observing the population dynamics of B. tabaci and its relationship with macroclimate and microclimate. The whitefly population was monitored on five randomly selected plants by inspecting three leaves (upper, middle, and lower) on each plant at seven-day intervals. The results showed that the highest population of whiteflies was found in brinjal, followed by chilli, tomato, and okra. The appearance of the pest was first observed at 21 DAS, and its peak population was recorded at 72 DAS, 79 DAS, 72 DAS, and 58 DAS for chilli, tomato, brinjal, and okra, respectively. The study revealed a positive correlation between whitefly population and relative humidity while a negative correlation with temperature. This study infers to make a pest calendar which ishelpful to adopt control measure in 70 time for different crops and also it will serve as a model for survey, surveillance and forecasting. Furthermore, the counts of all life stages of whitefly were performed on three strata of the plants, with three leaves observed from each stratum. The distribution pattern showed that eggs were predominantly found on upper leaves in chilli (2.823±1.055), tomato (0.553±0.360), and brinjal(0.292±0.189) crops, whereas they were more prevalent on lower leaves in okra (0.461±0.398). Nymphs were mainly distributed in the middle stratum in chilli (1.353±0.738), tomato (2.4±0.480) andokra (0.523±0.348) crops, whereas they were more abundant in the lower stratum for brinjal (3.184±0.799) crop. Adults, on the other hand, were primarily located on the upper leaves in all four crops, including chilli (2.823±1.055), tomato (2±0.437), brinjal (3.469±1.681), and okra (1.261±0.608). This study helps us to take specific strata wise management strategy or sampling for research purposes.ThesisItem Open Access POPULATION DYNAMICS AND BIO-INTENSIVE MANAGEMENT OF INSECT PEST COMPLEX IN HIGH-DENSITY MANGO ORCHARDS(DIVISION OF ENTOMOLOGY ICAR-INDIAN AGRICULTURAL RESEARCH INSTITUTE NEWDELHI– 110012, 2023) Arbud Lala; Dr. Jaipal Singh Choudhary; T-11291Mango, Mangifera indica L. (Anacardiaceae) is the national fruit of India and this fruit has developed its own importance all over the world due to its taste and aroma. The present study was conducted in the high-density mango orchard of National Germplasm Repository of Sub-tropical Fruit Crops at ICAR RCER, Farming System Research Centre for Hill and Plateau Region (FSRCHPR), Plandu, Ranchi from January to June, 2023 to study the insect pest population dynamics and formulate effective bio-intensive pest management strategies. A total of 24 species from 18 families of insect pest majority of Hemiptera, Lepidoptera, and Coleoptera orders were observed infesting mango flowers and fruits. The insect pests including, giantscale, Labioproctus poleii (Green), fog scale, Aulacaspistubercularis(Newstead),scale, Pulvinaria polygonata (Cockerell), mango hoppers, Amritodus atkinsoni (Lethierry), Idioscopus niveosparsus (Lethierry), Idioscopus nagpurensis (Pruthi), Fruit flies, Bactrocera zonata (Saunders), B. correcta (Bezzi), B. dorsalis (Hendel) were observed major from flowering to fruit harvest period. Application of Imidacloprid 17.8 % SL @ 0.005 %, Clothianidin 50% WDG @ 0.03% and Dinotefuran 20% SG @ 0.006 % were found most effective against sucking insect pest complex at flowering stage whereas Spinetoram 11.7 % SC @ 0.012% was effective against fruiting stage pest complex and comparatively safer towards natural enemies. The treatment Clothianidin 50% WDG recorded the highest benefit: Cost ratio (6.02) and was found to be the most economical among flowering stage treatments whereas Spinetoram 11.7 % SC was found as most economic (B: C ratio 3.91) at fruiting stage.ThesisItem Open Access Genetic diversity analysis in (Brassicaceae) germplasm using phenotypic Brassica juncea differences and molecular markers(DIVISION OF GENETICS ICAR-INDIAN ADRICULTURAL RESEARCH INSTITUTE NEW DELHI-110012, 2023) RANJIT SAROJ; Dr. D. K. Yadava; T-11289The response to selection in any crop improvement program depends on the degree of variance and heritability, and trait association. The objective of the current study was to explain variance, heritability components, genetic diversity, correlation among the traits, and marker trait association (MTA) in Indian mustard [ Czern & Coss] to recognize promising genotypes for effective breeding. Two hundred Brassica juncea (L). and eighty-nine diverse accessions of Indian mustard belonging to four continents were analyzed for yield and yield-related traits over two seasons (2017–2018 and 2018– 2019), using an alpha lattice design with two replications. The genetic variance was found to be significant (P ≤ 0.01) for the individual environments as well as under pooled analysis for all of the evaluated traits. High heritability combined with high genetic advance as percent of mean and genotypic coefficient of variation was observed for flowering traits, plant height traits, seed size, and seed yield/plant; hence, a better genetic gain is expected upon the selection for these traits over subsequent generations. Both correlation and stepwise regression analysis indicated that the main shoot length, biological yield, total seed yield, plant height up to the first primary branch, seed size, total siliqua count, days to flowering initiation, plant height at maturity, siliquae on the main shoot, main shoot length, and siliqua length were the most significant contributory traits for seed yield/plant. Genetic diversity using the phenotypic data revealed the genotypes grouped into five clusters and the most diverse cluster was cluster II (6.29). A high inter-cluster distance (D2 ) was recorded between cluster II and cluster IV (15.68), both the clusters can be used in hybridization breeding programs. Molecular genetic diversity of the 269 genotypes using 101 molecular markers (89 SSRs and 12 IPs) grouped the genotypes into five clusters. Structure analysis revealed that genotypes were grouped into two sub populations A and B, however, few genotypes had shown allele admixture representing genes carrying from both the sub-populations. Gene diversity revealed moderate diversity of the gene and the average number of alleles were also moderates in range. Linkage disequilibrium of the markers defined the low LD (0.127). Marker trait association revealed one marker (Na10A08) significantly associated with the seed yield per plant in pooled data analysis. Out of the total 101 markers, 20 markers were associated with the yield-related traits. IC-597867 was identified as promising genotype from the diversity study, which was the highest yielder, which can be used in future breeding programs for yield enhancement in Indian mustard.ThesisItem Open Access Developing intensification options to enhance productivity and resource use efficiency of conservation agriculture based pearlmillet mustard cropping system(DIVISION OF AGRONOMY ICAR-INDIAN AGRICULTURAL RESEARCH INSTITUTE NEW DELHI - 110 012, 2023) AKSHAY KUMAR YOGI; Dr. R. S. Bana; T-11287The present study addresses global agricultural challenges, focusing on rainfed systems in India, highlighting the importance of sustainable intensification through conservation agriculture, particularly zero tillage and residue management, within the context of the economically significant pearl millet-mustard cropping system, aiming to enhance productivity, resource-use efficiency, and sustainability while addressing climate change, biodiversity loss, and food security concerns. To combat micronutrient malnutrition and improve yields in rainfed cropping systems, this study explores climate-smart strategies like conservation agriculture and intensified millet cropping. ZT (zero tillage) systems with intercropping of legumes (clusterbean, cowpea, and chickpea) significantly increased productivity (7-12.5%), micronutrient biofortification [Fe (12.5%), Zn (4.9-12.2%), Mn (3.1-6.7%), and Cu (8.3-16.7%)], protein content (2.2-9.9%), oil content (1.3%) and fatty acid profile of pearl millet grains compared to conventional tillage (CT) based systems with sole cropping. Zero Tillage (ZT) systems consistently outperform conventional tillage, with a significant increase in mustard grain yield, major nutrient content (phosphorus and potassium), and micronutrient levels (iron, zinc, manganese, and copper). Mustard grain yield in ZT-P+CB-M surpasses conventional tillage. In conclusion, ZT with residue-recycling and legume intercropping is a recommended approach for enhancing pearl millet in South Asian rainfed agro ecosystems. system productivity (PEY and MEY) over the two-year study, with ZT-PCWM and ZT-PCLM exhibiting significant improvements of approximately 70.35% to 93.97% in the Kharif season and ZT-PCLM and ZT-PMC showcasing remarkable enhancements of approximately 57.46% to 130.08% in the Rabi season. The combination of ZT with intercropping and residue in both seasons significantly affect the soil bulk density, soil moisture extraction, MBC and carbon pools. The soil aggregates size distribution was higher with residue retention in zero tillage. ZT PCLM consistently delivered higher Gross Returns, Net Returns, Benefit-Cost Ratio, and lower Input Cost Ratio compared to other treatments, with notable grain yield increases over the control treatment (CT-PM). In contrast, Zero Tillage with intercropping and Crop Residue Management (ZT-PM) excelled in terms of Net Returns and ICR outperforming the control. Overall, these results emphasize the economic advantages of ZT-PCLM and ZT-PM in enhancing pearl millet crop profitability.ThesisItem Open Access Biocontrol potential of Beauveria bassiana (Balsamo) Vuillemin against soil borne pathogens of chickpea(DIVISION OF PLANT PATHOLOGY ICAR-INDIAN AGRICULTURAL RESEARCH INSTITUTE NEW DELHI – 110 012 (INDIA), 2023) CHERUKU ROSHINI; Dr. Tusar Kanti Bag; T-11286The biocontrol potential of four isolates of Beauveria bassiana BbR1, BbR2, BbR3, and BbR4 was explored against chickpea pathogens, Fusarium oxysporum f. sp. ciceris, Rhizoctonia bataticola, Rhizoctonia solani, Sclerotium rolfsii, and Sclerotinia sclerotiorum. All four isolates i.e., BbR1, BbR2, BbR3, and BbR4 were found antagonistic against Sclerotinia sclerotiorum and the isolate BbR2 displayed the highest inhibition percentage against stem rot of chickpea caused by Sclerotinia sclerotiorum. But BbR1 and BbR2 exhibited moderate inhibitory action against R. bataticola. However, none of the isolates exhibited antagonism against Fusarium oxysporum f. sp. ciceris, Rhizoctonia solani, and Sclerotium rolfsii. Further, the antagonistic ability of different isolates of B. bassiana was recorded to be more at 28oC than 20oC temperature, and the zone of inhibition was found to be greater when B. bassiana was inoculated 3 days and 5 days prior to S. sclerotiorum compared to their coinoculation on PDA. The B. bassiana BbR2 isolate showed the highest inhibition zone of 35% at 20°C and 37% at 28°C against the chickpea isolate; 22.95% at 20°C and 36.67% at 28°C for the mustard isolate, and 34.33% at 20°C and 35.58% at 28°C for the pea isolate, when inoculated 5 days prior to S. sclerotiorum. Hence, B. bassiana BbR2 was selected as the best antagonist against the stem rot pathogen of chickpea, S. sclerotiorum. The hydrolytic enzyme production capacity of BbR1, BbR2, BbR3, and BbR4 was studied to understand the mechanism of antagonistic properties of B. bassiana isolates. Amylase, protease, and cellulase activity were found to be the highest in the isolate BbR4 with an enzymatic index of 1.55, 1.60, and 1.31 respectively, followed by isolates BbR1, BbR2, and BbR3. Lipase activity was found to be the highest in isolate BbR2 with an enzymatic index of 1.32, followed by isolates BbR1, BbR3, and BbR4. The effect of seed treatment with spores of B. bassiana BbR2 on physiological and biochemical changes was monitored and it was observed that the reduction in chlorophyll a, chlorophyll b, and total chlorophyll content was found to be 28.57, 12.85 and 24.20% 88 respectively in treated plants, whereas they were 50.91, 39.76 and 47.85 % respectively in non treated chickpea plant. The enhanced activity of peroxidase (2.02fold), PPO (1.30fold), and total phenol content (2.81fold) was recorded to be higher in B. bassiana BbR2 treated chickpea seedlings than non-treated plants at 3 DAI. However, peroxidase, PPO activity, and total phenol content decrease later on with time in both treated and non-treated chickpea plants. All the biochemical parameters such as peroxidase, polyphenol oxidase activity, total phenol, and chlorophyll content, displayed a pattern of initial increase until 3 days post-inoculation, followed by a subsequent decline in successive time points indicating disease suppression with respect to average lesion length and PDI may be through induced systemic resistance. Chemical profiling of secondary metabolites of the isolates BbR1, BbR2, BbR3, and BbR4 indicated that the area under bassianolide and oosporein was relatively larger when compared to other compounds across the isolates. However, the area under various beauverolide compounds, including beauverolide KA, V, B, and L, as well as other compounds like bassiatin, beauvericin, and tenellin was relatively higher in BbR2 and BbR3 isolates compared to isolates BbR1 and BbR4. These findings suggest the potential involvement of these bioactive metabolites in the antagonistic interactions showing the highest inhibitory actions by BbR2 followed by BbR3.The Minimum inhibitory concentration (MIC) of secondary metabolites from BbR2 and BbR3 were estimated to be 4000 ppm, however, isolate BbR2 (67.04%) showed more inhibition than BbR3 (49.26%) at 2000 ppm. In-planta stem rot disease suppression data indicated that average lesion length on the stems of chickpea cv. JG 62 treated with B. bassiana BbR2 was consistently smaller than that on non-treated seedlings across time intervals. Additionally, the Percent Disease Index (PDI) reached 100 at 9 DAI for the non-treated plants, while the PDI for the treated plants was found to be 86.67. Overall, disease suppression for the treated plants was found to be 46.64%, 19.69%, and 14.33% at 3, 6, and 9 DAI respectively. From the present study it can be concluded that Beauveria bassiana isolates have properties similar to many other biological control agents in suppression of chickpea stem rot disease caused by Sclerotinia sclerotiorum. Therefore, BbR2 of B. bassiana could be included in the biological control of stem rot disease of chickpeas and may be included in integrated disease management practices.ThesisItem Open Access PHYSIOLOGICAL AND MOLECULAR CHARACTERIZATION FOR HIGH TEMPERATURE TOLERANCE IN GARDEN PEA(Division of Vegetable Science ICAR-Indian Agricultural Research InstituteNew Delhi – 110 012, 2023) JJANANII R; Dr. Brij Bihari Sharma; T-11285The garden pea is a cool-season legume crop commonly grown in temperate, subtropical, and mild tropical climates. The optimum temperature ranges from 15- 23℃, and growth stops above 30℃. The maximum day temperature exceeds 38℃ during the first week of April in North India, which affects the major morphological, physiological and biochemical processes of garden peas. Therefore, to extend its growing season and increase its profitability, there is a dire need to breed for heat tolerance in garden pea varieties. The present study, “Physiological and molecular characterization for high-temperature tolerance in Garden pea” characterized 86 garden pea genotypes for 11 qualitative and 11 quantitative yield- related traits followed by the screening at high temperatures in a growth chamber in phytotron (controlled) and field condition (uncontrolled). In controlled screening in the growth chamber, 34 and 7 genotypes were identified as tolerant during the seedling and reproductive stages, respectively. Independent field screening during heat stress season (Jan-April) identified 15 tolerant genotypes that survived and set pods at 39/16.4℃ and 15 moderately tolerant genotypes that survived with no pod set at 39/16.4℃. The identified fifteen tolerant genotypes were also classified as tolerant during seedling stage screening in the growth chamber except for two genotypes, while all the genotypes were classified as tolerant during reproductive stage screening in a growth chamber. Hence this study proposes that screening in controlled conditions could be used as a preliminary screening method in heat tolerant screening, which could efficiently reduce the space and time involved in field screening. Field screening also observed that only 19 genotypes flowered at 37/15.4℃, and only nine were found to have >60% pollen viability at this temperature. Genotypes with >60% pollen viability were also noted to have at least one pod set per plant. The morphological characterization of 86 garden pea genotypes showed that yield per plant and pod per plant were the most affected traits in heat stress season among quantitative and yield-related traits, with 93.22% and 82.24% reduction, respectively. The identified 15 tolerant, 15 moderately tolerant and 15 sensitive genotypes were further characterized using nine physiological and biochemical traits to understand their basis in heat tolerance. It was found that the average RWC and GI was found to be 27.58% and 26.01% lower in heat stress condition, and the reduction was highest in sensitive genotypes than in tolerant genotypes. The average canopy temperature in heat stress conditions was 56.32% higher than in the normal season, and sensitive genotypes showed 6.32 % higher canopy temperature than tolerant genotypes. Similarly, MSI was found to be decreased by 44.51%, and the rate of reduction was high in sensitive genotypes. The MDA was found to be increased by 4.71 times during heat stress conditions than normal conditions and tolerant genotypes showed lower accumulation of MDA. Similarly, H2O2 contents were also raised during heat stress conditions, and the highest increase was found in sensitive genotypes (262.92%). The antioxidant enzymes like superoxide dismutase showed increased activity of 69.61%, and catalase showed 8.89 times higher activity in heat stress season in tolerant genotypes. However, total sugar content was found to be decreased by 5.67% in tolerant genotypes and 11.75% in sensitive genotypes. Estimating the correlation coefficient showed that physiological and biochemical traits were very important in determining the yield parameters of plants under heat-stress conditions. Thus, the key physiological and biochemical traits like relative water content, greenness index, membrane stability index, malondialdehyde, hydrogen peroxide, superoxide dismutase and catalase could be used as an identification index for heat tolerance. It was also found that there was considerable morphological and molecular diversity among the studied garden pea genotypes. Of the 38 polymorphic SSR markers used, 55.26% showed intermediate polymorphism, while 34.21% showed high polymorphism. The markers 16213, psaa219, and psmpb16 recorded the highest number of alleles per loci (10 alleles), and the marker psmpaa67 had a major allele frequency of 0.95. The highest PIC of 0.81 was observed in the marker psmpsad141. The garden pea genotypes were grouped into four populations by structure analysis, and molecular variance among the population and within individuals was found to be significant. The population groups with higher allelic divergence could be used as parents for exploiting maximum heterosis. The identified tolerant genotypes viz. EC- 598646, EC-598638, 2019/PMPM-4, GP-61, GP-902, GP-912-II, EC-598649, GP-48, EC-677211, EC-598654, GP-1104, EC-677214, GP-57, GP-915-II and EC-598602 could be greatly helpful in the development of heat tolerant garden pea varieties.ThesisItem Open Access ‘Molecular insight into the protective role of green copper nanoparticle against Fusarium oxysporum in chickpea.(DIVISION OF MOLECULAR BIOLOGY AND BIOTECHNOLOGY ICAR-INDIAN INSTITUTE OF AGRICULTURAL BIOTECHNOLOGY, RANCHI- 834003 ICAR-INDIAN AGRICULTURAL RESEARCH INSTITUTE, 2023) PRATIK PRASAD SINGH; Dr. BIPLAB SARKAR; T-11284Copper is a potent antifungal agent for plant protection. Usually wilt disease caused by Fusarium oxysporium is considered as a unsolved paradox in the pulse’s cultivation. In the current study, the nano scale copper efficacy has been evaluated to nullify the fungal wilt infestation in the pulse crops. The synthesis of copper nanoparticles (CuO NPs) was carried out by green method and characterised by FTIR, UV-Vis and DLS. Through in- vitro study, the poisoned food technique was conducted to screen the different doses of nano-copper against the F. oxysporum. Further, selected doses (500 ppm, 750 ppm and 1000 ppm) were used in vivo model, the treatments containing 500 ppm showed the better morpho physiological outcomes which was well- supported by the histological as well as FACS evidences. It was reported that the copper responsive gene such as CHI F, CAO, SOD, GATA and LACCASE against the fungus causing wilt were upregulated in the treatment group containing 500 ppm. Hence, the CuO NPs can be an efficacious alternative to replace the conventional use of copper sulphate in wilt disease in the chickpeas.ThesisItem Open Access Genome-wide association study to identify marker-trait association(s) for morpho-physiological traits under contrasting production regimes in bread wheat(DIVISION OF GENETICS ICAR-INDIAN AGRICULTURAL RESEARCH INSTITUTE NEW DELHI- 110 012, 2023) AMIT KUMAR MAZUMDER; Dr. Kiran B. Gaikwad; T-11283Wheat (Triticum aestivum L. em. Thell) is the second most important global cereal crop, grown in diverse agro-climatic conditions. To sustainably increase wheat yield to meet the growing world population's food demand in the face of climate change, Conservation Agriculture (CA) is a promising approach. However, the adoption of CA is slow, primarily due to the lack of wheat varieties specifically designed for it. Previous studies have mainly focused on understanding genotype, tillage, and genotype-tillage interactions, with limited research on how wheat adapts to optimal CA conditions. Additionally, there's a lack of genomic studies investigating the genetic basis of crop adaptation to CA. To dissect the genetic architecture of 19 morpho-physiological traits that could be involved in the enhanced adaptation and performance of genotypes under CA, we performed genome wide association studies (GWAS) to identify marker trait associations (MTAs) under four contrasting production regimes viz., conventional tillage timely sown (CT-TS), conservation agriculture timely sown (CA-TS), conventional tillage late sown (CT-LS) and conservation agriculture late sown (CA-LS) using an association panel comprising of 183 advanced wheat breeding lines along with 5 checks. The physiological and agronomic evaluation of morpho-physiological traits under each production environment identified presence of ample amount of variations for the target traits among the experimental materials used in the present study. Through assessment of genotype by-environment (GxE) interaction for all morpho-physiological traits, the presence of GxE interaction was ascertained. The GGE biplot analysis summarised the best performing genotypes with high stability and mean for all target traits. Ideal genotypes for few of the important morpho-physiological traits identified as Phi2 (408), NPQ (311), RC (335), CTD (240), PS1 (424), DTH (359), DTM (165), TGW (404) and GY (434). The genotyping of the association panel was done using 35K Breeders’ Axiom array. The initial SNP data was filtered to obtained 9,771 highly informative SNPs which were utilised for further analyses. The population structure and kinship analyses identified the presence of two sub-populations in the association panel. Furthermore, LD decay rate was observed to be fastest for A subgenome (4.63Mb) followed by D subgenome (5.40Mb) and B subgenome (7.41Mb) with a whole genome LD decay of 3.75Mb. GWAS was performed using the BLINK model in R Studio. A - log10P value above 5.0 (Bonferroni threshold) was used as the significance criterion. In total, 80 MTAs were discovered for 19 morpho-physiological traits across the four production environments. CT-TS had the most significant MTAs (35), followed by CA-LS (25), CA-TS (11), and CT-LS (9). The phenotypic variation explained by these QTNs ranged from 2.15 to 40.22%. Gene annotation provided highly informative SNPs that associated with Phi2, NPQ, PS1 and RC which were linked with genes that play crucial roles in the physiological adaptation under both CA and CT. A highly significant SNP AX94651261 (9.43% PVE) was identified to be associated with Phi2, while two SNP markers AX94730536 (30.90% PVE) and AX94683305 (16.99% PVE) were associated with NPQ. Also, SNPs AX94476007 (19.45% PVE), AX94658713 (22.87%PVE) and AX94525104 (31.33% PVE) linked with stress tolerance were identified for DTH, DTM and GL, respectively. In addition, highly significant and informative SNPs were identified for DTH, DTM, PH, GY and GL being linked to genes, the products of which have been reported to play pivotal roles in stress tolerance.
