Farmers' management of rice varietal diversity in the mid-hills of Nepal: implications for on-farm conservation and crop improvement

Season-long monitoring of on-farm rice (Oryza sativa, L.) plots in Nepal explored farmers' decision-making process on the deployment of varieties to agroecosystems, application of production inputs to varieties, agronomic practices and relationship between economic return and area planted per variety. Farmers deploy varieties [landraces (LRs) and modern varieties (MVs)] to agroecosystems based on their understanding of characteristics of varieties and agroecosystems, and the interaction between them. In marginal growing conditions, LRs can compete with MVs. Within an agroecosystem, economic return and area planted to varieties have positive relationship, but this is not so between agroecosystems. LRs are very diverse on agronomic and economic traits; therefore, they cannot be rejected a priori as inferior materials without proper evaluation. LRs have to be evaluated for useful traits and utilized in breeding programmes to generate farmer-preferred materials for marginal environments and for their conservation on-farm

Appe mango: pickling the cultural and biological diversity of Uttara Kannada district in the Western Ghats

Uttara Kannada, one of the forest-rich districts of Karnataka, is well known for its biological diversity, rich cultural heritage and high level of awareness among its people on issues related to conservation. This flyer tells the story of Appe Mango and tackles questions such as, ‘What makes the people of Uttara Kannada tick for the conservation of biodiversity?’ and ‘How do they relate themselves to nature?

Isolation and characterization of microsatellite markers in Garcinia gummi-gutta by next-generation sequencing and cross-species amplification

Garcinia gummi-gutta (L.) Roxb. (Clusiaceae) is an endemic, semidomesticated, fruit-yielding tree species distributed in the Western Ghats of India and Sri Lanka. Various bioactive phytochemicals, such as garcinol, benzophenones and xanthones are isolated from G. gummi-gutta and have shown antibacterial, antiviral and antioxidant activities. We sequenced the total genomic DNA using Illumina Hiseq 2000 platform and examined 241,141,804 bp high quality data, assembled into 773,889 contigs. In these contigs, 27,313 simple-sequence repeats (SSRs) were identified, among which mononucleotide repeats were predominant (44.98%) followed by dinucleotide and trinucleotide repeats. Primers were designed for 9964 microsatellites among which 32 randomly selected SSR primer pairs were standardized for amplification. Polymerase chain reaction (PCR) amplification of genomic DNA in 30 G. gummi-gutta genotypes revealed polymorphic information content (PIC) across all 32 loci ranging from 0.867 to 0.951, with a mean value of 0.917. The observed and expected heterozygosity ranged from 0.00 to 0.63 and 0.896 to 0.974, respectively. Alleles per locus ranged from 12 to 27. This is the first report on the development of genomic SSR markers in G. gummi-gutta using next-generation sequencing technology. The genomic SSR markers developed in this study will be useful in identification, mapping, diversity and breeding studies

Isolation and characterization of microsatellite markers from Garcinia morella using next generation sequencing technology and cross-species amplification

The fruit-bearing medicinal tree, Garcinia morella, grows in the tropical rain forests of India’s Western Ghats, Indo-Chinese Himalayan regions and Sri Lanka. Its fruit rinds are used as a garnish and in seasoning during food preparation. In order to genetically exploit it and assess diversity, development of microsatellite markers was attempted. We partially sequenced genomic DNA using the Illumina Hiseq 2000 platform and examined sequence data for microsatellite loci. We obtained high-quality 10653 Mbp data and was assembled into 1613263 contigs. A total of 121199 SSRs were discovered, Di nucleotide repeats were predominant (42.5%), followed by mono and tri nucleotide repeats (30.4 and 7.9%, respectively). We were able to design primers for 52901 microsatellites. Genetic analysis of 48 SSR loci, showed PIC values ranging from 0.067 to 0.939 with a mean value of 0.7547. The allele per locus ranged from 2 to 24 with a mean of 13. These microsatellite markers can be employed for genetic diversity analysis, molecular characterization and mapping different traits

Rice landrace diversity in Nepal. Socio-economic and ecological factors determining rice landrace diversity in three agro-ecozones of Nepal based on farm surveys

In Nepal, in traditional rice farming systems many diverse landraces are grown in all of the rice agro-ecosystems from low to high altitude. Three case study sites were selected to represent the major rice agro-ecozones: Bara (100–150 m) for the low-altitude terai (plain); Kaski (700–1,206 m) for the mid-hill zone; and Jumla (2,200–3,000 m) for the high-hill zone. The diversity in rice varieties was compared in these three sites and nine survey villages in a series of surveys conducted in 1998, 1999 and 2006. The level and distribution of diversity on farm varied with the physical and socio-economic settings of the farming communities. The mid-hill site (Kaski) had the highest rice landrace diversity. This was adapted to the diverse agro-ecosystems found there and there was equal diversity in Kule khet (irrigated lands by seasonal canals) and Sim khet (marshy wet land). The next most diverse system was Nicha khet (irrigated lowlands) in Bara, the low-altitude site. The high-hill site (Jumla) had the lowest rice diversity. Across all sites many of the landraces were rarely grown and then only in small areas, reflecting the specialized uses to which they were put. At all sites the most common single landrace occupied less than half of the rice area. Resource-rich farmers were the more important custodians of on-farm rice varietal diversity across the sites. There was more rice diversity in favourable environments than in less favourable ones. This was true whether diversity was measured across sites or across rice domains within sites

Determinants of agriculture biodiversity in Western Terai landscape complex of Nepal

The study explored agriculture biodiversity around protected areas and identified factors affecting diversity of agriculture biodiversity in farming households. The study analyzed the data collected from household survey of about 907 farmers from Western-Terai Landscape Complex of Nepal. Intra-species and inter-species richness and evenness in agriculture landscape were estimated and compared across a spectrum of land-uses. The study identified different social, economic, technological and ecological factors affecting the richness of intra-species and inter-species diversity of agriculture biodiversity using generalized linear regression models. Technology index, information index, food security, animal holding, ethnicity, irrigation facility and land-use were found as major variables affecting agriculture. The results also indicated that buffer zones had higher diversity than other land-uses, indicating positive effects of protected-land on surrounding agriculture biodiversity. Results supported need of coordinated efforts to mainstream agriculture biodiversity conservation with landscape conservation plans and socio-economic developments of the region

Determinants of agriculture biodiversity in Western Terai landscape complex of Nepal

The study explored agriculture biodiversity around protected areas and identified factors affecting diversity of agriculture biodiversity in farming households. The study analyzed the data collected from household survey of about 907 farmers from Western-Terai Landscape Complex of Nepal. Intra-species and inter-species richness and evenness in agriculture landscape were estimated and compared across a spectrum of land-uses. The study identified different social, economic, technological and ecological factors affecting the richness of intra-species and inter-species diversity of agriculture biodiversity using generalized linear regression models. Technology index, information index, food security, animal holding, ethnicity, irrigation facility and land-use were found as major variables affecting agriculture. The results also indicated that buffer zones had higher diversity than other land-uses, indicating positive effects of protected-land on surrounding agriculture biodiversity. Results supported need of coordinated efforts to mainstream agriculture biodiversity conservation with landscape conservation plans and socio-economic developments of the region

Insight from the draft genome of Dietzia cinnamea P4 reveals mechanisms of survival in complex tropical soil habitats and biotechnology potential

The draft genome of Dietzia cinnamea strain P4 was determined using pyrosequencing. In total, 428 supercontigs were obtained and analyzed. We here describe and interpret the main features of the draft genome. The genome contained a total of 3,555,295 bp, arranged in a single replicon with an average G+C percentage of 70.9%. It revealed the presence of complete pathways for basically all central metabolic routes. Also present were complete sets of genes for the glyoxalate and reductive carboxylate cycles. Autotrophic growth was suggested to occur by the presence of genes for aerobic CO oxidation, formate/formaldehyde oxidation, the reverse tricarboxylic acid cycle and the 3-hydropropionate cycle for CO2 fixation. Secondary metabolism was evidenced by the presence of genes for the biosynthesis of terpene compounds, frenolicin, nanaomycin and avilamycin A antibiotics. Furthermore, a probable role in azinomycin B synthesis, an important product with antitumor activity, was indicated. The complete alk operon for the degradation of n-alkanes was found to be present, as were clusters of genes for biphenyl ring dihydroxylation. This study brings new insights in the genetics and physiology of D. cinnamea P4, which is useful in biotechnology and bioremediation