Genetic Resources Research Articles

Selective list of the Catalogues of the VIR Global Collection on vegetables and cucurbits published in 1962–2023

The Catalogue of the VIR Global Collection series is addressed to plant breeders and crop experts solving practical problems in plan breeding and seed production, plant scientists conducting fundamental and applied research, teachers and learners. The publications within this series help to disclose the potential of the VIR global collection of plant genetic resources and the VIR herbarium (WIR) as an important part of Russian bioresource collections (BRC). The editors of the journal Proceedings on Applied Botany, Genetics and Breeding decided to publish the Selective list of the Catalogues of the VIR Global Collection on vegetables and cucurbits published in 1962–2023 to throw light on VIR’s publishing activities, attract more attention to the Catalogue of the VIR Global Collection series, and specify the numbers and titles of the series’ issues for authors of scientific manuscripts. For the users’ convenience, the sources are arranged chronologically, following the order of issue numbers. The editors hope that this list will prove useful to our readers and authors.

Seeds and farmers' rights as drivers of change on food systems

In the heart of Kenya's vibrant agricultural landscape lies a fundamental aspect crucial for food security, cultural heritage, and economic resilience: the right to seed. Embedded within the fabric of traditional farming practices, the right to seed encompasses the freedom of farmers to save, exchange, and utilize traditional and farmer-bred seeds. In Kenya, as in many other countries, this right is not only a legal concept but a cornerstone of agricultural sovereignty. However, its preservation faces challenges in the face of globalization, corporate interests, and evolving intellectual property regimes. Yet, amidst these challenges, significant strides are being made, with collaborative efforts at the global level, particularly through initiatives led by the Convention on Biological Diversity (CBD) and the International Treaty on Plant Genetic Resources for Food and Agriculture (ITPGRFA), aimed at promoting and protecting farmers' rights. Every smallholder farmer has the right to safe, nutritious and healthy food and the ability to sustain themselves and their societies with the existing endorsed resources. The concept of farmers’ rights came out as a subject of debate in international agricultural circles, spearheaded by the Food and Agriculture Organisation of the United Nations (FAO). This includes the right to save, use, exchange and sell farm-saved seed and propagating materials, the right to protect traditional knowledge among others. In developing countries, the right to seed is a fundamental aspect of agricultural sovereignty and food security. This still emulates the subject debate from FAO. However, attention in scientific literature and policy circles for both seeds and farmers’ rights are compromised. This paper employs mediation analysis to explore the causal relationship between seed rights, farmers' rights, and food sovereignty, highlighting the pivotal role of smallholder farmers in shaping sustainable food systems. The findings underscore the importance of inclusive policies that prioritize farmers' rights and empower local communities to sustainably manage their seed resources. Key words: Farmer-managed seeds, seed banks, Access, smallholder farmers and benefit-sharing

Bio-Based Innovation and the Global Patent System: Exploring the WIPO Treaty on Intellectual Property, Genetic Resources and Associated Traditional Knowledge

Abstract This opinion critically examines the 2024 WIPO Treaty on Intellectual Property, Genetic Resources and Associated Traditional Knowledge, a new instrument addressing the use of genetic resources (GR), and traditional knowledge associated with GR (ATK) in the global patent system. Given the Treaty’s position at the intersection of intellectual property and environmental law, this article discusses its history and negotiation in the first part, including the Treaty’s links to the Convention on Biological Diversity (CBD) and the Agreement on Trade-Related Aspects of Intellectual Property Rights (TRIPS). It then discusses the concept of bio-based innovation and its role in the bioeconomy. Following this, the article assesses the Treaty’s contents, including its context and objectives, scope, the Patent Disclosure Requirement (PDR), sanctions and remedies for non-compliance with the PDR, information systems on GR and ATK, and its relationship with other international instruments. The article highlights the extensive diplomatic negotiations that shaped the final text and considers potential amendments that could be made during the Treaty’s review process. The Treaty is intended to improve the global patent system’s effectiveness, transparency, and quality concerning GR and ATK and to prevent Offices from granting patents erroneously. Its provisions present new challenges and complexities for stakeholders, and its long-term success will depend on ongoing international collaboration and engagement, both within and outside the Treaty’s framework, and ensuring equitable benefit-sharing from the use of GR and ATK as part of a global sustainable bioeconomy.

Effects of SPAD value variations according to nitrogen application levels on rice yield and its components

Nitrogen (N) is the most essential element for growth, development, and grain yield determination in crops. However, excessive nitrogen application can result in environmental pollution and greenhouse gas emissions that contribute to climate change. In this study, we used 158 rice genetic resources to evaluate the relationships between the soil and plant analysis development (SPAD) value and grain yield (GY) and its components. The SPAD value ranged between 30.5 and 55.8, with a mean of 41.7 ± 5.3, under normal nitrogen conditions (NN, 9 kg/10a), and between 27.5 and 52.3, with a mean of 38.6 ± 4.8, under low nitrogen conditions (LN, 4.5 kg/10a). Under NN conditions, the SPAD values were in the following order: japonica (43.5 ± 5.8), Tongil-type (41.7 ± 2.5), others (41.7 ± 5.2), and indica (38.3 ± 3.8). By contrast, under LN conditions, the SPAD values were in the following order: Tongil-type (40.4 ± 2.1), others (40.1 ± 4.5), japonica (39.6 ± 5.2), and indica (35.6 ± 3.9). The 158 genetic resources showed no correlation between SPAD and yield. Therefore, the low-decrease rate (LDR) and high-decrease rate (HDR) SPAD groups were selected to reanalyze the relationships between the surveyed traits. The SPAD values were positively correlated with 1000-grain weight (TGW) for both LDR and HDR groups (NN: 0.63, LN: 0.53), However, SPAD and GY were positively correlated only in the LDR group. For TGW, the coefficient of determination (R2) was 20% and 13% under NN and LN conditions, respectively. For GY, R2 values of 32% and 52% were observed under NN and LN conditions, respectively. Genetic resources with higher SPAD values in the LDR group exhibited the highest yield (NN: 1.19 kg/m2, LN: 1.04 kg/m2) under both NN and LN conditions. In conclusion, we selected 10 genetic resources that exhibited higher GY under both NN and LN conditions with minimal yield reductions. These genetic resources represent valuable breeding materials for nitrogen deficiency adaptation.

Outlook on nutritional importance and breeding strategies for oil and quality improvement in sesame (Sesamum indicum L.)

Sesame (Sesamum indicum L.), is a pivotal crop in global agriculture due to its high oil content (50-60 %), rich in quality unsaturated fatty acids and an array of bioactive compounds like sesamin and sesamol. This review is a compilation of information on sesame nutrition, mechanism of action of bioactive principles, health benefits in terms of unsaturated fats, antioxidants and essential nutrients to combat health disorders. The genetic resources are the base for any crop improvement programs. The genetic wealth of this crop as ex-situ conservation world-wide, traits of importance from its wild relatives, studies on genetic diversity through agronomic and molecular techniques for quality traits are focused. Both conventional and molecular breeding methods are examined. Conventional breeding efforts covers trait variability, correlations, gene action, combining ability studies, breeding methods and varieties released. The insights into molecular biology probes the novel QTLs, discovery of candidate genes, molecular markers for quality traits, genome sequencing, advancements in gene expression studies, genetic maps and pangemone. Despite the significant progress, the lacuna and future prospects in these areas are highlighted. Integrating the information from modern genomic technologies with conventional methods is the key to maximize the crop's potential for oil and nutritional security.

An experimental approach to farmer valuation of African rice genetic resources

AbstractGenebanks serve as both providers of valuable traits for breeding programs and repositories of diverse crop genetic material representing society's agricultural heritage. In this study, we use a Becker‐DeGroot‐Marschak mechanism to elicit the willingness‐to‐pay of rice farmers in Côte d'Ivoire for small amounts of African rice (Oryza glaberrima) landraces held by the genebank of the Rice Biodiversity Center for Africa, and for seed of newly developed ARICA rice varieties bred using genebank materials. Using a field experiment, we additionally investigate how randomized exposure to and experimentation with small amounts of African rice landrace seed or seed of advanced rice varieties developed by AfricaRice affect how smallholder rice farmers value these novel genetic resources. Surprisingly, we find that farmers generally value having access to African rice landraces at approximately the same level as for advanced rice varieties (and far above market rates for improved seed), and that those farmers who grew landrace seed in the offseason were willing to pay more than those who did not. Our results demonstrate the additional value provided by the conservation of African rice landrace varieties (apart from their use in breeding) and highlight the importance of experimentation in the adoption process.

GhASHH1.A and GhASHH2.A Improve Tolerance to High and Low Temperatures and Accelerate the Flowering Response to Temperature in Upland Cotton (Gossypium hirsutum).

The trithorax group (TrxG) complex is an important protein in the regulation of plant histone methylation. The ABSENT, SMALL, OR HOMEOTIC DISCS 1 (ASH1) gene family, as important family members of the TrxG complex, has been shown to regulate tolerance to abiotic stress and growth and development in many plants. In this study, we identified nine GhASH1s in upland cotton. Bioinformatics analysis revealed that GhASH1s contain a variety of cis-acting elements related to stress resistance and growth and development. The transcriptome expression profiles revealed that GhASHH1.A and GhASHH2.A genes expression were upregulated in flower organs and in response to external temperature stress. The results of virus-induced gene silencing (VIGS) indicated that GhASHH1.A and GhASHH2.A genes silencing reduced the ability of cotton to adapt to temperature stress and delayed the development of the flowering phenotype. We also showed that the silencing of these two target genes did not induce early flowering at high temperature (32 °C), suggesting that GhASHH1.A and GhASHH2.A might regulate cotton flowering in response to temperature. These findings provide genetic resources for future breeding of early-maturing and temperature-stress-tolerant cotton varieties.

Response of young rice panicles to salt stress: insights based on phenotype and transcriptome analysis

Saline-alkali soils limit rice growth and production. With an increasing global population, enhancing rice salt tolerance is crucial for improving yields in these areas. This study investigated the developmental characteristics of young panicles and pollen fertility in two rice varieties, 58M and 58L, under salt stress. Results showed that 58M had more substantial salt tolerance during panicle development. RNA sequencing of 18 samples from both varieties under high salt stress (0 h, 6 h, and 24 h) identified 469 common differentially expressed genes (DEGs) and 2,308 DEGs between the varieties. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment highlighted significant pathways such as phenylpropanoid biosynthesis, protein processing, and flavonoid biosynthesis. Six gene co-expression modules related to salt tolerance were identified, with six candidate genes (LOC_Os05g38530, LOC_Os04g07920, LOC_Os12g02105, LOC_Os01g06580, LOC_Os06g49250, and LOC_Os06g48300) potentially linked to salt tolerance. These findings provide insights into rice salt tolerance mechanisms and offer new genetic resources for breeding salt-tolerant rice.

Evaluation of oat accessions from different ecological groups in the steppe environments of Krasnodar Territory

Background. Studying genetic diversity and identifying sources of valuable agronomic traits for specific environmental conditions is of great importance for plant breeders when they select source material for crop improvement. Materials and methods. Three hundred and seven oat accessions of various ecogeographic origin were tested under the conditions of the Kuban Experiment Station, a branch of the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), in 2014–2019. Cv. ‘Valdin 765’ served as the reference. Weather conditions across the years of the study were contrasting in terms of the hydrothermal regime. Results. The inter-cultivar and year-to-year variability of the oat collection was analyzed in Krasnodar Territory and accessions promising for breeding were identified for a set of useful agronomic traits. The most significant differences among the studied oat accessions were recorded for the time of ripening and panicle characteristics. High yield of an accession under the conditions of Krasnodar Territory was associated with its high 1000 grain weight, which positively correlated with the duration of the period from panicle emergence to ripening and negatively with the length of the panicle, number of grains per panicle, plant height, and duration of the periods from germination to panicle emergence and from germination to ripening. Conclusion. The study of useful agronomic traits resulted in identifying oat accessions with the yield exceeding the reference (cv. ‘Valdin 765’) by 114–135%, that ripened 6–8 days earlier than the reference, were resistant to lodging, had short stems, manifested combined resistance (9 points) to crown and stem rust, low filminess (< 25%), good leafiness, high oil content (> 6%), increased protein content (> 14%), and high levels of yield structure components.

Cell wall remodeling confers plant architecture with distinct wall structure in Nelumbo nucifera.

Lotus (Nelumbo nucifera G.) is a perennial aquatic horticultural plant with diverse architectures. Distinct plant architecture (PA) has certain attractive and practical qualities, but its genetic morphogenesis in lotus remains elusive. In this study, we employ genome-wide association analysis (GWAS) for the seven traits of petiole length (PLL), leaf length (LL), leaf width (LW), peduncle length (PLF), flower diameter (FD), petal length (PeL), and petal width (PeW) in 301 lotus accessions. A total of 90 loci are identified to associate with these traits across 4 years of trials. Meanwhile, we perform RNA sequencing (RNA-seq) to analyze the differential expression of the gene (DEG) transcripts between large and small PA (LPA and SPA) of lotus stems (peduncles and petioles). As a result, eight key candidate genes are identified that are all primarily involved in plant cell wall remodeling significantly associated with PA traits by integrating the results of DEGs and GWAS. To verify this result, we compare the cell wall compositions and structures of LPA versus SPA in representative lotus germplasms. Intriguingly, compared with the SPA lotus, the LPA varieties have higher content of cellulose and hemicellulose, but less filling substrates of pectin and lignin. Additionally, we verified longer cellulose chains and higher cellulose crystallinity with less interference in LPA varieties. Taken together, our study illustrates how plant cell wall remodeling affects PA in lotus, shedding light on the genetic architecture of this significant ornamental trait and offering a priceless genetic resource for future genomic-enabled breeding.

Monitoring the genetic diversity in holothurian populations from the Italian coasts with mitochondrial DNA sequences

Sea cucumbers are deposit feeding members of marine benthic communities. The over-exploitation of sea cucumber natural stocks, especially in the Mediterranean basin, is having negative impacts on the marine ecosystem. This concerns had led the Italian government to take legal actions to preserve these important marine resources. The aim of this study was to evaluate the level of genetic diversity and population structures within two sympatric Holothuria sea cucumber species, H. polii and H. tubulosa, across ten Mediterranean areas along Italy. A 323 bp portion of the COI mitochondrial gene was sequenced in a total of 441 holothurians (251 H. polii, 177 H. tubulosa and 13 from other species). Genetic diversity analyses and analysis of molecular variance (AMOVA) suggest that H. polii and H. tubulosa species are distinct, but within and among populations are homogeneous, indicating active gene flows across the Mediterranean areas investigated. H. polii showed a lower genetic diversity than H. tubulosa, probably related to differences in life history traits. Phylogenetic analyses showed a clear differentiation between the two species, even if six specimens morphologically assigned to a species clustered within the other species, indicating a possible occurrence of hybridization events. These data will be useful in implementing conservation actions for these holothurian genetic resources.

Chromosomal Localization and Diversity Analysis of 5S and 18S Ribosomal DNA in 13 Species from the Genus Ipomoea

Background: Sweet potato (Ipomoea batatas (L.) Lam.), a key global root crop, faces challenges due to its narrow genetic background. This issue can be addressed by utilizing the diverse genetic resources of sweet potato’s wild relatives, which are invaluable for its genetic improvement. Methods: The morphological differences in leaves, stems, and roots among 13 Ipomoea species were observed and compared. Chromosome numbers were determined by examining metaphase cells from root tips. Fluorescence in situ hybridization (FISH) was used to identify the number of 5S and 18S rDNA sites in these species. PCR amplification was performed for both 5S and 18S rDNA, and phylogenetic relationships among the species were analyzed based on the sequences of 18S rDNA. Results: Three species were found to have enlarged roots among the 13 Ipomoea species. Chromosome analysis revealed that I. batatas had 90 chromosomes, Ipomoea pes-tigridis had 28 chromosomes, while the remaining species possessed 30 chromosomes. Detection of rDNA sites in the 13 species showed two distinct 5S rDNA site patterns and six 18S rDNA site patterns in the 12 diploid species. These rDNA sites occurred in pairs, except for the seven 18S rDNA sites observed in Ipomoea digitata. PCR amplification of 5S rDNA identified four distinct patterns, while 18S rDNA showed only a single pattern across the species. Phylogenetic analysis divided the 13 species into two primary clades, with the closest relationships found between I. batatas and Ipomoea trifida, as well as between Ipomoea platensis and I. digitata. Conclusions: These results enhance our understanding of the diversity among Ipomoea species and provide valuable insights for breeders using these species to generate improved varieties.

Alternative splicing and deletion in S-RNase confer stylar-part self-compatibility in the apple cultivar 'Vered'.

Although self-incompatibility in apples (Malus × domestica Borkh.) is regulated by a single S-locus with multiple S-haplotypes that comprise pistil S (S-RNase) and pollen S genes, it is not desirable in commercial orchards because it requires cross-pollination to achieve stable fruit production. Therefore, it is important to identify and characterize self-compatible apple cultivars. However, little is known about self-compatibility(SC) and its underlying molecular mechanisms in apples. In this study, we discovered that 'Vered', an early maturing and low chilling-requiring apple cultivar, exhibits stable SC, which was evaluated via self-pollination tests. The S-genotype of 'Vered' was designated as S24S39sm. Results of genetic analysis of selfed progeny of 'Vered' revealed that SC is associated with the S39sm-haplotype, and molecular analyses indicated that it is caused by alternative splicing and a 205-bp deletion in S39sm-RNase. These events induce frameshifts and ultimately produce the defective S39sm-RNase isoforms that lack their C-terminal half. These results enabled us to develop a 117-bp DNA marker that can be used to assist in the selection of self-compatible apples with the dysfunctional S39sm-RNase. Thus, analysis of 'Vered' provided insights into the molecular mechanism of the very rare trait of natural stylar-part SC. Moreover, 'Vered' is a valuable genetic resource for breeding cultivars with SC and/or low chilling requirement in apple. Our findings contribute to a better understanding of self-compatible molecular mechanisms in apple and provide for the accelerated breeding of self-compatible apple cultivars.

Identification of Soybean Mosaic Virus Resistant Soybean Genotypes using Gene-Linked Markers

Soybean is widely consumed legumes both in the form of food and feed. In the present scenario, the quality and quantity of soybean production is largely affected by different biotic factors, Soybean Mosaic Virus being one of the major biotic stress. Plant host resistance is an effective major to develop durable resistance from viral diseases, therefore understanding the molecular mechanism and identifying the resistant genotypes can contribute to resistance breeding in soybean. In 2020, ninety genotypes collected from Grain Legume Research Program, local collection and National Agricultural Genetic Resource Center were screened for the presence of resistant genes using gene linked molecular markers. Among them, three genotypes were identified with Soybean Mosaic Virus resistant loci, Rsv1 amplified by linked marker Satt114, four genotypes were identified with resistant loci, Rsv3 with linked marker Sat_424, and eight genotypes were identified with resistant loci, Rsv4 amplified by linked marker Satt558. Thus, showing expression of dominant resistance to some SMV strains. Interestingly, two genotypes (Co 175 and TGx1990-55) possessed both Rsv1 and Rsv3 loci thus showing potential of resisting broad spectrum SMV resistance to all SMV strains. Therefore, this study has identified potential genotypes that can be used as parental materials for resistant gene pyramiding in soybean breeding for SMV resistance

Genome-Wide Identification and Expression Analysis of the CLAVATA3/ESR-Related Gene Family in Tiger Nut

CLAVATA3 (CLV3)/EMBRYO SURROUNDING REGION (ESR)-related (CLE) genes encode a group of peptide hormones, which coordinate cell proliferation and differentiation in plants. Tiger nut (Cyperus esculentus L.) is a perennial monocot plant that produces oil-rich tubers. However, the mechanisms regulating tuber development in tiger nut are poorly understood, and nothing is known about CLE genes in tiger nut. In this study, we identified 34 CLE genes in the genomes, proteomes, and transcriptomes of C. esculentus (CeCLE). We analyzed their gene structures and expression profiles in different parts of the plant, at three stages of tuber development and in roots in response to dehydration stress. We found a relatively high expression level of CeCLE13 in growing tuber and suggested that the corresponding CLE peptide could be involved in the regulation of tuberization. We also analyzed CeCLE gene sequences in the genome of the most productive K-17 variety in the N. I. Vavilov All-Russian Institute of Plant Genetic Resources collection and found many single nucleotide polymorphisms, insertions, and deletions. Our data provides fundamental information for future research on tiger nut growth and tuberization.

Rapid assessment of main agronomic indicators in the grain of winter and spring forms of triticale using infrared spectroscopy

Background. Calibration models were developed for rapid assessment of crucial agronomic indicators in the grain of winter and spring triticale from the VIR collection using near-infrared spectroscopy (NIRS). These calibration models will enable users to find the most optimal utilization trends for individual triticale accessions. Materials and methods. Indicators of agronomic value (coloration, moisture, and the content of ash, protein, starch, amylose and fiber) were studied on a set of 32 grain samples collected from winter and spring triticale forms (Triticosecale Wittm. & A. Camus) reproduced in 2021–2022 at the Dagestan Experiment Station, a branch of the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR). Calibration models for the assessment of the said agronomic characters in triticale grain were developed on the platform of the MATRIX-I IR analyzer (Bruker Optics, Germany) and based on the values obtained by classical methods of biochemical analysis adopted at VIR. Results. Reliability of the calibration models was tested on a randomized batch of triticale grain samples: the results of the new calibrations were compared with those of the conventional biochemical analysis. This verification showed that the data obtained through the use of calibration curves were reliable for protein and ash content, while other models required further improvement. Conclusion. Calibration models for measuring protein and ash content developed on the basis of the MATRIX-I IR analyzer can be used to perform rapid assessment of the winter and spring triticale grain. This method makes it possible to accelerate the process of obtaining crop characteristics for a number of basic agronomic characters and preserve valuable breeding material.

Aspects of introduction and prospects for the use of Juglans L. representatives in Central Russia

Background. Human health security is an important goal of contemporary society. The combination of beneficial properties in Juglans nuts makes them one of the most valuable plant genetic resources, capable of ensuring a wholesome supply of nutrients required by the human organism. The Persian walnut (Juglans regia L.) has the largest set of useful agronomic traits among the representatives of the genus, except for winter hardiness. Its cultivation in areas farther to the north from the conventional area of distribution for commercial walnut orchards would be possible if Juglans spp. with higher resistance to unfavorable climate conditions could be involved. Interspecies hybridization can be used to increase winter hardiness in walnut. The objective of this study was to analyze the gene pool of Juglans L. and screen its bioresource collection at the arboretum of the Russian Research Institute of Fruit Crop Breeding (VNIISPK) in the context of useful agronomic indicators promising for plant breeding and landscaping. Materials and methods. The study was carried out in the VNIISPK arboretum (Orel Province, 53°00’N, 36°00’E) where 7 Juglans spp. are maintained. Results and conclusion. The results of the screening highlighted J. mandshurica Maxim., J. cordiformis Maxim., and Vekhov’s hybrid (J. cinerea L. × J. mandshurica Maxim.) as the most resistant to adverse environmental effects. They are recommended for use in plant breeding and landscaping programs under the conditions of Central Russia. A seedling of cv. ‘Astakhovsky’ demonstrated the best agronomic indicators among the Persian walnut (J. regia) genotypes. It can be used by breeders to develop new cultivars with useful agronomic traits for the environmental conditions of the region of study.

Clinical diagnosis and management of spinocerebellar Ataxia in a resource-constrained setting: a case report from Eastern Nepal

Introduction: Spinocerebellar ataxias (SCA) are a diverse group of neurodegenerative disorders with autosomal dominant inheritance, primarily affecting the cerebellum and its connections. Diagnosis typically involves genetic testing, but in resource-limited settings, clinical and neuroimaging assessments become critical. This case report highlights the role of non-genetic methods in diagnosing SCA and outlines management strategies in such settings. Case Presentation: A 41-year-old male presented with a two-year history of progressive gait imbalance, headache, and abnormal speech. He had a family history of similar symptoms in two siblings, but no significant past medical history. Clinical examination revealed scanning speech, dysmetria, and a broad-based gait. Clinical and neuroimaging findings, including cerebellar atrophy, led to a diagnosis of SCA in the absence of genetic testing. Patient management with speech, occupational, and physical therapies, showed gradual improvement. Discussion: SCA, characterized by cerebellar atrophy and a range of clinical symptoms, is typically diagnosed through genetic testing, but clinical and imaging assessments are crucial when genetic resources are limited. This case illustrates that a comprehensive clinical evaluation, including neuroimaging, can support the diagnosis of SCA even without genetic testing. Strategic management emphasizing symptomatic relief and functional improvement through a multidisciplinary approach, including regular follow-up and personalized therapy, are crucial, as evidenced by the timely improvement observed in our case. Conclusion: In resource-limited settings, a comprehensive clinical and neuroimaging assessment is essential for diagnosing Spinocerebellar Ataxia when genetic testing is not feasible. Effective management through multidisciplinary therapies can improve patient outcomes, underscoring the need for innovative strategies to enhance diagnostic and treatment capabilities in such environments.

Genetic diversity and parentage of cacao (Theobroma cacao L.) populations from Ghana using single nucleotide polymorphism (SNP) markers

Abstract Ortet selection remains an integral component of cacao breeding programme to develop improved clones and expand the gene pool of available germplasm. This study assessed the population structure of 168 cacao clones developed recently from selected ortets in on-station and on-farm progeny trials in Ghana using 45 SNP markers. Selection of ortets was primarily based on high bean yield, high yield efficiency, adaptability to marginal growing conditions, and low incidence of black pod and cocoa swollen shoot virus diseases. Additionally, 58 SNPs were employed to verify the parentage of 752 bi-clonal seedlings supplied to farmers for commercial plantations. Pairwise multilocus matching based on 45 SNPs showed that the 168 clones were all distinct. Overall, the clones had moderate genetic diversity (He = 0.349 ± 0.022) and shared ancestry with Marañón, Guiana, Contamana, Iquitos, Amelonado, Trinitario, Nanay and Purús based on Bayesian clustering, principal coordinates, and parentage analyses. Parentage analysis of bi-clonal seedlings assigned parent-offspring trios (>80% confidence level) to 65.2% of the farmers' varieties based on breeder's active clone collection. The results of the parentage analysis suggested the existence of mislabelled clones in the seed gardens, necessitating the need for correct clone identification or rogueing. Taken together, this study presents a new group of cacao genetic resources with potential to broaden the gene pool of cacao in cacao improvement programmes. Further, the study conveys evidence of the need for countries with established seed garden systems to constantly monitor the genetic purity of seedlings produced from the seed gardens.

Genotyping by sequencing; a strategy for identification and mapping of induced mutation in newly developed wheat mutant lines.

Exposing genetic material with physical mutagens can create novel genetic resources capable of combating different stresses. High throughput GBS-DArTseq™ assay was deployed to estimate genetic diversity of 33 newly developed stable wheat mutants as compared to the wild type. The identified 1,57,608 PAVs markers were randomly distributed across wheat chromosomes and sub-genomes with the highest number detected on Chr-7D (2877) and Chr-7B (2711). The B sub-genome contained the most PAVs followed by D and A-sub genome. Among mutant lines, Pb-M-2061 and Pb-M-59 had the highest PAV count, while Pb-M-605 and Pb-M-196 had the lowest. A total of 7,910 PAVs were consistently present over all replicates, with 3,252 specifically present in mutants and absent in wild type. The maximum PAVs (1480) were found in Pb-M-1027 and Pb-M-1323 (656). Functional characterization revealed that out of 3,252, 1,238 were found in wheat transcriptome database that contained 152 characterized and 1,196 uncharacterized genes. COGs and GO-terms analysis linked many PAVs with pathways involving signaling, metabolism and defense. Maximum number of gene-containing PAVs were identified in Pb-M-1027, Pb-M-2302 and Pb-M-1323 which were involved in tolerance to diseases and abiotic stresses, improved photosynthetic efficiency, larger grain size, increased grain yield and harvest index pathways. This study provides valuable insights into the genetic diversity and potential agronomic benefits of PAVs in wheat mutant lines. These findings can help molecular geneticist and breeders for exploiting the induced genetic diversity for unravelling the genetic circuits as well as exploiting in wheat breeding for developing resilient cultivars.