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This study aimed to explore transcriptomic distinctions between resistant (CS‐319) and susceptible (JAL‐42) groundnut (Arachis hypogaea) genotypes exposed to Sclerotium rolfsii infection across different developmental stages. Employing a de novo assembly‐based approach, we analysed the transcriptomic response in these groundnut plants under control and infected conditions at 24, 72 and 120 hours post‐inoculation (hpi). Our RNA‐Seq data yielded a total of 133,900,261 reads, revealing 7796 differentially expressed genes (DEGs). We constructed a gene regulatory network with 59 hub genes, identified 6783 transcription factors and uncovered 88,424 putative markers, including 17,236 simple‐sequence repeats (SSRs), 10,099 single‐nucleotide polymorphisms (SNPs) and 78,332 indels. Notably, the majority of DEGs were upregulated at 24 hpi in the resistant genotype, encompassing diverse functional categories such as pathogenesis‐related genes, defence‐related (R) genes, genes involved in plant–fungus interactions, oxidation–reduction‐related genes, transport, metabolism and proteolysis genes, along with transcription factors (FAR1, B3, GATA, NAC, WRKY, MYBC1 and bHLH), secondary metabolic pathway‐related genes and photosynthesis‐related genes. The up‐regulation of WRKY transcripts, associated with the activation of the jasmonic acid defence signalling pathway, potentially induced systemic acquired resistance (SAR). Conversely, these DEGs exhibited down‐regulation in the susceptible genotype. Furthermore, a total of 17,236 expressed sequence tag (EST)‐SSRs were identified from the unigenes, holding significant potential for advancing plant breeding through marker‐assisted methods, facilitating quantitative trait locus (QTL) mapping and evaluating genetic diversity among genotypes. This study's approach contributes to a more profound understanding of the molecular‐level defence mechanisms involved in the interaction between groundnuts and S. rolfsii. [ABSTRACT FROM AUTHOR]

Interspecific hybridization in the genus Rosa (Rosaceae) is a common natural phenomenon. Hybrids often exhibit heterosis and new combinations of traits, which can provide raw materials for horticultural breeding. DNA barcodes and microsatellites have been proposed to facilitate species discrimination and hybrid detection. However, most SSR markers developed for roses have been found unapplicable to Rosa sect. Synstylae because of null alleles or failed amplification. In this study, we designed 15 pairs of microsatellite primers, along with four previously developed primers specifically for Rosa sect. Synstylae; we then analyzed 174 individuals of three closely related and sympatrically distributed Rosa species as a test case to evaluate the consistency between morphological and genetic hybrid identifications and to compare the discrimination efficiency of the DNA barcodes versus SSRs in detecting admixture. Principle coordinate analysis identified several individuals with intermediate phenotypes among the three rose species. Hybridization, intraspecific morphological polymorphism, and sample collection at different growth stages or phenological phases may have hindered species identification based on morphology and distorted the morphological clustering results. The molecular analyses showed that 12 (6.8%), 13 (7.4%), and 15 (8.6%) individuals were identified as admixed by STRUCTURE, NewHybrids, and nrITS sequences, respectively, of which only seven hybrids showed signs of admixture across all three methods. About 81% of the morphologically identifiable hybrids exhibited admixture based on SSRs. Meanwhile, approximately 69% of morphologically identifiable hybrids were detected, but four morphologically pure species individuals were identified as genetically admixed based on nrITS sequences. Some morphologically pure species individuals were genetically identified as hybrids while some morphological hybrids were identified as pure individuals based on certain molecular markers. Overall, EST-SSRs discriminated morphological hybrids more accurately than nrITS. We inferred that there is ongoing interspecific gene exchange among the three wild Rosa species that obscures morphospecies boundaries. Combining multiple data types and analytical approaches offers powerful utility for hybrid detection, regardless of the level of hybridization. [ABSTRACT FROM AUTHOR]

Genetic profiling of the biodiversity in cultivated crop plants is necessary to preserve important genes and utilize them in a breeding program. Cucumber is used as a model plant to study various characteristics of Cucurbitaceae. Its adaptation to a wide range of climatic conditions suggested analyzing the landraces. The present study was conducted to evaluate the differences, at the genetic level, among landraces spanning five continents. DNA extracted from fifty-six landraces selected from USDA germplasm bank to cover a global representative sample of world cucumber landraces was used for polymerase chain reaction using twenty-eight polymorphic expressed sequence tags simple sequence repeat (EST-SSR) markers. Twenty-eight EST-SSR markers covering all seven chromosomes yielded 98 bands with an average of 3.42 bands per marker. Polymorphic information content ranged from 0.00 (EC35) to 0.74 (EC17) with an average of 0.34. Six clusters provided an appropriate summary of the variation among the landraces, with the two largest groups including 32 (Asiatic) and 17 (European and American) landraces, respectively. Four small groups, three with two members, and one with one member (PI 525155-Egypt) were dissimilar to the two main groups. Landraces from the same region were often clustered together. Genetic similarity of the landraces was revealed by marker banding patterns. The locations of genetic diversity for cucumber landraces can be identified from this study. Key message: Cucumber landraces have a broad genetic base distributed geographically. Genetic relationships among cucumber landraces were detailed. The route of the spread of cucumber from its center of origin to the rest of the world was elicited. The study confirmed that polymorphic EST-SSR markers are a valuable tool for assessing the genetic diversity of crops. [ABSTRACT FROM AUTHOR]

Mesona chinensis Benth (MCB), also known as Platostoma palustre, is a highly significant medicinal and edible plant in China and Southeast Asian countries. The cultivated seedlings of MCB are primarily local farm varieties propagated through cuttings, with many being domesticated from wild species. This has led to an unclear and mixed source, as well as uneven quality of MCB. Hence, it is imperative to collect, preserve, evaluate, and identify the germplasm resources of MCB. This study aimed to evaluate the genetic diversity and identify the germplasm of eight core MCB resources using morphology, cytology, and EST-SSR molecular markers. Morphological observations showed significant variation in the inflorescences, leaves, stems, and corolla tissues. Scanning electron microscope (SEM) observations demonstrated significant differences in the number of stomata between the abaxial and adaxial sides of leaves. Furthermore, out of 192 primer pairs of EST-SSR molecular markers, 9 were suitable for constructing fingerprints. A total of 31 alleles were detected, with an average of 3.444 alleles per locus. The number of effective alleles (Ne) of 9 EST-SSR loci ranged from 1.473 (TDF139) to 3.877 (TDF166), while the Shannon Information index (I) per locus ranged from 0.601 (TDF139) to 1.461 (TDF166). The average value of observed heterozygosity (Ho) was 0.681, while the expected heterozygosity (He) was 0.523. The mean value of fixation index (F) was -0.294, while the mean heterozygosity within populations (Hs) was 0.762. The polymorphism information content (PIC) ranged from 0.295 (TDF139) to 0.701 (TDF166) across the 9 loci, with an average PIC value of 0.466. These results indicated that the selected EST-SSR primers exhibited high levels of polymorphism. Notably, TDF166 played a prominent role in exploring the genetic diversity of MCB. Furthermore, the Nei's genetic distance among the eight germplasm resources exhibited significant variation, resulting in the division of all germplasm resources into six subclades. This suggested the presence of abundant genetic diversity within the MCB germplasm resources used in this study. This study provided a foundation for the conservation, management, and future breeding of MCB germplasm resources. [ABSTRACT FROM AUTHOR]

Abstract Genetic profiling of the biodiversity in cultivated crop plants is necessary to preserve important genes and utilize them in a breeding program. Cucumber is used as a model plant to study various characteristics of Cucurbitaceae. Its adaptation to a wide range of climatic conditions suggested analyzing the landraces. The present study was conducted to evaluate the differences, at the genetic level, among landraces spanning five continents. DNA extracted from fifty-six landraces selected from USDA germplasm bank to cover a global representative sample of world cucumber landraces was used for polymerase chain reaction using twenty-eight polymorphic expressed sequence tags simple sequence repeat (EST-SSR) markers. Twenty-eight EST-SSR markers covering all seven chromosomes yielded 98 bands with an average of 3.42 bands per marker. Polymorphic information content ranged from 0.00 (EC35) to 0.74 (EC17) with an average of 0.34. Six clusters provided an appropriate summary of the variation among the landraces, with the two largest groups including 32 (Asiatic) and 17 (European and American) landraces, respectively. Four small groups, three with two members, and one with one member (PI 525155-Egypt) were dissimilar to the two main groups. Landraces from the same region were often clustered together. Genetic similarity of the landraces was revealed by marker banding patterns. The locations of genetic diversity for cucumber landraces can be identified from this study.

Orchidantha chinensis T. L. Wu, an endemic species in China, is listed as a key protected wild plant in Guangdong Province. However, the lack of reports on the chloroplast genome and simple sequence repeat (SSR) markers has hindered the assessment of its genetic diversity and conservation strategies. The limited number of molecular markers to assess the genetic diversity of this species, and thus develop proper conservation strategies, highlighted the urgent need to develop new ones. This study developed new SSR markers and investigated genetic variation using 96 samples of O. chinensis from seven populations. Through high-throughput sequencing, a complete chloroplast genome of 134,407 bp was assembled. A maximum-likelihood phylogenetic tree, based on the chloroplast genome, showed that O. chinensis is closely related to Ravenala madagascariensis. The study identified 52 chloroplast SSRs (cpSSRs) and 5094 expressed sequence tag SSRs (EST-SSRs) loci from the chloroplast genome and leaf transcriptome, respectively. Twenty-one polymorphic SSRs (seven cpSSRs and fourteen EST-SSRs) were selected to evaluate the genetic variation in 96 accessions across seven populations. Among these markers, one cpSSR and 11 EST-SSRs had high polymorphism information content (>0.5). Cluster, principal coordinate, and genetic structure analyses indicated that groups G1 and G6 were distinct from the other five groups. However, an analysis of molecular variance showed greater variation within groups than among groups. The genetic distance among the populations was significantly positively correlated with geographical distance. These findings provide new markers for studying the genetic variability of O. chinensis and offer a theoretical foundation for its conservation strategies. [ABSTRACT FROM AUTHOR]

Key message: ARG6 and ARG10 pea accessions exhibited better tolerance to drought by keeping drought-associated attributes stable and higher, that is, stable chlorophyll content, high antioxidant activity, and the presence of polymorphic bands with stress-responsive EST-SSR markers. Each year, a significant portion of crops is lost due to various abiotic stresses, and even pea (Pisum sativum) crop growth and yield are severely affected by the challenges posed by drought stress. Drought is a critical factor that limits crop growth and development, and its impact is exacerbated by changes in the magnitude of climatic conditions. Drought induces oxidative stress in plants, leading to the accumulation of high concentrations of reactive oxygen species that damage cell structures and vital functioning of cells. The primary objective was to identify stress-tolerant plants by evaluating different morphological and biochemical attributes, such as biomass, chlorophyll content, relative water content, ascorbate peroxidase (APX), superoxide dismutase (SOD), and DPPH scavenging activity, as well as protein, proline, and phenolic content. Our study revealed that pea accessions (ARG6 and ARG10) were more resilient to drought stress as their chlorophyll, relative water, protein, and proline contents increased under drought conditions. Antioxidant enzymes, such as SOD, APX, and DPPH activities, also increased under drought stress in ARG10 and ARG6, suggesting that these accessions could bolster the antioxidant defense system in response to drought stress. Based on putative (cellular, biological, and metabolic) functions, ten EST-SSR primers were selected for the amplification study. Three EST-SSR primers, AUMP06_110, AUMP18_300, and AUMP31_250, were used for ARG6 and ARG10. Based on the correlation between the presence or absence of specific EST-SSR alleles, various physiological and morphological traits, and DPPH scavenging activity, both ARG10 and ARG6 demonstrated resistance to drought stress. [ABSTRACT FROM AUTHOR]

Eastern black walnut, Juglans nigra L., is an economically important tree species valued for its high-quality timber and edible nuts. A regional industry for the species' nut and kernel products resides in Missouri, where over 9 million kg of hulled in-shell nuts are purchased in masting years. The crop is primarily based upon nuts harvested from wild trees, placing a ceiling on nut volume and quality (e.g. small nut size, dark pellicle color, and 10–14% kernel by weight). Orchards of named cultivars, like 'Kwik Krop' and 'Sparrow', supply up to 22,000 kg of nuts with a higher kernel percentage (> 26%) and improved quality. Such cultivars often represent chance wild or on-farm seedlings, clonally propagated since the late 1800's by enthusiasts. Today, continued improvement of eastern black walnut as an orchard crop is limited by a long generation time, delayed expression of important traits, and space requirements – creating a strong need for marker-trait association studies that inform progeny selection. The first linkage map for J. nigra was recently created using the 'Sparrow' × 'Schessler' F1 population and loci for phenology traits discovered. The objective of this study is to utilize these genetic resources to detect quantitative trait loci (QTL) and report associated DNA markers for the spur-bearing habit, which promotes precocity and high yield. Using single-year data from the 11-year-old population, we observe that segregation for the spur-bearing habit appears to be recessive and multigenic. Three QTLs (p > 0.99) were identified on linkage group (LG) 8, LG11, and LG16 that explain 7.2%, 8.7%, and 10% of trait variation, respectively. Regions between flanking DNA markers were 3.16 cM, 4.32 cM, and 9.69 cM, respectively. This study is the first to examine the genetic control of bearing habit and yield in eastern black walnut and informs breeders' approach for their future genetic improvement. [ABSTRACT FROM AUTHOR]

To promote the selection of new Castanea henryi varieties, the identification of germplasm resources, and the healthy development of the industry, the genetic diversity of 22 excellent clones cultivated in Jian'ou city, Fujian province, were investigated using six pairs of polymorphic EST-SSR primers, and the fingerprints were constructed. Results showed that the average number of alleles per primer pair was 2. 667, average number of effective alleles was 2. 038, average observed heterozygosity was 0. 349, average expected heterozygosity was 0. 447, average Shannon's information index was 0. 721, average number of polymorphic loci was 11. 500, and average polymorphic information content was 0. 434, indicating high genetic diversity. The genetic similarity coefficient varied from 0. 754 to 1. 000, with an average value of 0. 856. At the genetic similarity coefficient of 0. 860, it could be divided into five major classes. Class Ⅰ included only HL19. Class Ⅱ included HL5, HL6, HL8, and HL21. Class Ⅲ included HL17 and HL18. Class Ⅳ included HL12 and HL13. Class Ⅴ included HL1, HL2, HL3, HL4, HL7, HL9, HL10, HL11, HL14, HL15, HL16, HL20, and HL22. Fingerprints of 22 clones were constructed using three pairs of polymorphic primers. It provided a reference for the selection of parents and superior germplasms. [ABSTRACT FROM AUTHOR]

Wheat leaf rust, caused by Puccinia triticina, is one of the most common fungal diseases of wheat in China and occurs widely in various wheat-growing regions. To clarify the epidemic, spread rules, and population structure of P. triticina among different regions, 217 isolates of P. triticina collected from Hebei, Shandong, Sichuan, and Xinjiang in China were tested by 34 Thatcher near-isogenic lines and 21 pairs of EST-SSR primers. A total of 83 races were identified, and THTT, PHTT, THTS, and PHJT were the most predominant races in the four provinces in 2009. We found enriched virulence and genetic diversity in the four P. triticina populations and a significant correlation between genetic polymorphism and geographic regions. However, no significant correlation was found between virulence phenotypes and molecular genotypes. Moreover, a notable high level of gene flow (Nm = 2.82 > 1) among four P. triticina populations was detected. The genetic relationship among Hebei, Shandong, and Sichuan populations was close, possibly due to the spread of P. triticina from Sichuan to Shandong and then to Hebei. In contrast, the Xinjiang population was relatively independent. Genetic differentiation analysis showed some level of differentiation among or within populations of P. triticina in the four provinces, and the genetic variation within populations (74.97%) was higher than across populations (25.03%). Our study provides a basis for a better understanding of the regional migration, epidemic, and population structure of P. triticina in China. [ABSTRACT FROM AUTHOR]

Chimonanthus praecox, a member of the Calycanthaceae family, is a unique, traditional, and famous flowering economic tree species in China. Despite the existence of several varieties, only a few cultivars have been formally named. Currently, expression sequence tag–simple sequence repeat (EST-SSR) markers are extensively used to identify different species and varieties; a large number of microsatellites can be identified from transcriptome databases. A total of 162,638 unigenes were assembled using RNA-seq; 82,778 unigenes were annotated using the Nr, Nt, Swiss-Prot, Pfam, GO, KOG, and KEGG databases. In total, 13,556 SSR loci were detected from 11,691 unigenes, with trinucleotide repeat motifs being the most abundant among the six repeat motifs. To develop the markers, 64,440 pairs of SSR primers with polymorphism potential were designed, and 75 pairs of primers were randomly selected for amplification. Among these markers, seven pairs produced amplified fragments of the expected size with high polymorphism. Using these markers, 12 C. praecox varieties were clustered into two monophyletic clades. Microsatellites in the transcriptome of C. praecox exhibit rich types, strong specificity, and great polymorphism potential. These EST-SSR markers serve as molecular technical methods for identifying different varieties of C. praecox and facilitate the exploration of a large number of candidate genes associated with important traits. [ABSTRACT FROM AUTHOR]

Mulberry (Morus L.) is an important crop for the sericulture industry, serving as the primary food source for the silkworm Bombyx mori L. Thailand has a long history of practicing sericulture and has imported and improved upon many indigenous cultivars to create new hybrid offspring. It is crucial to understand the genetic divergence of these accessions for their conservation and utilization in selection and breeding. In this study, 85 representative mulberry accessions in Thailand were observed morphology and analyzed for their genetic relationships using SRAP and EST-SSR markers. The findings indicate that the morphological traits of Thai mulberry are distinctive enough to differentiate between M. macroura Miq. and wild hybrid mulberry, and a group consisting of M. alba L. and M. australis Poir., and their hybrids. 12 SRAP primer combinations produced 193 polymorphic amplicons with an average of 17.0 bands per primer set, and the mean of PIC was 0.259. Eleven novel EST-SSR primers generated 35 amplicons with an average of 3.2 alleles per primer set, and the average PIC was 0.139. The dendrogram obtained using the UPGMA algorithm in R studio showed that the wild and wild hybrid mulberry were genetically distant from the domesticated species studied here. These findings have important implications for the characterization, improvement, molecular systematics, and conservation of Thai mulberry germplasm. [ABSTRACT FROM AUTHOR]

Soil pollution by heavy metals is a serious environmental concern globally. Hexavalent (VI) chromium (Cr) is one of the main pollutants causing groundwater and soil heavy metal pollution. Miscanthus sinensis is a C4 perennial grass species with a high level of heavy metal tolerance. This species can effectively remove Cr from soils and maintain desirable biomass production under Cr stress. This research aimed to characterize and compare Cr accumulation in 58 genotypes of M. sinensis and to develop Expressed Sequence Tag–Simple Sequence Repeat (EST-SSR) markers associated with Cr tolerance. The results show that the pattern of translocation of Cr in plants differed among the 58 M. sinensis genotypes following treatment of 200 mg/L of Cr6+; however, in most genotypes, the Cr was primarily accumulated in roots. A total of 43,367 EST-SSRs were identified, and 88 EST-SSR primer pairs corresponding to candidate genes involved in Cr accumulation in M. sinensis were selected for validation. Subsequently, 170 polymorphic loci generated from 24 validated EST-SSRs were used for the population structure and marker–trait association analysis. Based on a general linear model (GLM), a total of 46 associations were identified (p < 0.05), with 14 EST-SSRs markers associated with target traits. Among them, four genes related to ABC transporters, wall-associated receptor kinases, as well as two high-affinity sulfate transporters (ST), were identified under Cr stress (p < 0.05). The results of this study help to accelerate the screening across M. sinensis genotypes for desirable traits under Cr stress and provide a platform for M. sinensis genetic improvement and molecular-marker-assisted breeding. [ABSTRACT FROM AUTHOR]

Flax (Linum usitatissimum L.), as the earliest oil and fiber crop, is a model plant for genetic inferences of plant domestication processes involving multiple domestication events. However, a puzzle has emerged from several genetic studies, as dehiscent cultivated flax is genetically more related to its progenitor pale flax (L. bienne Mill.), and winter cultivated flax is well mixed with oil or fiber cultivated flax, while capsular dehiscence and winter hardiness are the major characteristics of pale flax. For this, a comparative analysis was conducted with 16 Linum samples representing pale flax and four domestication groups of cultivated flax (oil, fiber, winter, and dehiscent) using 454 pyrosequencing, Sanger resequencing and microsatellite data. It was found that the genomic sampling of genetic variants from the three applied methods yielded similar genetic information on pale flax and four groups of cultivated flax. The revealed genetic relationships did not show significant departures from the previous findings, but instead supported an early, independent domestication of a primitive flax lineage for oil use, followed by a subsequent flax domestication process with multiple domestication events for capsular dehiscence, oil, fiber and winter hardiness. Domestication on capsular dehiscence occurred earlier than domestication on winter hardiness. Domestication on winter hardiness was more complicated than domestication on capsular dehiscence. [ABSTRACT FROM AUTHOR]

Phaseolus coccineus L. is a highly valuable crop for human consumption with a high protein content and other associated health benefits. Herein, 14 P. coccineus L. landraces were selected for genetic characterization: two Protected Geographical Indication (PGI) landraces from the Prespon area, namely "Gigantes" ("G") and "Elephantes" ("E"), and 12 additional landraces from the Greek Gene Bank collection of beans (PC1–PC12). The genetic diversity among these landraces was assessed using capillary electrophoresis utilizing fluorescence-labeled Simple Sequence Repeat (SSR) and Expressed Sequence Tag (EST); Simple Sequence Repeat (SSR) is a molecular marker technology. The "G" and "E" Prespon landraces were clearly distinguished among them, as well as from the PC1 to PC12 landraces, indicating the unique genetic identity of the Prespon beans. Overall, the genetic characterization of the abundant Greek bean germplasm using molecular markers can aid in the genetic identification of "G" and "E" Prespon beans, thus preventing any form of fraudulent practices as well as supporting traceability management strategies for the identification of authenticity, and protection of the origin of local certified products. [ABSTRACT FROM AUTHOR]

A weedy rye, Secale cereale subsp. segetale found in Xinjiang, China, possess strong stress tolerance, tillering capacity and many useful traits. The study aims to better understand the genetic diversity of segetale rye from China at the molecular level. The genetic diversity of 92 populations (bulked samples) and further 168 plants (individual samples from 14 populations) in the segetale rye were analyzed using 47 polymorphic EST-SSR (expressed sequence tags derived microsatellite) molecular markers. A total of 211 bands were amplified by 47 EST-SSR primers in the 92 populations. Among them, there were 190 polymorphic bands, with an average of 4.04 bands per primer and an average polymorphic ratio of 88.4%. The variation range of PIC (polymorphic information content) was 0.16–0.94 with the average 0.75, indicating abundant genetic diversity of weedy rye populations. The clustering analysis of 92 populations based on Nei's genetic distance showed that their average genetic distance was near 0.35, and 92 populations from different regions of Xinjiang were relatively scattered, generally close genetic distance between populations in the same region. Similar rule was found between individual plants in same population using clustering and principal coordinate analysis (PCoA). To 168 individual plants from 14 populations, analysis found that the average genetic differentiation among populations was 0.143, and the genetic diversity of the segetale rye populations mainly existed within populations (85.7%). Abundant genetic diversity was found within different regions and populations of segetale rye from China. The research provides a theoretical basis on the application of elite genes of segetale rye to the genetic improvement of rye and wheat. [ABSTRACT FROM AUTHOR]

Pistacia lentiscus var. chia is a valuable crop for its high-added-value mastic, a resin with proven pharmaceutical and cosmeceutical properties harvested from the male tree trunk. To achieve the maximum economic benefits from the cultivation of male mastic trees, it is important to develop early sex diagnosis molecular tools for distinguishing the sex type. Thus far, the work on sex identification has focused on Pistacia vera with promising results; however, the low transferability rates of these markers in P. lentiscus necessitates the development of species-specific sex-linked markers for P. lentiscus var. chia. To our knowledge, this is the first report regarding: (i) the development of species-specific novel transcriptome-based markers for P. lentiscus var. chia and their assessment on male, female and monoecious individuals using PCR-HRM analysis, thus, introducing a cost-effective method for sex identification with high accuracy that can be applied with minimum infrastructure, (ii) the effective sex identification in mastic tree using a combination of different sex-linked ISSR and SCAR markers with 100% accuracy, and (iii) the impact evaluation of sex type on the genetic diversity of different P. lentiscus var. chia cultivars. The results of this study are expected to provide species-specific markers for accurate sex identification that could contribute to the selection process of male mastic trees at an early stage for mass propagation systems and to facilitate future breeding efforts related to sex-linked productivity and quality of mastic resin. [ABSTRACT FROM AUTHOR]

Introduction: Elymus nutans holds ecological and pastoral significance due to its adaptability and nutritional value, the Qinghai-Tibet Plateau (QTP) is a key hub for its genetic diversity. To conserve and harness its genetic resources in highland ecosystems, a thorough assessment is vital. However, a comprehensive phylogeographic exploration of E. nutans is lacking. The objective of this study was to unravel the genetic diversity, adaptation, and phylogenetics of E. nutans populations. Methods: Encompassing 361 individuals across 35 populations, the species' genetic landscape and dynamic responses to diverse environments were decoded by using four chloroplast DNA (cpDNA) sequences and nine microsatellite markers derived from the transcriptome. Results and discussion: This study unveiled a notable degree of genetic diversity in E. nutans populations at nuclear (I = 0.46, He = 0.32) and plastid DNA levels (Hd = 0.805, π = 0.67). Analysis via AMOVA highlighted genetic variation predominantly within populations. Despite limited isolation by distance (IBD), the Mekong-Salween Divide (MSD) emerged as a significant factor influencing genetic differentiation and conserving diversity. Furthermore, correlations were established between external environmental factors and effective alleles of three EST-SSRs (EN5, EN57 and EN80), potentially linked to glutathione S-transferases T1 or hypothetical proteins, affecting adaptation. This study deepens the understanding of the intricate relationship between genetic diversity, adaptation, and environmental factors within E. nutans populations on the QTP. The findings shed light on the species' evolutionary responses to diverse ecological conditions and contribute to a broader comprehension of plant adaptation mechanisms. [ABSTRACT FROM AUTHOR]

Brenneria goodwinii is a bacterial pathogen causing severe decline in Quercus brantii. We explored the effects of B. goodwinii on physiological traits of Q. brantii seedlings and assessed differences between families in the response to the pathogen. We examined 210 seedlings from 14 half-sib families. To evaluate disease resistance, foliar symptoms and several physiological traits, including chlorophyll fluorescence and electrolyte leakage were measured in pathogen-inoculated and mock-inoculated seedlings. In addition, seven EST-SSR markers associated with stress resistance were genotyped in two resistant and two susceptible families. All physiological traits were negatively affected by pathogen inoculation. There was significant genetic variation among the families, with the most susceptible ones showing a worse physiological condition. The heritability and coefficient of genotypic variation of the resistance increased during the experimental period reaching relatively high values (0.49 and 35%, respectively) five weeks after inoculation. EST-SSR analysis revealed that resistant families showed the highest heterozygosity. Two of the seven evaluated loci were associated with the measured physiological traits and showed high FST values. Our results support that resistant mother trees can be selected for disease management. The putative alleles of FIR053 locus could be useful for identifying resistant Q. brantii families to the pathogen. [ABSTRACT FROM AUTHOR]

SSR molecular markers were obtained based on abundant transcriptome data under different waterlogging conditions in order to develop appropriate biological tools and explore the molecular mechanism of hot pepper response to waterlogging stress in this experiment. The results were as follows: (1) A total of 128 939 Unigenes were obtained from transcriptome analysis of hot pepper. The total length, average length, and GC content were 55 082 725 bp, 1 101 bp and 40.57%, respectively. Compared with seven major functional databases, 102 123 (NR, 79.20%), 110 157 (NT, 85.43%), 70 203 (SwissProt, 54.45%), 73 539 (KOG, 57.03%), 77 646 (KEGG, 60.22%), 77 442 (GO, 60.06%) and 68 216 (Pfam, 52.91%) Unigenes obtained functional annotations. It was found that lipid metabolism, carbohydrate metabolism, amino acid metabolism, environmental adaptation, secondary metabolite biosynthesis, signal transduction and translation played important roles in the response to waterlogging stress. (2) A total of 26 574 SSR loci were found in 24 889 Unigenes from hot pepper transcriptome data. The frequency of SSR was 20.61%, of which single nucleotide repeat accounted for the highest ratio (37.26%), followed by tri-nucleotide (31.00%) and di-nucleotide (25.44%) repeat types, accounting for 93.70% of the total EST-SSR. The motifs A/T, AG/CT and TC/GA, followed by AT and TA, were the most abundant in mono-nucleotide and di-nucleotide. The most common types of tri-nucleotides were TTG/CAA and ACA/TGT. (3) 10 002 pairs of EST-SSR primers were designed with Primer 3. A total of 30 pairs of primers were randomly selected for amplification test, and all of them were effective. Seven pairs of primers could amplify the target bands in three hot pepper germplasms. To sum up, the motif structure of the most dominant SSR repeat type in hot pepper is basically similar to that of other varieties, and the molecular mechanism of hot pepper waterlogging stress response is preliminarily explored, and its EST-SSR markers are developed to provide reference for hot pepper waterlogging-tolerant genetic breeding.

Wheat leaf rust, caused by Puccinia triticina, is one of the most common fungal diseases of wheat in China and occurs widely in various wheat-growing regions. To clarify the epidemic, spread rules, and population structure of P. triticina among different regions, 217 isolates of P. triticina collected from Hebei, Shandong, Sichuan, and Xinjiang in China were tested by 34 Thatcher near-isogenic lines and 21 pairs of EST-SSR primers. A total of 83 races were identified, and THTT, PHTT, THTS, and PHJT were the most predominant races in the four provinces in 2009. We found enriched virulence and genetic diversity in the four P. triticina populations and a significant correlation between genetic polymorphism and geographic regions. However, no significant correlation was found between virulence phenotypes and molecular genotypes. Moreover, a notable high level of gene flow (Nm = 2.82 > 1) among four P. triticina populations was detected. The genetic relationship among Hebei, Shandong, and Sichuan populations was close, possibly due to the spread of P. triticina from Sichuan to Shandong and then to Hebei. In contrast, the Xinjiang population was relatively independent. Genetic differentiation analysis showed some level of differentiation among or within populations of P. triticina in the four provinces, and the genetic variation within populations (74.97%) was higher than across populations (25.03%). Our study provides a basis for a better understanding of the regional migration, epidemic, and population structure of P. triticina in China.

Chimonanthus praecox, a member of the Calycanthaceae family, is a unique, traditional, and famous flowering economic tree species in China. Despite the existence of several varieties, only a few cultivars have been formally named. Currently, expression sequence tag–simple sequence repeat (EST-SSR) markers are extensively used to identify different species and varieties; a large number of microsatellites can be identified from transcriptome databases. A total of 162,638 unigenes were assembled using RNA-seq; 82,778 unigenes were annotated using the Nr, Nt, Swiss-Prot, Pfam, GO, KOG, and KEGG databases. In total, 13,556 SSR loci were detected from 11,691 unigenes, with trinucleotide repeat motifs being the most abundant among the six repeat motifs. To develop the markers, 64,440 pairs of SSR primers with polymorphism potential were designed, and 75 pairs of primers were randomly selected for amplification. Among these markers, seven pairs produced amplified fragments of the expected size with high polymorphism. Using these markers, 12 C. praecox varieties were clustered into two monophyletic clades. Microsatellites in the transcriptome of C. praecox exhibit rich types, strong specificity, and great polymorphism potential. These EST-SSR markers serve as molecular technical methods for identifying different varieties of C. praecox and facilitate the exploration of a large number of candidate genes associated with important traits.

Zanthoxylum (Sichuan pepper), with its rich cultivars, has long been widely cultivated in China for its unique seasoning and medicinal uses, but most of its cultivars have similar morphological characteristics. Therefore, we hypothesized that the genetic diversity of Zanthoxylum cultivars is low because of their apomixis and long cultivation history. In this study, we aimed to investigate the genetic diversity of three Zanthoxylum species on the cultivar level based on express sequence tag–simple sequence repeat (EST-SSR) primers. In total, 121 samples of three Zanthoxylum species (Z. bungeanum, Z. armatum and Z. piperitum) were collected from different areas in China for genetic diversity analysis. A total of six specificity and polymorphism EST-SSR primers, which we selected from among 120 primers based on two transcriptomes (Z. bungeanum, Z. armatum) in our earlier study, were used to evaluate genetic diversity based on capillary electrophoresis technology. The results of our analysis using the unweighted pair group method with arithmetic mean (UPGMA) indicated that most of the samples are clustered in one clade in the UPGMA dendrogram, and the average genetic distance was 0.6409. Principal component analysis (PCA) showed that Z. piperitum may have a closer genetic relationship with Z. bungeanum than with Z. armatum. An analysis of molecular variation (AMOVA) showed that the genetic variation mainly stemmed from individuals within populations; the genetic differentiation coefficient (PhiPT) was 0.429, the gene flow (Nm) between populations was 0.333, and the differences among populations were not significant (p > 0.001). For the intraspecific populations of ZB, the percentage of genetic variation was 53% among populations and 47% within populations, with non-significant differences between populations (p > 0.001). The genetic differentiation coefficient (PhiT) was 0.529, and the gene flow (Nm) was 0.223. For the intraspecific populations of ZA, the results indicated that the percentage of genetic variation was 29% among populations and 71% within populations, with non-significant differences between populations (p > 0.001); the genetic differentiation coefficient (PhiPT) was 0.293, and the gene flow (Nm) was 0.223. Through genetic structure analysis (GSA), we predicted that these 121 samples belonged to two optimal subgroups, which means that all the samples probably originated from two gene pools. Above all, this indicated that the genetic diversity of the 121 Zanthoxylum samples was relatively low at both the species and cultivar levels, a finding which was consistent with our initial assumptions. This study provides a reference, with molecular-level data, for the further identification of Zanthoxylum species.

Copyright of Chinese Journal of Oil Crop Sciences is the property of Oil Crops Research Institute of Chinese Academy of Agricultural Sciences and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Sugarcane (Saccharum spp.) is a widely cultivated crop that fulfils approximately 75% of the sucrose demand worldwide. Owing to its polyploidy and complex genetic nature, it is difficult to identify and map genes related to complex traits, such as sucrose content. However, association mapping is one of the alternatives for identifying genes or markers for marker-assisted selection. In the present study, EST-SSR primers were obtained from in silico studies. The functionality of each primer was tested using Blast2Go software, and 30 EST-SSR primers related to sugar content were selected. These markers were validated using association analysis. A total of 70 F1 diverse genotypes for sugar content were phenotypes with two check lines. All parameters related to sugar content were recorded. The results showed a significant variation between the genotypes for sugar yield traits such as Brix value, purity, and sucrose content, etc. Correlation studies revealed that the Brix%, sucrose content, and sucrose recovery were significantly correlated. An association analysis was performed using mixed linear model to avoid false positive associations. The association analysis revealed that the SEM 407 marker was significantly associated with Brix% and sucrose content. The SEM 407 primers are putatively related to diphosphate-fructose-6-phosphate 1-phosphotransferase which is associated with Brix% and sucrose content. This functional marker can be used for marker-assisted selection for sugar yield traits in sugarcane that could accelerate the sugarcane breeding program. [ABSTRACT FROM AUTHOR]

SSR molecular markers were obtained based on abundant transcriptome data under different waterlogging conditions in order to develop appropriate biological tools and explore the molecular mechanism of hot pepper response to waterlogging stress in this experiment. The results were as follows: (1) A total of 128 939 Unigenes were obtained from transcriptome analysis of hot pepper. The total length, average length, and GC content were 55 082 725 bp, 1 101 bp and 40.57%, respectively. Compared with seven major functional databases, 102 123 (NR: 79.20%), 110 157 (NT: 85.43%), 70 203 (SwissProt: 54.45%), 73 539 (KOG: 57.03%), 77 646 (KEGG: 60.22%), 77 442 (GO: 60.06%) and 68 216 (Pfam: 52.91%) Unigenes obtained functional annotations. It was found that lipid metabolism, carbohydrate metabolism, amino acid metabolism, environmental adaptation, secondary metabolite biosynthesis, signal transduction and translation played important roles in the response to waterlogging stress. (2) A total of 26 574 SSR loci were found in 24 889 Unigenes from hot pepper transcriptome data. The frequency of SSR was 20.61%, of which single nucleotide repeat accounted for the highest ratio (37.26%), followed by tri-nucleotide (31.00%) and di-nucleotide (25.44%) repeat types, accounting for 93.70% of the total EST-SSR. The motifs A/T, AG/CT and TC/GA, followed by AT and TA, were the most abundant in mono-nucleotide and di-nucleotide. The most common types of tri-nucleotides were TTG/CAA and ACA/TGT. (3) 10 002 pairs of EST-SSR primers were designed with Primer 3. A total of 30 pairs of primers were randomly selected for amplification test, and all of them were effective. Seven pairs of primers could amplify the target bands in three hot pepper germplasms. To sum up, the motif structure of the most dominant SSR repeat type in hot pepper is basically similar to that of other varieties, and the molecular mechanism of hot pepper waterlogging stress response is preliminarily explored. The EST-SSR markers are developed to provide reference for hot pepper waterlogging-tolerant genetics breeding. [ABSTRACT FROM AUTHOR]

Soil pollution by heavy metals is a serious environmental concern globally. Hexavalent (VI) chromium (Cr) is one of the main pollutants causing groundwater and soil heavy metal pollution. Miscanthus sinensis is a C4 perennial grass species with a high level of heavy metal tolerance. This species can effectively remove Cr from soils and maintain desirable biomass production under Cr stress. This research aimed to characterize and compare Cr accumulation in 58 genotypes of M. sinensis and to develop Expressed Sequence Tag–Simple Sequence Repeat (EST-SSR) markers associated with Cr tolerance. The results show that the pattern of translocation of Cr in plants differed among the 58 M. sinensis genotypes following treatment of 200 mg/L of Cr6+; however, in most genotypes, the Cr was primarily accumulated in roots. A total of 43,367 EST-SSRs were identified, and 88 EST-SSR primer pairs corresponding to candidate genes involved in Cr accumulation in M. sinensis were selected for validation. Subsequently, 170 polymorphic loci generated from 24 validated EST-SSRs were used for the population structure and marker–trait association analysis. Based on a general linear model (GLM), a total of 46 associations were identified (p < 0.05), with 14 EST-SSRs markers associated with target traits. Among them, four genes related to ABC transporters, wall-associated receptor kinases, as well as two high-affinity sulfate transporters (ST), were identified under Cr stress (p < 0.05). The results of this study help to accelerate the screening across M. sinensis genotypes for desirable traits under Cr stress and provide a platform for M. sinensis genetic improvement and molecular-marker-assisted breeding.

Phaseolus coccineus L. is a highly valuable crop for human consumption with a high protein content and other associated health benefits. Herein, 14 P. coccineus L. landraces were selected for genetic characterization: two Protected Geographical Indication (PGI) landraces from the Prespon area, namely “Gigantes” (“G”) and “Elephantes” (“E”), and 12 additional landraces from the Greek Gene Bank collection of beans (PC1–PC12). The genetic diversity among these landraces was assessed using capillary electrophoresis utilizing fluorescence-labeled Simple Sequence Repeat (SSR) and Expressed Sequence Tag (EST); Simple Sequence Repeat (SSR) is a molecular marker technology. The “G” and “E” Prespon landraces were clearly distinguished among them, as well as from the PC1 to PC12 landraces, indicating the unique genetic identity of the Prespon beans. Overall, the genetic characterization of the abundant Greek bean germplasm using molecular markers can aid in the genetic identification of “G” and “E” Prespon beans, thus preventing any form of fraudulent practices as well as supporting traceability management strategies for the identification of authenticity, and protection of the origin of local certified products.

Daylilies (Hemerocallis spp.) are widely cultivated as perennial ornamentals worldwide with important edible, medicinal, and ornamental value. In this study, a total of 9139 SSR loci were detected in the daylily cultivar 'Autumn Red' through Single Molecular Real Time sequencing, of which 2604 unigenes contained two or more SSR loci. Tri-nucleotide repeats were predominated (5270, 57.66%) among the SSR loci, followed by di-nucleotide repeats (3253, 35.50%). Forty (44.44%) valid EST-SSR markers were identified from 90 synthesized EST-SSR markers by screening six accessions, including one daylily wild species, one daylily variant, two daylily cultivars and two night lily landraces cultivated in the National Hemerocallis Germplasm Resource Bank of China. Genetic diversity analysis of 104 Hemerocallis accessions was conducted using 30 polymorphic EST-SSR markers and a total of 98 alleles was identified with an average of 3.23, ranging from 2 to 8 alleles per loci. The polymorphism information content (PIC) values ranged from 0.01 to 0.70, with an average of 0.25. Five markers (XC007, XC057, XC058, XC068 and XC072) showed high polymorphism (PIC > 0.5). Cluster analysis showed that daylilies and night lilies were clustered into two phylogenetic groups, which was confirmed by population structure analysis and PCoA analysis. Among them, Cluster I was classified into six subclusters (Group A–F) in the NJ dendrogram. Combined with the analysis of morphological characteristics of accessions, it was found that the genetic distance may be affected by the source of accessions, which needs further research. Finally, DNA fingerprints of 104 Hemerocallis accessions were constructed using seven efficient EST-SSR markers. The EST-SSRs developed in this study provided useful tools for the identification of daylily accessions and molecular marker assisted breeding. [ABSTRACT FROM AUTHOR]

Cotton is a major source of natural fibre for the global textile industry and is also an important oilseed crop. Cotton fibre is the main source of textiles, the seeds are used for oil and the remaining bagasse is used as high-protein animal feed. In addition, cotton's so-called short fibre is used in more than 50 industries. Cotton breeding is generally based on crossing the best yielding and fibre quality genotypes. However, cotton breeding programmes are negatively affected by the narrow genetic diversity of varieties. It is for this reason that the identification of genetic resources and the disclosure of genetic diversity are so important. Here, the genetic diversity of G. hirsutum and G. barbadense genotypes was determined using high-resolution capillary gel electrophoresis. Using 19 EST-SSR markers, a total of 47 genotypes were screened. The PIC values of the markers used ranged from 0.268 to 0.889. The mean PIC value was calculated to be 0.603. In terms of clustering, PCoA and population structure analyses gave similar results, and the genotypes could be divided into three main groups. Genetic admixture with G. hirsutum was found in some genotypes of the G. barbadense species. We can conclude that (i) the EST-SSR markers used in this study are effective in the determination of genetic diversity, (ii) the genetic diversity should be increased through the collection of genetic resources and (iii) the genetic EST-SSR markers in this study should be considered in breeding programmes by using them in QTL studies. [ABSTRACT FROM AUTHOR]

The velvetbean caterpillar Anticarsia gemmatalis (VBC) is widely distributed in the Americas and causes severe damage to soybean foliage. This insect presents high ecological plasticity, a feature that is of great importance to understand its genetic diversity and potential gene flow to assist in resistance management strategies. With this objective, we developed microsatellite markers for VBC and applied them to five populations from Brazil. Nine primers were polymorphic, with high values of polymorphic information content (PIC > 0.5), and 134 alleles were identified in 155 individuals. These primers indicated deviation from the Hardy–Weinberg equilibrium for all populations (observed heterozygosity, Ho = 0.48, expected heterozygosity, He = 0.76), with moderate to high levels of genetic diversity and a moderate fixation index (FST = 0.14) among the populations. Analysis of population structure indicated the formation of two principal clusters. The northern one can be divided into the two populations that formed the cluster, with high genetic differentiation between them. The other cluster is formed by three populations, and we found evidence of low gene flow between them in the south–north direction, indicating that these populations may be migratory in certain conditions. These findings indicate that the designed primers were effective in describing the genetic diversity of VBC, with major implications for integrated pest management. Given the little gene flow and the high genetic diversity of populations, they present great potential to become resistant to control practices, which can lead to increased management costs. [ABSTRACT FROM AUTHOR]

Rhodomyrtus tomentosa Hassk is a flowering evergreen plant with traditional medicine and ornamental usages. This study aimed to develop a set of EST-SSRs markers for genetic diversity analysis of R. tomentosa. Transcriptome sequencing was performed to obtain the expressed sequence tags in different plant tissues. A total of 51,486 unigenes with a mean length of 1173 bp were achieved. 18,879 SSRs were identified in 14,132 unigenes, in which 3541 unigenes contained more than one SSR. The top three SSR repeat types were mononucleotide (8126, 43.04%), dinucleotide (5846, 31.06%) and trinucleotide (4610, 24.42%). The most abundance motifs were A/T (7816, 41.40%), followed by AG/CT (5002, 26.50%) and AAG/CTT (934, 4.95%). Of these SSRs, 11,726 SSRs were eligible for designing of flanking primers. Among the 100 randomly selected primers, 50 primers generated corresponding PCR products, whereas 23 primers were polymorphic. Thirteen primers with good reproducibility were used to characterize the genetic relationship of sixteen natural R. tomentosa plants. The mean value of observed heterozygosity (Ho), expected heterozygosity (He), fixation index (Fst), and Shannon information index (I) were 0.240, 0.414, 0.413, and 0.641, respectively. UPGMA (unweighted pair-group method with arithmetic averages) dendrogram divided the sixteen R. tomentosa plants into four groups, which were partially correlated with the geographical origin. This study presented a set of EST-SSRs that could be useful for population genetic relationship analysis in R. tomentosa. [ABSTRACT FROM AUTHOR]

Tropical lotus (Nelumbo) is an important and unique ecological type of lotus germplasm. Understanding the genetic relationship and diversity of the tropical lotus is necessary for its sustainable conservation and utilization. Using 42 EST-SSR (expressed sequence tag-simple sequence repeats) and 30 SRAP (sequence-related amplified polymorphism) markers, we assessed the genetic diversity and inferred the ancestry of representative tropical lotus from Thailand and Vietnam. In total, 164 and 41 polymorphic bands were detected in 69 accessions by 36 EST-SSR and seven SRAP makers, respectively. Higher genetic diversity was revealed in Thai lotus than in Vietnamese lotus. A Neighbor-Joining tree of five main clusters was constructed using combined EST-SSR and SRAP markers. Cluster I included 17 accessions of Thai lotus; cluster II contained three Thai accessions and 11 accessions from southern Vietnam; and cluster III was constituted by 13 accessions of seed lotus. Consistent with the results from the Neighbor-Joining tree, the genetic structure analysis showed that the genetic background of most Thai and Vietnamese lotus was pure, as artificial breeding has been rare in both countries. Furthermore, these analyses indicate that Thai and Vietnamese lotus germplasms belong to two different gene pools or populations. Most lotus accessions are genetically related to geographical distribution patterns in Thailand or Vietnam. Our findings showed that the origin or genetic relationships of some unidentified lotus sources can be evaluated by comparing morphological characteristics and the data of molecular markers. In addition, these findings provide reliable information for the targeted conservation of tropical lotus and parent selection in breeding novel cultivars of lotus.

Sugarcane (Saccharum spp.) is a widely cultivated crop that fulfils approximately 75% of the sucrose demand worldwide. Owing to its polyploidy and complex genetic nature, it is difficult to identify and map genes related to complex traits, such as sucrose content. However, association mapping is one of the alternatives for identifying genes or markers for marker-assisted selection. In the present study, EST-SSR primers were obtained from in silico studies. The functionality of each primer was tested using Blast2Go software, and 30 EST-SSR primers related to sugar content were selected. These markers were validated using association analysis. A total of 70 F1 diverse genotypes for sugar content were phenotypes with two check lines. All parameters related to sugar content were recorded. The results showed a significant variation between the genotypes for sugar yield traits such as Brix value, purity, and sucrose content, etc. Correlation studies revealed that the Brix%, sucrose content, and sucrose recovery were significantly correlated. An association analysis was performed using mixed linear model to avoid false positive associations. The association analysis revealed that the SEM 407 marker was significantly associated with Brix% and sucrose content. The SEM 407 primers are putatively related to diphosphate-fructose-6-phosphate 1-phosphotransferase which is associated with Brix% and sucrose content. This functional marker can be used for marker-assisted selection for sugar yield traits in sugarcane that could accelerate the sugarcane breeding program.

Kenaf is one of the most important natural cannabis plants. Molecular marker-assisted breeding is vital for accelerating the breeding process of kenaf. However, the number of kenaf markers is insufficient for molecular marker-assisted breeding. Using transcriptome sequencing data for salt-stressed kenaf plants, the number and distribution of simple sequence repeats (SSRs) and single nucleotide variations (SNVs) in the expressed sequences were determined. The objectives of this study were to elucidate the sequence variations in kenaf genes expressed in response to salt stress and to identify stable and dependable molecular markers. Primers were designed for SSR loci and then EST-SSR molecular markers were generated. The subsequent analyses revealed that 30.50% of the unigenes contained SSR motifs, most of which were single nucleotides followed by trinucleotides and dinucleotides. The unigenes containing SSRs were mostly associated with kenaf salt tolerance. Additionally, 10,483 SNVs were detected in contig sequences. Of the 3995 differentially expressed genes encoding interacting proteins, 1297 contained SSRs. Most of these genes were associated with metabolic pathways (e.g., 03000 transcription factors, B09132 signal transduction, and 04122 sulfur relay system). We designed 20 pairs of EST-SSR primers to genotype 30 kenaf varieties (lines), of which 9 primer pairs were ideal for genotyping (e.g., 1 highly polymorphic marker and 2 moderately polymorphic markers). The primer pairs designed for the EST-SSR markers in the kenaf genome may be useful SSR molecular markers for future research on kenaf. The verified polymorphic markers may be applicable to the molecular marker-assisted breeding of salt-tolerant kenaf varieties. [ABSTRACT FROM AUTHOR]

Molecular marker-based identification of Chinese orchids among species, genera, and hybrids before flowering has important breeding and genetic research value. In this study, the Cymbidium tortisepalum germplasm 'Lianbansu' was chosen for transcriptome sequencing, yielding 9,485 putative EST-SSRs discovered from 28,235 unigenes. Then, 192 primers were randomly selected from the designed primers, and 38 pairs of high-quality primers were screened out through experiments. These high-quality markers were used to examine the genetic diversity, population structure, and evolutionary history of 51 orchid germplasms. The number of alleles ranged from 3 to 12, with an average of 6. The observed and expected heterozygosity with an average of 0.4662 and 0.5973. The first two principal coordinates detected 39.66% of the total variation. It was found that the ΔK-value had one peak (When K = 2). Several germplasms of C. tortisepalum, Cymbidium sinense, Cymbidium hybridum, and some interspecific or intergeneric hybrids and unidentified germplasms could be effectively distinguished using these markers. In conclusion, a set of EST-SSR markers with outstanding transferability was created in this study that can be utilised for hybrid parent tracing and germplasm identification of orchids before flowering. [ABSTRACT FROM AUTHOR]

Yunzhou district, Datong, Shanxi province is the main production base of Hemerocallis citrina in China. In order to find out the main varieties of Hemerocallis citrina in Yunzhou district of Datong city and provide a theoretic basis for identification and breeding for the regional excellent varieties in Datong city, provide strong support for brand protection of the Hemerocallis citrina production area in Yunzhou district, in this experiment, Hemerocallis citrina seedlings from 33 villages in Yunzhou district of Datong city were collected, and morphological index and 43 pairs of highly polymorphic EST-SSR molecular markers previously developed by the research group on innovation and utilization of Hemerocallis citrina germplasm resources of Shanxi Agricultural University was used to conduct the genetic diversity analysis, genetic structure analysis, and cluster analysis of these seedlings. The results showed that the Hemerocallis citrina resources in Datong area could be divided into three groups by cluster analysis based on morphological index of flower bud traits.18 pairs of EST-SSR markers were screened out to be able to distinguish the tested germplasm. A total of 88 polymorphic fragments were amplified from 146 Hemerocallis citrina germplasm by these 18 pairs of EST-SSR markers, with an average of 4.89 polymorphic fragments amplified by each pair of primers. The average value of polymorphism information content(PIC) of primers was 0.298 2. The genetic similarity coefficient between most of the Hemerocallis citrina germplasm resources in Datong and the reference germplasm Datong Huanghua was 1.000 0. The results of cluster analysis and genetic structure analysis based on EST-SSR markers were similar, which could well classify the Hemerocallis citrina germplasm. Except for two Hemerocallis citrina germplasm from Fengyu village and two germplasm from Hedian village, the other 134 Hemerocallis citrina germplasm resources from Yunzhou district of Datong city were clustered with Datong Huanghua. The above results showed that except for four Hemerocallis citrina germplasm from Fengyu village and Hedian village, the other 134 Hemerocallis citrina germplasm resources from Yunzhou district of Datong city were all Datong Huanghua. [ABSTRACT FROM AUTHOR]

【Objective】 The study aimed to explore the SSR locus and distribution characteristics of Codonopsis tangshen Oliv transcriptome. 【Method】 Transcriptome sequencing was performed on C.tangshen leaves. The SSR locus of the transcriptome sequence was identified by MISA software, and functional annotation was performed on the Unigenes containing the SSR locus. Primer 3.0 was used to design EST-SSR primers, and the amplification stability of EST-SSR primers was verified based on C.tangshen germplasm from different regions. 【Result】 A total of 124 179 Unigenes were identified from the transcriptome sequences of C.tangshen, of which 26 084 Unigenes contained 35 827 SSR locus, with a SSR occurrence frequency of 21.01%.There were 165 types of SSR repeat elements in these SSR locus. From the distribution ratio of repeat elements in all the SSRs, the single nucleotide repeat elements A/T accounted for the highest percentage of 37.59%. In respect of the average distance of nucleotide repeat units, pentanucleotide showed the largest distance of 1288.54 kb. Concerning the proportion of primitive repetition times, the SSRs with that of ten accounted for the largest percentage of 21.55% (7722). The base count of SSR sequences was concentrated between 12 and 19 bp, with a total of 19 628 sequences (54.79%). There were 6933 potential polymorphic SSRs above 20 bp, accounting for 19.35% of all.27 SSR primers with stable amplification were selected to amplify the genomic DNA of C.tangshen, with the amplified fragment size ranging from 124 to 393 bp. Based on germplasm resources from different regions of C.tangshen, partial polymorphic markers with clear bands were selected. In addition, 26 084 Unigenes containing SSR locus were annotated by Go and KEGG analysis. These genes were highly enriched in biological processes such as transcriptional regulation, DNA binding, catalysis, and signal transduction. 【Conclusion】 SSR locus of C.tangshen transcriptome have high potential polymorphism, and developed potential polymorphic SSR markers will be used in research on genetic diversity analysis, germplasm identification, molecular assisted breeding, etc. of C.tangshen. [ABSTRACT FROM AUTHOR]

Copyright of Egyptian Journal of Agronomy is the property of Egyptian National Agricultural Library (ENAL) and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Abstract Background Monochasma savatieri Franch. ex Maxim is a medicinally valuable herb. However, the collection and protection of the wild germplasm resources of M. savatieri are still insufficient, and their genetic diversity and population structure have been poorly studied. Results We collected and examined 46 M. savatieri individuals from Fujian, Hunan, Jiangxi, and Zhejiang provinces for genetic diversity and population structure, using 33 newly developed expressed sequence tag-simple sequence repeat (EST-SSR) markers. Applying these markers, we detected a total of 208 alleles, with an average of 6.303 alleles per locus. The polymorphic information content varied from 0.138 to 0.884 (average: 0.668), indicating a high level of polymorphism. At the population level, there was a low degree of genetic diversity among populations (I = 0.535, He = 0.342), with Zhejiang individuals showing the highest genetic diversity among the four populations (Fst = 0.497), which indicated little gene flow within the M. savatieri populations (Nm = 0.253). Mantel test analysis revealed a significant positive correlation between geographical and genetic distance among populations (R 2 = 0.3304, p

Key message: This study developed and validated a set of polymorphic and cross-transferable EST-SSR markers in pecan. 31 polymorphic primers were qualified for genetic diversity evaluation. Pecan is a famous nut tree with high nutritional value. Nowadays, few EST-SSR markers have been developed for this species. Here, 31,074 protein-coding genes of pecan with 46.43 Mb were employed for EST-SSR identification. In total, 9522 EST-SSR loci were detected from 5752 genes with a distribution frequency of 16.69% of total genes and an average density of one SSR per 4.88 kb. Among them, the di-nucleotide (44.24%) was the most abundant motif, followed by mono-, tri-, tetra-, hexa-, and penta-nucleotide repeats. In addition, a total of 7764 EST-SSR loci were distributed in UTR regions, while the rest of the 1758 were located at CDS regions. Based on the flanked sequences surrounding SSR loci, 3586 primers were successfully developed and 250 pairs were randomly selected for verification using six pecan cultivars. After amplification, 171 (68.40%) primer pairs yielded the expected bands, of which, 159 showed polymorphisms. Among the polymorphic primers, 76 pairs could be cross-amplified in four other Carya species (Carya. laciniosa, C. ovata, C. hunanensis, and C. cathayensis). To further characterize the usefulness of EST-SSRs, 31 polymorphic primers were subjected to assess the genetic diversity and relationship of 40 pecan lines, in which the mean number of alleles per locus and polymorphism information content were 6.90 and 0.70, respectively, suggesting the capacity of the markers to monitor high level of informativeness. Cluster analysis indicated that some accessions in the corresponding subgroup were in good agreement with their genetic backgrounds and morphological traits. The EST-SSR resources offered here constitute a valuable tool for genetic diversity analysis in pecan. [ABSTRACT FROM AUTHOR]

Background: Lilium genus consists of approximately 100 species and numerous varieties, many of which are interspecific hybrids, which result in a complicated genetic background. The germplasm identification, genetic relationship analysis, and breeding of Lilium rely on exploiting genetic information among different accessions. Hence, an attempt was made to develop new EST-SSR markers and study the molecular divergence among 65 genotypes of Lilium. Methods and results: A total of 5509 EST-SSRs were identified from the high-throughput sequencing database of L. 'Elodie'. After primer screening, six primer pairs with the most abundant polymorphic bands were selected from 100 primer pairs. Combined with the other 10 reported SSR primers, a total of 16 pairs detected genetic information with an average PIC value of 0.7583. The number of alleles per locus varied from four to 33, the expected heterozygosity varied from 0.3289 to 0.9231, and the observed heterozygosity varied from 0.2857 to 0.5122. Based on the phylogenic results, 22 Asiatic hybrids (A), seven Longiflorum × Asiatic hybrids (LA), as well as two native species were grouped. Eighteen Oriental hybrids (O) and nine Oriental × Trumpet (OT) hybrids, four native species, one LO, and one LL (L. pardalinum × L. longiflorum) variety were grouped. Conclusions: Two major clusters were reported and a large number of genotypes were grouped based on UPGMA and STRUCTURE analysis methods. The PIC value as well as other parameters revealed that the EST-SSR markers selected were informative. In addition, the clustering pattern displayed better agreement with the cultivar's pedigree. The newly identified SSRs in this study provides molecular markers for germplasm characterization and genetic diversity for Lilium. [ABSTRACT FROM AUTHOR]

Wheat leaf rust, caused by Puccinia triticina, is one of the most important fungal diseases of wheat in China. However, little is known about the dynamic changes of population structure and genetic diversity of P. triticina during a period of time. In this study, 247 isolates of P. triticina collected from Hebei Province from 2001 to 2010 were tested on 36 Thatcher near-isogenic lines for virulence diversity and detected by 21 pairs of Expressed Sequence Tag derived Simple Sequence Repeat (EST-SSR) primers for genetic diversity. A total of 204 isolates were successfully identified as 164 races, and THTT, THST, PHRT, THTS, and PHTT were the most common races in Hebei Province from 2001 to 2010. The cluster analysis based on virulence showed that P. triticina has a rich virulence polymorphism, which had a certain correlation with the years, while the cluster analysis based on EST-SSR showed that the genetic diversity of the P. triticina population was significantly different between years in Hebei Province from 2001 to 2010. In addition, the population structure of P. triticina may have changed greatly in 2007 and 2009, which was significantly different from that of 2001–2006 on either virulence or genetic characteristics. The variation frequency of the population structure had an increasing trend during this period. From 2001 to 2010, there was a certain degree of gene flow among the P. triticina populations. No significant correlation was found between virulence and molecular polymorphism. The genetic differentiation analysis of the 10 tested populations (each year as a population) showed that the coefficient of genetic differentiation (Gst) was 0.27, indicating that there was a certain genetic differentiation among or within populations of P. triticina in Hebei Province. The genetic variation within populations (73.08%) was higher than that among populations (26.92%), which indicated that the genetic variations were mainly found within populations. Our study provides the foundation for a better understanding of the population structure change and genetic diversity of P. triticina over a period in Hebei Province of China. [ABSTRACT FROM AUTHOR]

Evaluating the contributions of geographic distance and environmental heterogeneity to the genetic divergence can inform the demographic history and responses to environmental change of natural populations. The isolation‐by‐distance (IBD) reveals that genetic differentiation among populations increases with geographic distance, while the isolation‐by‐environment (IBE) assumes a linear relationship between genetic variation and environmental differences among populations. Here, we sampled and genotyped 330 individuals from 18 natural populations of Cephalotaxus oliveri throughout the species' distribution. Twenty‐eight EST‐SSR markers were applied to analyze population genetics, for the investigation of the driving factors that shaped spatial structure. In addition, we identified the outlier loci under positive selection and tested their association with environmental factors. The results showed a moderate genetic diversity in C. oliveri and high genetic differentiation among populations. Population structure analyses indicated that 18 populations were clustered into two major groups. We observed that the genetic diversity of central populations decreased and the genetic differentiation increased towards the marginal populations. Additionally, the signatures of IBD and IBE were detected in C. oliveri, and IBE provided a better contribution to genetic differentiation. Six outlier loci under positive selection were demonstrated to be closely correlated with environmental variables, among which bio8 was associated with the greatest number of loci. Genetic evidence suggests the consistency of the central‐marginal hypothesis (CMH) for C. oliveri. Furthermore, our results suggest that temperature‐related variables played an important role in shaping genetic differentiation. [ABSTRACT FROM AUTHOR]

Aims: Quaternary climate changes dramatically affected species' distributions and thus impacted genetic diversity patterns, particularly for rear‐edge populations. Empirical studies have shown the southernmost (rear‐edge), fragmented populations of Japanese woody plants can harbour high genetic diversity owing to their origin in southern glacial refugia. The effect of Holocene climate warming on rear‐edge populations has, however, rarely been demonstrated. We assessed whether the genetic structure of populations of temperate plants in Japan can be interpreted to show legacies of both icy (Last Glacial Maximum, LGM) and warm (Holocene) climates. Location: Japanese Archipelago. Taxon: Hemerocallis middendorffii (Asphodelaceae). Methods: Population genetic profiles of 737 individuals from 41 populations were analysed to examine population structure and past population demography, using 12 EST‐SSR markers. Present and past suitable habitat areas during the LGM and the Holocene climatic optimum were estimated by ecological niche modelling (ENM). Reconstructed palaeodistribution was combined with population genetics to statistically predict population demographics in relation to past climate changes. Results: Genetic analysis of the 41 populations revealed 6 regional population groups. Four groups widely dominating the northern–central ranges harboured high genetic diversity, whereas genetic divergence within the groups was low. In contrast, the two groups at the southwestern edge were geographically and genetically isolated, and they showed the lowest genetic diversity. The estimated palaeodistributions showed a decrease in the suitable range during the Holocene in comparison with that at the LGM, and only habitat suitability in the Holocene was able to predict the genetic diversity across the range. Main conclusions Populations at the centre of the current distribution harbour high genetic diversity because they remained stable during both cold and warm periods. However, habitat fragmentation and population decline in relation to climate warming during the Holocene resulted in genetic isolation and impoverishment of the rear‐edge populations. [ABSTRACT FROM AUTHOR]

Juglans plant with important ecological and economic value is endangered in China, and the basis for its protection is the genetic diversity assessment. In the present study, the genetic diversity and the genetic structure of 134 samples from nine J. mandshurica populations with two related species were surveyed by EST-SSR markers. The results showed that 77 alleles were amplified within nine EST-SSR markers which had high polymorphism (PIC = 0.507). Compared with other Juglans species in China, the genetic diversity of J. mandshurica population in Shandong areas was relatively low (HO = 0.333, I = 0.705). The AMOVA analysis showed that 89% variation occurred within the population of J. mandshurica in Shandong areas while 11% occurred inter-populations. The low genetic differentiation (FST = 0.103) and the high gene flow (Nm = 2.894) among populations may be related to the long-distance transmission of pollen. The results of Mantel test showed that there was no significant correlation between geographic distance and genetic distance. UPGMA cluster analysis divided eight J. mandshurica populations in Shandong areas into two groups. The results of STRUCTURE analysis suggested interspecific introgression exists between J. mandshurica and common walnuts (J. regia L.). These genetic data would be great significance for biodiversity conservation for endangered J. mandshurica. [ABSTRACT FROM AUTHOR]

Chrysosplenium macrophyllum Oliv., belonging to the family Saxifragaceae, is a traditional and unique Chinese herbal medicine. However, the lack of adequate molecular markers has hampered the progress regarding population genetics and evolution within this species. In this research, we used the DNBSEQ-T7 Sequencer (MGI) sequencing assay to analyze the transcriptome profiles of C. macrophyllum. SSR markers were developed on the basis of transcriptomic sequences and further validated on C. macrophyllum and other Chrysosplenium species. The genetic diversity and structure of the 12 populations were analyzed by using polymorphic expressed sequence tag simple sequence repeat (EST-SSR) markers. A potential pool of 3127 non-redundant EST-SSR markers were identified for C. macrophyllum in this study. The developed EST-SSR markers had high amplification rates and cross-species transferability in Chrysosplenium. Our results also showed that the natural populations of C. macrophyllum had a high level of genetic diversity. Genetic distance, principal component analysis, and popular structure analysis revealed that all 60 samples clustered into two major groups that were consistent with their geographical origins. This study provided a batch of highly polymorphic EST-SSR molecular markers that were developed via transcriptome sequencing. These markers will be of great significance for the study of the genetic diversity and evolutionary history of C. macrophyllum and other Chrysosplenium species. [ABSTRACT FROM AUTHOR]

Eastern black walnut (Juglans nigra L.), one of the most valuable timber and veneer trees in North America, provides nut shells with unique industrial uses and nut kernels with distinctive culinary attributes. A mature F1 full-sib progeny orchard of 248 individuals from the cross of two eastern black walnut cultivars provides a long-term resource for discovering genetic mechanisms controlling life history, quality traits, and stress resistance. The genetic linkage map, constructed with 356 single nucleotide polymorphism (SNP) markers and 62 expressed sequence tag simple sequence repeats (EST-SSRs), is 1645.7 cM in length, distributed across the expected 16 linkage groups. In this first application of QTL mapping in J. nigra, we report QTL for budbreak, peak pistillate bloom, peak staminate bloom, and heterodichogamy. A dominant major QTL for heterodichogamy is reported, the sequence for which is syntenic with the heterodichogamy QTL on chromosome 11 of Persian walnut (J. regia L.). The mapping population parents are both protogynous, and segregation suggests a Mendelian component, with a 3:1-like inheritance pattern from heterozygous parents. Mapping the sequenced EST-SSR markers to the J. regia "Chandler" V2.0 genome sequence revealed evidence for collinearity and structural changes on two of the sixteen chromosomes. The inclusion of sequenced EST-SSR markers enables the direct comparison of this and subsequent J. nigra maps and other Juglandaceae genetic maps. This investigation initiates long-term QTL detection studies for quality and stress resistance traits in black walnut. [ABSTRACT FROM AUTHOR]