Enhancing the properties of swelling soils with lime, fly ash, and expanded polystyrene -A review.

This paper discusses efforts made by past researchers to steady the expansive (problematic) soils using mechanical and chemical techniques - specifically with EPS beads, lime and fly ash. Administering swelling of problematic soils is critical for civil engineers to prevent structural distress. This paper summarizes studies on reduction of swelling potential using EPS, lime and fly ash individually. Chemical stabilization with lime and fly ash are conventional methods for expansive soil stabilization, with known merits and demerits. This paper explores the suitability of different materials under various conditions and stabilization mechanisms, including cation exchange, flocculation, and pozzolanic reactions. The degree of stabilization is influenced by various factors such as the type and amount of additives, soil mineralogy, curing temperature, moisture content during molding, and the presence of nano-silica, organic matter, and sulfates. Additionally, expanded polystyrene (EPS) improves structural integrity by compressing when surrounded clay swells, reducing overall swelling. Thus, EPS addresses limitations of chemicals by mechanical means. Combining EPS, lime and fly ash creates a customized system promoting efficient, long-lasting, cost-effective and eco-friendly soil stabilization. Chemicals address EPS limitations like poor stabilization. This paper benefits civil engineers seeking to control expansive soil swelling and prevent structural distress. It indicates potential of an EPS-lime-fly ash system and concludes by identifying research gaps for further work on such combinatorial stabilizer systems.

Unraveling the genetics of heat tolerance in chickpea landraces (Cicer arietinum L.) using genome-wide association studies.

Chickpea, being an important grain legume crop, is often confronted with the adverse effects of high temperatures at the reproductive stage of crop growth, drastically affecting yield and overall productivity. The current study deals with an extensive evaluation of chickpea genotypes, focusing on the traits associated with yield and their response to heat stress. Notably, we observed significant variations for these traits under both normal and high-temperature conditions, forming a robust basis for genetic research and breeding initiatives. Furthermore, the study revealed that yield-related traits exhibited high heritability, suggesting their potential suitability for marker-assisted selection. We carried out single-nucleotide polymorphism (SNP) genotyping using the genotyping-by-sequencing (GBS) method for a genome-wide association study (GWAS). Overall, 27 marker-trait associations (MTAs) linked to yield-related traits, among which we identified five common MTAs displaying pleiotropic effects after applying a stringent Bonferroni-corrected p-value threshold of <0.05 [-log10(p) > 4.95] using the BLINK (Bayesian-information and linkage-disequilibrium iteratively nested keyway) model. Through an in-depth in silico analysis of these markers against the CDC Frontier v1 reference genome, we discovered that the majority of the SNPs were located at or in proximity to gene-coding regions. We further explored candidate genes situated near these MTAs, shedding light on the molecular mechanisms governing heat stress tolerance and yield enhancement in chickpeas such as indole-3-acetic acid-amido synthetase GH3.1 with GH3 auxin-responsive promoter and pentatricopeptide repeat-containing protein, etc. The harvest index (HI) trait was associated with marker Ca3:37444451 encoding aspartic proteinase ortholog sequence of Oryza sativa subsp. japonica and Medicago truncatula, which is known for contributing to heat stress tolerance. These identified MTAs and associated candidate genes may serve as valuable assets for breeding programs dedicated to tailoring chickpea varieties resilient to heat stress and climate change.

A Draft Transcriptome Announcement of Anguina tritici.

Anguina tritici, the wheat seed gall nematode, causes the 'ear-cockle' or seed gall disease of wheat (Triticum sp.), leading to an extensive decline of yield (30-70%) in underdeveloped wheat cultivating countries of the world. The nematode is known to survive in anhydrobiotic conditions for up to 32 years. Here, we present the first transcriptome assembly of A. tritici, which will be a valuable resource for understanding the genes responsible for nematode survival and above-ground plant parasitism. The final 133.2 Mb assembly consists of 105606 open reading frames (including isoforms) with the following BUSCO scores against Nematoda database: 80.3% complete (16.4% single copy and 63.9% duplicated), 2.1% fragmented, and 17.6% missing.

Nematode Genome Announcement: A Draft Genome of Seed Gall Nematode, Anguina tritici.

Anguina tritici is the first plant-parasitic nematode described in literature, dating back to the year 1743. It is responsible for causing earcockle (seed gall) and tundu diseases in wheat and rye. Notably, this nematode has been observed to survive in an anhydrobiotic state for up to 32 years within wheat seed galls. These exceptional characteristics have inspired the sequencing of the A. tritici genome. In this study, we present the initial draft genome of A. tritici, obtained using the Illumina MiSeq platform with coverage of 60-fold. The genome is estimated to have a size of 164 Mb and comprises 39,965 protein-coding genes, exhibiting a GC content of 39.1%. The availability of this genome data will serve as a foundation for future functional biological investigations, particularly for genes whose functions remain unknown to this day.

Whole chloroplast genome-specific non-synonymous SNPs reveal the presence of substantial diversity in the pigeonpea mini-core collection.

To unravel the plastid genome diversity among the cultivated groups of the pigeonpea germplasm, we characterized the SNP occurrence and distribution of 142 pigeonpea mini-core collections based on their reference-based assembly of the chloroplast genome. A total of 8921 SNPs were found, which were again filtered and finally 3871 non-synonymous SNPs were detected and used for diversity estimates. These 3871 SNPs were classified into 12 groups and were present in only 44 of the 125 genes, demonstrating the presence of a precise mechanism for maintaining the whole chloroplast genome throughout evolution. The Acetyl-CoA carboxylase D gene possesses the maximum number of SNPs (12.29%), but the Adenosine Tri-Phosphate synthatase cluster genes (atpA, atpB, atpE, atpF, atpH, and atpI) altogether bear 43.34% of the SNPs making them most diverse. Various diversity estimates, such as the number of effective alleles (1.013), Watterson's estimate (0.19), Tajima's D ( - 3.15), Shannon's information index (0.036), suggest the presence of less diversity in the cultivated gene pool of chloroplast genomes. The genetic relatedness estimates based on pairwise correlations were also in congruence with these diversity descriptors and indicate the prevalence of rare alleles in the accessions. Interestingly, no stratification was observed either through STRUCTURE, PCoA, or phylogenetic analysis, indicating the common origin of the chloroplast in all the accessions used, irrespective of their geographical distribution. Further 6194 Cleaved Amplified Polymorphic Sequences (CAPS) markers for 531 SNPs were developed and validated in a selected set of germplasm. Based on these results, we inferred that all of the cultivated gene pools of pigeonpea have a common origin for the chloroplast genome and they possess less diversity in protein-coding regions, indicating a stable and evolved plastid genome. At the same time, all diversity analysis indicates the occurrence of rare alleles, suggesting the suitability of the mini-core collection in future pigeonpea improvement programs. In addition, the development of chloroplast genome-based CAPS markers would have utility in pigeonpea breeding programs. Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-023-03785-8.

Cross species/genera transferability of simple sequence repeat markers, genetic diversity and population structure analysis in gladiolus (Gladiolus × grandiflorus L.) genotypes.

Background: Genetic analysis of gladiolus germplasm using simple sequence repeat (SSR) markers is largely missing due to scarce genomic information. Hence, microsatellites identified for related genera or species may be utilized to understand the genetic diversity and assess genetic relationships among cultivated gladiolus varieties. Methods: In the present investigation, we screened 26 genomic SSRs (Gladiolus palustris, Crocus sativus, Herbertia zebrina, Sysirinchium micranthum), 14 chloroplast SSRs (Gladiolus spp., chloroplast DNA regions) and 25 Iris Expressed Sequence Tags (ESTs) derived SSRs across the 84 gladiolus (Gladiolus × grandiflorus L.) genotypes. Polymorphic markers detected from amplified SSRs were used to calculate genetic diversity estimates, analyze population structure, cluster analysis and principal coordinate analysis (PCoA). Results: A total of 41 SSRs showed reproducible amplification pattern among the selected gladiolus cultivars. Among these, 17 highly polymorphic SSRs revealed a total of 58 polymorphic alleles ranging from two to six with an average of 3.41 alleles per marker. Polymorphic information content (PIC) values ranged from 0.11 to 0.71 with an average value of 0.48. A total of 4 SSRs were selectively neutral based on the Ewens-Watterson test. Hence, 66.66% of Gladiolus palustris, 48% of Iris spp. EST, 71.42% of Crocus sativus SSRs showed cross-transferability among the gladiolus genotypes. Analysis of genetic structure of 84 gladiolus genotypes revealed two subpopulations; 35 genotypes were assigned to subpopulation 1, 37 to subpopulation 2 and the remaining 12 genotypes could not be attributed to either subpopulation. Analysis of molecular variance indicated maximum variance (53.59%) among individuals within subpopulations, whereas 36.55% of variation among individuals within the total population. The least variation (9.86%) was noticed between two subpopulations. Moderate (FST = 0.10) genetic differentiation between two subpopulations was observed. The grouping pattern of population structure was consistent with the unweighted pair group method with arithmetic mean (UPGMA) dendrogram based on simple matching dissimilarity coefficient and PCoA. Conclusion: SSR markers from the present study can be utilized for cultivar identification, conservation and sustainable utilization of gladiolus genotypes for crop improvement. Genetic relationships assessed among the genotypes of respective clusters may assist the breeders in selecting desirable parents for crossing.

Integration of miRNA dynamics and drought tolerant QTLs in rice reveals the role of miR2919 in drought stress response.

To combat drought stress in rice, a major threat to global food security, three major quantitative trait loci for 'yield under drought stress' (qDTYs) were successfully exploited in the last decade. However, their molecular basis still remains unknown. To understand the role of secondary regulation by miRNA in drought stress response and their relation, if any, with the three qDTYs, the miRNA dynamics under drought stress was studied at booting stage in two drought tolerant (Sahbaghi Dhan and Vandana) and one drought sensitive (IR 20) cultivars. In total, 53 known and 40 novel differentially expressed (DE) miRNAs were identified. The primary drought responsive miRNAs were Osa-MIR2919, Osa-MIR3979, Osa-MIR159f, Osa-MIR156k, Osa-MIR528, Osa-MIR530, Osa-MIR2091, Osa-MIR531a, Osa-MIR531b as well as three novel ones. Sixty-one target genes that corresponded to 11 known and 4 novel DE miRNAs were found to be co-localized with the three qDTYs, out of the 1746 target genes identified. We could validate miRNA-mRNA expression under drought for nine known and three novel miRNAs in eight different rice genotypes showing varying degree of tolerance. From our study, Osa-MIR2919, Osa-MIR3979, Osa-MIR528, Osa-MIR2091-5p and Chr01_11911S14Astr and their target genes LOC_Os01g72000, LOC_Os01g66890, LOC_Os01g57990, LOC_Os01g56780, LOC_Os01g72834, LOC_Os01g61880 and LOC_Os01g72780 were identified as the most promising candidates for drought tolerance at booting stage. Of these, Osa-MIR2919 with 19 target genes in the qDTYs is being reported for the first time. It acts as a negative regulator of drought stress tolerance by modulating the cytokinin and brassinosteroid signalling pathway.

Genetic analysis of heat tolerance in hot pepper: insights from comprehensive phenotyping and QTL mapping.

High temperatures present a formidable challenge to the cultivation of hot pepper, profoundly impacting not only vegetative growth but also leading to flower and fruit abscission, thereby causing a significant reduction in yield. To unravel the intricate genetic mechanisms governing heat tolerance in hot pepper, an F2 population was developed through the crossing of two distinct genotypes exhibiting contrasting heat tolerance characteristics: DLS-161-1 (heat tolerant) and DChBL-240 (heat susceptible). The F2 population, along with the parental lines, was subjected to comprehensive phenotyping encompassing diverse morphological, physiological, and biochemical heat-related traits under high temperature conditions (with maximum temperature ranging from 31 to 46.5°C and minimum temperature from 15.4 to 30.5°C). Leveraging the Illumina Nova Seq-6000 platform, Double digest restriction-site associated DNA sequencing (ddRAD-seq) was employed to generate 67.215 Gb data, with subsequent alignment of 218.93 million processed reads against the reference genome of Capsicum annuum. Subsequent variant calling and ordering resulted in 5806 polymorphic SNP markers grouped into 12 LGs. Further QTL analysis identified 64 QTLs with LOD values ranging from 2.517 to 11.170 and explained phenotypic variance ranging from 4.05 to 19.39%. Among them, 21 QTLs, explaining more than 10% phenotypic variance, were identified as major QTLs controlling 9 morphological, 3 physiological, and 2 biochemical traits. Interestingly, several QTLs governing distinct parameters were found to be colocalized, suggesting either a profound correlation between the QTLs regulating these traits or their significant genomic proximity. In addition to the QTLs, we also identified 368380 SSR loci within the identified QTL regions, dinucleotides being the most abundant type (211,381). These findings provide valuable insights into the genetics of heat tolerance in hot peppers. The identified QTLs and SSR markers offer opportunities to develop heat-tolerant varieties, ensuring better crop performance under high-temperature conditions.

Genome wide identification and characterization of the amino acid transporter (AAT) genes regulating seed protein content in chickpea (Cicer arietinum L.).

Amino acid transporters (AATs), besides, being a crucial component for nutrient partitioning system are also vital for growth and development of the plants and stress resilience. In order to understand the role of AAT genes in seed quality proteins, a comprehensive analysis of AAT gene family was carried out in chickpea leading to identification of 109 AAT genes, representing 10 subfamilies with random distribution across the chickpea genome. Several important stress responsive cis-regulatory elements like Myb, ABRE, ERE were detected in the promoter region of these CaAAT genes. Most of the genes belonging to the same sub-families shared the intron-exon distribution pattern owing to their conserved nature. Random distribution of these CaAAT genes was observed on plasma membrane, vacuolar membrane, Endoplasmic reticulum and Golgi membranes, which may be associated to distinct biochemical pathways. In total 92 out 109 CaAAT genes arise as result of duplication, among which segmental duplication was more prominent over tandem duplication. As expected, the phylogenetic tree was divided into 2 major clades, and further sub-divided into different sub-families. Among the 109 CaAAT genes, 25 were found to be interacting with 25 miRNAs, many miRNAs like miR156, miR159 and miR164 were interacting only with single AAT genes. Tissues specific expression pattern of many CaAAT genes was observed like CaAAP7 and CaAVT18 in nodules, CaAAP17, CaAVT5 and CaCAT9 in vegetative tissues while CaCAT10 and CaAAP23 in seed related tissues as per the expression analysis. Mature seed transcriptome data revealed that genotypes having high protein content (ICC 8397, ICC 13461) showed low CaAATs expression as compared to the genotypes having low protein content (FG 212, BG 3054). Amino acid profiling of these genotypes revealed a significant difference in amount of essential and non-essential amino acids, probably due to differential expression of CaAATs. Thus, the present study provides insights into the biological role of AAT genes in chickpea, which will facilitate their functional characterization and role in various developmental stages, stress responses and involvement in nutritional quality enhancement.

Single trait versus principal component based association analysis for flowering related traits in pigeonpea.

Pigeonpea, a tropical photosensitive crop, harbors significant diversity for days to flowering, but little is known about the genes that govern these differences. Our goal in the current study was to use genome wide association strategy to discover the loci that regulate days to flowering in pigeonpea. A single trait as well as a principal component based association study was conducted on a diverse collection of 142 pigeonpea lines for days to first and fifty percent of flowering over 3 years, besides plant height and number of seeds per pod. The analysis used seven association mapping models (GLM, MLM, MLMM, CMLM, EMLM, FarmCPU and SUPER) and further comparison revealed that FarmCPU is more robust in controlling both false positives and negatives as it incorporates multiple markers as covariates to eliminate confounding between testing marker and kinship. Cumulatively, a set of 22 SNPs were found to be associated with either days to first flowering (DOF), days to fifty percent flowering (DFF) or both, of which 15 were unique to trait based, 4 to PC based GWAS while 3 were shared by both. Because PC1 represents DOF, DFF and plant height (PH), four SNPs found associated to PC1 can be inferred as pleiotropic. A window of ± 2 kb of associated SNPs was aligned with available transcriptome data generated for transition from vegetative to reproductive phase in pigeonpea. Annotation analysis of these regions revealed presence of genes which might be involved in floral induction like Cytochrome p450 like Tata box binding protein, Auxin response factors, Pin like genes, F box protein, U box domain protein, chromatin remodelling complex protein, RNA methyltransferase. In summary, it appears that auxin responsive genes could be involved in regulating DOF and DFF as majority of the associated loci contained genes which are component of auxin signaling pathways in their vicinity. Overall, our findings indicates that the use of principal component analysis in GWAS is statistically more robust in terms of identifying genes and FarmCPU is a better choice compared to the other aforementioned models in dealing with both false positive and negative associations and thus can be used for traits with complex inheritance.

A Systematic Phylogenomic Classification of the Multidrug and Toxic Compound Extrusion Transporter Gene Family in Plants.

Multidrug and toxic compound extrusion (MATE) transporters comprise a multigene family that mediates multiple functions in plants through the efflux of diverse substrates including organic molecules, specialized metabolites, hormones, and xenobiotics. MATE classification based on genome-wide studies remains ambiguous, likely due to a lack of large-scale phylogenomic studies and/or reference sequence datasets. To resolve this, we established a phylogeny of the plant MATE gene family using a comprehensive kingdom-wide phylogenomic analysis of 74 diverse plant species. We identified more than 4,000 MATEs, which were classified into 14 subgroups based on a systematic bioinformatics pipeline using USEARCH, blast+ and synteny network tools. Our classification was performed using a four-step process, whereby MATEs sharing ≥ 60% protein sequence identity with a ≤ 1E-05 threshold at different sequence lengths (either full-length, ≥ 60% length, or ≥ 150 amino acids) or retaining in the similar synteny blocks were assigned to the same subgroup. In this way, we assigned subgroups to 95.8% of the identified MATEs, which we substantiated using synteny network clustering analysis. The subgroups were clustered under four major phylogenetic groups and named according to their clockwise appearance within each group. We then generated a reference sequence dataset, the usefulness of which was demonstrated in the classification of MATEs in additional species not included in the original analysis. Approximately 74% of the plant MATEs exhibited synteny relationships with angiosperm-wide or lineage-, order/family-, and species-specific conservation. Most subgroups evolved independently, and their distinct evolutionary trends were likely associated with the development of functional novelties or the maintenance of conserved functions. Together with the systematic classification and synteny network profiling analyses, we identified all the major evolutionary events experienced by the MATE gene family in plants. We believe that our findings and the reference dataset provide a valuable resource to guide future functional studies aiming to explore the key roles of MATEs in different aspects of plant physiology. Our classification framework can also be readily extendable to other (super) families.

Identification and characterization of MADS box gene family in pigeonpea for their role during floral transition.

MADS box genes are class of transcription factors involved in various physiological and developmental processes in plants. To understand their role in floral transition-related pathways, a genome-wide identification was done in Cajanus cajan, identifying 102 members which were classified into two different groups based on their gene structure. The status of all these genes was further analyzed in three wild species i.e. C. scarabaeoides, C. platycarpus and C. cajanifolius which revealed absence of 31-34 MADS box genes in them hinting towards their role in domestication and evolution. We could locate only a single copy of both FLOWERING LOCUS C (FLC) and SHORT VEGETATIVE PHASE (SVP) genes, while three paralogs of SUPPRESSOR OF ACTIVATION OF CONSTANS 1 (SOC1) were found in C. cajan genome. One of those SOC1 paralogs i.e. CcMADS1.5 was found to be missing in all three wild relatives, also forming separate clade in phylogeny. This SOC1 gene was also lacking the characteristic MADS box domain in it. Expression profiling of major MADS box genes involved in flowering was done in different tissues viz shoot apical meristem, vegetative leaf, reproductive meristem, and reproductive bud. Gene-based time tree of FLC and SOC1 gene dictates their divergence from Arabidopsis before 71 and 23 million year ago (mya), respectively. This study provides valuable insights into the functional characteristics, expression pattern, and evolution of MADS box proteins in grain legumes with emphasis on C. cajan, which may help in further characterizing these genes. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-020-02605-7.

Forty years of clinical excellence at the Dr A Lakshmipathi Neurosurgical Centre and Post-Graduate Institute of Neurological Surgery, Voluntary Health Services (VHS) Hospital.

The Achanta Lakshmipathi Neurosurgical Center (ALNC) and Post Graduate Institute of Neurological Surgery is a private teaching neurosurgical institution located in the VHS (Voluntary Health Services) Hospital Chennai. It has been a leader and trendsetter among the private academic neurosurgical training institutions, and because of its unique legacy, has influenced the progress of Neurosurgery in India. The center was the second neurosurgical Institute to be created by Prof. B Ramamurthi and has trained neurosurgeons in the unique ALNC school of Neurosurgery. The Institute has grown to become a centre of excellence in microsurgery, and spinal surgery and has become a training centre for neurosurgery since 1985. The unique humanitarian aspects of the Voluntary Health Services Hospital helped in bringing the best of Neurosurgery to all strata of society. Forty years after its inception, the ALNC continues its delivery of excellence in clinical neurosurgery and academics.

Cytosine Methylation of Isoflavone Synthase Gene in the Genic Region Positively Regulates Its Expression and Isoflavone Biosynthesis in Soybean Seeds.

Plants, being sessile organisms, have evolved several dynamic mechanisms of gene regulation. Epigenetic modification especially cytosine methylation and demethylation actively regulates the expression of genes. To understand the role of cytosine methylation during isoflavonoid biosynthesis and accumulation, we performed cytosine methylation analysis in the coding region of two isoforms IFS1 and IFS2 gene, in two contrasting soybean genotypes differing in total isoflavone content (NRC37: high isoflavone; and NRC7: low isoflavone). The results indicated increased 5-mC in both the isoforms in NRC37 (∼20.51% in IFS2 and ∼85% in IFS1) compared with NRC7 (∼7.8% in IFS2 and ∼2.5% in IFS1) genotype, which signifies the positive role of 5-mC in the coding region of the gene leading to enhanced expression. In addition, temporal expression profiling [35 days after flowering (DAF), 45, 55, and 65 DAF] of both the isoforms showed increasing trend of accumulation in both the genotypes with maximum in NRC37 at 65 DAF. To further establish a correlation between methylation and expression of transcripts, we quantified the different isoforms of isoflavone in both the genotypes across all the stages. Therefore, the finding of this study would certainly increase our understanding of epigenetic regulation of isoflavone biosynthetic pathway mediated by the cytosine methylation that would assist molecular breeders to get high-performing soybean genotypes with better isoflavone yield.

Conserved miRNAs modulate the expression of potential transcription factors of isoflavonoid biosynthetic pathway in soybean seeds.

Despite the significant importance of soybean isoflavone, the regulatory mechanism of miRNAs during its biosynthesis is highly unexplored. In the present work, nine existing miRNAs along with their ten corresponding target genes were identified and validated in soybean for their possible role during isoflavonoid biosynthesis and accumulation. Temporal expression analysis at four key stages of seed development (35, 45, 55 and 65DAF) of all the miRNA-target pairs showed varying degree of differential accumulation in two soybean genotypes (NRC37: high isoflavone; and NRC7: low isoflavone). Differential expression of MYB65-Gma-miR159, MYB96-Gma-miRNA1534, MYB176-Gma-miRNA5030, SPL9-Gma-miRNA156, TCP3, TCP4-Gma-miRNA319, WD40-Gma-miRNA162, UDP-glucose: flavonoid 3-O-glucosyltransferase-Gma-miRNA396, and CHI3-Gma-miRNA5434 showed an important relationship with their targets in both the soybean genotypes across all the stages. Therefore, the finding of the present work would certainly increase our understanding of molecular regulation of isoflavone biosynthetic pathway mediated by the miRNA which would guide molecular breeder to develop isoflavone rich soybean cultivars.

Genome-wide analysis identifies chickpea (Cicer arietinum) heat stress transcription factors (Hsfs) responsive to heat stress at the pod development stage.

The heat stress transcription factors (Hsfs) play a prominent role in thermotolerance and eliciting the heat stress response in plants. Identification and expression analysis of Hsfs gene family members in chickpea would provide valuable information on heat stress responsive Hsfs. A genome-wide analysis of Hsfs gene family resulted in the identification of 22 Hsf genes in chickpea in both desi and kabuli genome. Phylogenetic analysis distinctly separated 12 A, 9 B, and 1 C class Hsfs, respectively. An analysis of cis-regulatory elements in the upstream region of the genes identified many stress responsive elements such as heat stress elements (HSE), abscisic acid responsive element (ABRE) etc. In silico expression analysis showed nine and three Hsfs were also expressed in drought and salinity stresses, respectively. Q-PCR expression analysis of Hsfs under heat stress at pod development and at 15 days old seedling stage showed that CarHsfA2, A6, and B2 were significantly upregulated in both the stages of crop growth and other four Hsfs (CarHsfA2, A6a, A6c, B2a) showed early transcriptional upregulation for heat stress at seedling stage of chickpea. These subclasses of Hsfs identified in this study can be further evaluated as candidate genes in the characterization of heat stress response in chickpea.

A part of the upstream promoter region of SHN2 gene directs trichome specific expression in Arabidopsis thaliana and heterologous plants.

A promoter trap mutant line of Arabidopsis carrying a promoterless ß-glucuronidase (uidA) gene exhibited GUS expression predominantly in all the trichomes. In this mutant, the T-DNA insertion was localized at 147bp upstream of the putative start codon, ATG, of the At5g11190 (SHN2) gene. Transcript profiling of the SHN2 suggested a constitutive expression of the gene in all the tissues. Deletion analysis of the upstream sequences established that a 565bp (-594/-30) region confers trichome-specific gene expression. The trichomes isolated from young, mature and senesced leaf tissues also showed the presence of SHN2 transcript. The occurrence of multiple TSSs on the SHN2 gene sequence, presence of the SHN2 transcript in the homozygous trip mutant, despite an insertional mutation event, and diverse reporter gene expression pattern driven by 5' and 3' promoter deletion fragments, suggest a complex transcriptional regulation of SHN2 gene in Arabidopsis. The promoter sequence -594/-30 showed a conserved functional role in conferring non-glandular trichome-specific expression in other heterologous systems like Brassica juncea and Solanum lycopersicon. Thus, in the present study T-DNA tagging has led to the identification of a trichome-specific regulatory sequence in the upstream region of a constitutively expressed SHN2 gene. The study also suggests a complex regulation of SHN2 gene. Isolated trichome specific region retains its functions in other systems like Brassica and tomato, hence could be effectively exploited in engineering trichome cells in heterologous crop plants to manipulate traits like biopharming and insect herbivory.

Isolation, cloning, and characterization of a cuticle collagen gene, Mi-col-5, in Meloidogyne incognita.

Cuticle collagens form a major part of the nematode cuticle and are responsible for maintaining the overall shape of the animal and its protection from the external environment. Although substantial research on cuticle collagen genes has been carried out in Caenorhabditis elegans, their isolation and characterization in plant parasitic nematodes have been limited to a few genes only. In this study, a cuticle collagen gene, Mi-col-5, was isolated from root-knot nematode, Meloidogyne incognita. A partial segment of 402 bp was first cloned and analyzed on Gbrowse followed by subsequent cloning of the 1047 bp long full cDNA specifying the open reading frame. The deduced amino acid sequence showed 92% sequence identity with that of Mj-col-5. However, a transmembrane helix was predicted in Mi-col-5 which was not present in Mj-col-5. The conserved pattern of cysteine residues in Mi-col-5 suggested that it belonged to group 2 of nematode cuticle collagens but with a longer carboxy terminal region as was the case with Mj-col-5. Domain prediction revealed the presence of a nematode cuticle collagen N terminal domain and a pfam collagen domain along with collagen triple helix repeats. A phylogenetic tree based on the amino acid sequences showed evolutionary relationship of Mi-col-5 with cuticle collagens genes of other nematodes. 3D models for Mi-col-5 were predicted with the best confidence score of -2.78. Expression of Mi-col-5 transcript was found to be maximum in egg masses followed by adult females and J2s suggesting its role in the early stages of the development of the nematode during its life cycle.

Identification and characterization of Wilt and salt stress-responsive microRNAs in chickpea through high-throughput sequencing.

Chickpea (Cicer arietinum) is the second most widely grown legume worldwide and is the most important pulse crop in the Indian subcontinent. Chickpea productivity is adversely affected by a large number of biotic and abiotic stresses. MicroRNAs (miRNAs) have been implicated in the regulation of plant responses to several biotic and abiotic stresses. This study is the first attempt to identify chickpea miRNAs that are associated with biotic and abiotic stresses. The wilt infection that is caused by the fungus Fusarium oxysporum f.sp. ciceris is one of the major diseases severely affecting chickpea yields. Of late, increasing soil salinization has become a major problem in realizing these potential yields. Three chickpea libraries using fungal-infected, salt-treated and untreated seedlings were constructed and sequenced using next-generation sequencing technology. A total of 12,135,571 unique reads were obtained. In addition to 122 conserved miRNAs belonging to 25 different families, 59 novel miRNAs along with their star sequences were identified. Four legume-specific miRNAs, including miR5213, miR5232, miR2111 and miR2118, were found in all of the libraries. Poly(A)-based qRT-PCR (Quantitative real-time PCR) was used to validate eleven conserved and five novel miRNAs. miR530 was highly up regulated in response to fungal infection, which targets genes encoding zinc knuckle- and microtubule-associated proteins. Many miRNAs responded in a similar fashion under both biotic and abiotic stresses, indicating the existence of cross talk between the pathways that are involved in regulating these stresses. The potential target genes for the conserved and novel miRNAs were predicted based on sequence homologies. miR166 targets a HD-ZIPIII transcription factor and was validated by 5' RLM-RACE. This study has identified several conserved and novel miRNAs in the chickpea that are associated with gene regulation following exposure to wilt and salt stress.