Linkage disequilibrium mapping: A journey from traditional breeding to molecular breeding in crop plants

434-442Germplasms are the reservoir of agronomically important traits traditionally maintained by various tribal communities over the year. Maintaining these germplasms generations after generations has little value unless exploited for the desired agronomic traits like biotic and abiotic stress, yield attributes and nutritional enrichment. Association mapping, otherwise called linkage disequilibrium mapping, is a molecular breeding approach for characterizing complex traits with agronomic importance in crop plants. It is a systematic method for identifying novel traits and is treated as an alternative tool to traditional QTL mapping approaches, which involves correlating molecular markers with the phenotypic trait in a diversified population. The map's resolution in association mapping is based on the candidate-gene approach or genome-wide association approach. Therefore, association mapping studies offer a great perspective on crop genetic improvement. Still, considerably large-scale research is required to determine the sensible implementation of association mapping analysis in most crop plants. Currently, there is considerable interest in using association mapping approaches in crop breeding programs, which can be achieved by advanced genomic technology and the development of statistical computer software packages. Here, the linkage disequilibrium approach and its usefulness in association mapping studies, including the steps associated with it are discussed. The current status and future challenges in complex trait dissection by utilizing the linkage disequilibrium mapping in crop plants are also discussed

Isolation and Identification of Pathogenic Bacteria from Brackish Waters of Chilika Lagoon, Odisha, India for Pharmaceutical Use

Aims: The present investigation was undertaken in order to isolate bacteria from eighteen different water samples collected from three different sectors of ‘Chilika’ lagoon of India and to study the resistance against ten different antibiotics viz., norfloxacin, tetracycline, ciprofloxacin, neomycin, nalidixic acid, ofloxacin, chloramphenicol, nitrofurantoin, streptomycin and amoxicillin as well as their serological implications.Methodology and Results: Four different pathogenic bacteria species viz., Shigella dysenteriae, Streptococcus lactis, Bacillus cereus and Klebsiella pneumoniae were isolated which showed a wide range of sensitivity to norfloxacin,tetracycline, ciprofloxacin, ofloxacin and nitrofurantoin. S. dysenteriae was sensitive to streptomycin where as other isolates were found to be resistant. Agarose gel electrophoresis failed to reveal plasmid DNA band indicating that theobserved resistance was perhaps encoded by nucleotide sequences harboured on the chromosomal DNA. Bacterial isolates were used as antigen for the production of polyclonal antibodies in rabbits.Conclusion, significance and impact of study:All the isolates exhibited strong antigenic character with specific serological relationship which can be implicated towards development of novel and pharmaceutically effective antibacterial products

Linkage disequilibrium mapping: A journey from traditional breeding to molecular breeding in crop plants

Germplasms are the reservoir of agronomically important traits traditionally maintained by various tribal communities over the year. Maintaining these germplasms generations after generations has little value unless exploited for the desired agronomic traits like biotic and abiotic stress, yield attributes and nutritional enrichment. Association mapping, otherwise called linkage disequilibrium mapping, is a molecular breeding approach for characterizing complex traits with agronomic importance in crop plants. It is a systematic method for identifying novel traits and is treated as an alternative tool to traditional QTL mapping approaches, which involves correlating molecular markers with the phenotypic trait in a diversified population. The map's resolution in association mapping is based on the candidate-gene approach or genome-wide association approach. Therefore, association mapping studies offer a great perspective on crop genetic improvement. Still, considerably large-scale research is required to determine the sensible implementation of association mapping analysis in most crop plants. Currently, there is considerable interest in using association mapping approaches in crop breeding programs, which can be achieved by advanced genomic technology and the development of statistical computer software packages. Here, the linkage disequilibrium approach and its usefulness in association mapping studies, including the steps associated with it are discussed. The current status and future challenges in complex trait dissection by utilizing the linkage disequilibrium mapping in crop plants are also discussed

Evaluation of Total Phenol Content of some Common Paddy Cultivars of Odisha with the Application of Biofertilizer in Assessing Resistance to Meloidogyne graminicola

The total phenol content of four common paddy cultivars of Odisha namely Abhisek (R), Manik (MR), Bas-12 (S) and Lalat (HS) were studied under pot culture condition in the net house following CRD design under different treatments using biofertilizer Azospirillum. brasilense alone or in combinations against rice root-knot nematode Meloidogyne graminicola. The objective of  the work was to study the quantitative changes in phenolic compounds content and the effect of  A.brasilense in the induction of phenolic compounds on the test nematode. It was observed  that there was a significant increase in total phenol content in both resistant and moderately resistant paddy cultivars Abhisek and Manik in treatment T2  (Azospirillum brasilense @ 12kg/ha at 15DAT + M. graminicola @ 1000J2 after 7days of Azospirillum inoculation) were seen higher than the susceptible variety Bas-12 and highly susceptible variety Lalat  as compared  to control T5 with increase percentage of 38.77%, 36.58%, 35.02% and 39.28% respectively in shoots. Similarly the trend was continued in roots containing total phenol content of 0.25mg/g  in Abhisek, 0.18mg/g  in Manik, 0.21mg/g in Bas-12 and 0.19mg/g in Lalat as compared to  other treatments. There were increase in percentage of change (p≤0.05) in roots under treatment T3 (A alone) in all the four varieties followed by T2 (A→N), and T1 (N→A) with respect to control T5. Basically, shoots of control plants in all four cultivars were observed more content of phenolic compounds than their roots. But after M. graminicola invasion and the action of A. brasilense the amount increased  in both the roots and shoots of all the cultivars. The T4 (N alone) treatment in all the R, MR, S and HS varieties were recorded higher as compare to T5 but less than the treatments T3, T2, and T1 in both roots and shoots against the test nematode, which could exacerbating for eco-friendly RKN management approach

Physiological, biochemical, and molecular responses of rice (Oryza sativa L.) towards elevated ozone tolerance

Rice (Oryza sativa L.) is one of the most important staple food crops that is cultivated in South East Asia. This crop is affected by a wide range of biotic and abiotic factors, each of which is contributing to a change in its physiology, biochemistry, and genetic makeup. Ozone is produced in the troposphere as a result of reactions between abiotic factors, such as oxides of nitrogen and carbon, and UV radiation. These reactions lead to the production of a wide variety of volatile organic compounds. Rice scientists have expressed a great deal of concern regarding the impact of ozone on rice, which has necessitated the development of strategies to combat the problem. The recent advances in rice genomics have led to the discovery of molecular biology approaches such as marker-assisted selection involving quantitative trait loci linked to genes that confer tolerance to ozone stress. This trait is thought to be controlled by a large number of loci with medium effects rather than by a single locus with a large effect. The current review is an effort to provide information on the physiological, biochemical, and molecular responses of rice towards elevated ozone tolerance and also to reflect the available strategies to minimize the effect

Seed Germination and Seedling Vigour of Spine Gourd (Momordica dioica Roxb.) in Response to Different Physical and Chemical Treatments

The present investigation was carried out at Department of Vegetable Science, OUAT, Bhubaneswar during 2019-2021. Five to six months old stored spine gourd seeds were exposed to various physical (T1: control, T2: 48 hours soaking in water, T3: hot water treatment for 20 minutes + 48 hourssoaking in water, T4: scarification by sand paper + 48 hours soaking in water, T5: removal of seed coat + 48 hours soaking in water) and chemical (C1: GA3 100 ppm, C2: GA3 200 ppm, C3: KNO3 1%, C4: KNO3 2%, C5: Thiourea 1%, C6: Thiourea 2% & C7: Control) treatments. The experiment was laid out in factorial CRD design with 35 treatment combinations replicated twice. The seeds were sown in plastic trays containing cocopeat media. The effect of these treatments on percentage of germination, length of seedling, seedling dry weight, seedling vigour index- I and II were studied. It was concluded that among the physical treatments, T5 (removal of seed coat + 48 hours soaking in water), among the chemical treatments, C1 (GA3 100 ppm) and between the interactions, T5C1 recorded highest germination percentage, seedling length, seedling dry weight, vigour index- I and vigour index – II. The lowest values were recorded in control. From the experimental results.it was observed that seed coat removed seeds soaked for 48 hours in water followed by treatment with GA3 100 ppm recorded highest germination percentage and seedling vigour in spine gourd

Structural investigation of Indica rice (<em>Oryza sativa</em> L.) <em>DREB1</em>AP2 domain in response to GCC-BOX DNA: an insight from molecular dynamics

47-56In adverse environmental conditions, genes show specific expression pattern according to their biological and physiological functions. Plant stress tolerance is a genetically complex trait that involves many genes and their expression patterns. Transcription factors (TFs) are vital for sustaining expression of certain genes by interacting with the basal transcription apparatus at target gene promoters to enhance or suppress the target gene functions. DREB proteins are having the conserved domains and functional motifs, which interact with 11 bp of GCC box of promoters and facilitate transcription of stress inducible gene(s). In the present investigation, we predicted the 3D-structure of rice DREB1-AP2 domain from isolated coding sequence of ten indica rice (Oryza sativa L.) cultivars and observed the dynamic interaction of GCC box (DREB1-AP2 domain). The dynamic properties of the DREB1-AP2 domain and its interaction with GCC box DNA were investigated by molecular dynamics simulations. Analysis of protein DNA interface showed that most of the conserved interactions were taking place in the residues of Gly85, Arg87, Arg89, Trp91, Lys93, Arg99, Arg106, Trp108, Ser111, and Tyr122 with GCC box DNA of promoter in Indica rice. In addition, another conserved residue, Arg103 (Lys166 of 1GCC) is interacting with GCC box. Global motion of the protein during MD simulation was analyzed, principal components of backbone atoms of the DREB1-AP2 domain in both apo and holo condition depicted that the higher motion in apo condition, than holo (or, DNA-bound) state. Overall, this study will help to understand the molecular mechanism of a DERB1 protein family in a broader prospective

Effect of Integrated Nutrient Management and Salicylic Acid Application on Relative Water Content, Plant Height and Grain Yield of Quinoa (Chenopodium quinoa Willd.)

Aims: A field study was conducted to quantify the effect of moisture deficit stress at different critical stages of quinoa and different mitigation approaches were adopted in order to alleviate moisture deficit stress. Study Design: The experiment was designed in split plot design comprising of six main plots (water management) and four sub plots (stress mitigation approaches). The treatments in main plots viz., no irrigation at branching (M1), at ear formation (M2), flowering (M3), grain filling (M4) stages, irrigating at all four stages (M5) and irrigating as and when required (M6), and sub plot treatments viz., soil test-based fertilizer recommendation (STBFR) (S1), STBFR + Salicylic acid spray at 100 ppm (S2), STBFR + rice straw mulching (S3) and integrated nutrient management (S4) were tested. Place and Duration of Study: The experiment was conducted at the Instructional Farm, Odisha University of Agriculture and Technology, Bhubaneswar during Rabi 2021-22. Methodology: Moisture deficit stress was imposed by withholding irrigation water and not irrigating in the defined period. The treatments in the subplots were imposed as per the schedule. Results: Optimal results, including significantly taller plants, elevated relative water content, and increased grain yield, were achieved when irrigation was applied on an as-needed basis (M6). Conversely, the lowest grain yield was observed when moisture deficit stress was imposed during the branching stage of quinoa. This outcome was primarily linked to a more substantial reduction in both relative water content and plant height. Among the various stress mitigation approaches, integrated nutrient management (S4) emerged as the most effective management practice, followed closely by STBFR + Salicylic acid spray at 100 ppm (S2). Conclusion: The result indicated that branching stage is the most critical stage for irrigation in quinoa and integrated nutrient management could be the best approach under moisture deficit stress in quinoa among the other treatments

Integrated Nutrient Management and Salicylic Acid Boost Quinoa (Chenopodium quinoa Willd.) Yield under Deficit Moisture Stress at Different Critical Stages

Aims: A field study was conducted to quantify the effect of moisture deficit stress at different critical stages of quinoa and different mitigation approaches were adopted in order to alleviate moisture deficit stress. Study Design: The experiment was designed in a split-plot design comprising six main plots (water management) and four subplots (stress mitigation approaches). The treatments in main plots viz., cut-off irrigation at branching (M1), at ear formation (M2), flowering (M3), grain filling (M4) stages, irrigating at all four stages (M5) and irrigating as and when required (M6), and subplot treatments viz., soil test-based fertiliser recommendation (STBFR) (S1), STBFR + Salicylic acid spray at 100 ppm (S2), STBFR + rice straw mulching (S3) and integrated nutrient management (S4) were tested. Place and Duration of Study: The experiment was conducted at the Instructional Farm, Odisha University of Agriculture and Technology, Bhubaneswar during Rabi 2021-22. Methodology: Moisture deficit stress was imposed by withholding irrigation water and not irrigating in the defined period. The treatments in the subplots were imposed as per the schedule. Results: The lowest leaf area index was recorded when irrigation was withheld at the branching stage (0.61) which was statistically similar to M2 (no irrigation at the ear formation stage) with an average leaf area index of 0.64. Similarly, plants under integrated nutrient management practices (S4) recorded a significantly higher leaf area index (0.92) which was statistically at par with S2 (STFBR + Salicylic acid spray) which was 0.87. The reduction in the TCC was the maximum when stress was applied at the branching and ear formation stage compared to the flowering and grain filling stage. The increment in grain yield by following INM (S4) and STBFR+SA (S2) under drought stress and irrigated control was 23.6% and 17.6%, respectively over fully inorganic nutrient management (S1). Conclusion: The result indicated that the branching stage is the most critical stage for irrigation in quinoa and integrated nutrient management could be the best approach under moisture deficit stress in quinoa among the other treatments

Biochemical characterization of maize (Zea mays L.) hybrids under excessive soil moisture stress

A set of 32 maize hybrids were evaluated under excessive soil moisture (ESM) stress. The plants were subjected to waterlogging for 12 days at the flowering stage by maintaining 3–5 cm water level. Physiological and biochemical traits were examined to analyze plants’ response to waterlogging stress. The chlorophyll a, b and total chlorophyll content declined due to ESM stress, and the decrease was relatively higher in the case of susceptible hybrids. The decrease in chlorophyll content had shown a significant impact on total carbohydrate content, but the tolerant hybrids thrive better under stress with a capacity to maintain higher carbohydrate concentration. Proline accumulation was enhanced in all hybrids in response to the above stress, but it was tremendously increased in tolerant hybrids to offer osmotic protection compared to the sensitive genotypes. Total chlorophyll, chlorophyll-a, carbohydrate, proline as well as an increase in proline content in response to stress, revealed a significant positive association with seed yield, while percentage decline in chlorophyll, decrease in carbohydrate and senescence percentage maintained the reverse trend. Further, the chlorophyll ‘a' followed by an increase in proline content can be considered as important parameters for assessing tolerance to ESM stress owing to their high positive direct effects on seed yield