Genetic Diversity Indices Research Articles

Genetic diversity and population structure analyses in barley (Hordeum vulgare) against corn-leaf aphid, Rhopalosiphum maidis (Fitch).

Corn-leaf aphid (CLA), Rhopalosiphum maidis (Fitch) (Hemiptera: Aphididae) is a serious economic pest of barley worldwide. Breeding for aphid resistance in plants is considered a cost-effective and environmentally safe approach for aphid control, compared to the use of chemical pesticides. One of the challenges in breeding for aphid resistance is the identification of resistant plant genotypes, which can be achieved through the use of molecular markers. In the present study, a set of aphid specific 10 simple-sequence repeats (SSR) markers were used to investigate genetic diversity and population structure analyses in 109 barley genotypes against R. maidis. Three statistical methods viz., multivariate hierarchical clustering based on Jaccard's similarity coefficient, principal coordinate analysis (PCoA) and the Bayesian approach were utilized to classify the 109 barley genotypes. The analyses revealed four subpopulations i.e., SubPop1, SubPop2, SubPop3 and SubPop4 with 19, 46, 20 and 24 genotypes including admixtures, respectively and represented 17.43%, 42.2%, 18.34% and 22.01% genotypes of the total population size, respectively. The studied SSR markers produced 67 polymorphic bands, with an average of 6.7 and ranging from 3 to 12 bands. Heterozygosity (H) was found to be highest in SSR28 (0.64) and lowest in SSR27 (0.89). The observed genetic diversity index varied from 0.10 to 0.34 (with an average of 0.19). Major allele frequency varied from 74.08% to 94.80%. On an average, 87.52% of the 109 barley genotypes shared a common major allele at any locus. Based on the Aphid Infestation Index (AII), only 2 genotypes were found to be resistant against CLA. SubPop2 also had lowest mean aphid population (28.83), widest genetic similarity index (0.60-1.00) and highest genetic similarity coefficient (0.82), which highlighted its potential for inclusion in future CLA resistance breeding programs.

Prospection of ISSR primers and population genetic characterization of Paratecoma peroba (Record) Kuhlm.

Abstract The objective of this study is to prospect ISSR primers (Inter Simple Sequence Repeats) and, further genetic characterization in Paratecoma peroba. For this, leaf samples of 20 individuals were collected in a forest fragment, located in a private area, close to the Instituto Federal de Educação, Ciência e Tecnologia do Espírito Santo, in the city of Alegre, ES, Brazil. For this, 43 ISSR primers were tested, and 10 primers were selected, which provided a total of 91 bands, with 57 polymorphic bands, resulting in 62.63% polymorphism. The polymorphic information content (PIC = 0.27) indicated moderate informativeness of the primers and, therefore, they are efficient in studies with the species. However, the values found for genetic parameters such as the number of observed (AO = 1.68) and effective (AE = 1.41) alleles and, the genetic diversity indices of Nei (H* = 0.23) and Shannon (I* = 0.35) indicate the occurrence of homozygous loci and low genetic diversity in the population. On the other hand, the genetic structure evaluated by the Bayesian approach revealed the formation of three genetic groups distributed in all sampled individuals, inferring once again about the occurrence of loci in homozygosity. Therefore, the connection of neighbouring fragments and the establishment of individuals obtained from other sources could increase the genetic diversity of the population and reduce the possible effects of depression by inbreeding and genetic drift.

Genetic Diversity and Population Structure in Ethiopian Mustard (Brassica carinata A. Braun) as Revealed by Single Nucleotide Polymorphism Markers.

Ethiopian mustard (Brassica carinata A. Braun) is currently one of the potential oilseeds dedicated to the production for biofuel and other bio-industrial applications. The crop is assumed to be native to Ethiopia where a number of diversified B. carinata germplasms are found and conserved ex situ. However, there is very limited information on the genetic diversity and population structure of the species. This study aimed to investigate the genetic diversity and population structure of B. carinata genotypes of different origins using high-throughput single nucleotide polymorphism (SNP) markers. We used Brassica 90K Illumina InfiniumTM SNP array for genotyping 90 B. carinata genotypes, and a total of 11,499 informative SNP markers were used for investigating the population structure and genetic diversity. The structure analysis, principal coordinate analysis (PcoA) and neighbor-joining tree analysis clustered the 90 B. carinata genotypes into two distinct subpopulations (Pop1 and Pop2). The majority of accessions (65%) were clustered in Pop1, mainly obtained from Oromia and South West Ethiopian People (SWEP) regions. Pop2 constituted dominantly of breeding lines and varieties, implying target selection contributed to the formation of distinct populations. Analysis of molecular variance (AMOVA) revealed a higher genetic variation (93%) within populations than between populations (7%), with low genetic differentiation (PhiPT = 0.07) and poor correlation between genetic and geographical distance (R = 0.02). This implies the presence of gene flow (Nm > 1) and weak geographical structure of accessions. Genetic diversity indices showed the presence of moderate genetic diversity in B. carinata populations with an average genetic diversity value (HE = 0.31) and polymorphism information content (PIC = 0.26). The findings of this study provide important and relevant information for future breeding and conservation efforts of B. carinata.

Characterization of prolamin storage protein profiles in Tunisian pearl millet landraces toward better utilization and improvement

AbstractBackground and ObjectivesThis study reports for the first time the variation of prolamin profiles among 51 pearl millet landraces representing seven populations prospected from contrasted bioclimatic areas of Tunisia.FindingsA total of 27 prolamins bands were detected, ranging from 11 to 245 kDa. Among them, 14 were polymorphic, resulting in a polymorphism rate of 51.85%. The bands with lower molecular weights are the most frequent. The biochemical marker M25.4 showed the highest value of Nei genetic diversity (h = 0.500), Shannon information index (I = 0.693), and effective number of alleles per locus Ne (2). At the population level, the polymorphism rates ranged between 50% (Mahdia) and 92.86% (Hammem Jebli, Kairouan, Medenine). The population of Kairouan showed the highest genetic diversity indices (I = 0.511 ± 0.054, h = 0.345 ± 0.041), while the lowest levels were recorded for the population of Mahdia (I = 0.268 ± 0.076, h = 0.177 ± 0.052). Analysis of molecular variance analysis indicated that the highest amount of genetic diversity was encompassed within the studied populations (89%). This was supported by low genetic differentiation (PhiPT = 0.110, p = .029) and Nei genetic distance values. The classification pattern using ward dendrogram and factorial analyses revealed the distinction of two clusters with a low genetic structure based on the geographic origins of landraces.Significance and NoveltyThe detected biochemical protein polymorphism could be a highly effective tool for the genetic resources characterization of pearl millet landraces, which will be further utilized in breeding investigations and taxonomic surveys of this cereal crop.

Genetic Structuring of One of the Main Vectors of Sylvatic Yellow Fever: Haemagogus (Conopostegus) leucocelaenus (Diptera: Culicidae).

Genetic diversity and population structuring for the species Haemogogus leucocelaenus, a sylvatic vector of yellow fever virus, were found to vary with the degree of agricultural land use and isolation of fragments of Atlantic Forest in municipalities in the state of São Paulo where specimens were collected. Genotyping of 115 mitochondrial SNPs showed that the populations with the highest indices of genetic diversity (polymorphic loci and mean pairwise differences between the sequences) are found in areas with high levels of agricultural land use (northeast of the State). Most populations exhibited statistically significant negative values for the Tajima D and Fu FS neutrality tests, suggesting recent expansion. The results show an association between genetic diversity in this species and the degree of agricultural land use in the sampled sites, as well as signs of population expansion of this species in most areas, particularly those with the highest forest edge densities. A clear association between population structuring and the distance between the sampled fragments (isolation by distance) was observed: samples from a large fragment of Atlantic Forest extending along the coast of the state of São Paulo exhibited greater similarity with each other than with populations in the northwest of the state.

Wolf genetic diversity compared across Europe using the yardstick method

Integrating data across studies with traditional microsatellite genetic markers requires careful calibration and represents an obstacle for investigation of wide-ranging species where populations require transboundary management. We used the “yardstick” method to compare results published across Europe since 2002 and new wolf (Canis lupus) genetic profiles from the Carpathian Mountains in Central Europe and the Dinaric Mountains in Southeastern Europe, with the latter as our reference population. We compared each population with Dinaric wolves, considering only shared markers (range 4–17). For each population, we calculated standard genetic diversity indices plus calibrated heterozygosity (Hec) and allelic richness (Ac). Hec and Ac in Dinaric (0.704 and 9.394) and Carpathian wolves (0.695 and 7.023) were comparable to those observed in other large and mid-sized European populations, but smaller than those of northeastern Europe. Major discrepancies in marker choices among some studies made comparisons more difficult. However, the yardstick method, including the new measures of Hec and Ac, provided a direct comparison of genetic diversity values among wolf populations and an intuitive interpretation of the results. The yardstick method thus permitted the integration of diverse sources of publicly available microsatellite data for spatiotemporal genetic monitoring of evolutionary potential.

Genetic diversity evaluation of core collection gene bank using simple sequence repeat marker of Acorus calamus L.: An important aromatic species

Acorus calamus L. is an important medicinal and aromatic plant having economic and medicinal properties. In the present research, molecular diversity analysis was performed using 138 Acorus calamus accessions obtained from the varied regions of Northeast India. All the collected germplasm was maintained at the Council of Scientific and Industrial Research-North East Institute of Science and Technology (CSIR-NEIST) experimental farm, Jorhat, India. A molecular diversity study was conducted by employing 30 primers screened from 55 simple sequence repeat (SSR) primers based on their polymorphic nature. An average of 99.58% polymorphism was exhibited with a total of 186 polymorphic alleles shown by the selected SSR primers. To estimate the variations among A. calamus accessions, an analysis of molecular variance (AMOVA) was also performed. The genetic diversity among the population was found to be 28% and genetic variations of 72% were observed within the population. Genetic variations within and among populations were found significant with P value of 0.001. The analysis of population-based genetic diversity parameters revealed an average value of 1.84 for the observed number of alleles (Na), 1.48 for an effective number of alleles (Ne), 0.28 for Nei’s genetic diversity index (h), and 0.42 for Shannon's information index in four grouped populations. All the 138 accessions of A. calamus were subdivided into three clusters of dendrogram based on unweighted pair group method with arithmetic mean (UPGMA) analysis. Principal component analysis (PCoA) was further performed and a biplot was constructed for the validation and confirmation of the clusters. Moreover, three genetically diverse populations were also detected by the use of structure harvester software. Until now, there are no such reports on the analysis of the genetic diversity of this industrially important crop using SSR markers. So, it can be considered as the first report on the molecular diversity of A. calamus which will be helpful for the crop improvement, conservation, and identification of the elite genotypes.

Genetic Diversity and Population Structure of Juniperus seravschanica Kom. Collected in Central Asia.

Juniperus seravschanica Kom. is a species that grows widely in the mountain ranges from Central Asia to Oman. It is an important tree for the formation of shrub-forest massifs in mountainous areas and for draining and fixing soils from middle to high altitudes. A comprehensive study of the species' genetic diversity and population structure is a basic approach to understanding the current status of J. seravschanica resources for the development of future conservation strategies. Samples from 15 populations of J. seravschanica were collected from the mountain ranges of Uzbekistan, Kyrgyzstan, and Kazakhstan. The genetic diversity and population structure of 15 Central Asian populations of J. seravschanica were assessed using 11 polymorphic simple sequence repeat (SSR) markers. Genetic diversity parameters, including the number of alleles (na), the effective number of alleles (ne), Shannon's information index (I), the percentage of polymorphic loci (PPL), Nei's genetic diversity index (Nei), principal coordinate analysis (PCoA), etc., were evaluated. The analysis of 15 J. seravschanica populations based on 11 polymorphic SSRs detected 35 alleles. The average PIC value was 0.432, and the highest value (0.662) was found in the JT_40 marker. Nei's genetic diversity index for the J. seravschanica populations was 0.450, ranging from 0.407 (population 14) to 0.566 (population 4). The analysis of molecular variance (AMOVA) showed that 90.3% of total genetic variation is distributed within the population. Using the alleles of all the populations, the gene flow (Nm) was found to be 4.654. Population structure analysis revealed poor clustering in the studied populations and confirmed our AMOVA results. The output of this work can be efficiently used for the maintenance of the species across the Central Asian region.

Genetic and morphological diversity in populations of Annona senegalensis Pers. occurring in Western (Benin) and Southern (Mozambique) Africa.

Understanding morpho-genetic diversity and differentiation of species with relatively large distributions is crucial for the conservation and sustainable management of their genetic resources. The present study focused on Annona senegalensis Pers., an important multipurpose wild plant, distributed exclusively in natural ecosystems but facing several threats. The study assessed the genetic and morphological diversity, structure, and differentiation of the species in populations from Western (Benin) and Southern (Mozambique) Africa. The material was evaluated to ascertain the environmental (climatic) determinants of the variation within this species. Four sub-populations comprised of 154 individuals were phenotyped based on nineteen plant, fruit, and leaf morphological traits and further genotyped using ten polymorphic nuclear microsatellite (nSSR) markers. The results indicated strong differences in plant, fruit, and leaf morphological traits between Western and Southern populations. Furthermore, the studied populations were characterized by high genetic diversity, with an average genetic diversity index of 1.02. Western populations showed higher heterozygosity values (0.61-0.71) than Southern populations (0.41-0.49). Western and Southern populations were clearly differentiated into two different genetic groups, with further genetic subdivisions reflecting four sub-populations. Genetic variation between regions (populations) was higher (69.1%) than among (21.3%) and within (9.6%) sub-populations. Four distinct morphological clusters were obtained, which were strongly associated with the four genetic groups representing each sub-population. Climate, mainly precipitation and temperature indexes, explained the relatively higher variation found in morphological traits from Western (40.47%) in relation to Southern (27.98%) populations. Our study suggests that both environmental and genetic dynamics play an important role in the development of morphological variation in A. senegalensis.

Genetic diversity analysis and fingerprints of Chrysanthemum×morifolium based on SSR molecular markers

The present study aims to explore the genetic diversity of germplasm resources of Chrysanthemum×morifolium (hereinafter, C.×morifolium) at the molecular level and to establish a fingerprint database of C.×morifolium varieties. We employed 12 pairs of primers with high levels of polymorphism, clear bands, and high degrees of reproducibility to analyze the SSR molecular markers and genetic diversity of 91 C.×morifolium materials and 14 chrysanthemum- related materials. With regard to constructing the fingerprints of the tested materials, we chose 9 pairs of core primers. The findings revealed that 12 primer pairs detected 104 alleles in 105 samples, ranging from 2 to 26. The average number of observed alleles (Na) per site was 9.25. The average number of effective alleles (Ne) per site was 2.745 6, with its range being 1.276 0 to 4.742 5. Shannon genetic diversity index (I) values ranged between 0.513 3 and 2.239 9 (M=1.209 0). Nei's gene diversity index (H) ranged between 0.216 3 and 0.789 1 (M=0.578 0). The observed heterozygosity (Ho) ranged between 0.223 3 and 0.895 2 (M=0.557 5). The expected heterozygosity (He) ranged between 0.217 4 and 0.793 3 (M=0.580 8). The polymorphism information content (PIC) ranged between 0.211 5 and 0.774 0 (M=0.532 9). The genetic similarity (GS) ranged between 0.228 5 and 1.000 0 (M=0.608 3). Cluster analysis revealed that when the genetic distance (GD) equals to 0.30, the tested materials can be classified into 2 groups. When the GD equals to 0.27, the first group can be divided into 6 subgroups; accordingly, 105 tested materials can be divided into 7 subgroups. The cophenetic correlation test was carried out based on the cluster analysis, and the corresponding results showed that the cluster map correlated with the genetic similarity coefficient (r=0.952 73). According to the results of Structure population analysis, we obtained the optimal population number, with the true number of populations (K) being 3 and the population being divided concerning Q≥0.5. Three subgroups, i.e., Q1, Q2 and Q3, included 34, 33 and 28 germplasms, respectively, and the remaining 10 germplasms were identified as the mixed population. During the experiment, 9 pairs of core primers were screened among the total of 12 for a complete differentiation regarding 105 tested materials, and the fingerprints of 91 C.×morifolium materials and 14 chrysanthemum-related materials were further constructed. Overall, there were significant genetic differences and rich genetic diversity among C.×morifolium materials, which would shed light on the garden application and variety selection fields of C.×morifolium. The fingerprint database of 105 C.×morifolium varieties and chrysanthemum-related species may provide technical support for future research regarding the identification and screening system of C.×morifolium varieties.

Genome-Wide RADseq Reveals Genetic Differentiation of Wild and Cultured Populations of Large Yellow Croaker.

Larimichthys crocea (also known as the large yellow croaker) is one of the most economically important marine fishes in China, and research on the ecology and genetics of this species is of immense significance. In this study, we performed restriction site-associated DNA sequencing (RAD-seq) of 54 individuals collected from four sites in China to analyze the genetic structure and diversity of large yellow croaker at the genome level. It revealed that the large yellow croaker populations in the Ningde and Zhoushan coastal waters can be clearly distinguished. Different genetic diversity indices were used to analyze the genetic diversity of the large yellow croaker, which showed that there was a differentiation trend between the wild and farmed populations in Ningde. Moreover, we identified genetically differentiated genomic regions between the populations. GO gene enrichment analysis identified genes that are related to fatty acid metabolism and growth. These findings enhance our understanding of genetic differentiation and adaptation to different living environments, providing a theoretical basis for the preservation and restoration of the genetic resources of the large yellow croaker.

Long-term effects of restoration on the links between above-and belowground biodiversity in degraded Horqin sandy grassland, Northern China

Long-term ecological restoration plays an important role in the sustainable development of degraded grassland ecosystem. In this study, the levels of species diversity, genetic diversity and soil microbial diversity in restored grassland were measured by vegetation survey, DNA barcoding and soil microbial high-throughput sequencing technology, so as to explore the relationship between above- and belowground biodiversity and its driving factors in Horqin sandy grassland. In this study, the results found that herb are dominated in restoration grassland types. Plant species richness (SR) from post-non-grazing restoration plot (NGR) communities was significantly higher than other restoration communities (10 ± 1.1, p = 0.004). Genetic diversity indices of dominant plant species in chloroplast DNA (cpDNA), were remarkable greater than nuclear DNA (nrDNA) in each recovering sandy grassland plots (amplitude of difference was 44.8%–70.5% in allelic richness (AR), 81.9%–128.1% in expected heterozygosity (HE)). The soil bacterial and fungal richness from natural mobile dune grassland (NM) communities was notably lower than that from recovering grassland types (1641.9 ± 100.4, p < 0.001; 533 ± 16.6, p < 0.001). In this study, heterogeneous levels of genetic variability among different recovering sandy grassland types were detected. Correlation analyses revealed that there were positive correlations between species diversity and genetic diversity (SR & AR: r = 0.56, R2 = 0.31, p < 0.001; SR & HE: r = 0.33, R2 = 0.11, p = 0.045) and a negative correlation between soil microbial diversity and genetic diversity (r = -0.44, R2 = 0.19, p = 0.005). The final structural equation model explained 38% of the variance in SR, 57% in AR, 52% in soil microbial diversity (SD), 49% in aboveground biomass (AGB), 87% in soil organic carbon (SOC), 47% in soil alkali-hydrolyzable nitrogen (SAN) and 69% in soil available phosphorus (SOP). Long-term ecological restoration had significant direct positive effects on AGB, SOC, SAN, SOP, AR, SR and SD. There was a negative correlation between above- and belowground biodiversity and biological and abiotic factors. The results of this study have clarified the above- and underground biodiversity levels of sandy grassland and the relationship with driving factors under long-term ecological restoration measures, and will provide effective support for the management and sustainable development of sandy grassland.

Genetic diversity and relatedness in captive collared peccaries Dicotyles tajacu (Linnaeus, 1758) (Cetartiodactyla: Tayassuidae) estimated by microsatellite genotyping using high-throughput sequencing: Implications for their conservation and reintroduction.

The global population of Dicotyles tajacu (Linnaeus, 1758) (Cetartiodactyla: Tayassuidae), commonly known as the collared peccary and distributed in the Neotropics, is currently in decline due to anthropogenic pressures. In this study, five microsatellite loci were used to genetically characterize a group of 20 captive-born collared peccaries intended for reintroduction. This study aimed to evaluate the genetic diversity and relatedness of captive individuals using microsatellite markers. The genetic data generated were used to evaluate the viability of the reintroduction and to propose measures for the management and conservation of this species. In this study, we found relatively high genetic diversity indices, indicating that the group was genetically diverse. Inbreeding coefficients with negative values were observed, indicating an excess of alleles in heterozygosis and an absence of inbreeding. One locus showed deviation from Hardy-Weinberg equilibrium, which may have been caused by the mixing of individuals from different origins. Relatedness analysis indicated that some individuals were highly related, with coefficients indicating they may be first-degree relatives. Our findings indicate that the studied group has enough genetic diversity to be released into nature, but the high individual relatedness found would require the adoption of strategies after the release of animals in the wild to ensure their persistence.

Molecular and genetic diversity in isolates of Trypanosoma evansi from naturally infected horse and dogs by using RoTat 1.2 VSG gene in Madhya Pradesh, India.

Trypanosoma evansi is a protozoan parasite that can infect a wide range of animals and is widespread around the world. In this study, we analyzed four fatal cases of T. evansi infection using clinical, parasitological, and molecular approaches. We also explored the genetic diversity, demographic history, and population-genetic structure of T. evansi using available Rode Trypanozoon antigenic type (RoTat) 1.2 gene sequences. Clinical findings of infected animals revealed high fever, anemia, weakness, and anorexia. The animals were treated with diminazene aceturate, which was moderately effective, and hematobiochemical parameters showed changes in hemoglobin and glucose levels. The molecular and genetic diversity of T. evansi was analyzed using the RoTat 1.2 VSG gene. Phylogenetic and haplotype analysis revealed two distinct clusters of T. evansi circulating in India. The genetic diversity indices, neutrality tests, gene flow, and genetic differentiation outcomes confirmed the genetic diversity of the T. evansi population, with a lack of uniformity. The identification of two distinct clusters, exhibiting differential demographic histories and evolutionary forces, implies that the clusters may have undergone independent evolutionary trajectories or experienced different environmental pressures. The present findings underlined the need of an early and precise diagnosis in order to treat and control T. evansi infections, and the RoTat 1.2 VSG gene is an important genetic marker for understanding the genetic diversity and evolutionary history of T. evansi. This knowledge can be used to create tailored strategies to control and manage the infection in an endemic region.

Molecular investigation of bovine tropical theileriosis outbreak in an organized dairy cattle farm in Madhya Pradesh, India.

The present study aimed to investigate an outbreak of Theileria annulata (T. annulata) infection in an organized dairy cattle farm in Madhya Pradesh, India, using clinical and molecular techniques. Following the deaths of two crossbred cattle in March 2021, 43 blood samples were collected from infected and apparently healthy animals and examined by blood smear and polymerase chain reaction (PCR) techniques. The blood smear examination showed that 23.25% of samples were positive for Theileria organisms, while conventional PCR targeting the 18S ribosomal RNA (18S rRNA) and T. annulata merozoite surface antigen-1 (TAMS-1) genes revealed that 32.55% of samples were positive for T. annulata. PCR targeting cytochrome b (Cytb) gene showed 46.51% of samples were positive for T. annulata. Haematological analysis confirmed clinical signs of infection in affected animals, which were treated with buparvaquone @ 2.5mg/kg body weight intramuscularly along with supportive medicine. Two 18S rRNA gene amplicons were sequenced and analysed in a phylogenetic tree and haplotype network with 54 Indian and 38 foreign sequences. The phylogenetic tree revealed two groups with a high posterior probability and bootstrap value, while the haplotype network revealed 35 haplotypes, with haplotype 1 (H1) being the most abundant and several single haplotypes clustering around it, indicating fast and widespread expansion. Genetic diversity indices and neutrality tests confirmed that the population was expanding. These studies highlight the significance of prompt and precise diagnosis and management of T. annulata outbreaks and provide insights into its evolutionary history and population dynamics of T. annulata in India, which could aid improving disease preventive and control strategies.

Evaluation of genetic variation of morphological and clubroot-resistance traits of radish and metabonomic analysis of clubroot-resistant cultivar

Global commercial production of radish (Raphanus sativus) is highly threatened by Plamodiophora brassicae. Germplasm evaluation and the deep analysis of variants with clubroot-resistant trait are needed to produce quality cultivars. The genetic diversity was analyzed for 97 radish germplasms based on 20 agronomic traits and the response to clubroot. Additionally, differentially regulated metabolites (DRMs) between healthy and P. brassicae-infected resistant cultivars were measured. The genetic diversity index values of quality traits varied from 0.396 to 1.350, and that of quantitative traits varied from 1.65–2.15. The variation of radish quantitative traits ranged from 19.18% to 54.44%. The principal component analysis indicated 8 comprehensive indicators, allowing classification of germplasms into 4 classes, with 71 in class I, 20 in class II, 4 in class III, and 2 in class IV. The results of classification of germplasms by the response to clubroot infection only or by comprehensive agronomic traits including response of plants to clubroot disease infection were similar. Among all traits assessed in the present study, the clubroot severity and the depth of in-soil root were closely linked. Metabolomic analysis revealed that the metabolites changes of clubroot resistant cultivar “DHBC” pre- and post- P. brassicae infection was relatively stable. P. brassicae infection resulted in limited DRMs, significant down-regulation was identified on ginsenoside, dihydro-2(3H)-thiophenone, proline, 1-pyrroline, while apiosylglucosyl 4-hydroxybenzoate, chrycolide, glucomalcomiin, and phosphocholine were significantly up-regulated. We revealed more extensive genetic variation in quantitative traits than in quality indexes in radish and we summarized that the response of radish to clubroot disease may be a dominate indicator in evaluation of radish varieties. Finally, untargeted metabolomic study confirmed the clubroot resistance of “DHBC” and revealed a sophisticated metabolites (including some precious pharmaceutical ingredients) variation in response to clubroot infection, offers new directions in the studies of clubroot resistance mechanism of radish.

Genetic diversity analysis of Centella asiatica L. Urban in Vietnam with RAPD marker

Centella asiatica (L.) Urb., belonging to the Apiaceae family, grows widely in shady, moist or marshy places. C. asiatica has been used in traditional medical systems in Asia for over 100 years. A better understanding of genetic diversity is essential for its conservation and use. In this study, we performed the genetic diversity analysis for 24 cultivars of Centella asiatica using 24 selected RAPD markers. There are genetic differences among the studied samples. However, the molecular screening with RAPD markers shows that genetic difference (0.0025–0.2194) and genetic diversity indices (%P = 42.02%, h = 0.1272, I = 0.1938) are relatively low. Besides, HUIB_CA06 and HUIB_CA26 (from Thua Thien Hue province) are genetically different from the remaining varieties, which warrants further analysis of these varieties.

Study on the Phenotypic Diversity of 33 Ornamental Xanthoceras sorbifolium Cultivars

Xanthoceras sorbifolium, belonging to the family Sapindaceae, has a beautiful tree shape, elegant leaves, large and many brightly colored flowers, and a long flowering duration. This plant is widely applied in gardens. In this study, 33 cultivars of Xanthoceras sorbifolium were selected from the perspective of ornamental properties, and their phenotypic traits, such as leaves, flowers, and branches, were measured and analyzed, and their phenotypic diversity was comprehensively evaluated using principal component analysis, in order to investigate the phenotypic diversity characteristics of Xanthoceras sorbifolium. The results showed that the genetic diversity index of the qualitative traits varied from 0.14 to 1.50, and that of quantitative traits varied from 1.76 to 2.05. The quantitative traits were more diverse than the qualitative traits. The coefficient of variation of the qualitative traits ranged from 16.90% to 57.96%, and that of quantitative traits ranged from 12.92% to 32.87%. The phenotypic traits of the tested cultivars had relatively rich variation. Furthermore, the level of the phenotypic diversity index of Xanthoceras sorbifolium was not consistent with the level of coefficient of variation, indicating large variation and uneven distribution of variation. Through principal component analysis, 17 quantitative characters were extracted into five principal components, with a cumulative contribution rate of 79.82%, representing the primary information on the quantitative characters of ornamental Xanthoceras sorbifolium cultivars. The F value of the 33 samples ranged from –2.79 to 1.93, and the comprehensive scores of seven cultivars were greater than 1, indicating that these cultivars had rich phenotypic diversity. Therefore, the screening, development, and utilization of fine germplasm resources of Xanthoceras sorbifolium should focus on these cultivars. The 33 cultivars were subsequently clustered into five categories through systematic clustering. The cluster analysis provided references for breeding ornamental Xanthoceras sorbifolium cultivars with different utilization values, such as large white flowers, small red flowers, large red flowers, large orange flowers, and double-petaled flowers.

Reduced genetic diversity and restricted gene flow of broadcast-spawning coral Galaxea fascicularis in the South China Sea reveals potential degradation under environmental change

Under the dual effects of climate change and anthropogenic activities, coral reefs in the South China Sea (SCS) are at serious risk of degradation. Galaxea fascicularis is a widely distributed species in the SCS, and the study of its genetics, survival, and adaptability is conducive to further understanding the future characteristics of coral reefs in the SCS. In this study, 146 G. fascicularis samples were selected from 9 survey stations across 12 latitudes in the SCS, and 8 pairs of microsatellite markers were used to characterize their genetic diversity and structure. The results showed moderate genetic diversity index values (Ar = 3.444–4.147, He = 0.634–0.782, Ho = 0.367–0.586). The AMOVA results and pairwise FST values showed a moderate level of genetic differentiation (ΦST = 0.119, P < 0.05) among G. fascicularis populations in the SCS, whereas its genetic structure showed high genetic differentiation (FST = 0.062–0.225) among relatively high-latitude populations (n = 3) and low genetic differentiation (FST = 0.012–0.064) in low-latitude populations (n = 6). The living environment of relatively high-latitude populations is disturbed by high-intensity human activities, leading to the specialization of local populations. Mantel test results showed a significant positive correlation between genetic differentiation among G. fascicularis populations and sea surface temperature (SST) variance (R2 = 0.4885; Mantel test, p = 0.010 < 0.05) in addition to geographical distance (R2 = 0.1134; Mantel, test p = 0.040 < 0.05), indicating that SST and geographical isolation were primary factors affecting the genetic structure of this species in the SCS. The lower genetic diversity and limited gene flow of G. fascicularis indicate limited genetic adaptation, and corresponding vulnerability may be more pronounced under future environmental changes. These findings provide a theoretical basis for the conservation and restoration of coral reefs in the SCS.

Genome wide analyses reveal the population distinctiveness of the ‘Nera del Mela’ sheep

Italy has a long history of sheep breeding and counts several local populations that may represent a unique source of genetic diversity. Among these, Nera del Mela is a sheep genetic resource historically reared in Sicily but not officially recognised as a breed. In this study, we genotyped 36 individuals of Nera del Mela using the OvineSNP50K array, in order to estimate the genetic diversity and evaluate the population structure and relatedness with other Italian sheep breeds. Genetic diversity indices, and inbreeding estimated from runs of homozygosity (FROH) revealed a moderate level of variability. Runs of homozygosity islands mapped candidate genes involved in the adaptation to local environment and immune response. Population genetic analyses using different approaches highlighted the hypothesis that this sheep possesses a defined genetic structure, especially if compared with other recognised breeds, despite the influence of other populations such as the Sicilian breeds. Overall, our findings represent a starting point for the possible official acknowledgement of this population, for the creation of a conservation plan, and thus for preserving this genomic heritage. HIGHLIGHTS Nera de Mela sheep can be considered as a reservoir of genetic diversity. The results indicated a clear genetic differentiation from other populations and moderate level of genetic variability. Our findings represent a starting point for the creation of conservation plans.