Management Of Germplasm Resources Research Articles

Phytochemical analysis of different Callicarpa species based on integrating metabolomics and chemometrics.

Traditionally, Callicarpa species have been utilized their anti-inflammatory and hemostatic properties. Prominently featured species in the 2020 Edition of the Chinese Pharmacopoeia were Callicarpa nudiflora (CN), Callicarpa macrophylla (CM), Callicarpa formosana (CF), and Callicarpa kwangtungensis (CK), which were formulated into several medicinal preparations. Extensive applications led to the significant depletion of CN's wild resources. The management of germplasm resources was significantly disordered. Adulteration issues were also prevalent. It is imperative that the study aims to identify alternative sources for CN and other pharmacopeial varieties and develop methods to distinguish different Callicarpa species. Data were acquired using three mass spectrometry modes: Data Dependent Analysis (DDA), Data-Independent Analysis (DIA), and full mass spectrometry (MS). The DDA mode identified or inferred information on 54 compounds. The Full MS mode identified or inferred 74 compounds, including 20 that were previously unreported in Callicarpa. These compounds were confirmed using standards. The DIA mode did not facilitate identification due to missing precursor ion data. With metabolomics, 19 differential compounds were identified or inferred. Luteolin, chrysoeriol, and quercetin were selected as potential markers, integrating the 10 active compounds from network pharmacology. Based on the relative abundance of these markers, it was proposed that Callicarpa giraldii Hesse ex Rehd. var. (CGHRV) and CM could serve as alternative resource species to CN, while CGHRV and Callicarpa giraldii Hesse ex Rehd. (CGHR) could substitute the pharmacopeial CM. Callicarpa longissimi (CLG) was suggested as an alternative to CK, while Callicarpa cathayana (CC) and Callicarpa rubella (CRL) could replace CF. Furthermore, the absence of certain compounds in CK presented a novel opportunity for the differentiation of various Callicarpa species.

Genome assembly of M. spongiola and comparative genomics of the genus Morchella provide initial insights into taxonomy and adaptive evolution.

Morchella spongiola is a highly prized mushroom for its delicious flavor and medical value and is one of the most flourishing, representative, and dominant macrofungi in the Qilian Mountains of the Qinghai-Tibet Plateau subkingdoms (QTPs). However, the understanding of M. spongiola remains largely unknown, and its taxonomy is ambiguous. In this study, we redescribed a unique species of M. spongiola, i.e., micromorphology, molecular data, genomics, and comparative genomics, and the historical biogeography of M. spongiola were estimated for 182 single-copy homologous genes. A high-quality chromosome-level reference genome of M. spongiola M12-10 was obtained by combining PacBio HiFi data and Illumina sequencing technologies; it was approximately 57.1Mb (contig N50 of 18.14Mb) and contained 9775 protein-coding genes. Comparative genome analysis revealed considerable conservation and unique characteristics between M. spongiola M12-10 and 32 other Morchella species. Molecular phylogenetic analysis indicated that M. spongiola M12-10 is similar to the M. prava/Mes-7 present in sandy soil near rivers, differentiating from black morels ~ 43.06 Mya (million years ago), and diverged from M. parva/Mes-7 at approximately 12.85 Mya (in the Miocene epoch), which is closely related to the geological activities in the QTPs (in the Neogene). Therefore, M. spongiola is a unique species rather than a synonym of M. vulgaris/Mes-5, which has a distinctive grey-brown sponge-like ascomata. This genome of M. spongiola M12-10 is the first published genome sequence of the species in the genus Morchella from the QTPs, which could aid future studies on functional gene identification, germplasm resource management, and molecular breeding efforts, as well as evolutionary studies on the Morchella taxon in the QTPs.

Assessing the population genetic structure of yellow croaker in China: Insights into the ecological and genetic consequences of artificial breeding on natural populations

The large yellow croaker, a crucial marine economic fish in China, experienced a drastic decline in wild resource in the early 1980s due to overfishing and habitat degradation. Since the year 2000, the government has implemented habitat protection measures and initiated long-term, large-scale releases aimed at restoring this ecologically and economically important fish resource. Despite these efforts, there has been no definitive success in increasing the biomass of this overexploited species, and the underlying reasons for this lack of success remain elusive. Leveraging whole-genome resequencing data from a large number of samples encompassing both cultured and wild populations, this study offers the most exhaustive analysis of the genetic structure of large yellow croaker to date. The results revealed no significant geographical structure among the wild populations along the coast of China, overturning the long-held belief that designated them into three genetic management units. Additionally, it highlighted the absence of genetic introgression from cultured to wild populations. Furthermore, this study identified adaptive changes in cultured populations due to artificial selection and aquaculture environments, potentially reducing their adaptability to natural environments. This reduced adaptability may impact the survival rate of released populations and their hybridization with wild populations, providing insights into the limited success of previous release efforts. In light of these findings, this study recommends implementing conservation and management strategies based on a single genetic management unit for the large yellow croaker. When selecting breeding populations for hatchery releases, emphasis should be placed on genetic background considerations rather than solely relying on the origin of individuals captured in the sea. These insights hold significant implications for conservation and restoration of the large yellow croaker resource, particularly in the management of germplasm resources.

The Genetic Diversity of Natural Ilex chinensis Sims (Aquifoliaceae) Populations as Revealed by SSR Markers

Ilex chinensis Sims. is an evergreen tree species native to China and mainly distributed in the region south of the Qinling Mountains and the Huai River. This species has important ornamental, medicinal, ecological, and economic values, and plays a positive role in improving the environment and people’s lives. To reveal the genetic diversity and genetic structure of 401 individuals from 14 populations in the major distribution area of I. chinensis, 11 pairs of SSR primers were selected for PCR amplification. The products were then subjected to capillary electrophoresis, and the genetic diversity of Ilex individuals was analyzed using relevant software. The results showed that the genetic diversity of I. chinensis was at a moderate-to-high level. A total of 54 alleles were detected at 11 SSR loci in the 14 Ilex populations, with an average of 4.831 alleles per locus. AMOVA analysis indicated that the genetic variation of I. chinensis populations mainly originated within populations. A STRUCTURE analysis divided the 401 I. chinensis individuals into four different genetic clusters. The unweighted pair group methods using arithmetic averages (UPGMA) clustering based on Nei’s genetic distance revealed that the population from Xinping of Yuxi, Yunnan Province (XP), and the population from Longan of Qianxinan, Guizhou Province (LoA) were located in the outermost layer of the phylogenetic tree, indicating the furthest genetic relationship between these two population and other populations. The remaining populations could be roughly divided into two groups. Principal coordinate analysis (PCoA) demonstrated that the 401 individuals were clearly divided into three groups, which was consistent with the results of the STRUCTURE analysis and UPGMA clustering. This study identified the hotspots of genetic diversity of I. chinensis, as well as units for the conservation of individuals. It also revealed the patterns of genetic variation and population distribution of I. chinensis in different regions, providing a molecular basis for the geographical zoning and formulation of breeding programs for I. chinensis, as well as germplasm resource management.

Quantitative 2D fruit shape analysis of a wide range of pear genetic resources toward shape design breeding

The shape of a fruit is one of the main characteristics of fruit morphology, and its quantitative description is crucial to improve fruit quality. However, the shape of a pear fruit is relatively complex, and difficult to describe comprehensively. This study aimed to quantitatively analyze the morphological diversity of 2D fruit shapes of 276 cultivars, covering 6 groups including Pyrus pyrifolia, Pyrus bretschneideri, Pyrus ussuriensis, Pyrus sinkiangensis, Pyrus communis and interspecific hybridization, and discover shape traits with high heritability. Through an automated image processing method, the fruit contour was first accurately extracted, and then geometrical parameters and Fourier descriptors of the pear fruit shape were obtained. Furthermore, principal components (PCs) of the Fourier descriptors were analyzed, and the broad-sense heritability (H2) of the PCs and standardized width (WSD) were estimated. After that, the pear shape stability was calculated, and cultivars were clustered by their shape characteristics. This paper mainly discusses the longitudinal section, as the cross-section variation among cultivars is small. For the longitudinal section, the results showed more than 95 % of the two-dimensional shape variation can be explained by only six principal components; WSD20, WSD30 and PC1 have high H2; the shape stability of western pear was the lowest; a new class of shape was found by clustering the shape traits. The results indicated that the proposed pipeline can provide an objective and comprehensive quantitative description of pear fruit shape for a wide range of cultivars, which is necessary to discover the key genes determining pear shape. This approach is also beneficial for research on pear breeding and germplasm resource management.

Deciphering the population structure and genetic basis of growth traits from whole-genome resequencing of the leopard coral grouper ( Plectropomus leopardus).

The leopard coral grouper ( Plectropomus leopardus) is a species of significant economic importance. Although artificial cultivation of P. leopardus has thrived in recent decades, the advancement of selective breeding has been hindered by the lack of comprehensive population genomic data. In this study, we identified over 8.73 million single nucleotide polymorphisms (SNPs) through whole-genome resequencing of 326 individuals spanning six distinct groups. Furthermore, we categorized 226 individuals with high-coverage sequencing depth (≥14×) into eight clusters based on their genetic profiles and phylogenetic relationships. Notably, four of these clusters exhibited pronounced genetic differentiation compared with the other populations. To identify potentially advantageous loci for P. leopardus, we examined genomic regions exhibiting selective sweeps by analyzing the nucleotide diversity ( θπ) and fixation index ( F ST) in these four clusters. Using these high-coverage resequencing data, we successfully constructed the first haplotype reference panel specific to P. leopardus. This achievement holds promise for enabling high-quality, cost-effective imputation methods. Additionally, we combined low-coverage sequencing data with imputation techniques for a genome-wide association study, aiming to identify candidate SNP loci and genes associated with growth traits. A significant concentration of these genes was observed on chromosome 17, which is primarily involved in skeletal muscle and embryonic development and cell proliferation. Notably, our detailed investigation of growth-related SNPs across the eight clusters revealed that cluster 5 harbored the most promising candidate SNPs, showing potential for genetic selective breeding efforts. These findings provide a robust toolkit and valuable insights into the management of germplasm resources and genome-driven breeding initiatives targeting P. leopardus.

Oolong tea cultivars categorization and germination period classification based on multispectral information.

Recognizing and identifying tea plant (Camellia sinensis) cultivar plays a significant role in tea planting and germplasm resource management, particularly for oolong tea. There is a wide range of high-quality oolong tea with diverse varieties of tea plants that are suitable for oolong tea production. The conventional method for identifying and confirming tea cultivars involves visual assessment. Machine learning and computer vision-based automatic classification methods offer efficient and non-invasive alternatives for rapid categorization. Despite advancements in technology, the identification and classification of tea cultivars still pose a complex challenge. This paper utilized machine learning approaches for classifying 18 oolong tea cultivars based on 27 multispectral characteristics. Then the SVM classification model was executed using three optimization algorithms, namely genetic algorithm (GA), particle swarm optimization (PSO), and grey wolf optimizer (GWO). The results revealed that the SVM model optimized by GWO achieved the best performance, with an average discrimination rate of 99.91%, 93.30% and 92.63% for the training set, test set and validation set, respectively. In addition, based on the multispectral information (h, s, r, b, L, Asm, Var, Hom, Dis, σ, S, G, RVI, DVI, VOG), the germination period of oolong tea cultivars can be completely evaluated by Fisher discriminant analysis. The study indicated that the practical protection of tea plants through automated and precise classification of oolong tea cultivars and germination periods is feasible by utilizing multispectral imaging system.

Chromosome-level genome assembly of the endangered plant Tetraena mongolica.

Tetraena mongolica is an endangered xerophytic shrub with high ecological value for the restoration of desert vegetation because of its high tolerance to drought and heat stress. Here, we generated a high-quality chromosome-level reference genome of T. mongolica by combining PacBio HiFi data and Hi-C sequencing technologies, which was approximately 1.12 Gb (contig N50 of 25.5 Mb) in size and contained 61,888 protein-coding genes; repetitive sequences comprised 44.8% of the genome. This genome of T. mongolica is the first published genome sequence of a member of the order Zygophyllales. Genome analysis showed that T. mongolica has undergone a recent whole genome duplication event, and a recent burst of long terminal repeat insertions afterward, which may be responsible for its genome size expansion and drought adaptation. We also conducted searches for gene homologues and identified terpene synthase (TPS) gene families and candidate genes involved in triacylglycerol biosynthesis. The T. mongolica genome sequence could aid future studies aimed at functional gene identification, germplasm resource management, molecular breeding efforts, as well as evolutionary studies of Fabids and angiosperm taxa.

Population Genomic Evidence for the Diversification of Bellamya aeruginosa in Different River Systems in China.

Clarifying the genetic structure can facilitate the understanding of a species evolution history. It is crucial for the management of germplasm resources and providing useful guidance for effective selective breeding. Bellamya is an economically and ecologically important freshwater snail for fish, birds and even humans. Population genetic structures of the Bellamya species, however, were unknown in previous studies. Population genomics approaches with tens to hundreds of thousands of single nucleotide polymorphisms (SNPs) make it possible to detect previously unidentified structures. The population genomic study of seven populations of B. aeruginosa across three river systems (Yellow River, Yangtze River and Pearl River) in China was conducted by SLAF-seq. SLAF-seq obtained a total of 4737 polymorphisms SLAF-tags and 25,999 high-consistency genome-wide SNPs. The population genetic structure showed a clear division among populations from the Yellow River basin (YH and WL) and the Pearl River basin (QSH and LB), as well as population YC from the Yangtze River basin using the SNPs data. However, there existed no distinct population structure using the mitochondrial DNA (mtDNA). The anthropogenic translocation from the Yangtze River basin to the Pearl River basin and the passive dispersion from the Yangtze River basin to the Yellow River basin by flooding have weakened the phylogeographic pattern of B. aeruginosa. The divergence of B. aeruginosa in the three river systems suggests that the anthropogenic dispersal for aquaculture and breeding requires serious consideration of the population structure for the preservation of genetic diversity and effective utilization of germplasm resources.

Comparison of Microsatellite DNA Fingerprints of Original Seed Files and Conserved Rice Germplasm Collections

The understanding of the genetic identity and composition of germplasm collections conserved in a genebank is vital for the proper management of germplasm resources and utilization in various plant breeding programs. A study was conducted at the Genebank of the Philippine Rice Research Institute (PhilRice) to examine the genetic similarity of the original seed files (SF) and regenerated seeds conserved as an active collection (AC) using 18 microsatellite DNA markers and to explore their underlying intra-varietal heterogeneity. Here, 74 rice germplasm collections regenerated from 1992–2012 were randomly selected for the comparative DNA fingerprinting. The genetic similarity between the original SF and regenerated AC was examined through the Dice coefficient (DC) analysis, while the extent of intra-varietal genetic heterogeneity was determined via average-linkage cluster analysis based on binary genetic distance. Of the 74 collections studied, 68 showed paired clustering of SF and AC, indicating high genetic similarity. The DCs of these collections ranged from 0.79–1. On the other hand, SF and AC comparison of six germplasm collections yielded very low DCs ranging from 0.62–0.77, with their corresponding SF and AC pair dissociated in the dendrogram owing to their high intra-varietal genetic heterogeneity. The intra-varietal polymorphic alleles between SF and AC were observed in all markers analyzed – especially in RM562, RM547, and RM154 microsatellite markers –suggesting their potential use in assessing the levels of intra-varietal genetic heterogeneity in rice cultivars. This pilot study provides baseline information that may be used for potential integration of intra-varietal similarity or variability tests in the Genebank which are important aspects for effective germplasm conservation, management, and utilization. Also discussed in this paper are other insights regarding the intra-varietal genetic heterogeneity of the selected rice accessions.

Identification and characterization of SSR markers in taro [Colocasia esculenta (L.) Schott] by RAD sequencing

Taro [Colocasia esculenta (L.) Schott] is an old crop with high genetic diversity. However, the breeding of taro is limited by the lack of well-developed genetic markers. To help further research on taro germplasm resource management, we developed a set of SSR marker primers. Restriction site-associated DNA sequencing (RAD-seq) was used to identify SSRs from a taro variety. PCR and capillary electrophoresis were applied to evaluate the efficiency of the primers. A phylogenetic tree was constructed to analyse the evolutionary relationship of 30 taro varieties. A total of 4438 SSRs (simple sequence repeats)were identified using RAD sequencing. A total of 3919 pairs of primers were designed based on the SSR data. Trinucleotide repeats (49.1%) were the most abundant type of SSR, while AT was the most common motif type (327 instances). Among 50 randomly selected primer pairs, 46 primer pairs were able to amplify the corresponding bands. A phylogenetic tree cluster analysis using SSR markers mainly supported the classification of taro varieties according to their phenotypes and ecological distribution. The SSR markers identified in this study provide a useful resource for taro genetic and germplasm research and genetic breeding.

Variation in Photosynthetic Traits and Correlation with Growth in Teak (Tectona grandis Linn.) Clones

In order to interpret the patterns of genetic variation of photosynthesis and the relationships with growth traits within gene resources of teak (Tectona grandis Linn.), gas exchange, and chlorophyll fluorescence parameters, growth traits of plants in nursery and field trials were measured for 20 teak clones originated from different countries. The results show that there was abundant genetic variation in gas exchange, chlorophyll fluorescence, and growth among the teak clones. The measured traits were found to have generally high heritability (h2) except for intercellular concentration of carbon dioxide (CO2) (Ci). The net photosynthetic rate (Pn), seedling height, and individual volume of wood were significantly correlated with each other, and seedling height was significantly correlated with plant height in field trials, suggesting that Pn and seedling height can be useful in teak breeding. Teak clones 7029, 71-5, 7219, 7412, and 7122, and provenances 3070, 3074, and 3071 had higher photosynthetic rates, and can be regarded as a key resource in teak improvement programs. This work provides useful information for teak breeding and germplasm resource management.

Validation of SSR Molecular Markers Linked to Drought Tolerant in Some Wheat Cultivars

The present study was carried out to conduct drought tolerance in three wheat cultivars including susceptible (Gemmiza7) and tolerant (Sakha93 and Sahel1). Molecular characterization was done by 26 SSR markers located on chromosome7 which was associated with drought tolerance in many previous studies. 26 SSR markers were polymorphic and thus showed 100% polymorphism. The number of alleles per locus varied from 2 to 3 alleles with an average (2.62). The polymorphism information content (PIC) value ranged from 0.34 to 0.59, with a mean of 0.51. The discrimination power (Dp) value ranged between 0.67 and 0.78 with an average of 0.71 per locus and Heterozygosity (He) value varied from 0.44 to 0.67 with an average of 0.59. The genetic relationships estimated by the polymorphism of SSR markers revealed a greater level of genetic variability in wheat cultivars of wide adaptability and applicability. Whereas an average of combined probability value for the SSR markers was 6.15 x 10-16, suggests the capability of the marker system to distinguish identity and purity of wheat cultivars. In addition to the SSR markers revealed various bands that were either absent or present within tolerant cultivars (Sakha93 and Sahel1) which were altogether absent in susceptible cultivar (Gemmiza7). Also, SSRs of diagnostic and curatorial importance were discerned as ‘stand-alone’ molecular descriptors for barcoding the application of DNA sequences of standardized genetic markers for the identification of wheat cultivars. However, the genetic information in this study could provide useful information to address breeding programs and germplasm resource management.

Evaluation of genetic diversity of Aegilops tauschii accessions using morphological characters

A collection of sixty-three accessions of Ae. tauschii belonging to different eco-geographical regions were used to evaluate its genetic diversity by 15 morphological characters. The data recorded were analyzed on all accessions using multivariate analyses. Principal component analysis (PCA) indicated that first six principal components with eigenvalues more than 1 explained 77.2% of the variability amongst accessions. Through cluster analysis according to Euclidian distance and UPGMA method, accessions divided into three groups. Knowledge of genetic diversity in Aegilops species provides different levels of information which is important in the management of germplasm resources.

Genetic and genomic resources of lentil: status, use and prospects

Extensive collections of lentil germplasm now exist in various genebanks around the world. This germplasm including wildLensspecies has been used in plant introduction strategies and in efforts to widen the potential sources of increasing genetic diversity in the breeding programmes of lentil. Improved techniques are emerging to overcome hybridization barriers between species and as a result, interspecific hybrids have been successfully obtained between species. Several interspecific recombinant inbred line populations have been developed. Selected and backcrossed lentil lines are currently in advanced yield trial stages, and desirable traits such as yield, disease resistance and agronomic traits have been incorporated into cultivated lentil especially fromLens ervoides, generating a wider spectrum of variability. Secondly, further expansion of the overall pool of germplasm and examination of allelic variation at the nucleotide level will benefit lentil-breeding programmes by augmenting phenotype-based variation to further advance cultivar development. Genomic resources for lentil are limited now, but this situation is changing rapidly as the cost of genotyping has declined. As a result, two successive expressed sequence tags (EST) projects were undertaken under the NAPGEN EST project initiative (http://www.nrc-cnrc.gc.ca/eng/programs/pbi/plant-products/napgen/.htm) and an Agricultural Development Fund project initiative. We emphasize that creation of intraspecific and interspecific genetic populations, genetic maps, association maps, quantitative trait loci and marker-assisted selection technologies for implementation in the breeding programme will enhance deployment of genes responsible for traits of interest. The economical use of genomic technologies for use in germplasm resource management and genetic improvement is on the near horizon.

Assessing Rosa persica genetic diversity using amplified fragment length polymorphisms analysis

The genetic diversity among 128 Iranian Rosa persica ( R. persica) accessions in the different populations was analyzed. Amplified fragment length polymorphisms (AFLP) technique was used to produce 171 polymorphic fragments. The number of polymorphic loci ranged from 101 to 147 and the polymorphism information content (PIC) varied from 0.289 to 0.073, with an average of 0.16. This shows extreme variability and genetic diversity among the studied R. persica populations. An indirect estimate of the number of migrants per generation ( Nm = 0.376) indicated that gene flow was relatively low among populations of the species. Cluster analysis using the UPGMA method grouped all accessions into six clusters. The results did not show relative agreement with the genotypes’ region of origin. Based on an analysis of molecular variance, 48% of the genetic variation of R. persica was within population and 52% was among populations. The present analysis revealed that Iranian R. persica genotypes are highly variable and genetically distinct from their origins. The apparent unique nature of the R. persica genotypes revealed by our results supports the case for the implementation of more intense characterization and conservation strategies, and provides useful information to address breeding programmes and germplasm resource management in Rosa spp.

Genetic diversity of the D-genome in T. aestivum and Aegilops species using SSR markers

Simple sequence repeats (SSRs), highly dispersed nucleotide sequences in genomes, were used for germplasm analysis and estimation of the genetic relationship of the D-genome among 52 accessions of T. aestivum (AABBDD), Ae. tauschii (D t D t ), Ae. cylindrica (CCD c D c ) and Ae. crassa (MMD cr1 D cr1 ), collected from 13 different sites in Iran. A set of 21 microsatellite primers, from various locations on the seven D-genome chromosomes, revealed a high level of polymorphism. A total of 273 alleles were detected across all four species and the number of alleles per each microsatellite marker varied from 3 to 27. The highest genetic diversity occurred in Ae. tauschii followed by Ae. crassa, and the genetic distance was the smallest between Ae. tauschii and Ae. cylindrica. Data obtained in this study supports the view that genetic variability in the D-genome of hexaploid wheat is less than in Ae. tauschii. The highest number of unique alleles was observed within Ae. crassa accessions, indicating this species as a great potential source of novel genes for bread wheat improvement. Knowledge of genetic diversity in Aegilops species provides different levels of information which is important in the management of germplasm resources.

Morphological diversity in brinjal (Solanum melongena L.) germplasm accessions

Brinjal (Solanum melongena L.) is an important solanaceous vegetable in many countries of Asia and Africa. It is a good source of minerals and vitamins in the tropical diets. Assessment of genetic resources is the starting point of any crop improvement programme. In India, the National Bureau of Plant Genetic Resources is the nodal institute for management of germplasm resources of crop plants and holds more than 2500 accessions of brinjal in its genebank. In the present study, morphological diversity in a set of 622 accessions, comprising 543 accessions from indigenous sources and 79 accessions of exotic origin, was assessed. Wide range of variations for 31 descriptors, 13 quantitative and 18 qualitative, were recorded. The wide regional variations for plant, flower and fruit descriptors revealed enough scope for improvement of yield characters by selection. The genetic differences among the landraces are potentially relevant to breeding programmes in that the variability created through hybridization of the contrasting forms could be exploited.