Biosafety education relevant to genetically engineered crops for academic and non-academic stakeholders in East Africa

Development and deployment of genetically engineered crops requires effective environmental and food safety assessment capacity. In-country expertise is needed to make locally appropriate decisions. In April 2007, biosafety and biotechnology scientists, regulators, educators, and communicators from Kenya, Tanzania, and Uganda, met to examine the status and needs of biosafety training and educational programs in East Africa. Workshop participants emphasized the importance of developing biosafety capacity within their countries and regionally. Key recommendations included identification of key biosafety curricular components for university students; collaboration among institutions and countries; development of informational materials for non-academic stakeholders and media; and organization of study tours for decision makers. It was emphasized that biosafety knowledge is important for all aspects of environmental health, food safety, and human and animal hygiene. Thus, development of biosafety expertise, policies and procedures can be a stepping stone to facilitate improved biosafety for all aspects of society and the environment

Genetic dissection of fruit quality traits in the octoploid cultivated strawberry highlights the role of homoeo-QTL in their control

Fruit quality traits are major breeding targets in the Rosaceae. Several of the major Rosaceae species are current or ancient polyploids. To dissect the inheritance of fruit quality traits in polyploid fleshy fruit species, we used a cultivated strawberry segregating population comprising a 213 full-sibling F1 progeny from a cross between the variety ‘Capitola’ and the genotype ‘CF1116’. We previously developed the most comprehensive strawberry linkage map, which displays seven homoeology groups (HG), including each four homoeology linkage groups (Genetics 179:2045–2060, 2008). The map was used to identify quantitative trait loci (QTL) for 19 fruit traits related to fruit development, texture, colour, anthocyanin, sugar and organic acid contents. Analyses were carried out over two or three successive years on field-grown plants. QTL were detected for all the analysed traits. Because strawberry is an octopolyploid species, QTL controlling a given trait and located at orthologous positions on different homoeologous linkage groups within one HG are considered as homoeo-QTL. We found that, for various traits, about one-fourth of QTL were putative homoeo-QTL and were localised on two linkage groups. Several homoeo-QTL could be detected the same year, suggesting that several copies of the gene underlying the QTL are functional. The detection of some other homoeo-QTL was year-dependent. Therefore, changes in allelic expression could take place in response to environmental changes. We believe that, in strawberry as in other polyploid fruit species, the mechanisms unravelled in the present study may play a crucial role in the variations of fruit quality

Additive QTLs on three chromosomes control flowering time in woodland strawberry (Fragaria vesca L.)

Flowering time is an important trait that affects survival, reproduction and yield in both wild and cultivated plants. Therefore, many studies have focused on the identification of flowering time quantitative trait locus (QTLs) in different crops, and molecular control of this trait has been extensively investigated in model species. Here we report the mapping of QTLs for flowering time and vegetative traits in a large woodland strawberry mapping population that was phenotyped both under field conditions and in a greenhouse after flower induction in the field. The greenhouse experiment revealed additive QTLs in three linkage groups (LG), two on both LG4 and LG7, and one on LG6 that explain about half of the flowering time variance in the population. Three of the QTLs were newly identified in this study, and one co-localized with the previously characterized FvTFL1 gene. An additional strong QTL corresponding to previously mapped PFRU was detected in both field and greenhouse experiments indicating that gene(s) in this locus can control the timing of flowering in different environments in addition to the duration of flowering and axillary bud differentiation to runners and branch crowns. Several putative flowering time genes were identified in these QTL regions that await functional validation. Our results indicate that a few major QTLs may control flowering time and axillary bud differentiation in strawberries. We suggest that the identification of causal genes in the diploid strawberry may enable fine tuning of flowering time and vegetative growth in the closely related octoploid cultivated strawberry.Peer reviewe

Phylogeographic and phylogenetic analyses of selected set of wild and naturalized <em>Solanum</em> spp. in Sri Lanka

Solanum spp. encompass a greater share of the biodiversity in the world. Sri Lanka, one of the biodiversity hotspots in the world, is the home for wide range of Solanum spp. which have been named and morphologically characterized.However, their origins and times of origin have not yet been resolved. Hence, this study was conducted to identify the origins and origination events of 13 wild and naturalized Solanum spp. found in Sri Lanka, using DNA barcoding locus matK in comparison to worldwide Solanum spp. with phylogenetics and divergence dating approaches. In this study, 13 Sri Lankan Solanum spp. were separated into four defined phylogenetic groups viz., Old world, Morelloids, Acanthophora and Trova. The studied Sri Lankan Solanum spp. would have been originated in Africa 2.007 million years ago (MYA) in the Pleistocene epoch through mammalian migration from Mediterranean land bridges. The Australian relatives of Sri Lankan Solanum spp. would have been colonized from South Asia through South East Asia. The floristic connectivity in Pleistocene epoch may have introduced Asian Solanum spp. to South East Asia where mid Miocenic collisions between Australian and Asian plates as well as over water Long Distance Dispersal (LDD) may have caused these species to colonize in Australia. Our analysis demonstrated that most of the Solanum spp. found in Sri Lanka were introduced from India during the Pleistocene ice age. We suggest that Pre Pleistocene migrations of Solanum spp. such as S. nigrum may have occurred through overwater LDD

Photosynthetic Phenomics of Field- and Greenhouse-Grown Amaranths vs. Sensory and Species Delimits

Consumers hesitate to purchase field-grown shoot-tops of amaranths in Sri Lanka, citing the low-cleanliness making growers focus on greenhouse farming. However, the photosynthetic and growth variations in relation to the organoleptic preference of the greenhouse-grown amaranths in comparison to field-grown counterparts have not been studied. Also, the species delimits of the amaranths in Sri Lanka have not been identified, limiting our ability to interpret species-specific production characteristics. Thus, we assessed the common types of amaranths under greenhouse and field conditions. The photosynthesis was measured using a MultispeQ device of the PhotosynQ phenomic platform, which records chlorophyll fluorescence-based parameters. The shoot-tops were harvested and prepared as dishes according to the typical recipe for amaranths in Sri Lanka. The dishes were subjected to an organoleptic assessment for the parameters color, aroma, bitterness, texture, and overall taste. The differences in plant and the shoot-top biomass were also assessed. The markers atpB-rbcL, matk-trnT, and ITS were used to define the species delimits. The field-grown and greenhouse-grown amaranths exhibited species/cultivar-specific photosynthetic variations. The texture and overall taste of the dishes were different among greenhouse and field-grown material. The tasters preferred the texture and the overall taste of the greenhouse-grown shoot-tops. The greenhouse-grown plants also yielded higher shoot-top harvests compared to field-grown counterparts. Out of the tested markers, ITS defines the delimits of amaranth species. The higher organoleptic preference, the appreciable yield levels, unique photosynthetic patterns of the greenhouse-grown amaranths, and species definitions provide the much-needed platform for clean shoot-top production guaranteeing the highest end-user trust

Where are we now as we merge genomics into plant breeding and what are our limitations? Experiences from RosBREED

The complete genome sequences of apple, peach, and diploid strawberry - one member of each of the three main fruit-producing branches of the Rosaceae tree - were available in 2010. Despite this achievement, virtually none of this genomics knowledge was being used to assist breeding efforts of these crops. Four years later, this gap has been bridged, with genetic information routinely used in many US apple, peach, and cherry breeding programs. For example, DNA tests predict apple crispness, peach maturity date, and cherry fruit size, enabling breeders to determine the best parents to combine and the best seedlings to advance. This application significantly reduces the wasted effort to eliminate entirely poor families and reduces the costs to grow and evaluate thousands of seedlings genetically destined to have unacceptable fruit quality or maturity date. This achievement was enabled by international community efforts, including the RosBREED project, funded by the USDA-National Institute of Food and Agriculture Specialty Crop Research Initiative (SCRI). DNA tests are now applied for high-value attributes where the targeted loci explain a large proportion of the trait variation. However, limitations to widespread adoption of these predictive tests still exist. Some limitations are due to lack of knowledge, such as an understanding of genotype by environment (G×E) interactions and loci associated with variation for other valuable attributes. Technical limitations include streamlined phasing of alleles from multiple families of pedigree-connected breeding germplasm and access to suitable commercial service providers.</p

Biosafety education relevant to genetically engineered crops for academic and non-academic stakeholders in East Africa

Development and deployment of genetically engineered crops requires effective environmental and food safety assessment capacity. In-country expertise is needed to make locally appropriate decisions. In April 2007, biosafety and biotechnology scientists, regulators, educators, and communicators from Kenya, Tanzania, and Uganda, met to examine the status and needs of biosafety training and educational programs in East Africa. Workshop participants emphasized the importance of developing biosafety capacity within their countries and regionally. Key recommendations included identification of key biosafety curricular components for university students; collaboration among institutions and countries; development of informational materials for non-academic stakeholders and media; and organization of study tours for decision makers. It was emphasized that biosafety knowledge is important for all aspects of environmental health, food safety, and human and animal hygiene. Thus, development of biosafety expertise, policies and procedures can be a stepping stone to facilitate improved biosafety for all aspects of society and the environment

Transboundary movements of foot-and-mouth disease from India to Sri Lanka: A common pattern is shared by serotypes O and C.

Foot-and-mouth disease (FMD) affects the livestock industry in a transboundary manner. It is essential to understand the FMD phylodynamics to assist in the disease-eradication. FMD critically affects the Sri Lankan cattle industry causing substantial economic losses. Even though many studies have covered the serotyping and genotyping of FMD virus (FMDV) in Sri Lanka, there is a significant knowledge gap exists in understanding the FMDV phylodynamics in the country. In the present study, the VP1 genomic region of FMD viral isolates belonging to serotype C from Sri Lanka and other South Asian countries were sequenced. All the published VPI sequences of serotype C and most of the published VP1 sequences for lineage ME-SA/Ind-2001d of serotype O from Sri Lanka, India, and other South Asian countries were retrieved. The datasets of serotype C and serotype O were separately analyzed using Bayesian, maximum likelihood, and phylogenetic networking methods to infer the transboundary movements and evolutionary aspects of the FMDV incursions in Sri Lanka. A model-based approach was used to detect any possible recombination events of FMDV incursions. Our results revealed that the invasions of the topotype ASIA of serotype C and the lineage ME-SA/Ind-2001d have a similar pattern of transboundary movement and evolution. The haplotype networks and phylogenies developed in the present study confirmed that FMDV incursions in Sri Lanka mainly originate from the Indian subcontinent, remain quiet after migration, and then cause outbreaks in a subsequent year. Since there are no recombination events detected among the different viral strains across serotypes and topotypes, we can assume that the incursions tend to show the independent evolution compared to the ancestral viral populations. Thus, we highlight the need for thorough surveillance of cattle/ruminants and associated product-movement into Sri Lanka from other regions to prevent the transboundary movement of FMDV

Analyses of phylogenetics, starch granule morphology and consumer preference of <i>Canna indica</i> L. grown in Sri Lanka

Canna indica is a tuber crop which has many medicinal values. In Sri Lanka, C. indica tubers are consumed in rural areas and mainly available in street-markets of Nuwara-Eliya and Kandy Districts. In the present study, we assessed the phylogenetics of C. indica, starch granule morphology and consumer preference of C. indica tubers in comparison to the popular tuber crops. The phylogenetic analysis was conducted based on the sequence polymorphism at rbcL, atpB gene, trnL-trnF and trnH-psbA marker-loci with respect to the ornamental Canna spp. in Sri Lanka and the previously published sequences of Canna spp. The starch granules were isolated and observed under optical and scanning electron microscopes. The diameter and the surface area of the starch granules were measured under the optical microscope and subjected to analysis of variance. As C. indica tubers are consumed as boiled tuber pieces in Sri Lanka, the consumer preference analysis was conducted using the boiled tuber pieces C. indica, Xanthosoma sagittifolium, Manihot esculenta, Solanum tuberosum, and Ipomoea batatas. The phylogenetic tree based on rbcL marker revealed that C. indica in Sri Lanka is slightly divergent from the other Canna spp. Only the polymorphism of the atpB gene can be used to differentiate C. indica from the ornamental Canna sp. in Sri Lanka. The morphological analysis of starch granules revealed that C. indica has the biggest scallop-seashell shaped starch granules compared to other tuber species. The boiled C. indica tubers were accepted better than that of X. sagittifolium, rated equally to the tubers of S. tuberosum and M. esculenta, and rated less than I. batatas. The hardy and fibrous nature of C. indica tubers must be the major limiting factors for achieving the highest consumer preference highlighting the need of breeding for better texture in tuber

Screening of segregating F2 progenies and validation of DNA markers through bulk segregant analysis for phosphorous deficiency tolerance in rice

Phosphorous deficiency (PD) tolerance is a polygenic trait. The underlying genetics of PD tolerance trait is important to provide the basis for detecting Quantitative Trait Loci (QTLs) and validating markers that could be used in Marker Assisted Breeding (MAB) in rice. The PD tolerance of Sri Lankan rice germplasm has been characterized. However, no attempts were taken to develop and validate the DNA markers for the breeding purposes and to understand the genetic basis of the traits. The present research project was conducted to assess the PD related traits and to validate internationally published DNA markers that are linked to PD tolerance using Sri Lankan rice cultivars. A total of 84 crosses were made and advanced to F2 and higher generations. Out of these crosses, an important subset of three crosses was selected based on the overall PD tolerance and sensitivity, importance as mega production varieties and pedigree connections between the cultivars. The plant height, number of tillers, shoot dry weight, leaf width, flag leaf width and the color metrics L*, a*, b*, hue (h*) and chroma (C*) were measured from 200 individuals each from the three populations grown under P deficient (Po) soil conditions. Except color traits, other traits were normally distributed and exhibited higher broad sensitivity. The color metrics indicate the presence of possible epistatic interactions between the major underlying loci. From each population, two extreme bulks were selected from the highest and lowest ends of shoot dry weight (SDW) for bulk segregant analyses (BSA) to validate the DNA markers for PD tolerance. It was observed that, DNA marker K46-K1 can be used for MAB of rice for PD tolerance. The genetic information generated in the present study can also be used for larger scale genomic studies such as SNPs, GBS and GWAS mapping