Ujjal K Nath - Academia.edu (original) (raw)

Papers by Ujjal K Nath

INTERNATIONAL JOURNAL OF SCIENTIFIC RESEARCH, Apr 1, 2023

Onion is one of the most popular spice crop, which is used for seasoning wide range of dishes as ... more Onion is one of the most popular spice crop, which is used for seasoning wide range of dishes as well as folk medicine. Assessment of genetic diversity helps to use the onion germplasm as breeding materials for its improvement. Molecular marker based diversity assessment is more powerful, rapid and reliable compared to morphology based genetic diversity assessment. Thirty eight onion germplasm were characterized by using 10 random amplied polymorphic DNA (RAPD) markers for estimating genetic diversity within the germplasm. The germplasm exhibited wide range of variability which could be used in cross breeding for getting superior F1 generation. Out of 10 primers, four gave polymorphism among onion germplasm. Genetic diversity of 38 germplasm was analyzed using variation at 34 RAPD loci, of which 91.89% were polymorphic. The highest pair wise genetic distance was 1.046 and the lowest was 0.056. The mean gene diversity among all the germplasm was 1.54 and Shannon's information index was 0.3188. The UPGMA dendrogram, based on Nei`s genetic diversity showed 6 clusters. The frequency of polymorphic loci ranged from 0.0263 to 1.0000, indicates that there exists a wide genetic diversity among the germplasm and corroborated the usefulness of RAPD markers for estimating genetic diversity in onion.

International Journal of Molecular Sciences, Jul 24, 2023

This article is an open access article distributed under the terms and conditions of the Creative... more This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY

Lettuce is the most important leafy vegetable. It is exclusively used as freshly raw form but som... more Lettuce is the most important leafy vegetable. It is exclusively used as freshly raw form but sometime also as cooked. However, its quality depends on several pre-and postharvest factors. The effects of growing conditions and cultivars on the postharvest quality of leaf lettuce were investigated. In this experiment the interaction of variable factor; like growing conditions and fixed factor; cultivars are also observed. The leaf lettuce cultivars 'Cheongchima', 'Cheongchuckmyeon', 'Geockchima' and 'Geockchuckmyeon' were grown under favourable (natural condition) and unfavorable growing condition (with excess soil water and 50% shading) to evaluate their shelf-life and postharvest qualities. Plant height and the number of leaves were significantly varied in different growing conditions and by cultivars. In addition, fresh weight was affected by only growing condition, whereas leaf thickness was influenced by cultivars, growing conditions and the cultivars influenced the degree of fresh weight loss and respiration rate during postharvest storage. However, the postharvest storage qualities differed with cultivars and in combination with growing conditions. Leaf thickness and quality of leaf lettuce before and after harvest were also varied by cultivars and growing conditions. It could be concluded that postharvest leaf lettuce quality remains acceptable when growing under excess soil water with 50% shading.

Journal of the Bangladesh Agricultural University, Oct 2, 2012

Genotype-environment interactions through different stability parameters and performance traits o... more Genotype-environment interactions through different stability parameters and performance traits of four fine rice genotypes were studied. The traits were; days to 50% flowering, days to maturity, plant height (cm), number of effective tillers per hill, panicle length (cm), number of fertile grains per panicle, number of sterile grains per panicle and yield (t/ha) in four fine rice genotypes across nine environments along with experimental farm of Genetics and Plant Breeding department, Bangladesh Agricultural University (BAU) Mymensingh. Significant differences were observed for genotypes, environments and genotypes-environment interaction. Stability analysis after Eberhat and Russell's model suggested that the genotypes used in study were more or less responsive to environmental changes. Most of the genotypes performed better in Comilla. BAU125 was found stable for effective tillers per hill and comparatively less sensitive to other genotypes in panicle length and number of sterile grains per panicle. BR5 was stable for days to maturity and plant height whereas Kalizira performed better than other genotypes for fertile grains per panicle. In general, only the genotype BAU125 was found stable for effective tillers per hill, panicle length and lowest number of sterile grains per panicle.

Journal of Biological Sciences, Feb 15, 2004

Garlic (Allium sativum) root tips were induced to regenerate shoots through callus culture and so... more Garlic (Allium sativum) root tips were induced to regenerate shoots through callus culture and somatic embryogenesis to obtain plantlets. The experiment was designed to investigate the regeneration potentiality of two garlic verities and also to develop an efficient protocol for regeneration of garlic via callus culture. Higher percentage of callus was initiated from the combination of 5 mg lG Kinetin and 1.5 mg lG 1 1 2,4-D. Embryogenic callus produced higher number of shoots in MS medium supplemented with 10 BAP. Rooting of individual shoots was induced after transfer to medium without growth regulator. The plantlets were established in the soil after acclimization. Cultivar differences in regeneration from root tips were observed.

한국원예학회 학술발표요지, Oct 1, 2016

Nuts have been used globally as health foods. However, because nuts cause allergies, people need ... more Nuts have been used globally as health foods. However, because nuts cause allergies, people need to be careful when eating food. Mostly foods are labeled, but sometimes intentional or unintentional mixing might occur. In the present study, we report DNA based on marker for the detection of four nuts almond, peanut, pine nut, and walnut using quantitative real-time polymerase chain reaction (qRT-PCR). Species-specific primer sets for four species were designed based on the single-nucleotide polymorphisms and insertion/deletion of the chloroplast gene, matK. The sensitivity of primer sets for the four species studied was assessed by analyzing DNA dilutions at concentration of 0.001-10 ng and binary mixtures of 0.1-100% of heat-treated and non-heat-treated samples. The four primer sets developed in the present study indicated appropriate amplification efficiency and correlation coefficients of the standard curves. In addition, to verify the applicability of these molecular markers, we performed a qRT-PCR with 14 commercial products and successfully detected the matK genes in several commercial food products that were declared to contain nuts. Thus, markers developed could be useful tools for confirming the presence of the four nut species in commercial products.

Horticulture Environment and Biotechnology, Nov 27, 2019

Bacterial fruit blotch (BFB), caused by Acidovorax citrulli, is an economically devastating disea... more Bacterial fruit blotch (BFB), caused by Acidovorax citrulli, is an economically devastating disease in melon. Molecular characterization of causal strains and identification of sources of resistance are necessary to control this important disease. Many strains of BFB were identified by partial sequencing and documented in GenBank. Recently, there was an outbreak of BFB strain NIHHS15-280 in melon fields (Goksung, Jeonnam, Korea) that severely hampered melon production in Korea. For this reason, we characterized NIHHS15-280 by partially sequencing the 16S rRNA gene using PCR-based markers. The partial sequence of the 16S rRNA gene of NIHHS15-280 was much more similar to A. citrulli strains associated with melon and watermelon hosts than other cucurbit hosts. A PCR-based assay identified the strain (NIHHS15-280) as belonging to A. citrulli group I, which predominantly infects non-watermelon cucurbits (virulent to melon). Thirty-five melon genotypes were screened against NIHHS15-280 in a detached-leaf inoculation assay. The lack of visible disease symptoms 11 days after inoculation in lines PI353814 and PI140471 indicated these to be highly resistant lines, whereas moderate resistance was observed in lines PI420145 and SCNU1154 and cultivars ME6 and ME5. Also, the most resistant lines were corroborated by a fruit inoculation assay. The characterized A. citrulli strain NIHHS15-280 (group I) and identified resistant lines will serve as a valuable resource for further genetic studies and improvement of BFB resistance in melon.

Rice Science, Nov 1, 2018

Grain shape is one of the important agronomic traits, which is closely related to the yield of ri... more Grain shape is one of the important agronomic traits, which is closely related to the yield of rice. A new rice mutant, named small and round grain (srg1), was isolated from an indica cultivar Zhenong 34 by ethyl methane sulfonate (EMS) mutagenesis. The microscopic analysis showed that the cell length of spikelet in srg1 was decreased compared with that in wild type (WT), which caused the grain length short. Meanwhile, the grains of srg1 were wider than those of WT because of the increased cell layers in spikelet in the lateral direction. Therefore, the inhibition of cell expansion and increased cell proliferation collectively led to the small and round grain. By map-based cloning, the gene SRG1 was located on the short arm of chromosome 9, which encodes a kinesin-4 protein, represented by the gene LOC_Os09g02650. A single nucleotide polymorphism, occurred in the 16th exon of SRG1, led to premature translation stop in mutant. The cell cycle-related genes were up-regulated in srg1, which conferred that SRG1 controlled grain width through the cell proliferation. Since the role of SRG1 in regulating grain shape was not clarified well before, it is valuable to explore the mechanism of grain development. This study could, hence, provide a morphogenesis and molecular basis for elucidating the function of SRG1, as well as a new germplasm resource for the further study of grain development.

Journal of Biological Sciences, Oct 15, 2002

BMC Genomics, Sep 6, 2017

Background: Zinc finger homeodomain proteins (ZHD) constitute a plant-specific transcription fact... more Background: Zinc finger homeodomain proteins (ZHD) constitute a plant-specific transcription factor family with a conserved DNA binding homeodomain and a zinc finger motif. Members of the ZHD protein family play important roles in plant growth, development, and stress responses. Genome-wide characterization of ZHD genes has been carried out in several model plants, including Arabidopsis thaliana and Oryza sativa, but not yet in tomato (Solanum lycopersicum). Results: In this study, we performed the first comprehensive genome-wide characterization and expression profiling of the ZHD gene family in tomato (Solanum lycopersicum). We identified 22 SlZHD genes and classified them into six subfamilies based on phylogeny. The SlZHD genes were generally conserved in each subfamily, with minor variations in gene structure and motif distribution. The 22 SlZHD genes were distributed on six of the 12 tomato chromosomes, with segmental duplication detected in four genes. Analysis of Ka/Ks ratios revealed that the duplicated genes are under negative or purifying selection. Comprehensive expression analysis revealed that the SlZHD genes are widely expressed in various tissues, with most genes preferentially expressed in flower buds compared to other tissues. Moreover, many of the genes are responsive to abiotic stress and phytohormone treatment. Conclusion: Systematic analysis revealed structural diversity among tomato ZHD proteins, which indicates the possibility for diverse roles of SlZHD genes in different developmental stages as well as in response to abiotic stresses. Our expression analysis of SlZHD genes in various tissues/organs and under various abiotic stress and phytohormone treatments sheds light on their functional divergence. Our findings represent a valuable resource for further analysis to explore the biological functions of tomato ZHD genes.

Journal of Integrative Agriculture, May 1, 2023

Journal of Biological Sciences, Nov 15, 2002

Genes, Feb 10, 2018

Plant growth and development can be adversely affected by cold stress, limiting productivity. The... more Plant growth and development can be adversely affected by cold stress, limiting productivity. The glutathione S-transferase (GST) family comprises important detoxifying enzymes, which play major roles in biotic and abiotic stress responses by reducing the oxidative damage caused by reactive oxygen species. Pumpkins (Cucurbita maxima) are widely grown, economically important, and nutritious; however, their yield can be severely affected by cold stress. The identification of putative candidate genes responsible for cold-stress tolerance, including the GST family genes, is therefore vital. For the first time, we identified 32 C. maxima GST (CmaGST) genes using a combination of bioinformatics approaches and characterized them by expression profiling. These CmaGST genes represent seven of the 14 known classes of plant GSTs, with 18 CmaGSTs categorized into the tau class. The CmaGSTs were distributed across 13 of pumpkin's 20 chromosomes, with the highest numbers found on chromosomes 4 and 6. The large number of CmaGST genes resulted from gene duplication; 11 and 5 pairs of CmaGST genes were segmental-and tandem-duplicated, respectively. In addition, all CmaGST genes showed organ-specific expression. The expression of the putative GST genes in pumpkin was examined under cold stress in two lines with contrasting cold tolerance: cold-tolerant CP-1 (C. maxima) and cold-susceptible EP-1 (Cucurbita moschata). Seven genes (CmaGSTU3, CmaGSTU7, CmaGSTU8, CmaGSTU9, CmaGSTU11, CmaGSTU12, and CmaGSTU14) were highly expressed in the cold-tolerant line and are putative candidates for use in breeding cold-tolerant crop varieties. These results increase our understanding of the cold-stress-related functions of the GST family, as well as potentially enhancing pumpkin breeding programs.

Scientific Reports, Oct 29, 2020

Lily belongs to family liliaceae, which mainly propagates vegetatively. Therefore, sufficient num... more Lily belongs to family liliaceae, which mainly propagates vegetatively. Therefore, sufficient number of polymorphic, informative, and functional molecular markers are essential for studying a wide range of genetic parameters in Lilium species. We attempted to develop, characterize and design SSR (simple sequence repeat) markers using online genetic resources for analyzing genetic diversity and population structure of Lilium species. We found di-nucleotide repeat motif were more frequent (4684) within 0.14 gb (giga bases) transcriptome than other repeats, of which was two times higher than tetra-repeat motifs. Frequency of di-(AG/CT), tri-(AGG/CTT), tetra-(AAAT), penta-(AGAGG), and hexa-(AGA GGG) repeats was 34.9%, 7.0%, 0.4%, 0.3%, and 0.2%, respectively. A total of 3607 non-redundant SSR primer pairs was designed based on the sequences of CDS, 5′-UTR and 3′-UTR region covering 34%, 14%, 23%, respectively. Among them, a sub set of primers (245 SSR) was validated using polymerase chain reaction (PCR) amplification, of which 167 primers gave expected PCR amplicon and 101 primers showed polymorphism. Each locus contained 2 to 12 alleles on average 0.82 PIC (polymorphic information content) value. A total of 87 lily accessions was subjected to genetic diversity analysis using polymorphic SSRs and found to separate into seven groups with 0.73 to 0.79 heterozygosity. Our data on large scale SSR based genetic diversity and population structure analysis may help to accelerate the breeding programs of lily through utilizing different genomes, understanding genetics and characterizing germplasm with efficient manner. Lily (Lilium sp.) is an economically important flowering monocots in the genus Lilium and family Liliaceae. Lilium sp. are originated in Asia, Europe, and North America 1. The Netherlands are the leading lily producer and exporter in the world 2 , lily also commercially cultivated in France, Chile, USA, Japan, and New Zealand. The Lilium genus consists of 100 species and more than 9000 cultivars (International Lily register, https ://www. lilyr egist er.com/). Based on 13 morphological characters the Lilium species are taxonomically classified into seven sections; Martagon, Pseudolirium, Lilium (Liriotypus), Archelirion, Sinomartagon, Leucolirion, and Oxypetalum 3,4. All cultivars from these sections were further categorized into three main groups: Longiflorum (L), Asiatic (A), and Oriental (O) hybrids 5. Longiflorum hybrids derived from intra-or inter-specific hybridization between L. formosanum and Leucolirion section 6 , whereas Asiatic hybrids originated from interspecies crosses among 12 species of the Sinomartagon section 7 and Oriental hybrids derived from hybridization among

Journal of Biological Sciences, Feb 15, 2004

International Journal of Molecular Sciences, May 13, 2017

Growth regulating factors (GRFs) are plant-specific transcription factors that are involved in di... more Growth regulating factors (GRFs) are plant-specific transcription factors that are involved in diverse biological and physiological processes, such as growth, development and stress and hormone responses. However, the roles of GRFs in vegetative and reproductive growth, development and stress responses in tomato (Solanum lycopersicum) have not been extensively explored. In this study, we characterized the 13 SlGRF genes. In silico analysis of protein motif organization, intron-exon distribution, and phylogenetic classification confirmed the presence of GRF proteins in tomato. The tissue-specific expression analysis revealed that most of the SlGRF genes were preferentially expressed in young and growing tissues such as flower buds and meristems, suggesting that SlGRFs are important during growth and development of these tissues. Some of the SlGRF genes were preferentially expressed in fruits at distinct developmental stages suggesting their involvement in fruit development and the ripening process. The strong and differential expression of different SlGRFs under NaCl, drought, heat, cold, abscisic acid (ABA), and jasmonic acid (JA) treatment, predict possible functions for these genes in stress responses in addition to their growth regulatory functions. Further, differential expression of SlGRF genes upon gibberellic acid (GA3) treatment indicates their probable function in flower development and stress responses through a gibberellic acid (GA)-mediated pathway. The results of this study provide a basis for further functional analysis and characterization of this important gene family in tomato.

The Scientific World Journal, 2014

Genetic diversity is important for crop improvement. An experiment was conducted during 2011 to s... more Genetic diversity is important for crop improvement. An experiment was conducted during 2011 to study genetic variability, character association, and genetic diversity among 27 soybean mutants and four mother genotypes. Analysis of variance revealed significant differences among the mutants and mothers for nine morphological traits. Eighteen mutants performed superiorly to their mothers in respect to seed yield and some morphological traits including yield attributes. Narrow differences between phenotypic and genotypic coefficients of variation (PCV and GCV) for most of the characters revealed less environmental influence on their expression. High values of heritability and genetic advance with high GCV for branch number, plant height, pod number, and seed weight can be considered as favorable attributes for soybean improvement through phenotypic selection and high expected genetic gain can be achieved. Pod and seed number and maturity period appeared to be the first order traits for higher yield and priority should be given in selection due to their strong associations and high magnitudes of direct effects on yield. Cluster analysis grouped 31 genotypes into five groups at the coefficient value of 235. The mutants/genotypes from cluster I and cluster II could be used for hybridization program with the mutants of clusters IV and V in order to develop high yielding mutant-derived soybean varieties for further improvement.

Physiology and Molecular Biology of Plants, Feb 21, 2020

Cytoplasmic male sterility (CMS) is maternally inherited trait, which hinders the ability to prod... more Cytoplasmic male sterility (CMS) is maternally inherited trait, which hinders the ability to produce viable pollen in plants. It serves as a useful tool for hybrid seed production via exploiting heterosis in crops. The molecular mechanism of CMS and fertility restoration has been investigated in different crops. However, limited number of reports is available on comparison of Ogura- and Polima-CMS with their shared maintainer in Chinese cabbage. We performed transcript profiling of sterile Ogura CMS (Tyms), Polima CMS (22m2) and their shared maintainer line (231–330) with an aim to identify genes associated with male sterility. In this work, we identified 912, 7199 and 6381 DEGs (Differentially Expressed Genes) in 22m2 Vs Tyms, 231–330 VS 22m2 and 231–330 Vs Tyms, respectively. The GO (Gene Ontology) annotation and KEGG pathway analysis suggested that most of the DEGs were involved in pollen development, carbon metabolism, lipase activity, lipid binding, penta-tricopeptide repeat (PPR), citrate cycle and oxidative phosphorylation, which were down-regulated in both CMS lines. This result will provide an important resource for further understanding of functional pollen development, the CMS mechanism and to improve molecular breeding in Chinese cabbage.Electronic supplementary materialThe online version of this article (10.1007/s12298-020-00775-5) contains supplementary material, which is available to authorized users.

Research Square (Research Square), Nov 17, 2022

Background and aim Clubroot is an infectious root disease caused by Plasmodiophora brassicae of B... more Background and aim Clubroot is an infectious root disease caused by Plasmodiophora brassicae of Brassica crops, which can cause immeasurable losses. We aimed to explore the infection mechanism under P. brassicae integrating transcriptome, small RNA, degradome and phytohormone technology. Result In this study, root samples of B. rapa resistant line BrT24 (R-line) and susceptible line Y510-9 (S-line) were collected at four different time points for cytological, transcriptome, miRNA and degradome investigations. We found the critical period of disease resistance and infection at 0-3 days and 9-20 days, respectively. Based on this finding we further analyzed the data of 9 d vs 20 d of S-line and predicted the key genes ARF8, NAC1, NAC4, TCP10, SPL14, REV and ATHB related to clubroot disease development and regulating disease resistance mechanisms. These genes are mainly related to auxin, cytokinin, jasmonic acid and ethylene cycles. We proposed a regulatory model of plant hormones under the mRNA-miRNA regulation in the critical period of Plasmodiophora brassicae infection based on the combination of 2 the present data of integrative transcriptome, small RNA, degradome and phytohormone with our previously published results. Conclusion Our integrative analysis found that the bra-miR164/NAC1/4, bra-miR319/TCP10 and bra-miR167/ARF8 were associated with clubroot symptoms development, which provide new insights into the regulation relationship of miRNA and plant hormones during the process of disease infection.

International Journal of Agricultural Research, Innovation and Technology, Feb 2, 2014

A 10×10 half diallel experiment was conducted on groundnut (Arachis hypogaea L.) to ascertain the... more A 10×10 half diallel experiment was conducted on groundnut (Arachis hypogaea L.) to ascertain the gene action and genetic parameters of ten traits including 50% flowering, no. of pods per plant, plant height, harvest index, pod index, 100 pod weight, 100 kernel weight, pod size, diseases infection and yield per plot. The experiments were carried out in the Department of Genetics and Plant Breeding, Bangladesh Agricultural University (BAU), Mymensingh during the cropping season of 2010-2011. The estimates of gene effects indicated that significance of both additive and non-additive variance for pod size, 100 pod weight and diseases infection among the traits and presence of over dominance satisfying assumptions of diallel except dormancy. However, both the additive and non-additive gene affects together importance to control of most quantitative traits in the groundnut. The average degree of dominance (H1/D) 1/2 (H1 = dominance variance, D = additive variance) was higher than one, indicating over dominance for all the traits. The narrow-sense heritability was high for 50% flowering (38%), harvest index (35%), pod size (52%), 100 pod weight (35%) and yield per plot (41%) indicating that great genetic gain could be achieved for them.

INTERNATIONAL JOURNAL OF SCIENTIFIC RESEARCH, Apr 1, 2023

Onion is one of the most popular spice crop, which is used for seasoning wide range of dishes as ... more Onion is one of the most popular spice crop, which is used for seasoning wide range of dishes as well as folk medicine. Assessment of genetic diversity helps to use the onion germplasm as breeding materials for its improvement. Molecular marker based diversity assessment is more powerful, rapid and reliable compared to morphology based genetic diversity assessment. Thirty eight onion germplasm were characterized by using 10 random amplied polymorphic DNA (RAPD) markers for estimating genetic diversity within the germplasm. The germplasm exhibited wide range of variability which could be used in cross breeding for getting superior F1 generation. Out of 10 primers, four gave polymorphism among onion germplasm. Genetic diversity of 38 germplasm was analyzed using variation at 34 RAPD loci, of which 91.89% were polymorphic. The highest pair wise genetic distance was 1.046 and the lowest was 0.056. The mean gene diversity among all the germplasm was 1.54 and Shannon's information index was 0.3188. The UPGMA dendrogram, based on Nei`s genetic diversity showed 6 clusters. The frequency of polymorphic loci ranged from 0.0263 to 1.0000, indicates that there exists a wide genetic diversity among the germplasm and corroborated the usefulness of RAPD markers for estimating genetic diversity in onion.

International Journal of Molecular Sciences, Jul 24, 2023

This article is an open access article distributed under the terms and conditions of the Creative... more This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY

Lettuce is the most important leafy vegetable. It is exclusively used as freshly raw form but som... more Lettuce is the most important leafy vegetable. It is exclusively used as freshly raw form but sometime also as cooked. However, its quality depends on several pre-and postharvest factors. The effects of growing conditions and cultivars on the postharvest quality of leaf lettuce were investigated. In this experiment the interaction of variable factor; like growing conditions and fixed factor; cultivars are also observed. The leaf lettuce cultivars 'Cheongchima', 'Cheongchuckmyeon', 'Geockchima' and 'Geockchuckmyeon' were grown under favourable (natural condition) and unfavorable growing condition (with excess soil water and 50% shading) to evaluate their shelf-life and postharvest qualities. Plant height and the number of leaves were significantly varied in different growing conditions and by cultivars. In addition, fresh weight was affected by only growing condition, whereas leaf thickness was influenced by cultivars, growing conditions and the cultivars influenced the degree of fresh weight loss and respiration rate during postharvest storage. However, the postharvest storage qualities differed with cultivars and in combination with growing conditions. Leaf thickness and quality of leaf lettuce before and after harvest were also varied by cultivars and growing conditions. It could be concluded that postharvest leaf lettuce quality remains acceptable when growing under excess soil water with 50% shading.

Journal of the Bangladesh Agricultural University, Oct 2, 2012

Genotype-environment interactions through different stability parameters and performance traits o... more Genotype-environment interactions through different stability parameters and performance traits of four fine rice genotypes were studied. The traits were; days to 50% flowering, days to maturity, plant height (cm), number of effective tillers per hill, panicle length (cm), number of fertile grains per panicle, number of sterile grains per panicle and yield (t/ha) in four fine rice genotypes across nine environments along with experimental farm of Genetics and Plant Breeding department, Bangladesh Agricultural University (BAU) Mymensingh. Significant differences were observed for genotypes, environments and genotypes-environment interaction. Stability analysis after Eberhat and Russell's model suggested that the genotypes used in study were more or less responsive to environmental changes. Most of the genotypes performed better in Comilla. BAU125 was found stable for effective tillers per hill and comparatively less sensitive to other genotypes in panicle length and number of sterile grains per panicle. BR5 was stable for days to maturity and plant height whereas Kalizira performed better than other genotypes for fertile grains per panicle. In general, only the genotype BAU125 was found stable for effective tillers per hill, panicle length and lowest number of sterile grains per panicle.

Journal of Biological Sciences, Feb 15, 2004

Garlic (Allium sativum) root tips were induced to regenerate shoots through callus culture and so... more Garlic (Allium sativum) root tips were induced to regenerate shoots through callus culture and somatic embryogenesis to obtain plantlets. The experiment was designed to investigate the regeneration potentiality of two garlic verities and also to develop an efficient protocol for regeneration of garlic via callus culture. Higher percentage of callus was initiated from the combination of 5 mg lG Kinetin and 1.5 mg lG 1 1 2,4-D. Embryogenic callus produced higher number of shoots in MS medium supplemented with 10 BAP. Rooting of individual shoots was induced after transfer to medium without growth regulator. The plantlets were established in the soil after acclimization. Cultivar differences in regeneration from root tips were observed.

한국원예학회 학술발표요지, Oct 1, 2016

Nuts have been used globally as health foods. However, because nuts cause allergies, people need ... more Nuts have been used globally as health foods. However, because nuts cause allergies, people need to be careful when eating food. Mostly foods are labeled, but sometimes intentional or unintentional mixing might occur. In the present study, we report DNA based on marker for the detection of four nuts almond, peanut, pine nut, and walnut using quantitative real-time polymerase chain reaction (qRT-PCR). Species-specific primer sets for four species were designed based on the single-nucleotide polymorphisms and insertion/deletion of the chloroplast gene, matK. The sensitivity of primer sets for the four species studied was assessed by analyzing DNA dilutions at concentration of 0.001-10 ng and binary mixtures of 0.1-100% of heat-treated and non-heat-treated samples. The four primer sets developed in the present study indicated appropriate amplification efficiency and correlation coefficients of the standard curves. In addition, to verify the applicability of these molecular markers, we performed a qRT-PCR with 14 commercial products and successfully detected the matK genes in several commercial food products that were declared to contain nuts. Thus, markers developed could be useful tools for confirming the presence of the four nut species in commercial products.

Horticulture Environment and Biotechnology, Nov 27, 2019

Bacterial fruit blotch (BFB), caused by Acidovorax citrulli, is an economically devastating disea... more Bacterial fruit blotch (BFB), caused by Acidovorax citrulli, is an economically devastating disease in melon. Molecular characterization of causal strains and identification of sources of resistance are necessary to control this important disease. Many strains of BFB were identified by partial sequencing and documented in GenBank. Recently, there was an outbreak of BFB strain NIHHS15-280 in melon fields (Goksung, Jeonnam, Korea) that severely hampered melon production in Korea. For this reason, we characterized NIHHS15-280 by partially sequencing the 16S rRNA gene using PCR-based markers. The partial sequence of the 16S rRNA gene of NIHHS15-280 was much more similar to A. citrulli strains associated with melon and watermelon hosts than other cucurbit hosts. A PCR-based assay identified the strain (NIHHS15-280) as belonging to A. citrulli group I, which predominantly infects non-watermelon cucurbits (virulent to melon). Thirty-five melon genotypes were screened against NIHHS15-280 in a detached-leaf inoculation assay. The lack of visible disease symptoms 11 days after inoculation in lines PI353814 and PI140471 indicated these to be highly resistant lines, whereas moderate resistance was observed in lines PI420145 and SCNU1154 and cultivars ME6 and ME5. Also, the most resistant lines were corroborated by a fruit inoculation assay. The characterized A. citrulli strain NIHHS15-280 (group I) and identified resistant lines will serve as a valuable resource for further genetic studies and improvement of BFB resistance in melon.

Rice Science, Nov 1, 2018

Grain shape is one of the important agronomic traits, which is closely related to the yield of ri... more Grain shape is one of the important agronomic traits, which is closely related to the yield of rice. A new rice mutant, named small and round grain (srg1), was isolated from an indica cultivar Zhenong 34 by ethyl methane sulfonate (EMS) mutagenesis. The microscopic analysis showed that the cell length of spikelet in srg1 was decreased compared with that in wild type (WT), which caused the grain length short. Meanwhile, the grains of srg1 were wider than those of WT because of the increased cell layers in spikelet in the lateral direction. Therefore, the inhibition of cell expansion and increased cell proliferation collectively led to the small and round grain. By map-based cloning, the gene SRG1 was located on the short arm of chromosome 9, which encodes a kinesin-4 protein, represented by the gene LOC_Os09g02650. A single nucleotide polymorphism, occurred in the 16th exon of SRG1, led to premature translation stop in mutant. The cell cycle-related genes were up-regulated in srg1, which conferred that SRG1 controlled grain width through the cell proliferation. Since the role of SRG1 in regulating grain shape was not clarified well before, it is valuable to explore the mechanism of grain development. This study could, hence, provide a morphogenesis and molecular basis for elucidating the function of SRG1, as well as a new germplasm resource for the further study of grain development.

Journal of Biological Sciences, Oct 15, 2002

BMC Genomics, Sep 6, 2017

Background: Zinc finger homeodomain proteins (ZHD) constitute a plant-specific transcription fact... more Background: Zinc finger homeodomain proteins (ZHD) constitute a plant-specific transcription factor family with a conserved DNA binding homeodomain and a zinc finger motif. Members of the ZHD protein family play important roles in plant growth, development, and stress responses. Genome-wide characterization of ZHD genes has been carried out in several model plants, including Arabidopsis thaliana and Oryza sativa, but not yet in tomato (Solanum lycopersicum). Results: In this study, we performed the first comprehensive genome-wide characterization and expression profiling of the ZHD gene family in tomato (Solanum lycopersicum). We identified 22 SlZHD genes and classified them into six subfamilies based on phylogeny. The SlZHD genes were generally conserved in each subfamily, with minor variations in gene structure and motif distribution. The 22 SlZHD genes were distributed on six of the 12 tomato chromosomes, with segmental duplication detected in four genes. Analysis of Ka/Ks ratios revealed that the duplicated genes are under negative or purifying selection. Comprehensive expression analysis revealed that the SlZHD genes are widely expressed in various tissues, with most genes preferentially expressed in flower buds compared to other tissues. Moreover, many of the genes are responsive to abiotic stress and phytohormone treatment. Conclusion: Systematic analysis revealed structural diversity among tomato ZHD proteins, which indicates the possibility for diverse roles of SlZHD genes in different developmental stages as well as in response to abiotic stresses. Our expression analysis of SlZHD genes in various tissues/organs and under various abiotic stress and phytohormone treatments sheds light on their functional divergence. Our findings represent a valuable resource for further analysis to explore the biological functions of tomato ZHD genes.

Journal of Integrative Agriculture, May 1, 2023

Journal of Biological Sciences, Nov 15, 2002

Genes, Feb 10, 2018

Plant growth and development can be adversely affected by cold stress, limiting productivity. The... more Plant growth and development can be adversely affected by cold stress, limiting productivity. The glutathione S-transferase (GST) family comprises important detoxifying enzymes, which play major roles in biotic and abiotic stress responses by reducing the oxidative damage caused by reactive oxygen species. Pumpkins (Cucurbita maxima) are widely grown, economically important, and nutritious; however, their yield can be severely affected by cold stress. The identification of putative candidate genes responsible for cold-stress tolerance, including the GST family genes, is therefore vital. For the first time, we identified 32 C. maxima GST (CmaGST) genes using a combination of bioinformatics approaches and characterized them by expression profiling. These CmaGST genes represent seven of the 14 known classes of plant GSTs, with 18 CmaGSTs categorized into the tau class. The CmaGSTs were distributed across 13 of pumpkin's 20 chromosomes, with the highest numbers found on chromosomes 4 and 6. The large number of CmaGST genes resulted from gene duplication; 11 and 5 pairs of CmaGST genes were segmental-and tandem-duplicated, respectively. In addition, all CmaGST genes showed organ-specific expression. The expression of the putative GST genes in pumpkin was examined under cold stress in two lines with contrasting cold tolerance: cold-tolerant CP-1 (C. maxima) and cold-susceptible EP-1 (Cucurbita moschata). Seven genes (CmaGSTU3, CmaGSTU7, CmaGSTU8, CmaGSTU9, CmaGSTU11, CmaGSTU12, and CmaGSTU14) were highly expressed in the cold-tolerant line and are putative candidates for use in breeding cold-tolerant crop varieties. These results increase our understanding of the cold-stress-related functions of the GST family, as well as potentially enhancing pumpkin breeding programs.

Scientific Reports, Oct 29, 2020

Lily belongs to family liliaceae, which mainly propagates vegetatively. Therefore, sufficient num... more Lily belongs to family liliaceae, which mainly propagates vegetatively. Therefore, sufficient number of polymorphic, informative, and functional molecular markers are essential for studying a wide range of genetic parameters in Lilium species. We attempted to develop, characterize and design SSR (simple sequence repeat) markers using online genetic resources for analyzing genetic diversity and population structure of Lilium species. We found di-nucleotide repeat motif were more frequent (4684) within 0.14 gb (giga bases) transcriptome than other repeats, of which was two times higher than tetra-repeat motifs. Frequency of di-(AG/CT), tri-(AGG/CTT), tetra-(AAAT), penta-(AGAGG), and hexa-(AGA GGG) repeats was 34.9%, 7.0%, 0.4%, 0.3%, and 0.2%, respectively. A total of 3607 non-redundant SSR primer pairs was designed based on the sequences of CDS, 5′-UTR and 3′-UTR region covering 34%, 14%, 23%, respectively. Among them, a sub set of primers (245 SSR) was validated using polymerase chain reaction (PCR) amplification, of which 167 primers gave expected PCR amplicon and 101 primers showed polymorphism. Each locus contained 2 to 12 alleles on average 0.82 PIC (polymorphic information content) value. A total of 87 lily accessions was subjected to genetic diversity analysis using polymorphic SSRs and found to separate into seven groups with 0.73 to 0.79 heterozygosity. Our data on large scale SSR based genetic diversity and population structure analysis may help to accelerate the breeding programs of lily through utilizing different genomes, understanding genetics and characterizing germplasm with efficient manner. Lily (Lilium sp.) is an economically important flowering monocots in the genus Lilium and family Liliaceae. Lilium sp. are originated in Asia, Europe, and North America 1. The Netherlands are the leading lily producer and exporter in the world 2 , lily also commercially cultivated in France, Chile, USA, Japan, and New Zealand. The Lilium genus consists of 100 species and more than 9000 cultivars (International Lily register, https ://www. lilyr egist er.com/). Based on 13 morphological characters the Lilium species are taxonomically classified into seven sections; Martagon, Pseudolirium, Lilium (Liriotypus), Archelirion, Sinomartagon, Leucolirion, and Oxypetalum 3,4. All cultivars from these sections were further categorized into three main groups: Longiflorum (L), Asiatic (A), and Oriental (O) hybrids 5. Longiflorum hybrids derived from intra-or inter-specific hybridization between L. formosanum and Leucolirion section 6 , whereas Asiatic hybrids originated from interspecies crosses among 12 species of the Sinomartagon section 7 and Oriental hybrids derived from hybridization among

Journal of Biological Sciences, Feb 15, 2004

International Journal of Molecular Sciences, May 13, 2017

Growth regulating factors (GRFs) are plant-specific transcription factors that are involved in di... more Growth regulating factors (GRFs) are plant-specific transcription factors that are involved in diverse biological and physiological processes, such as growth, development and stress and hormone responses. However, the roles of GRFs in vegetative and reproductive growth, development and stress responses in tomato (Solanum lycopersicum) have not been extensively explored. In this study, we characterized the 13 SlGRF genes. In silico analysis of protein motif organization, intron-exon distribution, and phylogenetic classification confirmed the presence of GRF proteins in tomato. The tissue-specific expression analysis revealed that most of the SlGRF genes were preferentially expressed in young and growing tissues such as flower buds and meristems, suggesting that SlGRFs are important during growth and development of these tissues. Some of the SlGRF genes were preferentially expressed in fruits at distinct developmental stages suggesting their involvement in fruit development and the ripening process. The strong and differential expression of different SlGRFs under NaCl, drought, heat, cold, abscisic acid (ABA), and jasmonic acid (JA) treatment, predict possible functions for these genes in stress responses in addition to their growth regulatory functions. Further, differential expression of SlGRF genes upon gibberellic acid (GA3) treatment indicates their probable function in flower development and stress responses through a gibberellic acid (GA)-mediated pathway. The results of this study provide a basis for further functional analysis and characterization of this important gene family in tomato.

The Scientific World Journal, 2014

Genetic diversity is important for crop improvement. An experiment was conducted during 2011 to s... more Genetic diversity is important for crop improvement. An experiment was conducted during 2011 to study genetic variability, character association, and genetic diversity among 27 soybean mutants and four mother genotypes. Analysis of variance revealed significant differences among the mutants and mothers for nine morphological traits. Eighteen mutants performed superiorly to their mothers in respect to seed yield and some morphological traits including yield attributes. Narrow differences between phenotypic and genotypic coefficients of variation (PCV and GCV) for most of the characters revealed less environmental influence on their expression. High values of heritability and genetic advance with high GCV for branch number, plant height, pod number, and seed weight can be considered as favorable attributes for soybean improvement through phenotypic selection and high expected genetic gain can be achieved. Pod and seed number and maturity period appeared to be the first order traits for higher yield and priority should be given in selection due to their strong associations and high magnitudes of direct effects on yield. Cluster analysis grouped 31 genotypes into five groups at the coefficient value of 235. The mutants/genotypes from cluster I and cluster II could be used for hybridization program with the mutants of clusters IV and V in order to develop high yielding mutant-derived soybean varieties for further improvement.

Physiology and Molecular Biology of Plants, Feb 21, 2020

Cytoplasmic male sterility (CMS) is maternally inherited trait, which hinders the ability to prod... more Cytoplasmic male sterility (CMS) is maternally inherited trait, which hinders the ability to produce viable pollen in plants. It serves as a useful tool for hybrid seed production via exploiting heterosis in crops. The molecular mechanism of CMS and fertility restoration has been investigated in different crops. However, limited number of reports is available on comparison of Ogura- and Polima-CMS with their shared maintainer in Chinese cabbage. We performed transcript profiling of sterile Ogura CMS (Tyms), Polima CMS (22m2) and their shared maintainer line (231–330) with an aim to identify genes associated with male sterility. In this work, we identified 912, 7199 and 6381 DEGs (Differentially Expressed Genes) in 22m2 Vs Tyms, 231–330 VS 22m2 and 231–330 Vs Tyms, respectively. The GO (Gene Ontology) annotation and KEGG pathway analysis suggested that most of the DEGs were involved in pollen development, carbon metabolism, lipase activity, lipid binding, penta-tricopeptide repeat (PPR), citrate cycle and oxidative phosphorylation, which were down-regulated in both CMS lines. This result will provide an important resource for further understanding of functional pollen development, the CMS mechanism and to improve molecular breeding in Chinese cabbage.Electronic supplementary materialThe online version of this article (10.1007/s12298-020-00775-5) contains supplementary material, which is available to authorized users.

Research Square (Research Square), Nov 17, 2022

Background and aim Clubroot is an infectious root disease caused by Plasmodiophora brassicae of B... more Background and aim Clubroot is an infectious root disease caused by Plasmodiophora brassicae of Brassica crops, which can cause immeasurable losses. We aimed to explore the infection mechanism under P. brassicae integrating transcriptome, small RNA, degradome and phytohormone technology. Result In this study, root samples of B. rapa resistant line BrT24 (R-line) and susceptible line Y510-9 (S-line) were collected at four different time points for cytological, transcriptome, miRNA and degradome investigations. We found the critical period of disease resistance and infection at 0-3 days and 9-20 days, respectively. Based on this finding we further analyzed the data of 9 d vs 20 d of S-line and predicted the key genes ARF8, NAC1, NAC4, TCP10, SPL14, REV and ATHB related to clubroot disease development and regulating disease resistance mechanisms. These genes are mainly related to auxin, cytokinin, jasmonic acid and ethylene cycles. We proposed a regulatory model of plant hormones under the mRNA-miRNA regulation in the critical period of Plasmodiophora brassicae infection based on the combination of 2 the present data of integrative transcriptome, small RNA, degradome and phytohormone with our previously published results. Conclusion Our integrative analysis found that the bra-miR164/NAC1/4, bra-miR319/TCP10 and bra-miR167/ARF8 were associated with clubroot symptoms development, which provide new insights into the regulation relationship of miRNA and plant hormones during the process of disease infection.

International Journal of Agricultural Research, Innovation and Technology, Feb 2, 2014

A 10×10 half diallel experiment was conducted on groundnut (Arachis hypogaea L.) to ascertain the... more A 10×10 half diallel experiment was conducted on groundnut (Arachis hypogaea L.) to ascertain the gene action and genetic parameters of ten traits including 50% flowering, no. of pods per plant, plant height, harvest index, pod index, 100 pod weight, 100 kernel weight, pod size, diseases infection and yield per plot. The experiments were carried out in the Department of Genetics and Plant Breeding, Bangladesh Agricultural University (BAU), Mymensingh during the cropping season of 2010-2011. The estimates of gene effects indicated that significance of both additive and non-additive variance for pod size, 100 pod weight and diseases infection among the traits and presence of over dominance satisfying assumptions of diallel except dormancy. However, both the additive and non-additive gene affects together importance to control of most quantitative traits in the groundnut. The average degree of dominance (H1/D) 1/2 (H1 = dominance variance, D = additive variance) was higher than one, indicating over dominance for all the traits. The narrow-sense heritability was high for 50% flowering (38%), harvest index (35%), pod size (52%), 100 pod weight (35%) and yield per plot (41%) indicating that great genetic gain could be achieved for them.