On protecting farmers' new varieties: new approaches to rights on collective innovations in plant genetic resources

"Current farmers' breeding goes beyond the gradual selection in landraces, and includes development and maintenance of major new farmers' varieties that are rather uniform, in particular in South-East Asia. Modern varieties developed in the formal sector have simply replaced landraces as the source of diversity, but have not abolished farmers' breeding practices. Interpretations of the new international agreements on plant genetic resources should protect the development of modern farmers' varieties. However, ensuring recognition of collective innovation, allowing access to relevant germplasm sources for farmers' breeding activities, keeping materials freely available, and arranging for effective benefit sharing, all form major challenges. This paper proposes a new protective measure: namely “origin recognition rights." Author's AbstractLandraces, Farmers' varieties, Collective rights, Declaration of origin, Origin recognition, Germplasm resources,

Mapping adaptation of barley to droughted environments

Identifying barley genomic regions influencing the response of yield and its components to water deficits will aid in our understanding of the genetics of drought tolerance and the development of more drought tolerant cultivars. We assembled a population of 192 genotypes that represented landraces, old, and contemporary cultivars sampling key regions around the Mediterranean basin and the rest of Europe. The population was genotyped with a stratified set of 50 genomic and EST derived molecular markers, 49 of which were Simple Sequence Repeats (SSRs), which revealed an underlying population sub-structure that corresponded closely to the geographic regions in which the genotypes were grown. A more dense whole genome scan was generated by using Diversity Array Technology (DArT®) to generate 1130 biallelic markers for the population. The population was grown at two contrasting sites in each of seven Mediterranean countries for harvest 2004 and 2005 and grain yield data collected. Mean yield levels ranged from 0.3 to 6.2 t/ha, with highly significant genetic variation in low-yielding environments. Associations of yield with barley genomic regions were then detected by combining the DArT marker data with the yield data in mixed model analyses for the individual trials, followed by multiple regression of yield on markers to identify a multi-locus subset of significant markers/QTLs. QTLs exhibiting a pre-defined consistency across environments were detected in bins 4, 6, 6 and 7 on barley chromosomes 3H, 4H, 5H and 7H respectivel

Inventory and history of the CIRAD cotton (Gossypium spp.) germplasm collection

The CIRAD Cotton Germplasm Col­lection was founded in 1978 through the pooling of a number of working collections. It is one of the largest collec­tions in the world representing genetic variability in the genus Gossypium L. In 2005, it contained 3070 accessions, including 1696 cultivars and 1374 wild and ancestral types, covering five tetra­ploid species and seven diploid species. The two main cultivated cotton spe­cies, G. hirsutum L. and G. barbadense L., accounted for 68% and 15% of the accessions, respectively. The cultivars originated from around a hundred countries, and the ancestral species ac­cessions were collected during expedi­tions conducted between 1980 and 1988. Part of the ancestral type collection (894 accessions) was assembled with fund­ing from IBPGR (now Bioversity In­ternational), and these accessions were handed over to CIRAD for conserva­tion, assessment and release

Multilocus haplotyping by parallel sequencing to decipher the interspecific mosaic genome structure of cultivated citrus

The most important economic Citrus species originated from natural interspecific hybridization between four ancestral taxa (C. reticulata, C. maxima, C. medica and C. micrantha) with limited further interspecific recombination due to apomixis and vegetative propagation. Such reticulate evolution coupled with vegetative propagation results in genomes that are mosaics of large chromosome fragments of the basic taxa, in frequent interspecific heterozygosity. Breeding of these species is hampered by their complex heterozygous genomic structures. Haplotyping of multiple gene fragments along the genome should be a powerful approach to resolve the evolutionary history of the gene pools, to reveal the admixture genomic structure of current species and to develop innovative breeding schemes. We have analysed the efficiency of parallel sequencing with 454 methodology to decipher the hybrid structure of modern citrus species and cultivars along chromosome 2. Four hundred fifty four amplicon libraries were established with the fluidigm array system for 48 genotypes and 16 gene fragments of chromosome 2. Haplotypes were established from the reads of each accession and phylogenetic analyses were performed from the haplotypic data of each gene fragment. The length of 454 reads and the level of differentiation between the ancestral taxa of modern citrus allowed efficient haplotype phylogenetic assignations for 12 of the 16 gene fragments. The analysis of the mixed genomic structure of modern species and cultivars (i) revealed C. maxima introgressions in modern mandarins; (ii) was consistent with previous hypothesis regarding the origin of secondary species; and (iii) provided a new picture of the evolution of chromosome 2. Perspectives to rebuild the main secondary species from the basic taxa are discussed. (Résumé d'auteur

Genetic Diversity of Selected Upland Rice Genotypes (Oryza sativa L.) for Grain Yield and Related Traits

Seventy-seven upland rice genotypes including popular cultivars in Nigeria and introduced varieties selected from across rice-growing regions of the world were evaluated under optimal upland ecology. These genotypes were characterised for 10 traits and the quantitative data subjected to Pearson correlation matrix, Principal Component Analysis and cluster analysis to determine the level of diversity and degree of association existing between grain yield and its related component traits. Yield and most related component traits exhibited higher PCV compared to growth parameters. Yield had the highest PCV (41.72%) while all other parameters had low to moderate GCV. Genetic Advance (GA) ranged from 9.88% for plant height at maturity to 41.08% for yield. High heritability estimates were recorded for 1000 grain weight (88.71%), days to 50% flowering (86.67%) and days to 85% maturity (71.98%). Furthermore, grain yield showed significant positive correlation with days to 50% flowering and number of panicles m-2. Three cluster groups were obtained based on the UPGMA and the first three principal components explained about 64.55% of the total variation among the 10 characters. The PCA results suggests that characters such as grain yield, days to flowering, leaf area and plant height at maturity were the principal discriminatory traits for this rice germplasm indicating that selection in favour of these traits might be effective in this population and environment

Molecular Genetic Diversity Study of Forest Coffee Tree (Coffea arabica L.) Populations in Ethiopia: Implications for Conservation and Breeding

Coffee provides one of the most widely drunk beverages in the world, and is a very important source of foreign exchange income for many countries. Coffea arabica, which contributes over 70 percent of the world's coffee productions, is characterized by a low genetic diversity, attributed to its allopolyploidy origin, reproductive biology and evolution. C. arabica has originated in the southwest rain forests of Ethiopia, where it is grown under four different systems, namely forest coffee, small holders coffee, semi plantation coffee and plantation coffee. Genetic diversity of the forest coffee (C. arabica) gene pool in Ethiopia is being lost at an alarming rate because of habitat destruction (deforestation), competition from other cash crops and replacement by invariable disease resistant coffee cultivars. This study focused on molecular genetic diversity study of forest coffee populations in Ethiopia using PCR based DNA markers such as random amplified polymorphic DNA (RAPD), inverse sequence-tagged repeat (ISTR), inter-simple sequence repeats (ISSR) and simple sequence repeat (SSR) or microsatellites. The objectives of the study are to estimate the extent and distribution of molecular genetic diversity of forest coffee and to design conservation strategies for it’s sustainable use in future coffee breeding. In this study, considerable samples of forest coffee collected from four coffee growing regions (provinces) of Ethiopia were analysed. The results indicate that moderate genetic diversity exists within and among few forest coffee populations, which need due attention from a conservation and breeding point of view. The cluster analysis revealed that most of the samples from the same region (province) were grouped together which could be attributed to presence of substantial gene flow between adjacent populations in each region in the form of young coffee plants through transplantation by man. In addition wild animals such as monkeys also play a significant role in coffee trees gene flow between adjacent populations. The overall variation of the forest coffee is found to reside in few populations from each region. Therefore, considering few populations from each region for either in situ or ex situ conservation may preserve most of the variation within the species. For instance, Welega-2, Ilubabor-2, Jima-2 and Bench Maji-2 populations should be given higher priority. In addition, some populations or genotypes have displayed unique amplification profiles particularly for RAPD and ISTR markers. Whether these unique bands are linked to any of the important agronomic traits and serve in marker assisted selections in future coffee breeding requires further investigations

Genetic control and geo-climate adaptation of pod dehiscence provide novel insights into the soybean domestication and expansion

Loss of pod dehiscence is a key step during soybean [Glycine max (L.) Merr.] domestication. Genome-wide association analysis for soybean shattering identified loci harboring Pdh1, NST1A and SHAT1-5. Pairwise epistatic interactions were observed, and the dehiscent Pdh1 overcomes the resistance conferred by NST1A or SHAT1-5 locus, indicating that Pdh1 predominates pod dehiscence expression. Further candidate gene association analysis identified a nonsense mutation in NST1A associated with pod dehiscence. Allele composition and population differential analyses unraveled that Pdh1 and NST1A, but not SHAT1-5, underwent domestication and modern breeding selections. Geographic analysis showed that in Northeast China (NEC), indehiscence at both Pdh1 and NST1A were required by cultivated soybean; while indehiscent Pdh1 alone is capable of coping shattering in Huang-Huai-Hai (HHH) valleys where it originated; and no specific indehiscence was required in Southern China (SC). Geo-climatic investigation revealed strong correlation between relative humidity and frequency of indehiscent Pdh1 across China. This study demonstrates that the epistatic interaction between Pdh1 and NST1A fulfills a pivotal role in determining the level of resistance against pod dehiscence. Humidity shapes the distribution of indehiscent alleles. Our results also suggest that HHH valleys, not NEC, was at least one of the origin centers of cultivated soybean.Comment: 17 pages 8 figure

Maize Germplasm Conservation in Southern California's Urban Gardens: Introduced Diversity Beyond ex situ and in situ Management.

Contemporary germplasm conservation studies largely focus on ex situ and in situ management of diversity within centers of genetic diversity. Transnational migrants who transport and introduce landraces to new locations may catalyze a third type of conservation that combines both approaches. Resulting populations may support reduced diversity as a result of evolutionary forces such as genetic drift, selection, and gene flow, yet they may also be more diverse as a result of multiple introductions, selective breeding and cross pollination among multiple introduced varietals. In this study, we measured the amount and structure of maize molecular genetic diversity in samples collected from home gardens and community gardens maintained by immigrant farmers in Southern California. We used the same markers to measure the genetic diversity and structure of commercially available maize varieties and compared our data to previously reported genetic diversity statistics of Mesoamerican landraces. Our results reveal that transnational dispersal creates an opportunity for the maintenance of maize genetic diversity beyond its recognized centers of diversity

Progress of guayule trials in Europe (Spain and France) : early evaluation

The main objectives of the project were to define the potential for cultivation of guayule (#Parthenium Argentatum#) in Southern Europe and to assess the economical justification as an alternative source for natural rubber produced in Europe. The best available subsets of guayule lines from Arizona germplasm were collected from USDA, National germplasm and US Universities (Arizona, Texas). The seeds from the germplasm collection both in France and Spain were used to produce enough guayule plants for local field trials and to settle a guayule collection of selected accessions to produce seeds for European projects. The genetic diversity of 40 guayule imported varieties was tested in two locations: Murcia in Spain, and Montpellier in France. The results showed clear genetic differences. First results showed that Mexican varieties are best adapted to South of Spain. Germination rates of seeds produced by the project varied from 5% to 60% depending on origin, age, line and seeds cleaning. A fertilization and irrigation trial was set-up in Murcia and Montpellier in May 2009. Three levels of irrigation and 3 levels of fertilization were compared using AZ2 seeds as genetic material. In Montpellier, different levels of irrigation did not alter the growth, but less watering reduced the mortality rate. While in Murcia, watering resulted in significantly higher yields. The low rubber content (3.2% in March 2010) and a high mortality of the plants (> 60%) observed in Montpellier after the 2009-2010 winter showed that France is not yet adapted for commercial cultivation of guayule. Rubber content of guayule plants in Murcia (Spain) harvested was 7.4% in March 2010 (for 17-months-old plants). Less than 1% mortality was observed, and the average yields of the irrigation trial was above 10 tons of dry matter (i.e.: 700 kg/ha of rubber) after two years, showing that the area is fully adapted for commercial cultivation of guayule, provided good watering. (Résumé d'auteur

Conservation and use of genetic resources of underutilized crops in the Americas - A continental analysis

Latin America is home to dramatically diverse agroecological regions which harbor a high concentration of underutilized plant species, whose genetic resources hold the potential to address challenges such as sustainable agricultural development, food security and sovereignty, and climate change. This paper examines the status of an expert-informed list of underutilized crops in Latin America and analyses how the most common features of underuse apply to these. The analysis pays special attention to if and how existing international policy and legal frameworks on biodiversity and plant genetic resources effectively support or not the conservation and sustainable use of underutilized crops. Results show that not all minor crops are affected by the same degree of neglect, and that the aspects under which any crop is underutilized vary greatly, calling for specific analyses and interventions. We also show that current international policy and legal instruments have so far provided limited stimulus and funding for the conservation and sustainable use of the genetic resources of these crops. Finally, the paper proposes an analytical framework for identifying and evaluating a crop’s underutilization, in order to define the most appropriate type and levels of intervention (international, national, local) for improving its statu