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Morinda (Rubiaceae) is considerably recognized for its multiple uses viz. food, medicine, dyes, firewood, tools, oil, bio-sorbent etc. The molecular characterization of such an important plant would be very useful for its multifarious enhanced utilization. In the present study, 31 Morinda genotypes belonging to two different species Morinda citrifolia and Morinda tomentosa collected from different regions of India were investigated using Inter Simple Sequence Repeat (ISSR) markers. Fifteen ISSR primers generated 176 bands with an average of 11.7 bands per primer, of which (90.34%) were polymorphic. The percentage of polymorphic bands, mean Nei’s gene diversity, mean Shannon’s information index in Morinda tomentosa and Morinda citrifolia was [(69.89%, 30.68%); (0.21 ± 0.19, 0.12 ± 0.20); (0.32 ± 0.27 0.17 ± 0.28)] respectively, revealing higher polymorphism and genetic diversity in Morinda tomentosa compared to Morinda citrifolia. Structure, and UPGMA cluster analysis placed the genotypes into well-defined separate clusters belonging to two species Morinda tomentosa and Morinda citrifolia revealing the utility of ISSR markers in species differentiation. Distinct ecotypes within a particular species could also be inferred emphasizing the collection and conservation of Morinda genotypes from different regions, in order to capture the overall diversity of respective species. Further higher diversity of M. tomentosa must be advanced for its utilization in nutraceutical, nutritional and other nonfood purposes.

Thaumatin-like protein (TLP) is the well-known sweetest protein which plays a crucial role in diverse developmental processes and different stress conditions in plants, fungi and animals. The TLP gene family is extensively studied in different plant species including crop plants. Watermelon (Citrullus lanatus) is an important cucurbit crop cultivated worldwide; however, the comprehensive information about the TLP gene family is not available in watermelon. In the present study, we identified the 29 TLP genes as gene family members in watermelon using various computational methods to understand its role in different developmental processes and stress conditions. ClaTLP gene family members were not uniformly distributed on 22 chromosomes. Phylogenetic analysis revealed that the ClaTLP gene family members were grouped into 10 sub-groups. Further, gene duplication analysis showed thirteen gene duplication events which included one tandem and twelve segmental duplications. Amino acid sequence alignment has shown that ClaTLP proteins shared 16 conserved cysteine residues in their THN domain. Furthermore, cis-acting regulatory elements analysis also displayed that ClaTLP gene family members contain diverse phytohormone, various defense, and stress-responsive elements in their promoter region. The expression profile of the ClaTLP gene family revealed the differential expression of gene family members in different tissues and abiotic stresses conditions. Moreover, the expression profile of ClaTLP genes was further validated by semi-quantitative reverse transcriptase PCR. Taken together, these results indicate that ClaTLP genes might play an important role in developmental processes and diverse stress conditions. Therefore, the outcome of this study brings forth the valuable information for further interpret the precise role of ClaTLP gene family members in watermelon.

We observed a harmonic noise (HN) in DEutscher Geräte-Pool für Amphibische Seismologie ocean-bottom seismometers (OBSs) data recorded from the Andaman–Nicobar region. The HN is characterized by sharp spectral peaks with a fundamental frequency and several overtones occurring at integer multiples of the fundamental frequency. We used an automated algorithm to quantify the occurrence of HN for the entire four-month deployment period (1 January 2014 to 30 April 2014). The algorithm detected more than 23 days of HN for some OBS stations. The spectral analysis of the hourly count of HN shows distinct lunar and solar tidal periodicities at 4.14, 6.1, 6.22, 12, and 12.4 hr as well as 13.66 days. The observed periodicities provide evidence of tidal triggering of HN. The HN is generated by the strumming of head buoys due to seafloor currents initiated by oceanic tides in the Andaman–Nicobar region.

Millets and pseudocereals are climate resilient (in terms of less water requirement, tolerance to biotic and abiotic stresses, adaptability to low input conditions) and also known as nutri-cereals crops because of nutritional superiority (rich in essential amino acids, minerals, vitamins, bioactive compounds, dietary fibre, resistant starch, etc.) over other major cereals. Among millets and pseudocereals sorghum, pearl millet, foxtail millet, finger millet, proso millet, amaranth, buckwheat and quinoa are extensively studied in terms of molecular characterization and generation of genomic resources. But in other millets like kodo millet, little millet, barnyard millet, browntop millet, fonio [Digitaria exilis (Kipp.) Stapf; (D. iburua Stapf)], etc., molecular studies are meagre and needs to be expedited at a large scale using next-generation sequencing approaches to generate genomic resources in terms of whole genome sequence, makers, genes/QTLs, alleles, etc. The present chapter is a comprehensive view of the molecular studies carried out till date in millets and pseudocereals. It also delivers information to the research community regarding progress made and future studies to be undertaken for enhanced utilization of existing genetic and genomic resources in these crops for future food and nutritional security.

Monitoring volcanic activity along the submarine volcanoes that are usually induced by subsurface magmatism is a challenge. We present fresh set of Ocean Bottom Seismometer (OBS) data that shows geophysical evidence indicative of subsurface magmatism along the submarine volcanoes in the off Nicobar region, Andaman Sea. In this region, we observed for the first time, hybrid very long-period earthquakes documented by passive OBS experiment. These events were initiated by high-frequency (5–10 Hz) with a clear onset of P-phase followed by low-frequency (0.01–0.5 Hz) oscillations in the range of 300–600 s with a prominent high-frequency (10–40 Hz) hydro-acoustic phase. A total of 141 high-frequency events were detected on 21st and 22nd March 2014 out of which 71 were of low-frequency oscillations. These events are distributed in the northwest–southeast direction along the submarine volcanic arc and Seulimeum strand of Great Sumatra fault. Off Nicobar region has been witnessing frequent earthquake swarms since 26th December 2004 tsunamigenic Sumatra earthquake. These swarms occurred in January 2005, March and October 2014, November 2015 and March 2019. The occurrence of low-frequency earthquakes and prominent hydro-acoustic phase are suggestive of sub-surface tectonic and magmatic influence. We propose that upward movement of magma pulses from deeper magma reservoir to the shallow magma chamber activated the strike-slip movement of sliver faults and induced earthquake swarms in the off Nicobar region.

Background: Kodo millet (Paspalum scrobiculatum L) is an annual hardy crop grown in India from Kerala and Tamil Nadu in the south, to Rajasthan, Uttar Pradesh, and West Bengal in the north. It is known to have high drought tolerance and, for its potential to sustain in marginally less fertile soil. The grain has high nutritional properties thus possess medicinal values. Owing to multiple utility factors and sustainable growth rate amidst climate change, makes it an ideal crop for cultivation. In the present study accessions of Kodo millet ((Paspalum scrobiculatum L) from twelve different geographical regions of India were evaluated for quantitative and qualitative traits to determine its growth conditions under varied climatic conditions. Methods: Total of 96 indigenous germplasm were collected across the country and were sown in a breeding farm to grow selectively healthy crops in a randomized block design manner during kharif 2012 and 2013. Observations of quantitative traits were recorded on five arbitrarily selected plants in each replication for different physiological traits. Results: The statistical data revealed significant differences among all the studied accessions. Mainly IC482729 and IC404789 from Tamil Nadu had high biomass, straw yield, and yield per plant. IC396004 from Chhattisgarh showed advantageous performance in earliness with medium plant height. Therefore, the present findings helped in identifying elite germplasm accessions and could be effectively used in the Kodo millet enhancement program.

Understanding the level of genetic diversity and structure of landraces is essential for economical use of genetic resources. In the present study, we investigated the genetic diversity of 36 representative sample of cucumber genotypes based on 10 quantitative traits and 17 polymorphic simple sequence repeat (SSR) markers. Our result revealed variability in flowering behavior, growth habit and fruit characters. We found that the traits, days to opening of first female flower varied from 39.03 to 51.94, fruit length 6.09 to 30.01(cm), fruit weight 104.39 to 277.05(g) and yield per plant 699.38 to 1670.93(g). Genetic distance based on 17 SSR markers among 36 genotypes was quantified ranging from 0.03 to 0.70 indicated a wide diversity among the genotypes selected for evaluation in the present study. These primers produced 2-4 number of alleles with an average 2.76. Polymorphism information content varied from 0.005 to 0.550 with an average of 0.348. The observed heterozygosity mean was 0.098, while gene diversity or expected heterozygosity was 0.625 to 0.057. The distinct genotypes found in this study based on morpho-molecular characters will great interest to cucumber breeder for selection of diverse parent or production of mapping population.

The off Nicobar region in the Andaman Sea is witnessing frequent earthquake swarms after December 2004 Tsunamigenic earthquake in January 2005, March and October 2014, November 2015 and April 2019. In this study, we present the geophysical evidence of active volcanism in the Off Nicobar back-arc region on 21st and 22nd March 2014 based on a passive Ocean Bottom Seismometer (OBS) experiment. We detected a series of hybrid earthquake events characterized by the onset of high–frequency signal (1-10 Hz) which is followed by a long period waveform of up to 600s having a range of 0.1-1 Hz. The waveforms appear to be emergent and lack the onset of a distinct S-phase. We also observed a very high frequency (10-40 Hz) hydro-acoustic phase in the coda of long-period events. These hybrid events are considered to be volcano-tectonic (VT) events that may trigger magmatic activities in the Off Nicobar region. We have identified and located 141 high-frequency events on 21st and 22nd March 2014 using hypocent v.3.2 program and they are distributed along NW-SE direction aligning with the submarine volcanoes defining the volcanic arc as observed in the high-resolution bathymetry data. The fault plane solution of the major high-frequency events suggests strike-slip faulting with the strike, dip and rake values of 334°, 89° and 171°, respectively along the direction of the prevalent sliver strike-slip faulting in the Andaman back-arc region. We propose that the upward movement of magma is a plausible mechanism which can explain the frequent occurrence of earthquake swarms in the off Nicobar region. The stress generated from magma movement may initially trigger shallow VT events such as faulting or dike intrusions and later generate long period ringing associated with the resonance of the magma chamber. The shallow nature of the events also generates a hydroacoustic wave which is detected in the OBS experiment as the source region is in the SOFAR channel.

Agriculture in the Central Himalayan Region depends on the availability of suitable germplasm as well as natural conditions. Due to extreme weather conditions, food and nutrition security is a major issue for communities inhabiting these remote and inaccessible areas. Millets are common crops grown in these areas. Foxtail millet (Setaria italica(L.) P. Beauv) is an important crop and forms a considerable part of the diet in this region. The aim of the present study was to explore, collect, conserve and evaluate the untapped genetic diversity of foxtail millet at the molecular level and discover variability in their nutritional traits. A total of 30 accessions having unique traits of agronomic importance were collected and molecular profiling was performed. A total of 63 alleles were generated with an average of 2.52 alleles per locus and average expected heterozygosity of 0.37 ± 0.231. Significant genetic variability was revealed through the genetic differentiation (Fst) and gene flow (Nm) values. Structure-based analysis divided whole germplasm into three sub-groups. Rich variability was found in nutritional traits such as dietary fibre in husked grains, carbohydrate, protein, lysine and thiamine content. The collected germplasm may be useful for developing nutritionally rich and agronomically beneficial varieties of foxtail millet and also designing strategies for utilization of unexploited genetic diversity for food and nutrition security in this and other similar agro-ecological regions.

In the present study, morphological, biochemical and molecular diversities were assessed for 62 accessions and four checks of Perilla frutescens collected from Meghalaya, Nagaland, Arunachal Pradesh, Manipur, Mizoram and Sikkim states of the North-eastern Hill (NEH) region of India. In the field, 8 qualitative and 13 quantitative traits were recorded to assess the diversity at the morphological level. Oil, protein, total phenol and fatty acids profiling was done to estimate diversity present at biochemical level and accessions namely IC524554, IC524504, IC52445, IC422885, IC275959, IC016443, IC006444, IC006442 and IC599246 were found with more than 50% oil content. Fourteen STMS markers which showed reproducible and clear amplification were selected for diversity study. Total 92 bands were amplified with 14 STMS primers out of which 92.85 (%) bands were polymorphic. Polymorphic information content (PIC) for STMS primers varied from 0.32 for primer GBFM75 to 0.92 for primer KWPE57. The average PIC was with an average of 0.62, and the gene diversity varied from 0.41 to 0.92. Cluster analysis based on biochemical and molecular characterization divided Perilla accessions into four groups whereas; morphological (qualitative and quantitative) markers divided accessions into three groups. Based on population structure analysis three clear populations were obtained. The principal coordinate analysis (PCoA) in Perilla accessions with STMS markers showed that the variation explained by the first three axes was 31.16%. Analysis of molecular variance (AMOVA), based on the hierarchical cluster showed 6% diversity among population, 87% among individual and 6% within the individual, whereas the model based approach showed 21% diversity among population, 73% among individual and 6% within the individual. The study based on genetic diversity and population structure showed that great extent of diversity exists in Perilla accessions collected from NEH region of India and accessions; more than 50% oil content can be utilized for oil improvement programme and industrial applications.

SUMMARYThe mountain ecosystem of the Central Himalayan Region is known for its diversity of crops and their wild relatives. In spite of adverse climatic conditions, this region is endowed with a rich diversity of millets. Hence, the aim of the present study was to explore, collect, conserve and evaluate the diversity of barnyard millet (Echinochloa frumentacea) to find out the extent of diversity available in different traits and the traits responsible for abiotic stress tolerance, and to identify trait-specific accessions for crop improvement and also for the cultivation of millets in the region as well as in other similar agro-ecological regions. A total of 178 accessions were collected and evaluated for a range of morpho-physiological and biochemical traits. Significant variability was noted in days to 50% flowering, days to 80% maturity, 1000 seed weight and yield potential of the germplasm. These traits are considered to be crucial for tailoring new varieties for different agro-climatic conditions. Variations in biochemical traits such as lipid peroxidation (0·552–7·421 nmol malondialdehyde formed/mg protein/h), total glutathione (105·270–423·630 mmol/g fresh weight) and total ascorbate (4·980–9·880 mmol/g fresh weight) content indicate the potential of collected germplasm for abiotic stress tolerance. Principal component analysis also indicated that yield, superoxide dismutase activity, plant height, days to 50% flowering, catalase activity and glutathione content are suitable traits for screening large populations of millet and selection of suitable germplasm for crop improvement and cultivation. Trait-specific accessions identified in the present study could be useful in crop improvement programmes, climate-resilient agriculture and improving food security in areas with limited resources.

Germin-like protein (GLP) genes in plants constitute a multigene family that functions in a variety of biological processes, such as plant growth and development and respond to abiotic and biotic stresses. Available genome sequences of foxtail millet (Setaria italica) have facilitated the identification and delineation of the GLP gene family, which is perhaps the first report in any millet crop. A total of 20 SiGLP genes were mapped in six of the nine foxtail millet chromosomes. The majority of these SiGLP genes, except six, clustered into five known germin (GER) groups and revealed group-specific variations in their gene structure and conserved protein motifs. The SiGLP genes shared homologous relationship within and across plant genomes as per their syntenic chromosomal regions, indicating gene duplication and expansion in course of plant evolution. Gene expression dynamics revealed four out of the 20 SiGLP genes having a putative functional role in different tissues. The presence of diverse cis-acting regulatory elements in the putative SiGLP promoter sequences and homology-based 3-D protein structure predictions revealed their possible functional diversity. The present work encompasses a molecular insight into the organization and functions of SiGLP gene family members. This may serve as a platform for functional analysis and their efficient utilizations in genetic improvement of foxtail millet and other related crops.

Notwithstanding the disadvantages of meager reproducibility and usual disassociation with any gene areas, ISSR, RAPD markers have been used for various molecular plant genetics analysis. Start codon targeted (SCoT) plant DNA markers, have principles of dominance and reproducibility but are advantageous as they mark the short conserved region flanking the ATG start codon in the genome that can further be used to target genes easily and efficiently. In the present study, we have used SCoT marker technique for genetic diversity analysis, estimating gene flow and population structure in the 39 bottle gourd germplasm collected from different regions of India. One hundred and sixty-one (161) amplicons were produced by 20 SCoT markers, generating 82.61% polymorphism. Using the marker data, we examined the distribution of genetic variation within and between populations. A Bayesian approach-based clustering program and population STRUCTURE analysis, proposed minor regional clustering based on geographical regions, with clear admixturing between both population signifying long-distance distribution measures between the populations. It is apparent from the results that SCoT markers are promising markers in research for diversity analysis and to target genes easily for the breeder, geneticist, and evolutionists.

Investigation of genetic diversity is essential for the selection of parents for crop breeding and conservation of genetic resources. To estimate the genetic variability and population structure in the midst of 45 accessions of sponge gourd brought together from different geographical areas of India, morphological traits and two molecular markers, ISSR and SCoT markers were compared. Principal components analysis of 20 morphological traits showed 72.70% variability and significant positive correlations between fruit traits. All three marker techniques clustered all accessions into two groups with few outgroups. High level of polymorphism was observed among ISSR (74.6%) and SCoT (71.5%) primers. The Bayesian model revealed the hidden grouping and showed admixture type of population. The diversity pattern is influenced by genetic marker used, as different molecular markers have different polymorphism evaluation efficiency. This study can be helpful in amplifying the genetic base and selection of specific traits for breeding. Thus, ISSR and SCoT markers are potential marker for identification in sponge gourd and provide valuable data on its genetic correlation and structure.

Fungal blast disease is one of the major constraints in finger millet production. Breeding for disease resistance in finger millet, needs characterization of genetic polymorphism among and between the resistant and susceptible genotypes. In total, 67 finger millet genotypes, which are resistant or susceptible to fungal blast disease, were analysed using sequence-related amplified polymorphism (SRAP) and simple sequence repeat (SSR) markers to assess genetic variations and select diverse parents. Twelve each of SRAP and SSR primers produced 95.1 and 93.1% polymorphic bands and grouped them into unweighted pair-group method with arithmetic average clusters. Two of the finger millet genotypes, IE 4709 (blast resistant) and INDAF 7 (susceptible) were distinguished as most diverse genotypes as parents. Several genotype-specific bands observed with SSR primers are potential in developing genotype-specific markers. A high genetic diversity within the resistant and susceptible genotypes, rather than between them, was revealed through Nei's gene diversity (h) index and analysis of molecular variance. The finding helps us to understand the extent of genetic polymorphism between blast disease resistant and susceptible finger millet genotypes to exploit in resistance breeding programs.

Bottle gourd [ Lagenaria siceraria (Mol.) Standl.] is an easy growing climber that has made great impact due to its medicinal importance. For estimating genetic diversity among accessions in breeding programs, SSR markers are an essential tool, but for the species that have meager number of these markers available, their development is a challenging aspect. In the present study a microsatellite-enriched library was constructed from the genotype ‘Pusa Santushti’. Sequencing of 100 putative SSR-positive clones from a total of 220 clones provided 44 SSR repeats and primer pairs could be designed for a total of 40 SSRs. Of these, 30 (75%) primer pairs yielded scorable amplicons and seven (17.5%) primers showed polymorphism among 40 bottle gourd accessions. The 20 polymorphic alleles from seven polymorphic markers were used for UPGMA dendrogram and population structure analysis; both revealed that five populations are present in the 40 accessions that did not group consistent with their geographical origins probably due to gene flow. The results of this study provide 30 novel SSR markers that would be valuable in agriculture via plant breeding, phylogenetic relationships, cultivar identification and linkage mapping in cultivated bottle gourd as well as related cucurbits species. Significantly, 49 partial genome sequences were also isolated that can be helpful in further gene based studies in this vegetable crop.

Luffa cylindrica(L.) M. Roem. is an underutilized vegetable and a potential biodiesel crop for future. Its fruits are edible and used as vegetable. To aid in the selection of lines for breeding, genetic variation and structure of ten populations ofL. cylindricawere determined with three morphological characters and 23 sequence-related amplified polymorphism (SRAP) markers. All the three morphological characters were found diverse among 45 accessions. The SRAP primers produced a total of 177 bands, out of which 129 were polymorphic. Informative markers assessed by different measures (polymorphism information content = 0.18, marker index = 1.26, resolving power = 2.87) will direct the selection of primers for cultivar identification inL. cylindrica. Low level of genetic differentiation among populations and higher level within populations (Gst= 0.4073,Nm= 0.7277,He= 0.124,I= 0.20) was detected that might be due to cross-pollinated nature ofL. cylindrica. The clustering pattern obtained through dendrogram and principal coordinate analysis was loosely concordant with the geographical distribution. The Bayesian structure analysis indicated an admixture type of population distribution. The results designate that SRAP and morphological markers are informative for characterization ofL. cylindricaand identification of distinctive cultivars.

Improved breeding for developing fruit quality in bottle gourd (Lagenaria siceraria (Mol.) Standl.) necessitates knowledge regarding its genetic diversity. To achieve this, a set of 108 locus-specific SSR markers has been developed in bottle gourd by cross-species transferability from 995 mapped Cucumis sativus SSR markers. During screening, 280 primer pairs amplified in the bottle gourd germplasm, which were further evaluated in a diverse set of 42 lines, resulting in 19 polymorphic, 89 monomorphic, 15 with multiple bands, and the rest 157 showed no or very non-specific amplification. The 19 polymorphic primer pairs produced a total of 54 alleles. Gene diversity, Shannon's information index, and Nei's coefficient of differentiation were calculated suggesting a moderate genetic variation at the species level. A model-based population structure analysis divided these germplasm into two subpopulations. This marker set will be applicable for evaluating the genetic structure for association mapping, DNA fingerprinting, and mounting linkage maps and will be a practical tool set for further genetics. This study provides one of the first quantitative views of population genetic variation in bottle gourd.

Morinda tomentosa Heyne (Rubiaceae) an evergreen small tree also known as Aal or Indian Mulberry or Nunaa has broad range of therapeutic and nutritional value and is broadly used for making morindone dye for the dyeing of silk, cotton and wool. This is the first report wherein twenty genotypes of M. tomentosa, an underutilized fruit plant collected from Madhya Pradesh, India were studied for genetic diversity analyses using 131 Start Codon Targeted Markers (SCoT) (gene based) and 97 Random Amplified Polymorphic DNA (RAPD) and 70 Inter Simple Sequence Repeat (ISSR) (neutral) markers. SCoT markers showed the highest level of polymorphism, Shannon’s Information Index and Polymorphism Information Content (70.23 %; 0.31 ± 0.27; 0.189 ± 0.103), while the total number of bands per primer (7.0) was highest for ISSR markers. Nei’s gene diversity (0.20) was found similar for both ISSR and SCoT markers. And geographical clustering was most pronounced with ISSR followed by SCoT and RAPD markers. Cumulative marker data revealed best clustering of genotypes based on their areas of the collection. And individually, our results showed the efficacy of both SCoT and ISSR (co-phenetic correlation values of 0.79 and 0.76 respectively) over RAPD (co-phenetic correlation value of 0.69) markers for genetic diversity and geographical patterning studies of M. tomentosa. Additionally, structure analysis grouped the twenty M. tomentosa genotypes into two sub-populations, this structuring and the identified markers can be utilized for making further strategies for collection and conservation of M. tomentosa from Madhya Pradesh and other states of India as well as for global collections.

Genetic diversity analysis was undertaken in 42 geographically distant genotypes accessions of bottle gourd (Lagenaria siceraria) from India northeastern (14) and northern region (28) using inter-simple sequence repeat (ISSR) markers. A total of 209 amplified bands were obtained from 20 ISSR primers used in this study, of which 186 were polymorphic with 89.00 % band polymorphism. Various parameters namely, observed number of alleles, effective number of alleles, Nei’s gene diversity/heterozygosity, resolving power, Shannon’s information index and gene flow were estimated under experiment. Jaccard’s similarity coefficient matrix was generated for pairwise comparisons between individual ISSR profiles and UPGMA cluster analysis based on this matrix showed clustering into six groups. Jaccard’s coefficient of similarity values ranged from 0.409 to 0.847, with a mean of 0.628 revealing a moderate level of genetic diversity. The Bayesian model-based approach to infer hidden genetic population structures using the multilocus ISSR markers revealed two populations among the 42 genotypes. This is the first report on the assessment of genetic variation using ISSR markers in this medicinal vegetable plant, and this study of diversity analysis will be helpful in analyzing future hybrid breeding strategy and devising effective germplasm exploration and conservation strategy.

Genetic diversity and population structure were analyzed in 67 diverse finger millet accessions of African and Indian origin. A total of 69 alleles were generated with a mean of 4.0 alleles per locus and with an average gene diversity of 0.471. Molecular diversity parameters showed higher values in African accessions. Nineteen rare and nine unique alleles were observed and the identified accessions can be a potential source for further improvement of finger millet. Clustering of south Indian accessions with African lowland types and north/highland Indian accessions with that of African highlands was also observed. Structure analysis revealed the distinctness of Ugandan accessions compared to other African accessions and five major sub-populations useful for parental selection, conservation, and utilization of finger millet.

We employed degenerate primers to amplify nucleotide-binding site (NBS) domain of resistance gene candidates (RGCs) from Tomato Leaf Curl New Delhi Virus (ToLCNDV) resistant Luffa cylindrica (sponge gourd) genotype, DSG-6. Sixteen non-redundant sequences of RGCs were identified with un-interrupted open reading frames (ORFs) and high amino acid sequence homologies (60–98%) to various nucleotide-binding site leucine-rich repeat (NBS-LRR) proteins from GenBank database. Alignment of the deduced amino acid sequence and phylogenetic analysis of the NBS domain revealed six and ten sponge gourd (sg) RGCs belong to the Toll Interleukin Receptor (TIR) and non-TIR group of NBS-LRR genes, respectively. The sgRGCs consisted of conserved NB-ARC [homologous region shared with APAF-1 (apoptotic protease-activating factor-1), R proteins and CED-4 (Caenorhabditis elegans death-4 protein)] domain from P-loop nucleoside triphosphatase (NTPase) family and characteristic P-loop, Kinase-2, RNBS-A, Kinase-3A and GLPL motifs. The comparative analysis of expression profiles of sgRGCs in asymptomatic and field-driven symptomatic leaf tissues of ToLCNDV resistant and susceptible genotypes revealed RGCLc28 is expressed consistently in resistant genotypes. The differentially expressed RGCLc28 of DSG-6 is predicted to have strong association with the resistance trait against the leaf curl and mosaic disease in sponge gourd and may serve as important genomic resource for candidate gene discovery.

SummarySponge gourd (Luffa cylindrica Roem.) is a popular cucurbitaceous vegetable on the Indian sub-continent. The crop is severely affected by Tomato Leaf Curl New Delhi Virus (ToLCNDV) a Geminivirus causing a yellow mosaic disease which results in 100% crop loss. Natural epiphytotic and challenge inoculation experiments revealed that DSG-6, an advanced inbred breeding line of L. cylindrica Roem., was resistant to ToLCNDV during both the Spring-Summer and rainy seasons of 2006 and 2007. Resistance was confirmed by PCR amplification with viral coat protein gene-specific primers that revealed a gene-specific band of 750 bp in susceptible (positive control) plants, but no 750 bp band in resistant plants. The inheritance of ToLCNDV resistance was studied through challenge inoculations in F2 and backcross (B1 and B2) populations of a cross between a resistant female (DSG-6) and a susceptible male parent (‘Pusa Sneha’). This revealed the dominant monogenic inheritance of the resistance gene. Two sequence-rela...

EST-SSR markers were developed using sequence information from 1740 expressed sequence tags (ESTs) of finger millet available in the public domain. A set of 31 SSR markers were synthesized based on di, tri, tetra and penta-nucleotide repeat sequences. These were used for PCR analysis of 11 elite germplasm lines of finger millet of Indian and African origin. Out of 31 SSR markers, amplification products were obtained for 17 primer pairs. Of these nine were found polymorphic with two alleles per locus. These 17 SSR primer pairs were also tested for amplification in three varieties of pearl millet (Pennisetum glaucum) and 11 could be transferred to pearl millet. The informative EST SSR markers developed, can be used in finger millet as well as pearl millet genetic improvement projects.

SummaryWatermelon, an important fruit crop in the family Cucurbitaceae, currently has few available Simple Sequence Repeat (SSR) markers. This study developed Expressed Sequence Tag-Simple Sequence Repeat (EST-SSRs) markers from watermelon and examined their transferability to Cucumis spp. We mined and characterised EST-SSRs from 1,762 watermelon Expressed Sequence Tags (ESTs) retrieved from the National Centre for Biotechnology Information (NCBI) database. Two hundred and thirty-two SSRs were detected following an analysis of the EST sequences and primer pairs were designed for these sequences using the “SSR Primer” programme. A subset of 40 new primer pairs flanking di-, tri-, tetra-, and penta-nucleotide repeat sequences were synthesised. These primer pairs were evaluated for amplification and polymorphism using DNA from seven watermelon varieties from India. Clear amplification products were obtained for 31 primer pairs, of which seven were found to be polymorphic with a mean allele number of two per ...

Kodo millet (Paspalum scrobiculatum L.) is known for its high nutritive value, dietary fiber, antioxidant activity, as well as for drought tolerance. It is primarily grown as a grain in India and in Africa it is either cultivated or harvested in wild. Neutral—ISSR (inter simple sequence repeat) as well as functional—SCoT (start codon targeted) and SRAP (sequence-related amplified polymorphism) markers were employed for genetic diversity studies in 96 accessions of kodo millet collected from diverse regions of India. The genetic diversity parameters like average bands per primer, Polymorphic information content, Nei’s gene diversity and Shannon’s information index of 11.22, 9.69; 0.12, 0.11; 0.15 ± 0.14, 0.13 ± 0.13 and 0.26 ± 0.21, 0.22 ± 0.19 was observed with neutral and functional markers respectively. Neutral markers were showing higher values as compared to functional markers for the genetic diversity parameters as discussed. Structure based analysis placed all the accessions into four sub-groups not strictly according to their geographical locations. The accessions from Bihar followed by Karnataka were showing high diversity based on both the marker systems useful for designing exploration, conservation and germplasm enrichment strategies. Further, the set of diverse accessions selected based on these markers would serve as potential sources of unique alleles and may be exploited in future for enhancement and utilization of kodo millet germplasm. Usage of African gene pool and wild species for broadening the genetic base of Indian kodo millet was also suggested based on the present studies.

Random Amplified Polymorphic DNA (RAPD) analysis was performed for the identification and assessment of genetic relationships in Indian sorghum comprising released varieties, hybrids and their parental lines (A, B and R-lines). Twenty-three random decamer primers generated 151 amplicons, of which 87 were found to be polymorphic (57.6%). The primer OPL-03 was the most informative as it could alone discriminate 13 accessions out of the 37 studied. The accessions 27B, C 43, CSV 14R and HC 6 were found to have specific bands. Four of the male sterile (27A, 296A, 2219A and AKMS 14A) lines and their respective maintainer (27B, 296B, 2219B and AKMS 14B) lines could be easily differentiated with thirteen random primers (OPA-09, OPC-02, OPD-07, OPE-04, OPE-16, OPG-09, OPL-01, OPL-03, OPL-05, OPL-15, OPL-18, OPV-01 and OPX-12). Based on Jaccard’s similarity coefficient values, the most distant two accessions were CS 3541 and CSV 14R and the closest were 104A and 104B, with similarity values of 0.64 and 1.00 respectively. The average Jaccard’s similarity coefficient of 0.78 revealed low level of genetic diversity in the investigated material. The dendrogram generated by UPGMA could group all the accessions into distinct clusters consistent with established classification viz. grain and forage sorghum and known pedigree information.

A total of 38 finger millet genotypes including 18 released varieties and 20 landraces from India were evaluated and compared based on RAPD, ISSR markers and morphological data collectively. RAPD markers showed higher polymorphism (61.62%) as compared to ISSR (57.00%) markers. The mean number of bands per primer and Jaccard's similarity coefficients generated for the markers RAPD, ISSR was 12.9; 0.810 and 14.3; 0.782 respectively. UPGMA clustering, and Structure analysis placed the landraces and varieties in separate groups with some exceptions. The data for 13 qualitative traits revealed diversity mainly for ear shape and ear size. ANOVA analysis of the 14 quantitative traits showed most of the characters to have signifi cant difference, representing the presence of genotypic differences among the 38 genotypes studied. The morpho-variability as well as variation based on molecular markers was higher in the landraces compared to the varieties. The usage of more diverse landraces as genitors to augment the genetic base and identify genes for adaptive and nutritional variations as well as conservation of more landraces to maximize the available genetic diversity of finger millet was emphasized.

Sixteen representative a ccessions of proso millet [Panicum miliaceum] having distinct traits of agronomic importance were collected from altitudinal range of 510–2,695 m asl in the Central Himalayan Region (CHR) of India. Considerable diversity was found in morpho-physiological traits viz., leaf length (16.80–32.00 cm), leaf width (1.7–2.1 cm), plant height (57.00–134.00 cm), days to 50 % flowering (34–54), days to 80 % maturity (111–144), and 1,000 seed weight (0.68–1.86 g). Collected accessions have been evaluated for a battery of biochemical parameters viz., chlorophyll, carotenoids, lipid peroxidation, cellular hydrogen peroxide, activity of nitrate reductase, lipoxygenase, catalase, peroxidase, superoxide dismutase along with super oxide free radical formation, glutathione (total, reduced, and oxidized), glutathione reductase, glutathione S-transferase, ascorbate (total, reduced, and oxidized), monodehydroascorbate reductase, and didehydroascorbate reductase. The sets of 12 genic-SSRs (simple sequence repeats), 54 ISSR (inter simple sequence repeats), and 40 SRAP (sequence related amplified polymorphism) markers were used to study the level of genetic diversity, and Nei’s gene diversity value of 0.20 was obtained with both ISSR and SRAP markers. SRAP markers showed higher average number of polymorphic bands, % polymorphism, polymorphic information content (PIC), and Shannon information index compared to ISSR markers; genic-SSRs showed no allelic variation. Cluster analysis shows close groupings of germplasm based on morpho-physiological traits as well as molecular markers. The diverse germplasm identified based on molecular markers with considerable diversity in morpho-physiological traits may be utilized for development of climate resilient cultivars.

With the advent of Next-generation sequencing and bioinformatic tools, gene expression studies have changed dramatically. Whole transcriptome studies are providing valuable resources for generating molecular markers like microsatellites and single-nucleotide polymorphisms and candidate genes. Transcriptome sequencing or RNA-Seq becomes more relevant in cases where whole-genome sequencing is not affordable. It provides cost-effective, functionally relevant information and generation of huge number of genomic resources in a reasonable time as compared to traditional approaches. The resulting information may be useful to address areas like differential gene expression, isoforms or allele-specific expression, characterization of regulatory elements, alternative splicing, RNA editing, population genetics and system biology etc.

Genetic diversity was studied in 47 Luffa genotypes with 17 EST-SSR primers, which generated 34 alleles, ranging 1–2 loci per primer. Forty seven genotypes were broadly classified into two different clusters. ClusterI comprised of genotypes DRG-98, Utkal Tripti, DRG-6, Sel-102, Pusa Nasdar, Pusa Nutan, Arka Sujat, DRG-73, DRG-61, DRG-42 and DRG-50, while Cluster II consisted of 36 genotypes, respectively. EST-SSR primer C90830_G3was found to be highly informative with PIC value of 0.3750. The variability in the species could be creditedto introgression and selection as a result of long history of cultivation under varied climatic conditions. Thepresent data provide adequate evidence of the applicability of EST-SSR markers for diversity analyses, cultivaridentification and characterization of the Luffa germplasm.

Population structure and genetic variation was estimated for 40 Indian and African finger millet genotypes using 237 random amplified polymorphic DNA (RAPD) and 16 morphological markers revealing differences between African and Indian groups. African genotypes showed 53.59%; 0.17±0.19; 0.27±0.27 compared to 48.10%; 0.15±0.19; 0.24±0.27 polymorphism, Nei's gene diversity and Shannon's Information index, respectively in Indian genotypes. Primers OPM-20, OPW-04, OPX-11 were identified as the most informative primers in terms of high % polymorphism and Nei's gene diversity values. Population structure analysis revealed the existence of two distinct sub-groups, correlated well with primary and secondary centers of finger millet diversity and can be utilized to enhance and widen finger millet germplasm base.