Genetic Diversity Information Research Articles

DbPepVar: A Novel Cancer Proteogenomics Database

Cancers arise from the acquisition of DNA mutations, such as substitutions, deletions, amplifications, and rearrangements. Understanding the distribution and correlation of such mutations in cancer may aid the characterization of the disease and subsequent identification of biomarkers for diagnosis and treatment. The proteogenomics database (dbPepVar) created here combines genetic variation information from dbSNP with protein sequences from NCBI’s RefSeq. Public mass spectrometry datasets (Ovarian, Colorectal, Breast, and Prostate) were used to perform a pan-cancer analysis, allowing the identification of unique genetic variations. As a result, 3,726 variant peptides were identified in samples from patients with ovarian cancer, 2,543 in prostate, 2,661 in breast and 2,411 in colon-rectal cancer patients. Data resulting from the proteogenomics approach employed and connected to other biological databases is now available in an intuitive and dynamic web portal where novice users can explore general aspects of the dataset in graph or table format, or dive in to filter the data with click and select options or using more advanced queries with regex. All data can be downloaded in csv or pdf format. In perspective, the web portal developed may direct studies to identify new therapeutic targets for different cancers, and one can also use our database for characterization of variants in samples of unknown genetic background, such as archived samples.

KERAGAMAN GENETIK Taxus SumatranaDARI POPULASI ALAM DI JAMBI MENGGUNAKAN PENANDA RAPD

The natural population of Taxus sumatrana in several areas in southern Asia, including Indonesia, has decreased in number. In Sumatra, populations of less than 20 trees/ha were found in the Gunung Kerinci and Gunung Tujuh areas, in Kerinci District, Jambi. Conservation efforts to protect this species from extinction are being carried out, for example, exploring seeds from natural populations for ex-situ plantations. The genetic diversity information of Taxus is required to develop conservation strategies for this species. This research aimed to observethe genetic diversity of Taxus from Gunung Tujuh and Gunung Kerinci populations in Jambi. The level of genetic diversity of 44 individuals from those populations was analyzed using ten markers of RAPD. The application of thosemarkers produced 104 loci used in data analysis using the GenAlex version 6.5 software. The result showed the heterozygosity value described the moderate level of genetic diversity of the two observed populations of 0,33±0.14 (Gunung Tujuh) and 0,35±0.14 (Gunung Kerinci). The genetic distance between the two populations (0,097) and genetic similarity (0,908) indicate that the two populations have a moderate variation in genetic structure. This study shows that the two populations have variations in geneticstructure at medium level although geographically close. Genetic conservation efforts for Taxus species in the future should involve more individuals from both populations and separate them as two different populations

Analysis of genetic diversity in selected sugarcane (Saccharum officinarum L.) accessions using inter simple sequence repeat (ISSR) markers

Genetic diversity information among a population is important in exploiting heterozygosity for the improvement of crop species through breeding programmes. This study was therefore, conducted to assess genetic diversity and establish molecular relationships among 20 selected exotic sugarcane accessions from the Unilorin Sugar Research Institute germplasm using Inter Simple Sequence Repeat (ISSR) molecular markers. Genomic DNA was extracted from the sugarcane leaf. Fragments amplification was then performed by polymerase chain reaction (PCR) with ISSR markers and the data obtained were analyzed using MEGA 4 software. Analysis of the electropherogram showed a total of 39 loci consisting of 369 bands, out of which 95.8% were polymorphic. The biplot analysis showed all the markers contributed to the observed diversity with the least achieved with ISSR6. The principal co-ordinate analysis grouped the accessions into four clusters, comprising mixtures of all the six collection sites. The polymorphism obtained in the present study showed that the ISSR markers are effective for assessment of genetic diversity of the sugarcane accessions as it reveals the genetic similarity or divergence of the accessions regardless their place of origin or cultivation.

Characterization of Brassica napus (Canola) Germplasm Based on Microsatellite Markers

Brassica napus L. is a major oilseed crop all over the world. The aim of this study was to investigate the genetic diversity of B. napus germplasm by using simple sequence repeats (SSR) markers. In the current study, ten SSR markers were used for studying genetic diversity of ten Brassica cultivars. Out of 110 total bands, 68 bands were polymorphic with 52.11% average polymorphism. Mean value of Nei’s genetic diversity and Polymorphism Information Content was 1.7, and 0.2630, respectively. These mean values show that there are moderate allelic differences between Brassica cultivars. The Nei’s genetic distance among various cultivars was 0.3281 and 0.125 which showed that germplasm of Brassica cultivars are different from each other, which is probably due to anthropogenic interventions and environmental factors. Thus, genetically different lines identified in this study could be employed in breeding programmes to develop higher-quality canola inbred varieties in future.

Genetic diversity in Terminalia arjuna from the North Western region of Himachal Pradesh, India

Terminalia arjuna Wight & Arn is used in the Indian traditional medicinal system for the treatment of various cardiac disorders and has been used for the treatment of various human problems like blood diseases, anemia, viral disease, fractures, ulcers, hepatic problems. This study was designed to understand the genetic variation in T. arjuna from different geographical regions of North-west Himalayas. Using the RAPD-PCR method, a total of 183 DNA bands were amplified from 30 accessions of T. arjuna with an average of 6.1 bands per primer. The amplified band size ranges from 150-1700 bp. The Polymorphic Information Content (PIC) value ranges from 0.244 (OPB-10) to 0.781 (OPA-02). The Marker Index (MI) values ranged from 0.6075 to 6.248, with an average of 3.1378. The effective multiplex ratio (EMR) values range from 1.33 (OPC-12) to 9 (OPC-20). A positive correlation was observed between PIC and MI (r = 0.83), MI and EMR (r = 0.873) values. The percentage of polymorphic loci among T. arjuna populations was found to be 71.17%, while AMOVA showed 85% variance within the populations and 15% among the populations. From UPGMA cluster analysis, intermixing of accessions of different populations was observed. This study concludes a genetic variation among different accessions of T. arjuna , indicating good cross-pollination, leading to gene flow between closely located accessions without affecting the gene pool. The genetic diversity information of T. arjuna reported in this study is a very important component for efficient conservation and effective management of its genetic resources.

Morphological characterization of 3 potential lines Cempo Ireng black rice result of Gamma-Ray irradiation

Gamma-ray irradiation on Cempo Ireng can lead to the variation of morphological characteristics; hence, morphological characterization is necessary to determine changes in potential lines. This research aimed to characterize the potential lines as one of the requirements for proposing plant variety release and add black rice genetic diversity information. The research was carried out in the rice fields of Pakahan Village, Jogonalan, Klaten in January-June 2020 with the arrangement of potential lines 8,13 and 44 of M6 in a row. In total 30 plants were selected randomly for each potential line and observed 19 morphological characters. Data analysis was carried out descriptively and qualitatively with the Chi-Square test. The results showed that gamma-ray irradiation affects the characters of leaf angle, auricle color, ligule color, leaf-blade color, leaf surface, panicle type, grain color, apiculus color, and rice length. Potential line 8 had different characteristics compared to non-irradiated Cempo Ireng in the characters of auricle color, leaf-blade color, leaf width, panicle length, grain width, rice length, and rice width, while on potential lines 13 and 44 occur in the characters of the leaf surface and panicle length.

Polyploidization and domestication

<p indent=0mm>Crop domestication is the process to domesticate and propagate wild plants into cultivated crops, and its essence is to purposefully preserve the genetic variation information on the genome through artificial selection. Domestication has played an important role in the origin and evolution of human farming civilization, and promoted the sustainable development of human civilization and the rapid progress of society, in which polyploidization is an important direction of crop domestication and improvement. Compared with the diploid ancestor species, polyploid crops often have obvious phenotypic advantages, relatively high biomass and economic yield, stronger resistance, as well as wider environmental adaptability. Important crops such as wheat (<italic>Triticum aestivum</italic> L.), cotton (<italic>Gossypium </italic>spp.), rape (<italic>Brassica napus</italic> L.) and potato (<italic>Solanum tuberosum </italic>L.) have experienced a long evolutionary process, and are comprehensive products of polyploidization and domestication. The evolution and domestication of polyploid crops and the molecular mechanism of important agronomic traits have always been important scientific issues in the field of crop genetics and breeding, which is of great significance for the molecular design and breeding of crops and sustainable development of agriculture.

Genetic and phenotypic diversity of selected Kenyan mung bean (Vigna radiata L. Wilckzek) genotypes

BackgroundMung bean is a pulse crop principally grown in the tropic and subtropic parts of the world for its nutrient-rich seeds. Seven mung beans accessions from Eastern Kenya were evaluated using thirteen phenotypic traits. In addition, 10 SSR markers were used to determine their genetic diversity and population structure. This aimed at enhancing germplasm utilization for subsequent mung bean breeding programs. ResultsAnalysis of variance for most of the phenology traits showed significant variation, with the yield traits recording the highest. The first three principal components (PC) explained 83.4% of the overall phenotypic variation, with the highest (PC1) being due to variation of majority of the traits studied such as pod length, plant height, and seeds per pod. The dendogram revealed that the improved genotypes had common ancestry with the local landraces. The seven mung beans were also genotyped using 10 microsatellite markers, eight of which showed clear and consistent amplification profiles with scorable polymorphisms in all the studied genotypes. Genetic diversity, allele number, and polymorphic information content (PIC) were determined using powermarker (version 3.25) and phylogenetic tree constructed using DARWIN version 6.0.12. Analysis of molecular variance (AMOVA) was calculated using GenALEx version 6.5. A total of 23 alleles were detected from the seven genotypes on all the chromosomes studied with an average of 2.875 across the loci. The PIC values ranged from 0.1224 (CEDG056) to 0.5918 (CEDG092) with a mean of 0.3724. Among the markers, CEDG092 was highly informative while the rest were reasonably informative except CEDG056, which was less informative. Gene diversity ranged from 0.1836 (CEDG050) to 0.5102 (CDED088) with an average of 0.3534. The Jaccards dissimilarity matrix indicated that genotypes VC614850 and N26 had the highest level of dissimilarity while VC637245 and N26 had lowest dissimilarity index. The phylogenetic tree grouped the genotypes into three clusters as revealed by population structure analysis (K = 3), with cluster III having one unique genotype (VC6137B) only. AMOVA indicated that the highest variation (99%) was between individual genotype. In addition, marker traits association analysis revealed 18 significant associations (P < 0.05). ConclusionThese findings indicate sufficient variation among the studied genotypes that can be considered for germplasm breeding programs.

Influence of Interspecific Interference Competition on the Genetic Structure of Calopteryx splendens Populations

Understanding the effects of interspecific competition on genetic diversity will deepen our knowledge on species evolution. In the case of Calopteryx splendens and C. virgo, sympatric damselfly species, interspecific interference competition by C. virgo has remarkable effects on territoriality of C. splendens resulting in reproductive character displacement. Since territoriality is correlated with phenotype and mating success, we investigated the effects of interspecific interference competition on genetic diversity of C. splendens populations. Using amplified fragment length polymorphisms (AFLP), we determined the population genetic structure of 12 C. splendens populations and used the genetic diversity information to relate heterozygosity of C. splendens to abundance of C. virgo in sympatric populations. We found that heterozygosity of C. splendens males decreased with increasing abundance of C. virgo males. This result most likely reflects changes in effective population size due to interspecific interference competition and shows an effect on genetic structure in damselfly populations.

Assessment of genetic diversity on tomato (Lycopersicon esculentum Mill.) landraces using SSR molecular markers in Turkey

Genetic diversity is getting have been increasingly narrowed by the dense bred cultivar usage for production, on the other hand, genetic variation created by the landraces is known as the raw material of plant breeding. A collection of 21-landrace and three-commercial tomato (Lycopersicon esculentum Mill.) genotypes were screened for allele profile, genetic definition and genetic similarity with the aim of identifying genetic variability in genetic level with 40 SSR loci. Number of alleles per locus ranged from 3 (SSR50, SSR80, SSR9, LEtat002) to 13 (LEat018). Expected and observed heterozygosity values were scored between He: 0.753 and Ho: 0.714 respectively and the mean value of polymorphism information content (PIC) value of these loci was found as 0.694. Considering distribution of alleles at loci, the highest allele frequency was observed from SSR75 with % 62.5 LEat014 with % 58.3 LEga004 with % 50.0 locus, while the lowest was in AI491065 with 16.6% LEta024 locus. UPGMA (Unweighted Pair-Group Method using Arithmetic Means) method was conducted for cluster analysis. The dendrogram was consisted 2 main groups; Group 2 was the largest and contained many sub-groups. The highest genetic similarity level of genotypes from Bafra-Merkez and Sivas-Yukarıkale Village was found as 0.776. The lowest similarity ratio was observed between Sivas-Yıldızeli-Emirler Village and Samsun-Carsamba genotypes with 0.136. The obtained results are indicated that genetic diversity information of landraces with effective SSR loci will help to manage tomato genetic resources for tomato breeding.

Genetic Analysis and Selection Criteria in Bambara Groundnut Accessions Based Yield Performance

The knowledge of genetic variability and breeding techniques is crucial in crop improvement programs. This information is especially important in underutilized crops such as Bambara groundnut, which have limited breeding systems and genetic diversity information. Hence, this study evaluated the genetic variability and established the relationship between the yield and its components in Bambara groundnut based on seed weight using multivariate analysis. A field trial was conducted in a randomized complete block design with three replications on 28 lines. Data were collected on 12 agro-morphological traits, and a statistical analysis was conducted using SAS version 9.4 software, while the variance component, genotypic and phenotypic coefficient variation, heritability, and genetic advance values were estimated. A cluster analysis was performed using NT-SYS software to estimate the genetic relations among the accessions. The results showed significant variability among the accessions based on the yield and yield component characteristics. The evaluated lines were grouped into seven primary clusters based on the assessed traits using the UPGMA dendrogram. Based on the overall results, G5LR1P3, G1LR1P3, G4LR1P1, G2SR1P1 and G3SR1P4 performed the best for the yield and yield components. These improved lines are recommended for large-scale evaluation and utilization in future breeding programs to develop high-yield Bambara groundnut varieties.

Genome assembly of the popular Korean soybean cultivar Hwangkeum.

Massive resequencing efforts have been undertaken to catalog allelic variants in major crop species including soybean, but the scope of the information for genetic variation often depends on short sequence reads mapped to the extant reference genome. Additional de novo assembled genome sequences provide a unique opportunity to explore a dispensable genome fraction in the pan-genome of a species. Here, we report the de novo assembly and annotation of Hwangkeum, a popular soybean cultivar in Korea. The assembly was constructed using PromethION nanopore sequencing data and two genetic maps and was then error-corrected using Illumina short-reads and PacBio SMRT reads. The 933.12 Mb assembly was annotated as containing 79,870 transcripts for 58,550 genes using RNA-Seq data and the public soybean annotation set. Comparison of the Hwangkeum assembly with the Williams 82 soybean reference genome sequence (Wm82.a2.v1) revealed 1.8 million single-nucleotide polymorphisms, 0.5 million indels, and 25 thousand putative structural variants. However, there was no natural megabase-scale chromosomal rearrangement. Incidentally, by adding two novel subfamilies, we found that soybean contains four clearly separated subfamilies of centromeric satellite repeats. Analyses of satellite repeats and gene content suggested that the Hwangkeum assembly is a high-quality assembly. This was further supported by comparison of the marker arrangement of anthocyanin biosynthesis genes and of gene arrangement at the Rsv3 locus. Therefore, the results indicate that the de novo assembly of Hwangkeum is a valuable additional reference genome resource for characterizing traits for the improvement of this important crop species.

ANALYSIS OF GENETIC DIVERSITY OF PALM OIL PLANT (Elaeis guineensis Jacq.) PALM OIL RESEARCH CENTER (PPKS) BASED ON PRIMARY SSR (Simple Sequence Repeats)

The background of this research was to obtain information of genetic diversity within and among populations of E. guineensis using SSR markers. This research was conduted in Biology Molecular Laboratory, Indonesian Oil Palm Research Institute, Marihat, Pematangsiantar, North Sumatra from March 2016 to January 2017. A total of 100 palm oil samples used in this research, including 20 samples from the populations of E. guineensis TR01S, including 20 samples from the populations of E. guineensis BJ022S, including 20 samples from the populations of E. guineensis BJ42S, including 20 samples from the populations of E. guineensis BO52S, and including 20 samples from the populations of E. guineensis MA19S. Calculation and Desciptive analysis in this research using software GeneMarker® version 2.40, software DARwin version 6.0.13 and Microsoft Excel 2007. Research shows that the number of banding patterns detected 104 The banding patterns WITH range 8-9 per primary banding pattern, and the size of the banding patterns ranging from 101 bp -328 bp. mEgCIR2569 primary is the most widely primer to amplify DNA and the average of the percentage of polymorphism in the primer being used by 71%. Analysis dendogram 100 samples All 3 hearts big group of Jatropha genetic WITH BETWEEN Yang ranged from 0.03 to 1.00 Based on the findings of the analysis of genetic relationships WITH Matrix Method using differences Simple Matching Value factorial analysis (PCoA) declared WITH axis I and axis II ON 12 primary SSR of 20.3%. mEgCIR2569 primary is the most widely primer to amplify DNA and the average of the percentage of polymorphism in the primer being used by 71%. Analysis dendogram 100 samples All 3 hearts big group of Jatropha genetic WITH BETWEEN Yang ranged from 0.03 to 1.00 Based on the findings of the analysis of genetic relationships WITH Matrix Method using differences Simple Matching Value factorial analysis (PCoA) declared WITH axis I and axis II ON 12 primary SSR of 20.3%. mEgCIR2569 primary is the most widely primer to amplify DNA and the average of the percentage of polymorphism in the primer being used by 71%. Analysis dendogram 100 samples All 3 hearts big group of Jatropha genetic WITH BETWEEN Yang ranged from 0.03 to 1.00 Based on the findings of the analysis of genetic relationships WITH Matrix Method using differences Simple Matching Value factorial analysis (PCoA) declared WITH axis I and axis II ON 12 primary SSR of 20.3%.

Elucidating SNP-based genetic diversity and population structure of advanced breeding lines of bread wheat (Triticum aestivum L.).

Genetic diversity and population structure information are crucial for enhancing traits of interest and the development of superlative varieties for commercialization. The present study elucidated the population structure and genetic diversity of 141 advanced wheat breeding lines using single nucleotide polymorphism markers. A total of 14,563 high-quality identified genotyping-by-sequencing (GBS) markers were distributed covering 13.9 GB wheat genome, with a minimum of 1,026 SNPs on the homoeologous group four and a maximum of 2,838 SNPs on group seven. The average minor allele frequency was found 0.233, although the average polymorphism information content (PIC) and heterozygosity were 0.201 and 0.015, respectively. Principal component analyses (PCA) and population structure identified two major groups (sub-populations) based on SNPs information. The results indicated a substantial gene flow/exchange with many migrants (Nm = 86.428) and a considerable genetic diversity (number of different alleles, Na = 1.977; the number of effective alleles, Ne = 1.519; and Shannon’s information index, I = 0.477) within the population, illustrating a good source for wheat improvement. The average PIC of 0.201 demonstrates moderate genetic diversity of the present evaluated advanced breeding panel. Analysis of molecular variance (AMOVA) detected 1% and 99% variance between and within subgroups. It is indicative of excessive gene traffic (less genetic differentiation) among the populations. These conclusions deliver important information with the potential to contribute new beneficial alleles using genome-wide association studies (GWAS) and marker-assisted selection to enhance genetic gain in South Asian wheat breeding programs.

Development of GBTS and KASP Panels for Genetic Diversity, Population Structure, and Fingerprinting of a Large Collection of Broccoli (Brassica oleracea L. var. italica) in China.

Broccoli (Brassica oleracea var. italica) is one of the most important and nutritious vegetables widely cultivated in China. In the recent four decades, several improved varieties were bred and developed by Chinese breeders. However, the efforts for improvement of broccoli are hindered by limited information of genetic diversity and genetic relatedness contained within the available germplasms. This study evaluated the genetic diversity, genetic relationship, population structure, and fingerprinting of 372 accessions of broccoli representing most of the variability of broccoli in China. Millions of SNPs were identified by whole-genome sequencing of 23 representative broccoli genotypes. Through several stringent selection criteria, a total of 1,167 SNPs were selected to characterize genetic diversity and population structure. Of these markers, 1,067 SNPs were genotyped by target sequencing (GBTS), and 100 SNPs were genotyped by kompetitive allele specific PCR (KASP) assay. The average polymorphism information content (PIC) and expected heterozygosity (gene diversity) values were 0.33 and 0.42, respectively. Diversity analysis revealed the prevalence of low to moderate genetic diversity in the broccoli accessions indicating a narrow genetic base. Phylogenetic and principal component analyses revealed that the 372 accessions could be clustered into two main groups but with weak groupings. STRUCTURE analysis also suggested the presence of two subpopulations with weak genetic structure. Analysis of molecular variance (AMOVA) identified 13% variance among populations and 87% within populations revealing very low population differentiation, which could be attributed to massive gene flow and the reproductive biology of the crop. Based on high resolving power, a set of 28 KASP markers was chosen for DNA fingerprinting of the broccoli accessions for seed authentication and varietal identification. To the best of our knowledge, this is the first comprehensive study to measure diversity and population structure of a large collection of broccoli in China and also the first application of GBTS and KASP techniques in genetic characterization of broccoli. This work broadens the understanding of diversity, phylogeny, and population structure of a large collection of broccoli, which may enhance future breeding efforts to achieve higher productivity.

Norovirus passive surveillance as an alternative strategy for genetic diversity assessment in developing countries

In developing countries, the acute gastroenteritis outbreaks submitted for viral testing are limited due to deficient surveillance programs. The aim of this study was to analyze a passive surveillance strategy for monitoring the molecular epidemiology of norovirus (NV) and counterbalance the genetic diversity data gap.Laboratory-confirmed rotavirus negative sporadic stool samples (N = 523) collected between 2010 and 2017 from children were selected from our archival collection and were tested for NV and sequencing was performed on the positive samples. Passive surveillance information was compared with the genetic diversity data that was available from local norovirus-confirmed gastroenteritis outbreaks.Each year, norovirus detection in the sporadic samples ranged from 12 to 29%. GI and GII norovirus were detected in 7 (1.3%) and 101 (19.3%) of the specimens, respectively. Four GI and six GII capsid genotypes were identified. Six out of 9 strains detected in the NV outbreaks panel were also identified in the set of sporadic samples either coincidently in the same year, the previous or the later year. Also, this set of samples depicted even better the circulating epidemic strain. Thus, implementing norovirus testing and genotyping in stool samples collected with other purposes represent a suitable strategy for providing genetic diversity information.

IDENTIFICATION AND CHARACTERISATION OF COI GENE IN FEMALE SUMATRAN ELEPHANT (Elephas maximus sumatranus) IN ELEPHANT TRAINING CENTRE, WAY KAMBAS NATIONAL PARK

Sumatran elephant is a subspecies of endemic Asian elephants on the island of Sumatra and is included in the Red List of the International Union for Conservation of Nature (IUCN) with critically endangered status. The building of the Elephant Training Centre (ETC) in Way Kambas National Park (WKNP) is one of the conservation efforts of Sumatran elephants. Small and closed population size lead to an increased risk of inbreeding that triggers reduction in genetic variation and viability and increases the risk of extinction. The phylogenetic pattern of Sumatran elephants in Indonesia has shown a low population genetic diversity. Genetic diversity information is indispensable to support the direction of decision making in Sumatran elephant conservation policy. The DNA isolation of Sumatran elephants in ETC, WKNP has performed as a first step to trace its genetic variation. The advanced step of DNA isolation is the use of cytochrome oxidase subunit I (COI) gene for identification of genetic characteristics in Sumatran elephants. The COI gene is one of the genes on the mitochondrial genome and in molecular studies it is used as a genetic marker to study genetic characteristics between species and individuals. Identification and characterisation are done by sequencing process and data analysis in the form of electroforegram using Molecular Evolution Genetics Analysis (MEGA) software version 6.0. to see the genetic diversity of the female Sumatran elephant population in ETC, WKNP. Based on the results of the analysis it is indicated that the genetic distance of 24 individual female Sumatran elephant from PLG, TNWK is 0.000 with a homology value of 100%, strengthened by the construction of phylogenetic tree. The absence of genetic distance indicates a close genetic relationship, so it can be concluded all individual female Sumatran elephants in the PLG, TNWK is derived from one population group.

Genetic diversity and relatedness analysis of nine wild species of tree peony based on simple sequence repeats markers

Tree peony has nine wild species, but the evolutionary relationship of them is still unclear. Here, a total of 274 specimens from 22 natural populations of nine wild species were collected, and their genetic diversity and similarity was analyzed based on Simple Sequence Repeats (SSR) molecular markers. A total of 106 alleles were generated based on 20 primers and with an average of 5.3 alleles per primer. Shannon's information index (I) ranged from 0.6333 to 1.7842, and the average of Nei's genetic diversity coefficient (H) was 0.5771. Polymorphism Information Content (PIC) value varied from 0.29 to 0.77, ten of these primers had high polymorphism (PIC ≥ 0.50). All the above genetic parameters of primers reflect more rich genetic diversity information compared with other researches using SSR molecular markers to study the genetic diversity of tree peony wild species. At the population level, the lowest and highest degree of genetic diversity occurred in Paeonia ludlowii-P1 and P. delavayi-P3 population, respectively. Whereas at species level, the genetic diversity of 9 wild peony species was as follows: P. lutea > P. delavayi > P. rockii > P. qiui > P. ostii > P. decomposita > P. potaninii > P. spontanea > P. ludlowii. Furthermore, cluster analysis at species level divided the nine wild tree peony species into two branches. In branch I, the closest phylogenetic relationship was found between P. ostii and P. rockii, followed by P. spontanea, P. qiui, and P. decomposita. In branch II, the closest relationship occurred between P. lutea and P. delavayi, followed by P. potaninii and P. ludlowii. Clustering results supported the division of tree peonies into two subsects (Delavayanae and Vaginatae), it also supported P. potaninii and P. ludlowii as independent species. The results provided novel insight into the genetic diversity and phylogenetic relationship of nine wild tree peony species. It will help formulate comprehensive protection measures of wild germplasm resources and select proper parents for distant hybridization in the future.

Genetic Diversity and Population Assessment of Musa L. (Musaceae) Employing CDDP Markers

Sixty-six accessions of Musa genus with different genomic groups that consisted of wild relatives and cultivated lines were obtained from the International Transit Center, Belgium, for DNA extraction using Cetyl trimethylammonium bromide method, followed by amplification with Conserved DNA-derived Polymorphism (CDDP) markers for genetic diversity and population assessment. A total of 421 alleles with major allele frequency of 2.051 were detected from the reproducible markers. High genetic diversity (GD, 11.093) and polymorphic information content (0.918) were revealed. The number of polymorphic loci and percentage of polymorphic loci ranged from 59 to 66 and 89.34 to 100, respectively. Using the potential genetic indicators including effective number of alleles, Nei’s genetic diversity, and Shannon’s information index, the AS genomic group was identified to have the highest GD, while the AAA accessions had the lowest GD indices. The GD parameters identified in the accessions were ranked as AS > AAB > AAAA > AA > ABB > wild diploidy > BB > AB > AAA from high to low based on polymorphic loci of the markers. Total intraspecific GD, interspecific GD, and estimate gene flow identified were 0.433, 0.404, and 7.113, respectively. The coefficient of gene differentiation of 0.066 was obtained, indicating 6.57% among the population and 93.43% within the population. Dendrogram analysis produced nine major groups with subgroups at similarity index of 0.814. These CDDP functional gene-based markers were informative and very efficient in resolving GD, and population indices among the banana and plantain accessions of different genomes. The identified CDDP markers might serve as potential tools for selecting suitable training populations for breeding and conservation of Musa species.

Adding leaves to the Lepidoptera tree: capturing hundreds of nuclear genes from old museum specimens

AbstractMuseum collections around the world contain billions of specimens, including rare and extinct species. If their genetic information could be retrieved at a large scale, this would dramatically increase our knowledge of genetic and taxonomic diversity information, and support evolutionary, ecological and systematic studies. We here present a target enrichment kit for 2953 loci in 1753 orthologous nuclear genes + the barcoding region of cytochrome C oxidase 1, for Lepidoptera and demonstrate its utility to obtain a large number of nuclear loci from dry, pinned museum material collected from 1892 to 2017. We sequenced enriched libraries of 37 museum specimens across the order Lepidoptera, many from higher taxa not yet included in high‐throughput molecular studies, showing that our kit can be used to generate comparable data across the order, and provides resolution both for shallower and deeper nodes. The filtered datasets (172 taxa, 234 464 amino acid positions and corresponding nucleotides from 1835 CDS regions) were used to infer a phylogeny of Lepidoptera, which is largely congruent in topology to recent phylogenomic studies, but with the addition of some key taxa. We furthermore present our TEnriAn (Target Enrichment Analysis) workflow for processing and combining target enrichment, transcriptomic and genomic data.