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, ßLIM1, 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, ßLIM1, 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.

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.

Biocontrol potential of three novel Trichoderma strains: isolation, evaluation and formulation.

We have isolated three novel strains of Trichoderma (two T. harzianum and one T. atroviride) from wild mushroom and tree bark, and evaluated their biocontrol potential against Sclerotium delphinii infecting cultivated cotton seedlings. T. harzianum strain CICR-G, isolated as a natural mycoparasite on a tree-pathogenic Ganoderma sp. exhibited the highest disease suppression ability. This isolate was formulated into a talcum-based product and evaluated against the pathogen in non-sterile soil. This isolate conidiated profusely under conditions that are non-conducive for conidiation by three other Trichoderma species tested, thus having an added advantage from commercial perspective.

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.