Advances in identifying GM plants: toward the routine detection of ‘hidden’ and ‘new’ GMOs

In 2018 the Court of Justice of the European Union recalled that organisms with genomes modified by artifactual techniques should be considered GMOs under European regulations. GMOs derived from cultures of cells isolated in vitro or from new genomic techniques must therefore be traceable. This chapter reviews the various technical steps and characteristics of those techniques causing genomic and epigenomic scars and signatures. These intentional and unintentional traces, some of which are already used for varietal identification, and are being standardized, can be used to identify these GMOs and differentiate them from natural mutants. The chapter suggests a routine procedure for operators and control laboratories to achieve this without additional costs.

Study Of Genetic Diversity And Resistance Of Fruit Crops To Main Pathogens Using DNA Markers

Breeding modern varieties of fruit crops requires the study of their biodiversity as a source of genes for useful traits, with the aim of transferring them to genome of commercial varieties. Application of genomic technologies can significantly speed up the breeding process. Identification and application of DNA markers for the study of genetic diversity, varietal identification, as well as the transfer of genes of valuable economic traits through marker assisted selection programs is of great applied importance. The article discusses the results of studies to identify genes and DNA markers associated with resistance of some fruit crops to major diseases.

How to Choose a Good Marker to Analyze the Olive Germplasm (Olea europaea L.) and Derived Products

The olive tree (Olea europaea L.) is one of the most cultivated crops in the Mediterranean basin. Its economic importance is mainly due to the intense production of table olives and oil. Cultivated varieties are characterized by high morphological and genetic variability and present a large number of synonyms and homonyms. This necessitates the introduction of a rapid and accurate system for varietal identification. In the past, the recognition of olive cultivars was based solely on analysis of the morphological traits, however, these are highly influenced by environmental conditions. Therefore, over the years, several methods based on DNA analysis were developed, allowing a more accurate and reliable varietal identification. This review aims to investigate the evolving history of olive tree characterization approaches, starting from the earlier morphological methods to the latest technologies based on molecular markers, focusing on the main applications of each approach. Furthermore, we discuss the impact of the advent of next generation sequencing and the recent sequencing of the olive genome on the strategies used for the development of new molecular markers.

Deciphering the Taxonomic Delimitation of Ottelia acuminata (Hydrocharitaceae) Using Complete Plastomes as Super-Barcodes

Accurate species delimitation and identification, which is a challenging task in traditional morphology-based taxonomy, is crucial to species conservation. Ottelia acuminata (Hydrocharitaceae) is a severely threatened submerged macrophyte endemic to southwestern China. The taxonomy of O. acuminata, which has long been in dispute, remains unresolved, impeding effective conservation and management practices. Here, we aim to address the long-standing issues concerning species boundary and intraspecific subdivision of O. acuminata using complete plastome sequences as super-barcodes. The taxonomic delimitation of O. acuminata was explored using phylogenetic inference and two independent sequence-based species delimitation schemes: automatic barcode gap discovery (ABGD) and multi-rate Poisson tree processes (mPTP). The reciprocally reinforcing results support the reduction of the closely related congeneric species, O. balansae and O. guanyangensis, as two conspecific varieties of O. acuminata. Within the newly defined O. acuminata, accurate varietal identification can be achieved using plastome super-barcodes. These findings will help inform future decisions regarding conservation, management and restoration of O. acuminata. This case study suggests that the use of plastome super-barcodes can provide a solution for species delimitation and identification in taxonomically difficult plant taxa, thus providing great potential to lessen the challenges of inventorying biodiversity, as well as biologically monitoring and assessing threatened species.

A Multidisciplinary Fingerprinting Approach for Authenticity and Geographical Traceability of Portuguese Wines

The interest in developing reliable wine authenticity schemes is a hot-topic, especially for wines with recognized added-value. In order to accomplish this goal, two dimensions need to be considered: the grapevine variety determination and the geographical provenance. The aim of this study was to develop a multidisciplinary approach applicable to wines from the sub region Melgaço and Monção of the demarcated Vinho Verde region and from the demarcated Douro region. The proposed scheme consists on the use of DNA-based assays to detect Single Nucleotide Polymorphisms (SNPs) on three genes of the anthocyanin pathway (UFGT, F3H and LDOX) coupled with High-resolution melting (HRM) analysis aiming the varietal identification. The Alvarinho wines revealed to have the same haplotype using this marker set, demonstrating its applicability for genetic identification. In addition, to assess their geographical provenance, a multi-elemental approach using Sr and Pb isotopic ratios of wine, soil and bedrock samples was used. The isotopic data suggest a relation between Sr and Pb uptake by vine roots and soil’s texture and clay content, rather than with the whole rock’s isotopic ratios, but also highlights the potential of a discriminating method based on the combination of selected isotopic signatures.

Varietal identification and fingerprinting of Pearl Millet (Pennisetum glaucum L.) varieties and hybrid using morphological descriptors and SSR markers

Pearl Millet (Pennisetum glaucum) is the sixth most important cereal crop in the world. The genomic resources available in Pearl millet can be utilized for fingerprinting and screening of hybrids using SSR markers and will be helpful for the assessment of seed purity. Hence, the present study was focused on fingerprint popular pearl millet varieties and hybrids of Tamil Nadu for varietal identification and hybrid purity test. The varieties used for DNA fingerprinting were CO (Cu) 9, CO 10, Pearl Millet hybrid CO 9 along with the parents, A' line ICMA 93111A and R' line PT 6029-30. The morphological features were recorded to screen the cultivars. The Pearl millet hybrid CO 9 scored the highest value for more than four quantitative characters via., Number of productive tillers (4-6), Leaf blade length (60-68cm), Leaf blade width (4.0-4.5cm), number of nodes (8-10), and 1000 seed weight (13-14g) which is at par and comparable with the composite CO 10 and higher than that of the variety CO (Cu) 9. PCR was performed using 36 SSR primers to find out polymorphism among the varieties. The SSR markers ICMP3021 and PSMP2089 were able to selectively identify CO (Cu) 9 from the other varieties. Whereas, the SSR markers ICMP3018, PSMP2219, and PSMP2220 were used to distinguish CO 10 from the other varieties. Further, the CO10 variety produced additional alleles for all the markers due to its composite nature. Among the thirty-six SSR primers screened, none of them were found suitable to distinguish the TNAU hybrid CO 9 from its parents. The unique DNA fingerprints developed in the present study can be utilized for seed purity testing and varietal identification.

Genotyping of Avasirkhva, an indigenous Abkhasian grapevine variety

Molecular genotyping of native varieties of Vitis vinifera L. from different winegrowing areas is a current trend in the grapevine genetic diversity research. Abkhazia is among the world cradles of tamed grape, and its indigenous gene pool is of particular interest. Avasirkhva is a native Abkhasian grapevine variety mainly grown in the Gudauta District. Te research aimed to obtaining a genetic passport of Avasirkhva grapevine using microsatellite polymorphism data. Te study sampled grape plants from private farmsteads of the Gudauta District. Te plant phenotype corresponded to the variety’s ampelographic description. DNA was isolated from young shoot tip leaves with a CTAB-based protocol. Genotyping was performed with polymerase chain reaction (PCR) followed by capillary fragment separation. High-polymorphic SSR loci (VVS2, VVMD5, VVMD7, VVMD25, VVMD27, VVMD28, VVMD32, VrZAG62, VrZAG79) recommended for grapevine varietal identification were used as markers. Te amplicon size was estimated with an ABI Prism 3130 automated genetic analyser using the GeneMapper and PeakScanner soſtware and Pinot Noir as a reference variety genotype. Four samples exhibited an identical microsatellite profile. Te microsatellite assay-based genetic passport of the Avasirkhva variety is as follows: VVS2141-145 VVMD5234-242 VVMD7239- 249, VVMD25239-249, VVMD27184-190, VVMD28234-248, VVMD32248- 262, VrZAG62200-204, VrZAG79251-257. Te obtained passport is unique with respect to the known genotypes in the Vitis International Variety Catalogue (VIVC). A Principal Coordinate Analysis of microsatellite data was used to infer the genetic relationships between Avasirkhva and the Abkhasian varieties Kachich and Azhizhkvakva genotyped in our earlier studies, as well as nine native grapevines of Georgia, the nearest viticultural area. Te Avasirkhva genetic passport can be used in grapevine genotyping studies to clarify the varietal identity.

Adoption of improved cassava varieties in Nigeria: Insights from DNA fingerprinting versus self-reporting varietal identification approaches

Much of the empirical studies on crop varietal adoption in Sub-Saharan Africa relied on self-reported adoption in farm-household surveys, which is prone to measurement errors. In addition, farmers’ perceptions of consumption-related varietal traits in adoption studies has received limited attention compared with production-related traits. Using DNA-based and self-reported adoption measures, we analyze the adoption of improved cassava varieties (ICVs) with a focus on the extent of varietal misidentification, the sensitivity of the drivers of adoption to varietal misidentification and the role of farmers’ perceptions of biofortification trait in adoption decisions. We find that the adoption rate of ICVs is relatively high using both DNA-based and self-reported adoption measures, but there is notable misclassification in varietal adoption. We find that the mismatch in DNA-based and self-reported adoption measures leads to some variation in the factors that influence the likelihood and intensity of adoption of ICVs. This suggests that appropriate varietal identification helps in better understanding of the drivers of adoption. In addition, we find that despite the observed varietal misclassification, farmers’ perceptions of biofortification trait is significantly correlated with the probability and intensity of adoption of ICVs using both DNA-based and self-reported varietal identification. This suggests that inclusion of biofortification trait in cassava matters for both the likelihood and extent of adoption of ICVs. The latter lends credence to the emerging policy interests in breeding programs for biofortified crops to address hidden hunger in Nigeria.