Genome-wide identification and expression analysis of the plant specific LIM genes in Gossypium arboreum under phytohormone, salt and pathogen stress

Asiatic cotton (Gossypium arboreum) cultivated as ‘desi cotton’ in India, is renowned for its climate resilience and robustness against biotic and abiotic stresses. The genome of G. arboreum is therefore, considered as a valued reserve of information for discovering novel genes or gene functions for trait improvements in the present context of cotton cultivation world-wide. In the present study, we carried out genome-wide analysis of LIM gene family in desi cotton and identified twenty LIM domain proteins (GaLIMs) which include sixteen animals CRP-like GaLIMs and four plant specific GaLIMs with presence (GaDA1) or absence (GaDAR) of UIM (Ubiquitin Interacting Motifs). Among the sixteen CRP-like GaLIMs, eleven had two conventional LIM domains while, five had single LIM domain which was not reported in LIM gene family of the plant species studied, except in Brassica rapa. Phylogenetic analysis of these twenty GaLIM proteins in comparison with LIMs of Arabidopsis, chickpea and poplar categorized them into distinct αLIM1, βLIM1, γLIM2, δLIM2 groups in CRP-like LIMs, and GaDA1 and GaDAR in plant specific LIMs group. Domain analysis had revealed consensus [(C-X₂-C-X₁₇-H-X₂-C)-X₂-(C-X₂-C-X₁₇-C-X₂-H)] and [(C-X₂-C-X₁₇-H-X₂-C)-X₂-(C-X₄-C-X₁₅-C-X₂-H)] being conserved as first and/or second LIM domains of animal CRP-like GaLIMs, respectively. Interestingly, single LIM domain containing GaLIM15 was found to contain unique consensus with longer inter-zinc-motif spacer but shorter second zinc finger motif. All twenty GaLIMs showed variable spatio-temporal expression patterns and accordingly further categorized into distinct groups of αLIM1, βLIM1, γLIM2 δLIM2 and plant specific LIM (DA1/DAR). For the first time, response of GaDA1/DAR under the influence of biotic and abiotic stresses were studied in cotton, involving treatments with phytohormones (Jasmonic acid and Abscisic acid), salt (NaCl) and wilt causing pathogen (Fusarium oxysporum). Expressions patterns of GaDA1/DAR showed variable response and identified GaDA2 as a probable candidate gene for stress tolerance in G. arboreum.

Morpho-physiological and molecular characterization of drought tolerance traits in Gossypium hirsutum genotypes under drought stress

Drought stress is one of the major abiotic stresses affecting lint yield and fibre quality in cotton. With increase in population, degrading natural resources and frequent drought occurrences, development of high yielding, drought tolerant cotton cultivars is critical for sustainable cotton production across countries. Six Gossypium hirsutum genotypes identified for drought tolerance, wider adaptability and better fibre quality traits were characterized for various morpho-physiological and biochemical characters and their molecular basis was investigated under drought stress. Under drought conditions, genotypes revealed statistically significant differences for all the morpho-physiological and biochemical traits. The interaction (genotype × treatment) effects were highly significant for root length, excised leaf water loss and cell membrane thermostability indicating differential interaction of genotypes under control and stress conditions. Correlation studies revealed that under drought stress, relative water content had significant positive correlation with root length and root-to-shoot ratio while it had significant negative correlation with excised leaf water loss, epicuticular wax, proline, potassium and total soluble sugar content. Analysis of expression of fourteen drought stress related genes under water stress indicated that both ABA dependent and ABA independent mechanisms of drought tolerance might be operating differentially in the studied genotypes. IC325280 and LRA5166 exhibited ABA mediated expression of stress responsive genes and traits. Molecular basis of drought tolerance in IC357406, Suraj, IC259637 and CNH 28I genotypes could be attributed to ABA independent pathway. Based on physiological phenotyping, the genotypes IC325280 and IC357406 were identified to possess better root traits and LRA5166 was found to have enhanced cellular level tolerance. Variety Suraj exhibited good osmotic adjustment and better root traits to withstand water stress. The identified drought component trait(s) in specific genotypes would pave way for their pyramiding through marker assisted cotton breeding.

Author Correction: Long-term impacts of Bt cotton in India

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Long-term impacts of Bt cotton in India

Most scholarship on the closely-watched case of genetically modified Bacillus thuringiensis (Bt) cotton in India has focused on short-term impacts and has also ignored other major changes in India's cotton agriculture. This Perspective combines several data sources over a 20-year span to provide long-term comparisons of Bt adoption with yields and other inputs at both countrywide and state-specific scales. Bt cotton adoption is shown to be a poor indicator of yield trends but a strong indicator of initial reductions in pesticide use. Yield increases correspond to changes in fertilizer and other inputs. Bt cotton has continued to control one major cotton pest, but with Bt resistance in another pest and surging populations of non-target pests, farmers now spend more on pesticides today than before the introduction of Bt. Indications are that the situation will continue to deteriorate.

Population genetic structure of cotton pink bollworm, Pectinophora gossypiella (Saunders) (Lepidoptera: Gelechiidae) using mitochondrial cytochrome oxidase I (COI) gene sequences from India

Pink bollworm (PBW), Pectinophora gossypiella is one of the most destructive pest's globally inflicting huge economic losses in cotton even during later stages of crop growth. In the present investigation, the population genetic structure, distribution, and genetic diversity of P. gossypiella in cotton growing zones of India using partial mitochondrial DNA cytochrome oxidase-I (COI) gene was addressed. The overall haplotype (Hd), number of nucleotide differences (K), and nucleotide diversity (π) were 0.3028, 0.327, and 0.00047, respectively which suggest that entire population exhibited low level of genetic diversity. Zone-wise clustering of population revealed that central zone recorded low level of Hd (0.2730) as compared to north (0.3619) and south (0.3028) zones. The most common haplotype (H1) reported in all 19 locations could be proposed as ancestral/original haplotype. This haplotype with one mutational step formed star-like phylogeny connected with 11 other haplotypes. The phylogenetic relationship studies revealed that most haplotypes of populations are closely related to each other. Haplotype 5 was exclusively present in Dharwad (South zone) shared with populations of Hanumangarh and Bathinda (North zone). The result indicated that there is no isolation by distance effect among the Indian populations of PBW. The present study reports a low genetic diversity among PBW populations of India and H1, as ancestral haplotype from which other haplotypes have evolved suggests that the migration and dispersal over long distance and invasiveness are major factors.

Regional odontodysplasia

Regional odontodysplasia (ROD) is a rare developmental anomaly involving both mesodermal and ectodermal components in a group of contiguous teeth. It affects the primary and permanent dentitions in the maxilla and the mandible or both, however, the maxilla is frequently involved. Although the etiology of the ROD is uncertain, it has been suggested that numerous other factors play a role. The treatment plan should be based on the degree of involvement as well as the functional and esthetic needs in each case. This article reports the case of a 5-year-old boy presenting a rare anomaly on the right side of the maxillary arch. The treatment performed was rehabilitation with temporary partial acrylic denture and periodic checkups. The extraction was followed by rehabilitation with dental implants. The main aim of this article is to provide valuable information to pediatric dentists about the review and treatment alternatives for ROD.

Biology of the mealybug, Phenacoccus solenopsis on cotton in the laboratory

Phenacoccus solenopsis Tinsley (Hemiptera: Pseudococcidae) has been the current topic of research for insect taxonomists and applied entomologists in India due to its invasiveness, rapid spread, morphological and biological variations and the need for establishing an effective control strategy. The biology of the mealybug P. solenopsis was studied on cotton under laboratory conditions between August and October of 2009 with mean temperature and relative humidity of 23.3–30.2° C and 40.5–92.5% RH, respectively, in central India. Neonate crawlers that emerged from a field population were collected and constituted the study population. The developmental period from immature crawler to adult stage was greater for males (18.7 ± 0.9 days) compared to females (13.2 ± 1.8 days), probably due to the additional molt to the pupal stage in males. Survival of second instars was lower (45.5%) than first and third instars (71.4%). Females showed dynamic patterns of fecundity with the number of crawlers produced per female ranging between 128 and 812, with a mean of 344 ± 82. The reproductive period lasted 30.2 ± 8.2 days. Parthenogenesis with ovoviviparity (96.5%) was dominant over the oviparous (3.5%) mode of reproduction. Adult females lived 42.4 ± 5.7 days. Males accounted for less than 5% of the population, and lived 1.5 ± 0.1 days. The life history parameters of P. solenopsis adult females are discussed relative to the appearance of symptoms on the cotton crop, and the importance of making management interventions during the effective reproductive period of the insect.

Widespread infestation of the exotic mealybug species, Phenacoccus solenopsis (Tinsley) (Hemiptera: Pseudococcidae), on cotton in India

A survey was conducted in 47 locations in nine cotton-growing states of India to identify the composition of mealybug species occurring on cotton. Results of the taxonomic study showed that two mealybug species, the solenopsis mealybug, Phenacoccus solenopsis (Tinsley), and the pink hibiscus mealybug, Maconellicoccus hirsutus (Green), were found to infest cotton plants from all nine cotton growing states of the country. However, P. solenopsis was found to be the predominant mealybug species, comprising 95% of the samples examined. P. solenopsis, which was hitherto not reported to occur in India, now appears to be widespread on cotton in almost all cotton-growing states of the country. P. solenopsis is an exotic species originated from the USA and was reported to damage cotton and crops of 14 families. This report discusses the implications of the introduction of this exotic polyphagous pest species and the necessary steps to mitigate its potential threat to agriculture in India.

Pyrethroid resistance and mechanisms of resistance in field strains of Helicoverpa armigera (Lepidoptera: Noctuidae)

Pyrethroid resistance was found in 54 field strains of Helicoverpa armigera collected between 1995 and 1999 from 23 districts in seven states of India. LD50 values of the field strains ranged from 0.06 to 72.2 microg/larva with slopes of 0.5-3.1. Resistance was highest in regions where pyrethroid use was frequent (four to eight applications per season). Resistance to deltamethrin was exceptionally high with resistance ratios of 13,570 and 27,160 in two strains collected during February 1998 in central India. Resistance to cypermethrin, fenvalerate and cyhalothrin also was high with resistance ratios of >1,000 in four strains collected from central and southern India. Resistance ratios were below 100 in >50% of the strains tested. Pyrethroid resistance was high in strains collected from the districts in Andhra Pradesh where a majority of the cotton farmer suicide cases in India were reported. Resistance to pyrethroids appeared to have increased over 1995-1998 in most of the areas surveyed. Studies carried out through estimation of detoxification enzyme activity and synergists indicated that enhanced cytochrome p450 and esterase activities were probably important mechanisms for pyrethroid resistance in field strains. Pyrethroid nerve insensitivity also was found to be a major mechanism in some parts of the country where the use of pyrethroids was high. The information presented illustrates the importance of proper insect management programs to avoid the consequences associated with improper insecticide use.

Carbamate and organophosphate resistance in cotton pests in India, 1995 to 1999

Monitoring for organophosphate and carbamate resistance was carried out on five major insect pests of cotton collected from 22 cotton-growing districts across India. Resistance was monitored in Helicoverpa armigera (Hübner) and Pectinophora gossypiella (Saunders) for the period 1995-1999 and for Spodoptera litura (Fabricius), Earias vittella (Fabricius) and Bemisia tabaci (Gennadius) in a survey conducted during the 1997-98 cropping season. Of the 53 field strains of H. armigera, only four were found to exhibit resistance to quinalphos, the highest 15-fold, whereas all 16 field strains tested were found to be resistant to monocrotophos. Similarly, out of 40 field strains tested, only eight were found to express appreciable resistance to methomyl. Resistance in P. gossypiella to quinalphos was high in the majority of the strains tested. Of the seven strains of E. vittella tested, two strains from northern India exhibited > 70-fold resistance to monocrotophos. Of the 11 S. litura strains tested, only four were found to exhibit resistance factors of 10 to 30-fold to quinalphos and monocrotophos. All of the B. tabaci field strains exhibited resistance to methomyl and monocrotophos and susceptibility to triazophos. Practical implications for pest control resulting from the observed patterns of cross-resistance between quinalphos, monocrotophos and methomyl are discussed.