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Assam, a north-eastern state in India contributes the largest share in India’s total tea production. However, the workers in the tea gardens of the state are considered as one of the poor and margi...

Persistent organic pollutants (POPs) of soil mainly exhibit toxic characteristics that posses hazard to whole mankind. These toxic pollutants includes several group of compound viz., polychlorinated biphenyls, polybrominated biphenyls, polychlorinated dibenzofurans, polycyclic aromatic hydrocarbons, organophosphorus and carbamate insecticides, herbicides and organic fuels, especially gasoline and diesel. They can also be complex mixture of organic chemicals, heavy metals and microbes from septic systems, animal wastes and other sources of organic inputs. Phytoremediation is an emerging technology which can be used for remediation of soil from organic pollutants. In this chapter an attempt has been made to discuss about the sources of organic pollutants, factors that influenced the uptake of organic pollutants by plants, the different mechanism responsible for organic pollutants, phytoremediation of organic pollutants and their advantages and limitation.

Background Anthocyanins are plant secondary metabolites with key roles in attracting insect pollinators and protecting against biotic and abiotic stresses. They have potential health-promoting effects as part of the human diet. Anthocyanin biosynthesis has been elucidated in many species, enabling the development of anthocyanin-enriched fruits, vegetables, and grains; however, few studies have investigated Brassica napus anthocyanin biosynthesis. Results We developed a high-anthocyanin resynthesized B. napus line, Rs035, by crossing anthocyanin-rich B. rapa (A genome) and B. oleracea (C genome) lines, followed by chromosome doubling. We identified and characterized 73 and 58 anthocyanin biosynthesis genes in silico in the A and C genomes, respectively; these genes showed syntenic relationships with 41 genes in Arabidopsis thaliana and B. napus. Among the syntenic genes, twelve biosynthetic and six regulatory genes showed transgressively higher expression in Rs035, and eight structural genes and one regulatory gene showed additive expression. We identified three early-, four late-biosynthesis pathways, three transcriptional regulator genes, and one transporter as putative candidates enhancing anthocyanin accumulation in Rs035. Principal component analysis and Pearson’s correlation coefficients corroborated the contribution of these genes to anthocyanin accumulation. Conclusions Our study lays the foundation for producing high-anthocyanin B. napus cultivars. The resynthesized lines and the differentially expressed genes we have identified could be used to transfer the anthocyanin traits to other commercial rapeseed lines using molecular and conventional breeding. Electronic supplementary material The online version of this article (10.1186/s40709-018-0090-6) contains supplementary material, which is available to authorized users.

Bacterial blight (BB) is caused by Xanthomonas oryzae pv. oryzae and is one of the most important diseases in rice. It results in significantly reduced productivity throughout all rice-growing regions of the world. Four BB resistance genes have been reported, however, introgression of a single gene into rice has not been able to sufficiently protect rice against BB infection. Pyramiding of effective BB resistance genes (i.e., Xa genes) into background varieties is a potential approach to controlling BB infection. In this study, combinations of four BB resistance genes, Xa4, xa5, xa13, and Xa21, were pyramided into populations. The populations were derived from crossing Ciherang (a widespread Indonesian rice variety) with IRBB60 (resistance to BB). Promising recombinants from the F6 generation were identified by scoring the phenotype against three virulent bacterial strains, C5, P6, and V, which cause widespread BB infection in most rice-growing countries. Pyramiding of genes for BB resistance in 265 recombinant introgressed lines (RILs) were confirmed through marker-assisted selection (MAS) of the F5 and F6 generations using gene-specific primers. Of these 265 RILs, 11, 34 and 45 lines had four, three, or two BB resistance genes, respectively. The RILs had pyramiding of two or three resistance genes, with the Xa4 resistance gene showing broad spectrum resistance against Xoo races with higher agronomic performance compared to their donor and recipients parents. The developed BB-resistant RILs have high yield potential to be further developed for cultivation or as sources of BB resistance donor material for varietal improvement in other rice lines.

Pink-fruited tomato is characterized by transparent peel with lack of flavonoid NC (Naringenin Chalcone). SlMYB12 is a transcription regulator of NC biosynthesis and marked as candidate gene regulating pink color trait of tomato. Causative allelic variations have been reported previously in the SlMYB12 as 603-bp deletion in promoter region, two SNPs (− > A) and (C > T) in the second exon and (G > T) nucleotide substitution in the second intron. Here, we tested these variations in eighty-five pink inbred lines and two red lines. Among them fifty lines were homozygous for the 603-bp deletion and twenty-eight for the insertion (− > A). No variations were observed in pink lines (16NWS01, 16NWS24, 16NWS28, 16NWS29, 16NWS30, 16NWS34 and 16NWS82). Cloning and sequencing of SlMYB12 gene revealed two new SNPs G > A at 1794 bp and 1851 bp positions of genomic sequence in six lines. While 44.75 Kb deletion was identified proximate to SlMYB12 region in the line 16NWS82. These new variations together with previously reported markers could serve as valuable markers in pink tomato breeding.

Anthocyanins are the resultant end-point metabolites of phenylapropanoid/flavonoid (F/P) pathway which is regulated at transcriptional level via a series of structural genes. Identifying the key genes and their potential interactions can provide us with the clue for novel points of intervention for improvement of the trait in strawberry. We profiled the expressions of putative regulatory and biosynthetic genes of cultivated strawberry in three developmental and characteristically colored stages of fruits of contrastingly anthocyanin rich cultivars: Tokun, Maehyang and Soelhyang. Besides FaMYB10, a well-characterized positive regulator, FaMYB5, FabHLH3 and FabHLH3-delta might also act as potential positive regulators, while FaMYB11, FaMYB9, FabHLH33 and FaWD44-1 as potential negative regulators of anthocyanin biosynthesis in these high-anthocyanin cultivars. Among the early BGs, Fa4CL7, FaF3H, FaCHI1, FaCHI3, and FaCHS, and among the late BGs, FaDFR4-3, FaLDOX, and FaUFGT2 showed significantly higher expression in ripe fruits of high anthocyanin cultivars Maehyang and Soelhyang. Multivariate analysis revealed the association of these genes with total anthocyanins. Increasingly higher expressions of the key genes along the pathway indicates the progressive intensification of pathway flux leading to final higher accumulation of anthocyanins. Identification of these key genetic determinants of anthocyanin regulation and biosynthesis in Korean cultivars will be helpful in designing crop improvement programs.

The color of tomato (Solanum lycopersicum) fruit flesh is often used as an indicator of quality. Generally, fruit color is determined by the accumulation of carotenoids and flavonoids, along with concomitant degradation of chlorophylls during ripening. Several genes, such as phytoenesynthetase1 (Psy1), STAY-GREEN (SGR), and SlMYB12, have been extensively studied to elucidate the genes controlling fruit coloration. In this study, we observed low carotenoid levels without degradation of chlorophylls in green-fruited tomato caused by mutations in three genes, Psy1, SGR, and SlMYB12. We crossed two inbred lines, BUC30 (green-fruited) and KNR3 (red-fruited), to confirm the causal effects of these mutations on fruit coloration. The F2 population segregated for eight different fruit colors in the proportions expected for three pairs of gene, as confirmed by a chi-square test. Therefore, we developed a population of tomato with diverse fruit colors and used molecular markers to detect the genes responsible for the individual fruit colors. These newly-designed DNA-based markers can be used for selecting desired fruit color genotypes within adapted breeding materials and cultivars for breeding.

Eukaryotic chromosomes are organized into heterochromatin and euchromatin domains. Heterochromatin domains are transcriptionally repressed and prevented from spreading into neighbouring genes by chromatin boundaries. Previously, we identified 55 boundary-related genes in Saccharomyces cerevisiae. In this study, we describe the characterization of one of these boundary genes, named SGF29, which was previously reported as a component of the SAGA, SLIK, ADA and HAT-A2 complex. A domain analysis of Sgf29 identified two minimal regions that can function as individual boundaries. The N-terminal minimal region comprising amino acids 1-12, which has not been defined as a functional domain, showed stronger boundary formation ability than the C-terminal minimal region comprising amino acids 110-255, which contains Tudor domains. Together with Ada2, Ada3 and Sgf29, which are all components of SAGA, Gcn5 acetylates multiple lysine residues on nucleosomal histone H3, which is associated with an open chromatin structure. However, the results presented in this study suggest that the boundary formation ability of the Sgf29 minimal regions is independent of Gcn5. An in vivo analysis also revealed that Sgf29 and Gcn5 perform distinct functions at native telomere boundary regions on the chromosome.

Erucic acid (22:1) is a valuable renewable resource for the oleochemical industry. Currently available high erucic acid rapeseed cultivars contain only about 50% erucic acid in the seed oil. A substantial increase of the erucic acid content of the rapeseed oil could increase market prospects. The transgenic line TNKAT, over expressing the rapeseed fatty acid elongase gene (fae1) and expressing the Ld-LPAAT gene from Limnanthes douglasii was crossed with the line 6575-1 HELP (high erucic and low polyunsaturated fatty acid). A from the F1 plants produced population of 90 doubled haploid (DH) lines was tested in a greenhouse with three replicates. Parental lines TNKAT and 6575-1 HELP contained 46 and 50% erucic acid in the seed oil, respectively. In the DH population the erucic acid content ranged between 35 and 59%. The Ld-LPAAT + Bn-fae1.1 transgene showed a 1:1 segregation. The transgenic DH lines contained up to 8% trierucolyglycerol, but surprisingly had a by 2.3% lower erucic acid content compared to the non-transgenic segregants. Results indicated that the ectopically expressed fae1.1 gene may not be functional. The DH population also showed a large quantitative variation for PUFA content ranging from 6 to 28% (TNKAT: 21%, 6575-1 HELP: 8%). Regression analysis showed that in the DH population a 10% reduction in PUFA content led to a 4.2% increase in erucic acid content. Development of locus specific PCR primers for the two resident erucic acid genes fae1.1 (A-genome) and fae1.2 genes (C-genome) of rapeseed allowed sequencing of the respective alleles from TNKAT and 6575-1 HELP. Single nucleotide polymorphisms were only found for the fae1.1 gene. Use of allele specific fae1.1 PCR primers, however, did not reveal a significant effect of the fae1.1 allele from either parent on erucic acid content. The high erucic acid low polyunsaturated fatty acid DH lines and the fae1 locus specific primers developed in the present study should be useful in future studies aimed at increasing erucic acid content in rapeseed. peerReviewed

The budding yeast Saccharomyces cerevisiae contains active and inactive chromatin separated by boundary domains. Previously, we used genome-wide screening to identify 55 boundary-related genes. Here, we focus on Sgf73, a boundary protein that is a component of the Spt-Ada-Gcn5 acetyltransferase (SAGA) and SLIK (SAGA-like) complexes. These complexes have histone acetyltransferase (HAT) and histone deubiquitinase activity, and Sgf73 is one of the factors necessary to anchor the deubiquitination module. Domain analysis of Sgf73 was carried out, and the minimum region (373-402 aa) essential for boundary function was identified. This minimum region does not include the domain involved in anchoring the deubiquitination module, suggesting that the histone deubiquitinase activity of Sgf73 is not important for its boundary function. Next, Sgf73-mediated boundary function was analyzed in disruption strains in which different protein subunits of the SAGA/SLIK/ADA complexes were deleted. Deletion of ada2, ada3 or gcn5 (a HAT module component) caused complete loss of the boundary function of Sgf73. The importance of SAGA or SLIK complex binding to the boundary function of Sgf73 was also analyzed. Western blot analysis detected both the full-length and truncated forms of Spt7, suggesting that SAGA and SLIK complex formation is important for the boundary function of Sgf73.

Distribution of various fractions of soil zinc (Zn) and their relationships with soil properties in rice growing soils of Assam were studied with twenty five geo-referenced soil samples (0-30 cm) with variable Zn status from rice growing areas of Assam, representing 3 major soil orders viz., Entisol, Inceptisol and Alfisol. The distribution of different forms of Zn in rice soils revealed that water soluble and exchangeable Zn (WSEx-Zn) fraction in soils ranged from 0.32 to 1.92, complexed Zn (COMP-Zn) from 1.46 to 4.5, amorphous sesquioxide bound Zn from 1.30 to 6.21, crystalline sesquioxide bound Zn (CBD-Zn) from 0.45 to 2.25 and residual Zn (Res-Zn) from 101.7 to 285.2 mg kg-1 with mean values of 0.87, 2.71, 2.92, 1.12 and 186.98 mg kg-1, respectively. Residual Zn was the dominant fraction among all Zn fractions studied, which ranged from 101.7 to 285.2 mg kg-1 and the mean value was 186.9 mg kg-1. The WSEx-Zn, COMP-Zn, amorphous sesquioxide bound Zn, CBD-Zn and Res-Zn constituted 0.45, 1.57, 1.62, 0.63 and 95.7 per cent of total Zn. Multiple regression of physicochemical properties of soil with different Zn-fractions showed the highest R2 value (0.616) with COMP-Zn. Multiple regression of different Zn fractions with plant parameters showed the highest contribution of WSEx-Zn to plant Zn concentration (76.7%), Zn-uptake (63.0%) and dry matter yield (36.1%) of rice. Path coefficient analysis of different Zn-fractions with Zn-concentration in rice plant showed the highest direct effect (0.5610) of WSEx-Zn on Zn concentration and indirect effect of COMP-Zn (0.3731) and amorphous sesquioxide bound Zn (0.2508) via WSEx-Zn. Significant positive correlation was also observed between WSEx-Zn and plant Zn uptake (r=0.668**), plant Zn concentration (r=0.647**) and drymatter yield (r=0.401*), suggesting that water soluble plus exchangeable Zn fraction is of great importance in Zn nutrition of lowland rice. Major portion of Zn was in the residual fraction which contributed very little to plant uptake. Significant positive correlation among WSEx, organic complex and amorphous sesquioxide bound Zn indicated that they are possibly in dynamic equilibrium with each other.

A field experiment was carried out at instructional-cum-research farm of Assam Agricultural University, Jorhat, Assam to enrich grains of some popular high yielding rice varieties with soil and soil plus foliar application of zinc (Zn). Three different levels of Zn viz., 0, 21 kg ha−1 as soil application, and 21 kg ha−1 as soil application + foliar spray of 0.5% of ZnSO4 thrice at heading, flowering and panicle initiation stages were evaluated. Irrespective of varieties, highest mean Zn concentration of 29.3 mg kg−1 was observed in rice grain with soil + foliar application of Zn. The mean Zn content varied from 17.6 to 34.2 mg kg−1 and it increased from 5.8 to 20.3 per cent over control with soil application and 13.2 to 32.3 per cent with soil + foliar application of Zn. Amongst the varieties, the highest concentration was found in variety Kushal (34.3 mg kg−1) followed by Moniram (33.5 mg kg−1). Variety Kushal also recorded highest Zn uptake (140.9 g ha−1) followed by the variety Ranjit (127.1 g ha−1). However, in terms of Zn use efficiency and apparent Zn recovery efficiency, varieties Moniram and Ranjit, respectively performed best. Thus, Ranjit recorded the highest Zn accumulation efficiency by grains over other varieties.

The eukaryotic nucleus is organized into structurally and functionally distinct domains that are often located in close proximity to one another. The euchromatin form of DNA is transcriptionally active and maintains an open chromatin structure via the actions of promoter, enhancers, and locus control region sequences. By contrast, heterochromatin is composed of a condensed chromatin structure that is generally transcriptionally repressed. Chromatin barriers prevent silenced chromatin domains from spreading into active domains. In S. cerevisiae telomeres, HML, HMR and ribosomal DNA (rDNA) are transcriptionally silent regions. The Sir (Silent Information Regulator) protein complex, consisting of Sir2, Sir3 and Sir4, plays a key role in transcriptional repression. The regulation of gene expression is crucial for proper development and survival of all organisms; chromatin structure is a central regulator of gene expression. Histone modifications, such as acetylation and ubiquitination, play a crucial role to facilitate a number of cellular events, including gene regulation. Histones acetylation is largely associated with open chromatin structure to support the entry of transcriptional machinery to genomic loci for activation, whereas ubiquitination of histone has been linked to gene activation and repression both. The budding yeast Saccharomyces cerevisiae contains active and inactive chromatin separated by boundary domains. Previously, we used genome-wide screening to identify 55 boundary-related genes. In this study, firstly I have focused on Sgf73, a boundary protein that is a component of the SAGA (Spt-Ada-Gcn5 acetyltransferase) and SLIK (SAGA-like) complexes. These complexes have histone acetyltransferase (HAT) and histone deubiquitinase activity, and Sgf73 is one of the factors necessary to anchor the deubiquitination module. Domain analysis of Sgf73 was performed and the minimum region (373?402 aa) essential for boundary function was identified. This minimum region does not include the domain involved in anchoring the deubiquitination module, suggesting that the histone deubiquitinase activity of Sgf73 is not important for its boundary function. Next, Sgf73-mediated boundary function was analyzed in disruption strains in which different protein subunits of the SAGA/SLIK/ADA complexes were deleted. Deletion of ada2, ada3 or gcn5 (a HAT module component) caused complete loss of the boundary function of Sgf73. The importance of SAGA or SLIK complex binding to the boundary function of Sgf73 was also analyzed. Western blot analysis detected both the full-length and truncated forms of Spt7, suggesting that SAGA and SLIK complex formation is important for the boundary function of Sgf73. Secondly, in the present study, 90 DH lines derived from F1 plants of the cross Ld-LPAAT- Bn-fae1 over expressing transgenic rapeseed plants with high erucic acid and low polyunsaturated fatty acid (HELP) plant material were analyzed. Erucic acid (22:1) is a major component in the seed oil of wild type rapeseed. But this erucic acid is toxic for consumption. However, from the last decade, high erucic acid rapeseed (HEAR) cultivars have regained interest for industrial purposes. Here, I study the inheritance of erucic acid content in the segregating transgenic DH population and evaluate the variation and heritability for different phenological and quality traits such as: days to flowering and maturity, oil, protein and different fatty acids content in the DH population. Large variation was found for erucic acid content in DH population varied from 34.6% to 59.1%. Genetic variance components were large and significant for all traits. The segregation pattern of erucic acid content showed 1:3:3:1 separation suggesting erucic acid content was controlled by the alleles of three loci in the DH population. Transgene Ld-LPAAT-Bn-fae1 showed negative effect (-2.7%) to change the erucic acid content in the DH population. This result suggesting that there was no effect of Bn-fae1 for increasing the erucic acid content or the absence of β-ketoacyl-CoA synthase (KCS) activities required for initiating fatty acid elongation from 18:1 to 22:1. On the other hand PUFA (Poly Unsaturated Fatty Acid) had effect to increase the erucic acid content up to 3.7%. In presence of transgene Ld-LPAAT showed limited activities to produce trierucin (8% instead of probable 20%) in the selected best DH line. The selected DH lines showed increase in erucic acid content (59.1%) compared to parental lines TNKAT (46.1%) and HELP (50.4%). Highest amount of erucic acid might be achieved due to introgression of PUFA alleles with those of the strong alleles of the indigenous erucic acid loci, because transgene showed negative effect on erucic acid. There was no adverse effect of the high erucic content on other phenological traits in the selected best DH line. In conclusion the result of this study showed that erucic acid is inherited by alleles of three loci. The variation of erucic acid has been achieved due to the combination of alleles of two indigenous erucic acid loci with alleles of PUFA. Low in PUFA content could contribute markedly to increase erucic acid than the transgene construct present in DH lines. The selected DH line having 59% erucic acid could be source material for crossing to other high erucic acid transgenic line to increase the erucic acid content

Persistent organic pollutants (POPs) of soil mainly exhibit toxic characteristics that posses hazard to whole mankind. These toxic pollutants includes several group of compound viz., polychlorinated biphenyls, polybrominated biphenyls, polychlorinated dibenzofurans, polycyclic aromatic hydrocarbons, organophosphorus and carbamate insecticides, herbicides and organic fuels, especially gasoline and diesel. They can also be complex mixture of organic chemicals, heavy metals and microbes from septic systems, animal wastes and other sources of organic inputs. Phytoremediation is an emerging technology which can be used for remediation of soil from organic pollutants. In this chapter an attempt has been made to discuss about the sources of organic pollutants, factors that influenced the uptake of organic pollutants by plants, the different mechanism responsible for organic pollutants, phytoremediation of organic pollutants and their advantages and limitation.