Development of a multiplex DNA-based traceability tool for crop plant materials

The authenticity of food is of increasing importance for producers, retailers and consumers. All groups benefit from the correct labelling of the contents of food products. Producers and retailers want to guarantee the origin of their products and check for adulteration with cheaper or inferior ingredients. Consumers are also more demanding about the origin of their food for various socioeconomic reasons. In contrast to this increasing demand, correct labelling has become much more complex because of global transportation networks of raw materials and processed food products. Within the European integrated research project ‘Tracing the origin of food’ (TRACE), a DNA-based multiplex detection tool was developed—the padlock probe ligation and microarray detection (PPLMD) tool. In this paper, this method is extended to a 15-plex traceability tool with a focus on products of commercial importance such as the emmer wheat Farro della Garfagnana (FdG) and Basmati rice. The specificity of 14 plant-related padlock probes was determined and initially validated in mixtures comprising seven or nine plant species/varieties. One nucleotide difference in target sequence was sufficient for the distinction between the presence or absence of a specific target. At least 5% FdG or Basmati rice was detected in mixtures with cheaper bread wheat or non-fragrant rice, respectively. The results suggested that even lower levels of (un-)intentional adulteration could be detected. PPLMD has been shown to be a useful tool for the detection of fraudulent/intentional admixtures in premium foods and is ready for the monitoring of correct labelling of premium foods worldwide

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Not AvailableThe Wild Abortive (WA) system is the major cytoplasmic male sterility (CMS) source for hybrid rice production in indica rice and its fertility restoration is reported to be controlled by two major loci viz. Rf3 on chromosome 1 and Rf4 on chromosome 10. With the availability of the rice genome sequence, an attempt was made to fine map, develop candidate gene based markers for Rf3 and Rf4 and validate the developed marker system in a set of known restorer lines. Using polymorphic markers developed from microsatellite markers and candidate gene based markers from Rf3 and Rf4 loci, local linkage maps were constructed in two mapping populations of ~1,500 F2 progeny from KRH2 (IR58025A/KMR3R) and DRRH2 (IR68897A/DR714-1-2R) hybrids. QTLs and their interactions for fertility restoration in Rf3 and Rf4 loci were identified. The identified QTL in both mapping populations together explained 66–72 % of the phenotypic variance of the trait suggesting their utility in developing a marker system for identification of fertility restorers for WA-CMS. Sequence comparison of the two candidate genes from the Rf3 and Rf4 regions in male sterile (A) and restorer (R) lines showed 2–3 bp indels and a few substitutions in the Rf3 region and indels of 327 and 106 bp in the Rf4 region respectively. The marker system identified in the present study was validated in 212 restorers and 34 maintainers along with earlier reported markers for fertility restoration of WA-CMS. Together DRCG-RF4-14 and DRCG-RF4-8 for the Rf4 locus and DRRM-RF3-5/DRRM-RF3-10 for the Rf3 locus showed a maximum efficiency of 92 % for identification of restorers.Not Availabl

Indel polymorphism in sugar translocation and transport genes associated with grain filling of rice (Oryza sativa L.)

Not AvailableDepending on the position on the panicle, grain filling differs for spikelets on primary branches and secondary branches of upper and lower portions in rice (Oryza sativa L.). With the objective of identifying candidate genes associated with the grainfilling process across the panicle, a candidate gene (CG) - based mapping approach was attempted in an F2 population derived from the cross between Rasi, a rice variety known for its good grain filling, and IC114927, a local landrace. The grain filling (%) was characterized for 444 F2 individual plants across the panicle. Within the F2 population, thirteen plants were identified with [90% grain filling across the panicle]. For 120 markers designed from 1 kb upstream and within the candidate genes reported to be involved in translocation process of sugars, 18.3% polymorphism was observed. Using a selective genotyping approach comprising 24 individuals from eight groups based on their filling and position, two associated CG markers were identified. Further analysis of the mapping population showed a CG marker based on the sucrose phosphate synthase gene on chromosome 2 to be significantly associated with filling of grains on primary branches of the upper half of the panicle and another CG marker based on the transporter gene on chromosome 11 to be associated with filling of grains on primary branches of the lower half; secondary branches of the upper half and lower half of the panicle. Both the positive alleles were contributed by the variety Rasi. With a candidate gene - based marker mapping approach, two genes involved in sugar translocation and transport were identified to be directly associated with grain filling in rice.Not Availabl

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