Single Sequence Repeat Research Articles

Multiple functions of the herpesvirus UL14 gene product in viral infection.

Herpesviruses are a family of double-stranded DNA viruses with a tegument structure and a genome composed of a single sequence and terminal repeat (TR) sequences. The herpesvirus UL14 gene encodes the protein UL14 (pUL14), which has various subcellular localizations and plays a vital role in regulating immediate-early (IE) gene transcription and expression, influences the intracellular localization patterns of several proteins belonging to the capsid and the DNA packaging machinery, participates in secondary envelopment, and influences viral particle release. Additionally, pUL14 has roles in maintaining cellular homeostasis and preventing apoptosis. This review discusses how pUL14 engages in the life cycle of herpesviruses and provides new ideas for further research on pUL14's function in viral infection.

Development of SSR markers for genetic diversity analysis and species identification in Polygonatum odoratum (Mill.) Druce based on transcriptome sequences.

Polygonatum odoratum (Mill.) Druce is a well-known traditional Chinese herb belonging to the Polygonatum. However, the understanding of the genetic diversity of this species at the molecular level is limited due to the lack of transcriptomic and genomic information. In this study, 37,387 unigenes were assembled based on the transcriptome sequencing of the rhizome of Polygonatum odoratum (Mill.) Druce., and 11,021 single- sequence repeats (SSR) motifs, mainly consisting of single-nucleotide repeats (44.44%), dinucleotides (31.06%), and trinucleotides (22.59%), were identified. Based on these SSR motifs, 9,987 primer pairs of SSR markers were designed and 68 SSR markers were randomly selected for verification, of which 21 SSR markers showed polymorphisms among the 24 Polygonatum odoratum germplasms. Ninety-four alleles were detected: the observed alleles ranged from 2 to 11, the effective alleles varied from 1.086 8 to 4.916 8, the Shannon diversity index was 0.173 2~1.749 7, and the polymorphism information content PIC ranged from 0.076 7 to 0.803 9. Based on our analysis of genetic diversity (SSR genotypes) and population structure, we divided the 24 germplasm resources into two groups, indicating that the germplasm with similar geographical origins can be grouped together. In addition, the primers 'YZ14' and 'YZ47' could effectively distinguished the related species: Polygonatum kingianum Coll.et Hemsl., Polygonatum sibiricum Red., Polygonatum cyrtonema Hua, Polygonatum zanlanscianense Pamp. and Polygonatum odoratum (Mill.) Druce. This is the first study in which a dataset of expressed sequence tag (EST)-SSR markers is constructed for the Polygonatum odoratum (Mill.) Druce, and these newly developed EST-SSR markers provided a very efficient tool for genetic relationship analysis, species identification and marker-assisted selection breeding of Polygonatum odoratum (Mill.) Druce.

Unveiling the genetic landscape: Exploring the SSR-based genetic architecture and amino acid dissection of Gossypium barbadense and G. darwinii genomes

Genetic maps highlight the genome organization and structure but also provide the chance of tagging superior traits for crop improvement through marker-assisted selection. Amino acids are building blocks of proteins and perform crucial function in regulating the signaling of molecules involved in the development and growth of plants. Plant architecture also have an impact on crop productivity. In order to select elite cultivars for breeding and identification of favorable alleles and their functional properties, a deep understanding of genetic architecture and development of genetic map is essential. In present investigation, an interspecific cross of Gossypium barbadense XH-18 × G. darwinii 5-7 was made to develop a genetic map utilizing single sequence repeat markers for the dissection of amino acids involved in genetic architecture of G. barbadense and G. darwinii. We measured chromosomal distribution of 20 amino acids across the whole genome of both species. The map consists of 613 markers spread across all 26 chromosomes, covering 2371.4 cM of cotton genome with an average inter-marker distance of 9.35 cM. The marker number anchored on the chromosomes varied from 5 to 76 with an average of 23.57 on each chromosome. The Dt sub-genome had more markers (83.03%) than the At sub-genome (15.66%). Moreover, the longest chromosome was 143.387 cM, the shortest was 58.430 cM, and the average length was 91.207 cM. The Dt subgenome spans a greater genomic distance than the At subgenome. A sum of 21,035 genes were discovered, covering the complete genome of G. barbadense; G. darwinii and have been found to be involved in tRNA 3'-trailer cleavage, macromolecule modification, peptide deformylase activity, response to biotic stimulus and defense response. The minimum Glutamic acid (Glu), Histidine (His), and Lysine (Lys) were found on Chr.13 (0.00-17.74), Chr.02 (0.00-8.01), and Chr.06 (0.00-17.97), respectively found through chromosomal amino acid dissection. The genome-wide SSR interspecific genetic map of G. barbadense and G. darwinii is first of its kind, and studying chromosomal distribution of amino acids will set a landmark step to dissect the genome structure of G. darwinii.

RAG1/2 induces double-stranded DNA breaks at non-Ig loci in the proximity of single sequence repeats in developing B cells.

In developing B cells, V(D)J gene recombination is initiated by the RAG1/2 endonuclease complex, introducing double-stranded DNA breaks (DSBs) in V, D, and J genes and resulting in the formation of the hypervariable parts of immunoglobulins (Ig). Persistent or aberrant RAG1/2 targeting is a potential threat to genome integrity. While RAG1 and RAG2 have been shown to bind various regions genome-wide, the in vivo off-target DNA damage instigated by RAG1/2 endonuclease remains less well understood. In the current study, we identified regions containing RAG1/2-induced DNA breaks in mouse pre-B cells on a genome-wide scale using a global DNA DSB detection strategy. We detected 1489 putative RAG1/2-dependent DSBs, most of which were located outside the Ig loci. DNA sequence motif analysis showed a specific enrichment of RAG1/2-induced DNA DSBs at GA- and CA-repeats and GC-rich motifs. These findings provide further insights into RAG1/2 off-target activity. The ability of RAG1/2 to introduce DSBs on the non-Ig loci during the endogenous V(D)J recombination emphasizes its genotoxic potential in developing lymphocytes.

Tidings from the Tides–De novo transcriptome assembly of the endemic estuarine bivalve Villorita cyprinoides

The Indian black clam Villorita cyprinoides Gray, 1825, is an economically valuable estuarine bivalve that faces challenges from multiple stressors and anthropogenic pressures. However, limited genomic resources have hindered molecular investigations into the impact of these stressors on clam populations. Here, we have generated the first transcriptomic reference datasets for V. cyprinoides to address this knowledge gap. A total of 25,040,592 and 22,486,217 million Illumina paired-end reads generated from two individuals were assembled using Trinity and rnaSPAdes. From the 47,607 transcripts identified as Coding Domain Sequences, 37,487 returned positive BLAST hits against six different databases. Additionally, a total of 14,063 Single Sequence Repeats were identified using GMATA. This study significantly enhances the genetic understanding of V. cyprinoides, a potential candidate for aquaculture that supports the livelihoods of many people dependent on small-scale fisheries. The data generated provides insights into broader genealogical connections within the family Cyrenidae through comparative transcriptomics. Furthermore, this transcriptional profile serves as baseline data for future studies in toxicological and conservation genetics.

Use of SSR markers and FTIR chemometrics to assess the nobility of kava cultivars from the Pacific

According to the FAO/WHO Codex Alimentarius regional standards for kava (Piper methysticum Forst. f.), only Noble cultivars shall be used as raw material. Other P. methysticum cultivars and wild forms (P. m. var. wichmannii C.DC.) are excluded from trade. There is a need for accurate identification tools as morpho-agronomic descriptors are influenced by growing conditions and once kava roots have been harvested, it is visually impossible to differentiate Noble cultivars from others. In the present study, 163 leaf samples originating from Papua New Guinea, the Solomon Islands, Vanuatu, Fiji, Tahiti, Hawaii and Pohnpei were analyzed using 13 microsatellite (Single Sequence Repeat, SSR) markers. Hierarchical Clustering Analysis (HCA) and Multiple Correspondence Analysis (MCA) clearly differentiated five groups: Nobles from Polynesia, Nobles from Vanuatu, Two-day cultivars from Vanuatu, var. wichmannii from Vanuatu and P. methysticum cultivars for Papua New Guinea. Fourier Transform InfraRed (FTIR) was used to assess its potential as a high throughput analytical tool to detect nobility. FTIR spectra (1800-800 cm−1) from 138 root powder samples were analyzed using Principal Component Analysis (PCA). Nobles from Vanuatu and from Polynesia were not differentiated from each other but were differentiated from poor quality P. methysticum cultivars and from var. wichmannii. Linear Discriminant Analysis (LDA) improved the differentiation of Nobles from others. Samples were then classified in two groups: Nobles (Vanuatu + Polynesia) and non-Nobles. A learning and a test sets were composed at random. PLS-DA (Partial Least Square Discriminant Analysis) allowed the differentiation of Nobles with a prediction accuracy over 96.9%. FTIR has potential for kava quality control. The method described here is simple, fast, eco-friendly, and requires less than 0.5 g of root powder. Its routine application could greatly contribute to guarantee kava quality and protect the international markets.

Determining the Relationships Between Genotype and Phenotype Using Molecular Genetic Tools in Chickens

Context: Chicken meat is one of the rich sources of protein and is considered one of the most commonly consumed meats in the world. Enhancing poultry production and its products is achievable through chicken breeding. Effective breeding projects for future genetic improvement require an understanding of the genetic potential of a given population. Evidence Acquisition: Articles were selected based on novel molecular markers related to economic traits of chicken in Animal quantitative trait loci (QTL) database, Ensemble genome browser, CorrDB, ChickVD, Galbase, and Google Scholar. These databases contain QTLs, markers, and reference genomes of chicken. Galbase provides research communities with updated possibilities to conduct thorough functional genomics research on chickens. ChickVD manages high-quality sequence variation data, variation analysis in relation to chicken genes, cDNAs, genetic markers, and QTLs. CorrDB compiles all available chicken genetic and phenotypic trait correlation data to aid in the analysis of genetic networks and facilitate systems biology research. Animal Quantitative Trait Loci Database (Animal QTLdb) gathers and compiles all existing data on trait mapping, including QTL (phenotype/expression, eQTL), candidate gene, association data (GWAS), and copy number variations (CNV) for livestock animal genomes. This comprehensive database facilitates the easier identification and comparison of discoveries within and across species. Ensemble genome browser is a powerful tool for analyzing vertebrate genomes, offering valuable insights into comparative genomics, evolutionary processes, sequence variations, and transcriptional regulation. Results: Valuating the relatedness of the studied broilers and layers is important for maintaining and improving the genetic reserves of the same population. Candidate genes (CGs) are used to determine genes related to economic traits in chickens. Molecular genetic techniques such as whole-genome re-sequencing (WGRS) can identify single nucleotide polymorphisms (SNPs), insertion/deletion polymorphisms (indels), structural variations (SV), CNV, and simple sequence repeats (SSRs) and their chromosomal regions in terms of QTL. Recently, the pan-genome (PG) has become one of the most important tools to study genome variation and changes in important traits. The use of molecular markers and CGs can aid in evaluating the genetic relationships between phenotype and genotype of broilers and layers. Conclusions: This review introduces molecular genetic methods and new approaches to identify novel genes related to important biological pathways and significant production and reproductive traits.

Durum wheat (Triticum turgidum L. var. durum) root system response to drought and salt stresses and genetic characterization for root-related traits.

Abiotic stresses such as drought and salt are significant threats to crop productivity. The root system adaptation and tolerance to abiotic stresses are regulated by many biochemical reactions, which create a complex and multigenic response. The present study aims to evaluate the diversity of root responses to cyclic abiotic stress in three modern durum wheat varieties and one hydric stress-tolerant landrace in a pot experiment from seedling to more advanced plant development stages. The genotypes responded to abiotic stress during the whole experiment very differently, and at the end of the experiment, nine out of the 13 traits for the landrace J. Khetifa were significantly higher than other genotypes. Moreover, single sequence repeat (SSR) genetic analysis revealed high polymorphism among the genotypes screened and interesting private alleles associated with root system architecture traits. We propose that the markers used in this study could be a resource as material for durum wheat breeding programs based on marker-assisted selection to increase the vegetal material with high drought and salt stress tolerance and to identify candidates with strong early vigor and efficient root systems. This study provides appropriate genetic materials for marker-assisted breeding programs as well as a basic study for the genetic diversity of root traits of durum wheat crops.

Genotypic and allelic variability of the calpain CAPN1-316 gene in the Tropical Milking criollo breed and indication of its meat tenderness

Background: Genes and their variants related to milk and beef production in cattle can be identified through molecular markers. In particular, the Calpain gene CAPN1-316 has been linked to meat tenderness. The males of the Tropical Milking Criollo cattle not assigned as breeding animals are destined for commercial beef production. Objective: To estimate the genotypic and allelic frequencies in the calpain gene CAPN1-316 and its relation to meat tenderness in the Tropical Milking criollo breed. Methods: Molecular marker microsatellites of single sequence repeats (SSR) from DNA were extracted from blood samples of 423 purebred animals from three farms to identify the variants of the CAPN1-316 gene using the polymerase chain reaction (PCR). Genotypic and Allelic frequencies within populations, genetic distance, heterozygosity, and Xi squared (X2) test were performed using Pop Gene V.4. Results: The genotypic frequencies of the whole population were CC 0.31, GG 0.18, and CG 0.51. The allelic frequencies of variant C per farm were 0.62, 0.60, and 0.52. The genotypic and allelic frequencies of the CAPN1-316 polymorphisms were in Hardy-Weinberg equilibrium (X2, p>0.05). The CC genotype showed indication of greater tenderness. Conclusion: In the Tropical Milking criollo cattle, the C variant of the CAPN1-316, favorable to meat tenderness, had a bigger frequency than the G variant.

Quantitative Trait Loci Mapping Identified Candidate Genes Involved in Plant Height Regulation in Rice

Rice plant height is an agricultural trait closely related to biomass, lodging tolerance, and yield. Identifying quantitative trait loci (QTL) regions related to plant height regulation and developing strategies to screen potential candidate genes can improve agricultural traits in rice. In this study, a double haploid population (CNDH), derived by crossing ‘Cheongcheong’ and ‘Nagdong’ individuals, was used, and a genetic map was constructed with 222 single-sequence repeat markers. In the RM3482-RM212 region on chromosome 1, qPh1, qPh1-1, qPh1-3, qPh1-5, and qPh1-6 were identified for five consecutive years. The phenotypic variance explained ranged from 9.3% to 13.1%, and the LOD score ranged between 3.6 and 17.6. OsPHq1, a candidate gene related to plant height regulation, was screened in RM3482-RM212. OsPHq1 is an ortholog of gibberellin 20 oxidase 2, and its haplotype was distinguished by nine SNPs. Plants were divided into two groups based on their height, and tall and short plants were distinguished and clustered according to the expression level of OsPHq1. QTLs and candidate genes related to plant height regulation, and thus, biomass regulation, were screened and identified in this study, but the molecular mechanism of the regulation remains poorly known. The information obtained in this study will help develop molecular markers for marker-assisted selection and breeding through rice plant height control.

Complete chloroplast genomes of six neotropical palm species, structural comparison, and evolutionary dynamic patterns

The Arecaceae family has a worldwide distribution, especially in tropical and subtropical regions. We sequenced the chloroplast genomes of Acrocomia intumescens and A. totai, widely used in the food and energy industries; Bactris gasipaes, important for palm heart; Copernicia alba and C. prunifera, worldwide known for wax utilization; and Syagrus romanzoffiana, of great ornamental potential. Copernicia spp. showed the largest chloroplast genomes (C. prunifera: 157,323 bp and C. alba: 157,192 bp), while S. romanzoffiana and B. gasipaes var. gasipaes presented the smallest (155,078 bp and 155,604 bp). Structurally, great synteny was detected among palms. Conservation was also observed in the distribution of single sequence repeats (SSR). Copernicia spp. presented less dispersed repeats, without occurrence in the small single copy (SSC). All RNA editing sites were C (cytidine) to U (uridine) conversions. Overall, closely phylogenetically related species shared more sites. Almost all nodes of the phylogenetic analysis showed a posterior probability (PP) of 1.0, reaffirming the close relationship between Acrocomia species. These results elucidate the conservation among palm chloroplast genomes, but point to subtle structural changes, providing support for the evolutionary dynamics of the Arecaceae family.

Assessment of genetic variation among wheat genotypes for drought tolerance utilizing microsatellite markers and morpho-physiological characteristics

Drought is a major abiotic stress that severely limits sustainable wheat (Triticum aestivum L.) productivity via morphological and physio-biochemical alterations of cellular processes. The complex nature and polygenic control of drought tolerance traits make breeding tolerant genotypes quite challenging. However, naturally occurring variabilities among wheat germplasm resources could potentially help combating drought. The present study was conducted to assess the drought tolerance of 18 Bangladeshi hexaploid wheat genotypes, focusing on the identification of potent sources of diversity by combining microsatellite markers, also known as single sequence repeat markers, and morpho-physiological characteristics that might help accelerating wheat crop improvement programs. Initially, the genotypes were evaluated using 25 microsatellite markers followed by an on-field evaluation of 7 morphological traits (plant height, spike number, spike length, grains per spike, 1000-grain weight, grain yield, biological yield) and 6 physiological traits (SPAD value, membrane stability index, leaf relative water content, proline content, canopy temperature depression, and leaf K+ ion content). The field-trial was conducted in a factorial fashion of 18 wheat genotypes and two water regimes (control and drought) following a split-plot randomized complete block design. Regardless of genotype, drought was significantly damaging for all the tested traits; however, substantial variability in drought stress tolerance was evident among the genotypes. Spike length, 1000-grain weight, SPAD value, leaf relative water content, canopy temperature depression, proline content, and potassium (K+) ion content were the most representative of drought-induced growth and yield impairments and also correlated well with the contrasting ability of genotypic tolerance. Microsatellite markers amplified 244 alleles exhibiting 79% genetic diversity. Out of 25 markers, 23 was highly polymorphic showing 77% average polymorphism. Morpho-physiological trait-based hierarchical clustering and microsatellite marker-based neighbor-jointing clustering both revealed three genotypic clusters with 71% co-linearity between them. In both cases, the genotypes Kanchan, BAW-1147, BINA Gom 1, BARI Gom 22, BARI Gom 26, and BARI Gom 33 were found to be comparatively more tolerant than the other tested genotypes, showing potential for cultivation in water-deficit environments. The findings of this study would contribute to the present understanding of drought tolerance in wheat and would provide a basis for future genotype selection for drought-tolerant wheat breeding programs.

A Simplified, Efficient and Rapid DNA Extraction Protocol from Rice Grains and Leaf

DNA extraction is very complicated with different plant species because the presence of secondary metabolites that hinder with DNA isolation processes and application like DNA restriction, Gene amplification, as well as gene cloning. A simple method for preparation of rice genomic DNA was developed. The current study expressed comparatively rapid, cost-effective, less time consuming, methods for DNA extraction from seed, young leaves and old leaves of rice genotypes without using liquid nitrogen, phenol, and β–mercaptoethanol in extraction buffer. Using this method, high quality and quantity of genomic DNA was get from 0.5 g of rice seed, young leaves and 75 days old leavesand extracted total nucleic acids (genomic DNA) were amplified by employing single sequence repeats (SSR) or microsatellite markers, which produced reproducible results.This protocol resolves the problems of DNA degradation, contamination, and low yield due to binding and/or coprecipitation with starches and polysaccharides.

Resource Status of Wild Hawthorn in Xinjiang and Research Progress of Genetic Diversity in Hawthorn

Wild hawthorn is a rare wild plant resource endemic to the western Tianshan Mountain in Xinjiang, containing three species: Crataegus songorica, C. alorocarpa and C. sanguirnta. However, the area of wild hawthorn forest has shrunken under the disturbance of human activities, genetic diversity has also suffered serious damage. Therefore, it is urgent to carry out the present status investigation of genetic diversity and assess the genetic differentiation of geographic populations of wild hawthorns. This paper summarizes the resource status of wild hawthorn in Xinjiang and research progress of genetic diversity in hawthorn, and developed an approach to screen molecular markers of single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) using Restriction-site Associated DNA sequencing (RAD-seq). SNP and SSR markers will be used to assess genetic diversity, genetic differentiations and genetic relationships of different populations of wild hawthorns.

Assessing the Genetic Variability of Sweet Chestnut Varieties from the Tuscan Apennine Mountains (Italy)

Castanea sativa Mill. is a valuable species with historical and economic importance in Europe, particularly in the Mediterranean area. In Italy, chestnut cultivation has been developed for centuries, leading to the recognition of more than 300 varieties. Nevertheless, a profusion of local names has been assigned by growers, causing the occurrence of synonyms and homonyms across the country. This research focused on genetic characterization and identification using 21 single sequence repeats (SSRs) for four chestnut varieties (i.e., Pastinese, Nerattino, Carpinese, and Rossola) commonly used for flour production in the Tuscan Apennine Mountains (Pistoia Province). A comprehensive number of 55 accessions identified by local growers as belonging to the four varieties were analyzed, in addition to a few “Marrone” accessions as outgroups. The 21 microsatellites were highly informative, detecting 98 alleles and displaying an average polymorphism information content (PIC) equal to 0.582. In addition, a considerable amount of genetic diversity was revealed, as shown by the heterozygosity levels (He = 0.634 and Ho = 0.475). The STRUCTURE analysis provided clear distinctions among the different varieties, splitting them into four separate groups. This result was also confirmed by UPGMA dendrogram and principal co-ordinates analysis (PCoA). However, one accession (Carp_5), previously identified as Carpinese, showed an allelic profile attributable to Pastinese, suggesting that farmers might have performed mislabeling or grafting propagation errors. Thus, our results confirm the use of SSRs to allocate the accessions of different varieties, uncovering possible synonyms and homonyms. Specifically, in the context of the Pistoiese mountain region, this tool can favor the traceability of processed products, such as flour, enhancing the quality and economic value of the local market. Lastly, our findings have revealed a considerable genetic variability within the Tuscan chestnut varieties whose preservation is mandatory to face climate change challenges through sustainable forest management practices.

Morphological and molecular characterization of flax (Linum usitatissimum L.) accessions obtained from different locations in Turkey

Flax (Linum usitatissimum L.) is one of the most significant industrial crops due to its oil and fiber, which have a plethora of uses. Because of this, the characterization and introduction/adaptation of flax crops are of great interest. For this reason, we aimed to investigate the genetic diversity and patterns of flax cultivars/genotypes (a 63-cultivar/genotype was used) employing single sequence repeat microsatellite markers via 16 strong amplicon loci, and by estimating their morphological attributes. We determined the quality of the flax, in terms of oil content and composition, and its fiber quality using scanning electron microscopy and strength-linked attributes. For assessment, a series of statistical analyses were carried out in order to cluster and scatter the relevant parameters corresponding to the cultivars/genotypes. Of the assayed flax cultivar/genotypes, Eckendorfi was found to have promising agromorphological values. The average polymorphic information content values were recorded (= 0.689), and the smallest and largest loci with allele dimensions were Lu9(2) and Lu19-Lua613(6) respectively. Overall, the agromorphological attributes were consistent with the microsatellite-based markers in decoding the genetic diversity and population structure of the flax germplasm.

Analysis of Selected Marker Studies on Minor Poaceae Forages

Pastures are very important for agriculture since the main feeding source of the enormous cattle herd in the world is forage. Pastures comprise plants from several genera of grasses and legumes. In terms of the physical variety, ecology, and economic significance, the Poaceae is among the most significant families of Angiosperms. Regarding stress tolerance, species within this family exhibit a very wide range of variation. In recent years, the importance of using molecular markers in phylogenetic analyses of numerous organisms has increased. The development of genomic technologies and infrastructure has progressed sufficiently for their use in marker- aided selection (MAS) to be studied in several important perennial fodder species. Differences can be directly attributed to minor variations in the genetic code such as phenotype, single sequence repeats (SSRs), and single nucleotide polymorphisms (SNPs). Therefore, breeders can benefit significantly from developing and characterizing new genetic markers. This paper gives a brief analysis of some international studies on some minor Poacea forages.

Complete Chloroplast Genome of Endangered Bruguiera hainesii C.G.Rogers 1919 and Phylogenetic Analysis with Associated Species

Abstract Background: Bruguiera hainesii C.G. Rogers 1919, a true mangrove tree is a critically endangered species (CR) in Vietnam. This species is restricted to the Con Dao National Park, Ba Ria-Vung Tau province, where it occurs in very tiny populations. However, the exploration of the chloroplast genome of B. hainesii in Vietnam has a serious lack of information. It is extremely challenging to promote the conservation of B. hainesii. Therefore, urgently required to discover and comprehend the chloroplast genome of B. hainesii. Methods: To detect evolutionary analysis between mangroves, we sequenced the complete chloroplast genome of B. hainesii using next-generation sequencing technology (Illumina Hiseq X Ten). Results: We sequenced and assembled the complete chloroplast genome of B. hainesii, which was deposited in GenBank as accession number OR086085. The DNA was circular with 164,305 bp length, comprising 37% GC. The genome contained a large single-copy region of 91,724 bp, inverted repeat regions of 26,360 bp, and a short single-copy region of 19,861 bp. Furthermore, it contained 130 genes, consisting of 83 protein-coding genes, 37 tRNAs, and 8 rRNAs. We detected 131 single-sequence repeats, including 119 mononucleotides, 11 dinucleotides, and one trinucleotide. Phylogenetic analysis showed strong support that B. hainesii was sister to B. cylindrica. Conclusions: The findings in this study provide a foundation for species identification, evolutionary genetics, and the conservation of endangered B. hainesii in Vietnam.

Deciphering Early Movements and Domestication of Coffea arabica through a Comprehensive Genetic Diversity Study Covering Ethiopia and Yemen

The coffee species Coffea arabica is facing numerous challenges regarding climate change, pests and disease pressure. Improved varieties will be part of the solution. Making optimal use of the scarce genetic diversity of the species is hence essential. In this paper, we present the first study of C. arabica genetic diversity covering its complete native habitat in Ethiopia together with its main domestication centers: Yemen and Hararghe region in Ethiopia. All in all, 555 samples were analyzed with a set of Single Sequence Repeat markers. Through admixture genetic analysis, six clusters were identified. A total of two “Core Ethiopian” clusters did not participate in the domestication of the species. There were four clusters that were part of the “Domestication Pathway” of C. arabica. The first one was named “Ethiopian Legacy” as it represents the genetic link between “Core Ethiopia” and the “Domestication Pathway” in Yemen and Hararghe. The geographic origin of this cluster in Ethiopia was the south of Ethiopia, namely Gedio, Guji and Sidama, which hence appears as the source of coffee seeds that led to the domestication of C. arabica. In Yemen, in addition to the “Ethiopian Legacy” cluster, we confirmed the “Typica/Bourbon” and “New-Yemen” clusters. In Hararghe, the “Harrar” cluster, never described before, likely originates from a re-introduction of domesticated coffee from Yemen into this region of Ethiopia. Cultivated varieties around the world today originate from the “Ethiopian Legacy” and “Typica/Bourbon” clusters and but none are related to the “new-Yemen” and “Harrar” clusters. Implications for breeding strategies are discussed.

Assessment of Wild Rocket (Diplotaxis tenuifolia (L.) DC.) Germplasm Accessions by NGS Identified SSR and SNP Markers.

Rocket is the common designation for two baby-leaf salad crops of the Brassicaceae family: Eruca sativa (L.) Cav., usually referred to as annual garden rocket, and Diplotaxis tenuifolia (L.) DC. commonly named to as perennial wild rocket. E. sativa is used for human consumption since antiquity. However, the growing consumer preference for D. tenuifolia is being accompanied by the fast increase in its production area and commercialization of new cultivars. Nevertheless, the worldwide number of wild rocket accessions maintained in germplasm collections is very reduced, the solution for which situation the project "REMIRucula" intends to contribute, establishing a germplasm collection at the INIAV, Oeiras, Portugal. Herein, we report on the establishment via next generation sequencing (NGS) of the first genome assembly of D. tenuifolia and the identification of specific single sequence repeat (SSR) and single nucleotide polymorphisms (SNP) loci for the establishment of specific DNA-markers for this species. A representative set of 87 D. tenuifolia and 3 E. sativa accessions were assessed by 5 SSR and 9 SNP-CAPS markers, allowing a drastic discrimination between both species and the establishment of unequivocal molecular fingerprints for the analyzed accessions. The non-discrimination within six pairs and one trio of D. tenuifolia accessions is discussed.