Genetic Resources Research Articles

Analysis of ddRAD-seq data provides new insights into the genomic structure and patterns of diversity in Italian donkey populations.

With more than 150 recognized breeds, donkeys assume relevant economic importance, especially in developing countries. Even if the estimated number of heads worldwide is 53M, this species received less attention than other livestock species. Italy has traditionally been considered one of the cradles of European donkey breeding, and despite a considerable loss of biodiversity, today still counts nine autochthonous populations. A total of 220 animals belonging to 9 different populations were genotyped using the double-digest restriction site associated DNA (ddRAD) sequencing to investigate the pattern of diversity using a multi-technique approach. A total of 418,602,730 reads were generated and successfully demultiplexed to obtain a medium-density SNP genotypes panel with about 27K markers. The diversity indices showed moderate levels of variability. The genetic distances and relationships, largely agree with the breeding history of the donkey populations under investigation. The results highlighted the separation of populations based on their genetic origin or geographical proximity between breeding areas, showed low to moderate levels of admixture, and indicated a clear genetic difference in some cases. For some breeds, the results also validate the success of proper management conservation plans. Identified ROH islands, mapped within genomic regions related to immune response and local adaptation, are consistent with the characteristics of the species known for its rusticity and adaptability. This study is the first exhaustive genome-wide analysis of the diversity of Italian donkey populations. The results emphasized the high informativeness of genome-wide markers retrieved through the ddRAD approach. The findings take on great significance in designing and implementing conservation strategies. Standardized genotype arrays for donkey species would make it possible to combine worldwide datasets to provide further insights on the evolution of the genomic structure and origin of this important genetic resource.

The Identification Standard of “Serious Circumstances” in the Crime of Infringing Human Genetic Resources

The Identification Standard of “Serious Circumstances” in the Crime of Infringing Human Genetic Resources

Phylogeographic Structure and Population Dynamics of Baoxing Osmanthus (Osmanthus serrulatus), an Endemic Species from the Southwest Sichuan Basin, China.

The mountainous regions of southwest China are recognized as pivotal centers for the origin and evolution of Osmanthus species. Baoxing Osmanthus (Osmanthus serrulatus Rehder), a rare and endemic species known for its spring blooms, is sparsely distributed within the high altitude evergreen broad-leaved forests surrounding the southwestern Sichuan Basin. However, persistent anthropogenic disturbances and habitat fragmentation have precipitated a significant decline in its natural population size, leading to the erosion of genetic resources. To assess the genetic status of O. serrulatus and formulate effective conservation strategies, we conducted sampling across ten wild populations, totaling 148 individuals in their natural habitats. We employed two cpDNA fragments (matK and trnS-trnG) to elucidate the phylogeographic structure and historical population dynamics. The results revealed low species-level genetic diversity, alongside pronounced regional differentiation among populations (FST = 0.812, p < 0.05) and a notable phylogeographic structure (NST = 0.698 > GST = 0.396, p < 0.05). Notably, genetic variation was predominantly observed among populations (81.23%), with no evidence of recent demographic expansion across the O. serrulatus distribution range. Furthermore, divergence dating indicated a timeline of approximately 4.85 Mya, corresponding to the late Miocene to early Pleistocene. This temporal correlation coincided with localized uplift events in the southwestern mountains and heightened Asian monsoons, suggesting pivotal roles for these factors in shaping the current phylogeographic pattern of O. serrulatus. These findings support the effective conservation of O. serrulatus germplasm and offer insights into the impact of Quaternary climate oscillations on companion species within evergreen broad-leaved forests. They also enhance our understanding of the origin and evolution of these forests in the southwestern mountains, aiding biodiversity conservation efforts in the region.

Mitochondrial DNA (mtDNA) genetic variability of cytochrome B gene (CYTB) in three populations of native rabbits in Egypt

The current study aimed to detect the genetic variability of mitochondrial DNA (mtDNA) cytochrome B (CYTB) gene in 80 native Egyptian rabbits (NER) belonging to three populations in three different agriculture regions (Delta, Middle, and Upper Egypt) and also investigate the origin of these breeds by phylogenetic relationship analysis. A total of 62 haplotypes were recorded among the three NER populations. The native Upper Egypt rabbits (NUER) expressed the highest number of haplotypes, mutations, polymorphic sites, and haplotype diversity (23, 55, 51, and 1.00, respectively). While it gave the lowest values of nucleotide diversity (0.0262) and Tajima's D (−0.01435), the percentage of mutual haplotypes was 4.8 % between the Middle and Delta Egypt populations. The phylogenetic analysis showed that there were more separated haplotypes of NUER compared to other populations. The same finding was also observed when supported by 31 sequences of different rabbit breeds retrieved from the GeneBank database. A mutual haplotype was observed between native Delta Egyptian rabbits (NDER) and New Zealand (NWZ) rabbits. The results of this study shed light on the importance of indigenous breeds in rural areas through mtDNA, which contributes to finding sustainable strategies to conserve and improve genetic resources in Egyptian rural areas.

Nomenclatural standards of barley cultivars bred by the Ural Research Institute of Agriculture – Branch of the Ural Federal Agrarian Scientific Research Center, Ural Branch of the Russian Academy of Sciences

As part of the present work, nomenclatural standards of spring barley cultivars ‘Krauf’ and ‘Pamyati Chepeleva’ were created by the Ural Research Institute of Agriculture.The plant material for these nomenclatural standards was collected at the Research and Production Base “Pushkin and Pavlovsk laboratories of VIR”.The article presents descriptions of morphological and biological and economic properties of the cultivars.The nomenclatural standard of cultivar ‘Krauf’ is represented by one herbarium sheet and has one duplicate sheet, while that of cultivar ‘Pamyati Chepeleva’ is represented by one herbarium sheet and two duplicates.Every sheet contains the entire plant at the milky ripeness stage collected at the Pushkin Laboratories of RPB “Pushkin and Pavlovsk Laboratories of VIR”, as well as mature spikes and grains samples collected at the Ural Research Institute of Agriculture. The plant material for the herbaria was taken from the offspring of one seed sample.The nomenclatural standard specimens were prepared in accordance with the recommendations of the International Code of Nomenclature of Cultivated Plants (ICNCP) and registered in the VIR Herbarium database. The herbarium specimens were deposited at the Herbarium of Cultivated Plants of the World, their Wild Relatives and Weeds (WIR) at the National Center for Plant Genetic Resources.

Complete Organelle Genome of the Desiccation-Tolerant (DT) Moss Tortula atrovirens and Comparative Analysis of the Pottiaceae Family.

Tortula atrovirens (Sm.) Lindb. is an important component of biological soil crusts and possesses an extraordinary tolerance against desiccation in dryland habitats. However, knowledge of the organelle genome of this desiccation-tolerant (DT) moss is still lacking. Here, we assembled the first reported Tortula organelle genome and conducted a comprehensive analysis within the Pottiaceae family. T. atrovirens exhibited the second largest chloroplast genome (129,646 bp) within the Pottiaceae, whereas its mitogenome (105,877 bp) and those of other mosses were smaller in size compared to other land plants. The chloroplast and mitochondrial genomes of T. atrovirens were characterized by the expansion of IR boundaries and the absence of homologous recombination-mediated by large repeats. A total of 57 RNA editing sites were detected through mapping RNA-seq data. Moreover, the gene content and order were highly conserved among the Pottiaceae organelle genomes. Phylogenetic analysis showed that bryophytes are paraphyletic, with their three lineages (hornworts, mosses, and liverworts) and vascular plants forming successive sister clades. Timmiella anomala is clearly separated from the monophyletic Pottiaceae, and T. atrovirens is closely related to Syntrichia filaris within the Pottioideae. In addition, we detected four hypervariable regions for candidate-molecular markers. Our findings provide valuable insights into the organelle genomes of T. atrovirens and the evolutionary relationships within the Pottiaceae family, facilitating future discovery of DT genetic resources from bryophytes.

GhGASA14 regulates the flowering time of upland cotton in response to GA3.

The silencing of GhGASA14 and the identification of superior allelic variation in its coding region indicate that GhGASA14 may positively regulate flowering and the response to GA3. Gibberellic acid-stimulated Arabidopsis (GASA), a member of the gibberellin-regulated short amino acid family, has been extensively investigated in several plant species and found to be critical for plant growth and development. However, research on this topic in cotton has been limited. In this study, we identified 38 GhGASAs that were dispersed across 18 chromosomes in upland cotton, and all of these genes had a GASA core domain. Transcriptome expression patterns and qRT-PCR results revealed that GhGASA9 and GhGASA14 exhibited upregulated expression not only in the floral organs but also in the leaves of early-maturing cultivars. The two genes were functionally characterized by virus-induced gene silencing (VIGS), and the budding and flowering times after silencing the target genes were later than those of the control (TRV:00). Compared with that in the water-treated group (MOCK), the flowering period of the different fruiting branches in the GA3-treated group was more concentrated. Interestingly, allelic variation was detected in the coding sequence of GhGASA14 between early-maturing and late-maturing accessions, and the frequency of this favorable allele was greater in high-latitude cotton cultivars than in low-latitude ones. Additionally, a significant linear relationship was observed between the expression level of GhGASA14 and flowering time among the 12 upland cotton accessions. Taken together, these results indicated that GhGASA14 may positively regulate flowering time and respond to GA3. These findings could lead to the use of valuable genetic resources for breeding early-maturing cotton cultivars in the future.

Environment influences the genetic structure and genetic differentiation of Sassafras tzumu (Lauraceae)

BackgroundSassafras tzumu, an elegant deciduous arboreal species, belongs to the esteemed genus Sassafras within the distinguished family Lauraceae. With its immense commercial value, escalating market demands and unforeseen human activities within its natural habitat have emerged as new threats to S. tzumu in recent decades, so it is necessary to study its genetic diversity and influencing factors, to propose correlative conservation strategies.ResultsBy utilizing genotyping-by-sequence (GBS) technology, we acquired a comprehensive database of single nucleotide polymorphisms (SNPs) from a cohort of 106 individuals sourced from 13 diverse Sassafras tzumu natural populations, scattered across various Chinese mountainous regions. Through our meticulous analysis, we aimed to unravel the intricate genetic diversity and structure within these S. tzumu populations, while simultaneously investigating the various factors that potentially shape genetic distance. Our preliminary findings unveiled a moderate level of genetic differentiation (FST = 0.103, p < 0.01), accompanied by a reasonably high genetic diversity among the S. tzumu populations. Encouragingly, our principal component analysis painted a vivid picture of two distinct genetic and geographical regions across China, where gene flow appeared to be somewhat restricted. Furthermore, employing the sophisticated multiple matrix regression with randomization (MMRR) analysis method, we successfully ascertained that environmental distance exerted a more pronounced impact on genetic distance when compared to geographical distance (βE = 0.46, p < 0.01; βD = 0.16, p < 0.01). This intriguing discovery underscores the potential significance of environmental factors in shaping the genetic landscape of S. tzumu populations.ConclusionsThe genetic variance among populations of S. tzumu in our investigation exhibited a moderate degree of differentiation, alongside a heightened level of genetic diversity. The environmental distance of S. tzumu had a greater impact on its genetic diversity than geographical distance. It is of utmost significance to formulate and implement meticulous management and conservation strategies to safeguard the invaluable genetic resources of S. tzumu.

Revealing critical mechanisms in determining sorghum resistance to drought and salt using mRNA, small RNA and degradome sequencing

BackgroundPlant growth and development are severely threatened by drought and salt stresses. Compared with structural genes, transcription factors (TFs) play more pivotal roles in plant growth and stress adaptation. However, the underlying mechanisms of sorghum adapting to drought and salt are insufficient, and systematic analysis of TFs in response to the above stresses is lacking.ResultsIn this study, TFs were identified in sorghum and model plants (Arabidopsis thaliana and rice), and gene number and conserved domain were compared between sorghum and model plants. According to syntenic analysis, the expansion of sorghum and rice TFs may be due to whole-genome duplications. Between sorghum and model plants TFs, specific conserved domains were identified and they may be related to functional diversification of TFs. Forty-five key genes in sorghum, including four TFs, were likely responsible for drought adaption based on differently expression analysis. MiR5072 and its target gene (Sobic.001G449600) may refer to the determination of sorghum drought resistance according to small RNA and degradome analysis. Six genes were associated with drought adaptation of sorghum based on weighted gene co-expression network analysis (WGCNA). Similarly, the core genes in response to salt were also characterized using the above methods. Finally, 15 candidate genes, particularly two TFs (Sobic.004G300300, HD-ZIP; Sobic.003G244100, bZIP), involved in combined drought and salt resistance of sorghum were identified.ConclusionsIn summary, the findings in this study help clarify the molecular mechanisms of sorghum responding to drought and salt. We identified candidate genes and provide important genetic resource for potential development of drought-tolerant and salt-tolerant sorghum plants.

Inhibition of Prolactin Affects Epididymal Morphology by Decreasing the Secretion of Estradiol in Cashmere Bucks.

Yanshan Cashmere bucks are seasonal breeding animals and an important national genetic resource. This study aimed to investigate the involvement of prolactin (PRL) in the epididymal function of bucks. Twenty eleven-month-old Cashmere bucks were randomly divided into a control (CON) group and a bromocriptine (BCR, a prolactin inhibitor, 0.06 mg/kg body weight (BW)) treatment group. The experiment was conducted from September to October 2020 in Qinhuangdao City, China, and lasted for 30 days. Blood was collected on the last day before the BCR treatment (day 0) and on the 15th and 30th days after the BCR treatment (days 15 and 30). On the 30th day, all bucks were transported to the local slaughterhouse, where epididymal samples were collected immediately after slaughter. The left epididymis was preserved in 4% paraformaldehyde for histological observation, and the right epididymis was immediately preserved in liquid nitrogen for RNA sequencing (RNA-seq). The results show that the PRL inhibitor reduced the serum PRL and estradiol (E2) concentrations (p < 0.05) and tended to decrease luteinizing hormone (LH) concentrations (p = 0.052) by the 30th day, but no differences (p > 0.05) occurred by either day 0 or 15. There were no differences (p > 0.05) observed in the follicle-stimulating hormone (FSH), testosterone (T), and dihydrotestosterone (DHT) concentrations between the two groups. The PRL receptor (PRLR) protein was mainly located in the cytoplasm and intercellular substance of the epididymal epithelial cells. The PRL inhibitor decreased (p < 0.05) the expression of the PRLR protein in the epididymis. In the BCR group, the height of the epididymal epithelium in the caput and cauda increased, as did the diameter of the epididymal duct in the caput (p < 0.05). However, the diameter of the cauda epididymal duct decreased (p < 0.05). Thereafter, a total of 358 differentially expressed genes (DEGs) were identified in the epididymal tissues, among which 191 were upregulated and 167 were downregulated. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses revealed that ESR2, MAPK10, JUN, ACTL7A, and CALML4 were mainly enriched in the estrogen signaling pathway, steroid binding, calcium ion binding, the GnRH signaling pathway, the cAMP signaling pathway, and the chemical carcinogenesis-reactive oxygen species pathway, which are related to epididymal function. In conclusion, the inhibition of PRL may affect the structure of the epididymis by reducing the expression of the PRLR protein and the secretion of E2. ESR2, MAPK10, JUN, ACTL7A, and CALML4 could be the key genes of PRL in its regulation of epididymal reproductive function.

Overexpression of PavHIPP16 from Prunus avium enhances cold stress tolerance in transgenic tobacco

BackgroundThe heavy metal-associated isoprenylated plant protein (HIPP) is an important regulatory element in response to abiotic stresses, especially playing a key role in low-temperature response.ResultsThis study investigated the potential function of PavHIPP16 up-regulated in sweet cherry under cold stress by heterologous overexpression in tobacco. The results showed that the overexpression (OE) lines’ growth state was better than wild type (WT), and the germination rate, root length, and fresh weight of OE lines were significantly higher than those of WT. In addition, the relative conductivity and malondialdehyde (MDA) content of the OE of tobacco under low-temperature treatment were substantially lower than those of WT. In contrast, peroxidase (POD), superoxide dismutase (SOD), catalase (CAT) activities, hydrogen peroxide (H2O2), proline, soluble protein, and soluble sugar contents were significantly higher than those of WT. Yeast two-hybrid assay (Y2H) and luciferase complementation assay verified the interactions between PavbHLH106 and PavHIPP16, suggesting that these two proteins co-regulated the cold tolerance mechanism in plants. The research results indicated that the transgenic lines could perform better under low-temperature stress by increasing the antioxidant enzyme activity and osmoregulatory substance content of the transgenic plants.ConclusionsThis study provides genetic resources for analyzing the biological functions of PavHIPPs, which is important for elucidating the mechanisms of cold resistance in sweet cherry.

Plant Genetic Resources for Food and Agriculture: The Role and Contribution of CREA (Italy) within the National Program RGV-FAO

Conservation, characterization and exploitation of agrobiodiversity are key factors to guarantee food security and face future challenges such as climate changes. These issues are the subject of a series of international agreements, such as the Convention of Biological Diversity, with its Nagoya Protocol, and the International Treaty on Plant Genetic Resources for Food and Agriculture (ITPGRFA) adopted in 2001 and entered into force in 2004. Italy ratified the Treaty in 2004 and instituted a long-lasting program, RGV-FAO, to implement it. CREA is one of the three organizations involved in the RGV-FAO Program, together with the National Research Council (CNR) and Reti Semi Rurali. CREA maintains a total of 40,186 accessions including cereals, vegetables, fruits, forages, industrial crops, forest and woody crops, medicinal and aromatic plants, and their wild relatives. Accessions are conserved using different ex situ conservation systems (seeds, in vivo plants, vegetative organs and in vitro plantlets), and characterized using genetic, morpho-phenological and/or biochemical methods. Herein, we will present the CREA long-lasting program RGV-FAO with some examples of the use of plant genetic resources in breeding programs, including molecular approaches. Some critical issues related to access and benefit sharing in PGRFA, such as the Nagoya Protocol and the Digital Sequence Information, will be discussed, highlighting their potential impact on food security and on the advancement of knowledge.

Genome-wide identification, molecular evolution and expression analysis of the B-box gene family in mung bean (Vigna radiata L.)

BackgroundMung bean (Vigna radiata L.) is an important warm-season grain legume. Adaptation to extreme environmental conditions, supported by evolution, makes mung bean a rich gene pool for stress tolerance traits. The exploration of resistance genes will provide important genetic resources and a theoretical basis for strengthening mung bean breeding. B-box (BBX) proteins play a major role in developmental processes and stress responses. However, the identification and analysis of the mung bean BBX gene family are still lacking.ResultsIn this study, 23 VrBBX genes were identified through comprehensive bioinformatics analysis and named based on their physical locations on chromosomes. All the VrBBXs were divided into five groups based on their phylogenetic relationships, the number of B-box they contained and whether there was an additional CONSTANS, CO-like and TOC1 (CCT) domain. Homology and collinearity analysis indicated that the BBX genes in mung bean and other species had undergone a relatively conservative evolution. Gene duplication analysis showed that only chromosomal segmental duplication contributed to the expansion of VrBBX genes and that most of the duplicated gene pairs experienced purifying selection pressure during evolution. Gene structure and motif analysis revealed that VrBBX genes clustered in the same group shared similar structural characteristics. An analysis of cis-acting elements indicated that elements related to stress and hormone responses were prevalent in the promoters of most VrBBXs. The RNA-seq data analysis and qRT-PCR of nine VrBBX genes demonstrated that VrBBX genes may play a role in response to environmental stress. Moreover, VrBBX5, VrBBX10 and VrBBX12 are important candidate genes for plant stress response.ConclusionsIn this study, we systematically analyzed the genomic characteristics and expression patterns of the BBX gene family under ABA, PEG and NaCl treatments. The results will help us better understand the complexity of the BBX gene family and provide valuable information for future functional characteristics of specific genes in this family.

Unraveling the mechanism of flower color variation in Brassica napus by integrated metabolome and transcriptome analyses.

Brassica napus is one of the most important oil crops in the world. Breeding oilseed rape with colorful flowers can greatly enhance the ornamental value of B. napus and thus improve the economic benefits of planting. As water-soluble flavonoid secondary metabolites, anthocyanins are very important for the synthesis and accumulation of pigments in the petals of plants, giving them a wide range of bright colors. Despite the documentation of over 60 distinct flower shades in B. napus, the intricacies underlying flower color variation remain elusive. Particularly, the mechanisms driving color development across varying flower color backgrounds necessitate further comprehensive investigation. This research undertook a comprehensive exploration through the integration of transcriptome and metabolome analyses to pinpoint pivotal genes and metabolites underpinning an array of flower colors, including beige, beige-red, yellow, orange-red, deep orange-red, white, light-purple, and purple. First, we used a two-way BLAST search to find 275 genes in the reference genome of B. napus Darmor v10 that were involved in making anthocyanins. The subsequent scrutiny of RNA-seq outcomes underscored notable upregulation in the structural genes F3H and UGT, alongside the MYB75, GL3, and TTG1 transcriptional regulators within petals, showing anthocyanin accumulation. By synergizing this data with a weighted gene co-expression network analysis, we identified CHS, F3H, MYB75, MYB12, and MYB111 as the key players driving anthocyanin synthesis in beige-red, orange-red, deep orange-red, light-purple, and purple petals. By integrating transcriptome and weighted gene co-expression network analysis findings with anthocyanin metabolism data, it is hypothesized that the upregulation of MYB75, which, in turn, enhances F3H expression, plays a pivotal role in the development of pigmented oilseed rape flowers. These findings help to understand the transcriptional regulation of anthocyanin biosynthesis in B. napus and provide valuable genetic resources for breeding B. napus varieties with novel flower colors.

Prototype biodiversity digital twin: crop wild relatives genetic resources for food security

Amidst population growth and climate-driven crop stresses such as drought, extreme weather, fungal and insect pests, as well as various crop diseases, ensuring food security demands innovative strategies. Crop wild relatives (CWR), wild plants in the same genus as the crop as well as wild populations belonging to the same species as the crop, offer novel genetic resources crucial for enhancing crop resilience against these stress factors. Here, we introduce a prototype digital twin (pDT) to aid in searching and utilising CWR genetic resources. Using the MoDGP (Modelling the Germplasm of Interest) tool, the pDT enables mapping geographic areas where stress-tolerant CWR populations can be found. With its graphical user interface, it offers flexibility in selecting genetic resources from CWR tailored to enhance resilience of various crops against diverse stress factors.

Utilising soybean [Glycine max (L.) Merr.] wild and untapped genetic resources through pre‐breeding: Challenges and opportunities

AbstractSoybean is an economically important oilseed crop with diverse uses as food, feed, biofuel and so forth. Although the demand for soybean is growing rapidly worldwide, the narrow genetic base of released cultivars due to meagre utilisation of available wild and untapped genetic resources is a major factor contributing to stagnant production and productivity levels of soybean. Considering the continuously increasing global population, changing dietary habits, ongoing climatic fluctuations, rapidly evolving biotic stresses and shrinking land and water resources, utilisation of novel and diverse sources of variation is required for the genetic enhancement of soybean. To widen the genetic base of commercial soybean cultivars and to improve the genetic gain of the crop focused and systematic pre‐breeding efforts can play a game‐changing role by supplying novel genes in crop improvement programs. This article discusses the rationale of tapping wild and untapped genetic resources of soybean, gene pools, soybean genetic resources conserved ex‐situ and its utilisation status, genetic base of commercial soybean cultivars, identified novel genes and genomic regions in wild genetic resources, pre‐breeding efforts in India and strategies for incorporating desirable traits in the elite cultivated gene pool for fulfilling the requirements of farmers and other end‐users.

Genomic and phenomic predictions help capture low-effect alleles promoting seed germination in oilseed rape in addition to QTL analyses

Key messagePhenomic prediction implemented on a large diversity set can efficiently predict seed germination, capture low-effect favorable alleles that are not revealed by GWAS and identify promising genetic resources.Oilseed rape faces many challenges, especially at the beginning of its developmental cycle. Achieving rapid and uniform seed germination could help to ensure a successful establishment and therefore enabling the crop to compete with weeds and tolerate stresses during the earliest developmental stages. The polygenic nature of seed germination was highlighted in several studies, and more knowledge is needed about low- to moderate-effect underlying loci in order to enhance seed germination effectively by improving the genetic background and incorporating favorable alleles. A total of 17 QTL were detected for seed germination-related traits, for which the favorable alleles often corresponded to the most frequent alleles in the panel. Genomic and phenomic predictions methods provided moderate-to-high predictive abilities, demonstrating the ability to capture small additive and non-additive effects for seed germination. This study also showed that phenomic prediction estimated phenotypic values closer to phenotypic values than GEBV. Finally, as the predictive ability of phenomic prediction was less influenced by the genetic structure of the panel, it is worth using this prediction method to characterize genetic resources, particularly with a view to design prebreeding populations.

SNP genotyping Dutch heritage apple cultivars allows for germplasm characterization, curation, and pedigree reconstruction using genotypic data from multiple collection sites across the world

The curation and preservation of Dutch apple germplasm depends on reliable accession level information. However, many accessions of Dutch heirloom apple cultivars maintained publicly by the “Centre for Genetic Resources, the Netherlands” (CGN) and privately by Dutch pomological societies lack information regarding true-to-typeness and pedigree ancestry. The aim of this study was to address this knowledge gap by genotyping 652 apple accessions maintained in the CGN collection and Dutch private collections, compare their genotypic information to each other and to a large database of apple cultivars from around the world to identify genotypic duplicates and pedigree relationships for the Dutch apple cultivars. Towards this aim, accessions were genotyped on the 20 K Illumina Infinium(R) apple SNP array and with 15 SSR markers. Each accession was assigned to a genotypic profile code (MUNQ codes, as used in previous studies) facilitating communication regarding genotypic duplicates. There were 211 (51.1%) genotypic profiles in the Dutch germplasm which were not identified in other germplasm collections. Private collections maintained many of these unique accessions, including important pedigree ancestors. The study identified a number of common pedigree ancestors of Dutch cultivars, such as ‘Herfst Bloem Soete’, ‘Huismanszoet’ (2), and ‘Reinette Rouge Étoilée’. The duplicate and pedigree reconstruction results and relevant literature descriptions were used to pomologically verify the identity of relevant accessions. The results of this study resolved identity disputes, helped to decide which accessions should be retained or included in the CGN collection, and benefited ongoing pomological studies in ancestry and provenance of traditional Dutch cultivars.

Molecular and agro-morphological characterization of new barley genotypes in arid environments

BackgroundGenetic diversity, population structure, agro-morphological traits, and molecular characteristics, are crucial for either preserving genetic resources or developing new cultivars. Due to climate change, water availability for agricultural use is progressively diminishing. This study used 100 molecular markers (25 TRAP, 22 SRAP, 23 ISTR, and 30 SSR). Additionally, 15 morphological characteristics were utilized to evaluate the optimal agronomic traits of 12 different barley genotypes under arid conditions.ResultsSubstantial variations, ranging from significant to highly significant, were observed in the 15 agromorphological parameters evaluated among the 12 genotypes. The KSU-B101 barley genotype demonstrated superior performance in five specific traits: spike number per plant, 100-grain weight, spike number per square meter, harvest index, and grain yield. These results indicate its potential for achieving high yields in arid regions.The Sahrawy barley genotype exhibited the highest values across five parameters, namely leaf area, spike weight per plant, spike length, spike weight per square meter, and biological yield, making it a promising candidate for animal feed. The KSU-B105 genotype exhibited early maturity and a high grain count per spike, which reflects its early maturity and ability to produce a high number of grains per spike. This suggests its suitability for both animal feed and human food in arid areas. Based on marker data, the molecular study found that the similarity coefficients between the barley genotypes ranged from 0.48 to 0.80, with an average of 0.64. The dendrogram constructed from these data revealed three distinct clusters with a similarity coefficient of 0.80. Notably, the correlation between the dendrogram and its similarity matrix was high (0.903), indicating its accuracy in depicting the genetic relationships. The combined analysis revealed a moderate correlation between the morphological and molecular analysis, suggesting alignment between the two characterization methods.ConclusionsThe morphological and molecular analyses of the 12 barley genotypes in this study effectively revealed the varied genetic characteristics of their agro-performance in arid conditions. KSU-B101, Sahrawy, and KSU-B105 have emerged as promising candidates for different agricultural applications in arid regions. Further research on these genotypes could reveal their full potential for breeding programs.

Chloroplast Genomes of Vitis flexuosa and Vitis amurensis: Molecular Structure, Phylogenetic, and Comparative Analyses for Wild Plant Conservation.

The chloroplast genome plays a crucial role in elucidating genetic diversity and phylogenetic relationships. Vitis vinifera L. (grapevine) is an economically important species, prompting exploration of wild genetic resources to enhance stress resilience. We meticulously assembled the chloroplast genomes of two Korean Vitis L. species, V. flexuosa Thunb. and V. amurensis Rupr., contributing valuable data to the Korea Crop Wild Relatives inventory. Through exhaustive specimen collection spanning diverse ecological niches across South Korea, we ensured comprehensive representation of genetic diversity. Our analysis, which included rigorous codon usage bias assessment and repeat analysis, provides valuable insights into amino acid preferences and facilitates the identification of potential molecular markers. The assembled chloroplast genomes were subjected to meticulous annotation, revealing divergence hotspots enriched with nucleotide diversity, thereby presenting promising candidates for DNA barcodes. Additionally, phylogenetic analysis reaffirmed intra-genus relationships and identified related crops, shedding light on evolutionary patterns within the genus. Comparative examination with chloroplast genomes of other crops uncovered conserved sequences and variable regions, offering critical insights into genetic evolution and adaptation. Our study advances the understanding of chloroplast genomes, genetic diversity, and phylogenetic relationships within Vitis species, thereby laying a foundation for enhancing grapevine genetic diversity and resilience to environmental challenges.