Lal Babu Chaudhary

Universal plant DNA barcode loci may not work in complex groups: a case study with Indian berberis species.

Background The concept of DNA barcoding for species identification has gained considerable momentum in animals because of fairly successful species identification using cytochrome oxidase I (COI). In plants, matK and rbcL have been proposed as standard barcodes. However, barcoding in complex genera is a challenging task. Methodology and Principal Findings We investigated the species discriminatory power of four reportedly most promising plant DNA barcoding loci (one from nuclear genome- ITS, and three from plastid genome- trnH-psbA, rbcL and matK) in species of Indian Berberis L. (Berberidaceae) and two other genera, Ficus L. (Moraceae) and Gossypium L. (Malvaceae). Berberis species were delineated using morphological characters. These characters resulted in a well resolved species tree. Applying both nucleotide distance and nucleotide character-based approaches, we found that none of the loci, either singly or in combinations, could discriminate the species of Berberis. ITS resolved all the tested species of Ficus and Gossypium and trnH-psbA resolved 82% of the tested species in Ficus. The highly regarded matK and rbcL could not resolve all the species. Finally, we employed amplified fragment length polymorphism test in species of Berberis to determine their relationships. Using ten primer pair combinations in AFLP, the data demonstrated incomplete species resolution. Further, AFLP analysis showed that there was a tendency of the Berberis accessions to cluster according to their geographic origin rather than species affiliation. Conclusions/Significance We reconfirm the earlier reports that the concept of universal barcode in plants may not work in a number of genera. Our results also suggest that the matK and rbcL, recommended as universal barcode loci for plants, may not work in all the genera of land plants. Morphological, geographical and molecular data analyses of Indian species of Berberis suggest probable reticulate evolution and thus barcode markers may not work in this case.

Analysis of genetic diversity, population structure and linkage disequilibrium in elite cotton (Gossypium L.) germplasm in India

An understanding of the level of genetic diversity is a prerequisite for designing efficient breeding programs. Fifty-one cultivars of four cotton species (Gossypium hirsutum, G. barbadense, G. herbaceum and G. arboreum) representing core collections at four major cotton research stations with a wide range of eco-geographical regions in India were examined for the level of genetic diversity, distinct subpopulations and the level of linkage disequilibrium (LD) using 1100 amplified fragment length polymorphism (AFLP) markers with 16 primer pairs combinations. The AFLP markers enabled a reliable assessment of inter- and intra-specific genetic variability with a heterogeneous genetic structure. Higher genetic diversity was noticed in G. herbaceum, followed by G. arboreum. The genetic diversity in tetraploid cotton species was found to be less than that in the diploid species. The genotypes VAGAD, RAHS14, IPS187, 221 557, Jayhellar of G. herbaceum and 551, DLSA17, 221 566 of G. arboreum were identified as the most diverse parents, useful for quantitative trait loci (QTL) analysis in diploid cotton. Similarly, LRA 5166, AS3 and MCU5 of G. hirsutum and B1, B3, Suvin of G. barbadense were most diverse to develop mapping populations for fibre quality. The internal transcribed spacer sequences were sufficient to resolve different species and subspecies of diploid cotton. Low level of genome-wide LD was detected in the entire collection (r2 = 0.07) as well as within the four species (r2 = 0.11–0.15). A strong agreement was noticed between the clusters constructed on the basis of morphological and genotyping data.

Tree species of the Himalayan Terai region of Uttar Pradesh, India: a checklist

The study catalogues a sum of 278 tree species belonging to 185 genera and 57 families from the Terai region of Uttar Pradesh. The family Fabaceae has been found to exhibit the highest generic and species diversity with 23 genera and 44 species. The genus Ficus of Moraceae has been observed the largest with 15 species. About 50% species exhibit deciduous nature in the forest. Out of total species occurring in the region, about 63% are native to India. Almost all tree species have some importance in one and another way for the local people. In the study area about 80 species flower in the spring, 74 in the summer, 73 in the winter and 30 in rainy season. As per the existing IUCN Red List, 24 species of the area fall under different categories. Presence of these red listed trees in the study area enhances the importance of their proper management and conservation plan.

Isolated Ficus trees deliver dual conservation and development benefits in a rural landscape

Many of the world’s rural populations are dependent on the local provision of economically and medicinally important plant resources. However, increasing land-use intensity is depleting these resources, reducing human welfare, and thereby constraining development. Here we investigate a low cost strategy to manage the availability of valuable plant resources, facilitated by the use of isolated Ficus trees as restoration nuclei. We surveyed the plants growing under 207 isolated trees in Assam, India, and categorized them according to their local human-uses. We found that Ficus trees were associated with double the density of important high-grade timber, firewood, human food, livestock fodder, and medicinal plants compared to non-Ficus trees. Management practices were also important in determining the density of valuable plants, with grazing pressure and land-use intensity significantly affecting densities in most categories. Community management practices that conserve isolated Ficus trees, and restrict livestock grazing and high-intensity land-use in their vicinity, can promote plant growth and the provision of important local resources.

Periodicity of different phenophases in selected trees from Himalayan Terai of India

The temporal phenology of leaf bud bursting, leaf initiation, leaf maturation, leaf fall, flower initiation, fruit initiation and fruit fall was recorded for eight tree species (Ficus hispida, F. squamosa, Mallotus nudiflorus, M. philippensis, Shorea robusta, Schleichera oleosa, Pongamia pinnata and Terminalia arjuna) in the tropical moist deciduous forest of Himalayan Terai region from November 2009 to October 2012. The study revealed that a short low temperature dry period, sufficient winter rain and temperature rise are the triggering factors for summer leaf flushing and, the increased soil water availability for second leaf flushing in rains. Initiation of flowering with leaf emergence in the dry period supports higher rate of fruit setting due to maximum availability and activities of pollinators. The dispersal and post dispersal success of fruits increased by their ripening before and/or in the rainy season. In T. arjuna, no correlation has been found between the fruiting and rains. M. nudiflorus and M. philippensis initiate leaves and flowers with the first significant increase in temperature and photoperiod and are thus suggested as the potential tree species for climate change studies in tropics.

Relation of Forest Structure and Soil Properties in Natural, Rehabilitated and Degraded Forest

Relation of Forest Structure and Soil Properties in Natural, Rehabilitated and Degraded Forest Plant community structure, species diversity and soil properties of natural, rehabilitated and degraded forests were studied in order to assess relationship of different forests structure and soil properties in upper Indo-Gangetic plain of Uttar Pradesh state of India. The composition of species, population bundance and importance value of the woody species were investigated in each forest; the representative soil samples from 30 cm depth of each forest were also analyzed for the soil properties. Dominant families at the natural forest are Moraceae (21.9%) and Rubiaceae (15.6%) while at the rehabilitated forest are Moraceae (53.8%) and Fabaceae (23%). In the degraded forest, the Moraceae and Fabaceae are dominant families occupy 33% each. These among forest community structure indicate that degraded forests are less complex ecosystems than natural forest stands.

The UPLC–ESI–QqQLIT–MS/MS method for quantitative determination of phytochemicals in ethanolic extracts of different parts of eight Ficus species: Development and validation

ABSTRACT Ficus and validation of the ultra performance liquid chromatography–electrospray ionization hybrid triple quadrupole–linear ion trap–tandem mass spectrometry (UPLC–ESI–QqQLIT–MS/MS) method in a multiple-reaction monitoring (MRM) mode for the quantitative determination of 19 phytochemicals. The chromatographic separation of targeted phytochemicals was performed using the Waters ACQUITY UPLC BEH™ C18 column (1.7 μm, 2.1 mm × 50 mm) with 0.1% formic acid with water and acetonitrile as a mobile phase at a flow rate of 0.25 mL/min. The validation parameters showed the overall recoveries from 95.78−101.44% (RSD ≤ 3.25%), precision (intra-day: RSD ≤ 2.96%; inter-day: RSD ≤ 2.89%), linearity (R2 ≥ 0.9982), limit of detection (8.60 × 10–10−2.18 × 10–6 mg/mL), and the limit of quantitation (2.60 × 10–9–6.63 × 10–6 mg/mL) in the concentration range from 0.5 to 1000 × 10–6 mg/mL. This method was successfully applied in ethanolic extracts of different parts (fruits, leaves, and barks) of selected eight Ficus species. Quinic acid was predominant followed by rutin and chlorogenic acid among the studied nineteen phytochemicals. Ficus benjamina showed the maximum total content in fruits and leaves. The UPLC–ESI–QqQLIT–MS/MS method combined with principal component analysis (PCA) was successfully used for Ficus species discrimination on the basis of the contents of 15 compounds. The UPLC–ESI–QqQLIT–MS/MS method combined with PCA could be used for quality control.