Trait specific marker-based characterization and population structure analysis in rice (Oryza sativa L.) germplasm of Kashmir Himalayas.

BACKGROUND: Rice is a key food grain contributor to the global food grain basket and is considered the main food crop in India with a large number of varieties released every year. SSR markers have proven to be an excellent tool for studying genetic diversity. As a result, the present study was done to characterize and assess genetic diversity as well as population structural aspects. METHODS AND RESULTS: Fifty genotypes of rice were characterized using 40 SSR markers to assess the genetic diversity and genetic relationship. A total of 114 alleles were amplified with an average of 2.85 alleles per locus. The Polymorphism Information Content (PIC) values varied from 0.30 (RM162) to 0.58 (RM413) with an average of 0.44. Gene diversity was in the range of 0.35 (RM162) to 0.66 (RM413), with an average value of 0.52, while heterozygosity ranged from 0.18 (RM27) to 0.74 (RM55), with an average of 0.39. The population structure revealed a narrow genetic base with only three major subpopulations. Analysis of molecular variance revealed that 74% of the variation was attributed within individuals, 23% was among individuals, and 3% was among populations. Pairwise Fst value of population A & B is 0.024, population B & C is 0.120 and population A & C is 0.115. Dendrogram grouped the genotypes into three clusters with wide variation among the accessions. CONCLUSION: Genotyping combined with phylogeny and population structure analysis proved to be a powerful method for characterizing germplasm in this study. There is significant gene flow within populations, as well as the presence of different combinations of alleles, and that allelic exchange rates within the populations are higher than among the populations. Assessing the genetic diversity among individual genotypes within populations is quite useful in selecting candidate parents for future breeding programs to improve the target traits in rice for the Himalayan region.

Explicating genetic diversity based on ITS characterization and determination of antioxidant potential in sea buckthorn (Hippophae spp.).

BACKGROUND: Sea buckthorn (Hippophae) is in the focus of interest mainly for its positive effects on health of both human and animal organisms. Due to the similarities in vegetative morphology, Hippophae species are often misidentified. Therefore, current study was focused on ITS based sequence characterization of sea buckthorn species and comparative biochemical evaluation for its antioxidant properties. METHODS AND RESULTS: DNA was extracted from leaf samples. Primer pairs K-Lab-SeaBukRhm-ITS1F1- K-Lab-SeaBukRhm-ITS1R1 and K-LabSeaBukTib- ITSF1- K-LabSeaBukTib-ITSR1 were used for PCR amplification. The purified PCR products were outsourced for sequencing. Phylogenetic tree was constructed based on neighbor-joining (NJ) method. Moreover, comparison of antioxidant potential of leaves of two sea buckthorn species (Hippophae rhamnoides and Hippophae tibetana) collected from different regions of Ladakh viz., Stakna, Nubra, DRDO Leh and Zanskar was determined by 2,2-diphenyl-1-picrylhydrazyl (DPPH), 2,2-azino-bis (3- ethylbenzothiazoline-6-sulphonic acid) diammonium salt (ABTS), and Total antioxidant capacity (TAC) by phosphomolybdenum assays. The present investigation led to the differentiation of two sea buckthorn species viz., H. rhamnoides and H. tibetana based on Internal Transcribed Spacer (ITS) region. Moreover, significant variation was observed in antioxidant potential of leaf extracts collected from different regions. CONCLUSIONS: Primary ITS sequence analysis was found to be powerful tool for identification and genetic diversity studies in sea buckthorn. Leaves of sea buckthorn have pronounced antioxidant properties and can be used in food, neutraceuticals and pharmaceutical industries etc. The current study will pave the way to discover small bioactive molecules responsible for antioxidant and anticancer properties in sea buckthorn.

Improved protocol for efficacious in vitro androgenesis and development of doubled haploids in temperate japonica rice.

DH (Doubled haploid) is the immortal mapping population and an outcome of single meiotic cycle, contributed from male partner. An improved procedure was developed for high frequency androgenesis in japonica genotypes, K-332 and GS-88 and their F1s. A total of 207 fertile, green, di-haploid plants were generated from K-332 × GS-88 hybrids using the improved anther culture protocol. The investigation was carried out to evaluate callus induction potential and regeneration response for the genotypes and the derived F1s on N6 media and modified N6 media (N6M). Whereas, N6 failed to induce callusing, agarose solidified N6M media supplemented with 4% maltose, growth regulators; NAA (2 mg/l), 2, 4-D (0.5 mg/l), Kinetin (0.5 mg/l), and silver nitrate induced high calli percentage of 27.6% in F1s, 9.5% and 6.7% in GS-88 and K-332 respectively. Murashige and Skoog (MS) media supplemented with 3% sucrose, and the hormonal combination BAP (2 mg/l), Kinetin (1 mg/l) and NAA (1 mg/l) induced high green shoot regeneration rates (0-60.0%). The effect of cold pre-treatment at 4°C and the stage of anther collection and their interaction was studied. The effect of cold pre-treatment (CP) of collected boots at 4°C (for CP2: 2, CP4: 4, CP6: 6 and CP8: 8 days) at different stages of panicle emergence (BES4-6: 4-6, BES7-10: 7-10, BES11-13: 11-13, BES>13: more than 13 inches was worked out in relation to the effect on response of calli induction, albino regeneration, green plant regeneration and number of shoots/green calli. CP referred to the number of days for which the collected boots were incubated before they were inoculated. BES was the length (inches) between flag leaf and penultimate leaf at the time of boot collection. We concluded that CP6 and BES7-10 showed better response to callus proliferation and regeneration of plantlets across genotypes. The appropriate pre-treatment, stage of anther collection and favourable media composition resulted in high calli induction and green plant regeneration rates in recalcitrant japonica genotypes. The modified N6 media resulted into efficient callus induction and is expected to be useful for studies which aim at rapid generation of mapping populations for genetic studies.

Contact dermatitis in saffron workers: clinical profile and identification of contact sensitizers in a saffron-cultivating area of Kashmir Valley of North India.

BACKGROUND: Saffron, a bulbous perennial plant belonging to Iridaceae family, is the most expensive cultivated herb that is widely used for industrial and nonindustrial purposes. However, besides its attractive and valuable properties, contact dermatitis due to saffron is an uncommon reported entity. OBJECTIVES: The aims of this study were to determine the clinical pattern patch-testing profile of contact dermatitis in saffron workers and to identify the most common allergens/sensitizers. MATERIAL AND METHODS: One hundred ten saffron workers were patch-tested with 39 allergens, which included Indian standard series antigens, plant series antigens, and extracts from different parts of saffron flower. RESULTS: The allergens in Indian standard series accounted for 52.44% of positive reactions. Plant series and different parts of saffron accounted for 47.56% of the positive reactions. Among those patients with positive responses to the supplemental saffron allergens, 83.3% were of present or past relevance. CONCLUSIONS: The data observed in the present study confirm that the saffron dermatitis is a distinct clinical entity with characteristic clinical presentation and has a strong significance as an occupational allergen in those handling this plant. Patch testing with different parts of saffron flower has a role to play in finding out the etiological cause.