Development of genic SSR marker resources from RNA-seq data in Camellia japonica and their application in the genus Camellia

AbstractCamellia is a genus of flowering plants in the family Theaceae, and several species in this genus have economic importance. Although a great deal of molecular makers has been developed for molecular assisted breeding in genus Camellia in the past decade, the number of simple sequence repeats (SSRs) publicly available for plants in this genus is insufficient. In this study, a total of 28,854 potential SSRs were identified with a frequency of 4.63 kb. A total of 172 primer pairs were synthesized and preliminarily screened in 10 C. japonica accessions, and of these primer pairs, 111 were found to be polymorphic. Fifty-one polymorphic SSR markers were randomly selected to perform further analysis of the genetic relationships of 89 accessions across the genus Camellia. Cluster analysis revealed major clusters corresponding to those based on taxonomic classification and geographic origin. Furthermore, all the genotypes of C. japonica separated and consistently grouped well in the genetic structure analysis. The results of the present study provide high-quality SSR resources for molecular genetic breeding studies in camellia plants.

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Genetic relationships within the Cucurbitaceae as assessed by consensus chloroplast simple sequence repeats (ccSSR) marker and sequence analyses

Canadian Journal of Botany ◽

10.1139/b03-074 ◽

2003 ◽

Vol 81 (8) ◽

pp. 814-832 ◽

Cited By ~ 24

Author(s):

Sang-Min Chung ◽

Deena S Decker-Walters ◽

Jack E Staub

Keyword(s):

Simple Sequence Repeats ◽

Genetic Relationships ◽

Morphological Data ◽

Insertion And Deletion ◽

Nicotiana Tabacum L ◽

The Family ◽

Pcr Products ◽

Species Comparisons ◽

Sequence Substitution ◽

Simple Sequence

To investigate genetic relationships in Benincaseae (19 accessions), Cucurbiteae (1), Joliffieae (2), Melothrieae (2), and Sicyeae (3) tribes of the family Cucurbitaceae, consensus chloroplast simple sequence repeats (ccSSR) primer pairs obtained from tobacco (Nicotiana tabacum L.) chloroplast DNA were used. Variation in the length and putative sequence substitution events of polymerase chain reaction (PCR) products were analyzed. Sequencing of four fragments (ccSSR-1, -7, -8, and -19) revealed that convergence in fragment length occurs in more distant species comparisons. In ccSSR-1 and -8, the same fragment lengths occurred as the result of different insertion and deletion events. Nevertheless, the examination of a large number of ccSSR fragments suggested that this apparent homoplasy could be overshadowed by evolutionary relationships among taxa. This hypothesis is supported by the relative degree of positive congruence of taxon groupings after cluster and principal components analyses performed on both base pair length and sequence substitution data. Moreover, these analyses support previous biochemical and morphological data indicating that distinct lineages exist within the Benincaseae. Likewise, data support the hypotheses that the genus Benincasa is descended from an ancient African ancestor and that the progenitor of the New World Sicyeae tribe shares a common ancestor with the genus Luffa of the Old World Benincaseae.Key words: Benincaseae, chloroplast, consensus, homoplasy, microsatellite, simple sequence repeats.

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Management of Vitis and Brassica Germplasm

HortScience ◽

10.21273/hortsci.31.4.692d ◽

1996 ◽

Vol 31 (4) ◽

pp. 692d-692

Author(s):

James R. McFerson ◽

Warren F. Lamboy ◽

Steve Kresovich

Keyword(s):

Genetic Markers ◽

Genetic Relationships ◽

Molecular Genetic ◽

Geographic Origin ◽

Small Subset ◽

Molecular Genetic Markers ◽

Germplasm Collections ◽

Diversity Assessment ◽

Ssr Loci ◽

The Individual

We discuss a series of studies in our units employing molecular genetic markers in collection management, primarily for identity and diversity assessment and partitioning of genetic variation. Isozymes, random amplified polymorphic DNAs (RAPDs), and simple sequence repeat DNAs (SSRs) have been used for these purposes. We analyzed a range of Brassica oleracea accessions at six isozyme loci. Unique isozyme profiles (or fingerprints) were found for 40% of the individual genotypes within accessions. While isozymes were extremely valuable for partitioning genetic variability between and among subspecies, they failed to identify accessions and subspecies. Furthermore, relationships found did not correspond to those predicted by taxonomy. In a study of three species of Chinese vegetable brassicas using 112 RAPD markers, we were able to unambiguously distinguish all 52 accessions studied, despite some intra-accession variability. In addition, cluster analysis correctly grouped all individuals of the same species, but below that rank, taxonomic groupings occasionally broke down. RAPD profiles were found that unambiguously distinguished the three Brassica species from one another, but, for subspecies, no such profiles were found. In another RAPD study of B. oleracea subsp. capitata (cabbage), a closely related set of cultivars were not distinguishable, although more distantly related cultivars were. We had disappointing results with a RAPD study of Vitis accessions. DNA was extracted from the leaves of 23 greenhouse-grown and 52 field-grown vines. Twelve of the 23 greenhouse vines were rooted cuttings collected from 12 of the field-grown vines. Unfortunately, the RAPD profiles of all vines grown in the same location (whether greenhouse or vineyard) were more similar to one another than were profiles from the same clone grown in the two different locations. We are studying whether this result is due to physiological differences in plants growing under different conditions, to differences between PCR reagent lots, to pathogen infestation, or to DNA sample contamination. In a study of 23 accessions representing 15 Vitis species and three species hybrids, we used six different SSR markers to identify individual genotypes. We were able to unambiguously distinguish all genotypes, except two that were identical at all six loci. Review of planting records revealed that the two genotypes were probably the same grape clone. SSR results were not congruent with known taxonomic relationships or geographic origin of genotypes. The SSR polymorphisms found in even this small subset of the Vitis collection in principle make possible the identification of more than 130 trillion different genotypes. This high level of polymorphism, however, makes our particular SSR loci of limited use for identification of species and for the determination of genetic relationships. Molecular genetic markers offer a powerful, efficient approach to assessing questions of identity, relationship, and diversity in germplasm collections, but markers need to be selected based on their suitability for the particular task.

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Diversity Among a Wide Asian Collection of Bitter Gourd Landraces and their Genetic Relationships with Commercial Hybrid Cultivars

Journal of the American Society for Horticultural Science ◽

10.21273/jashs03748-16 ◽

2016 ◽

Vol 141 (5) ◽

pp. 475-484 ◽

Cited By ~ 10

Author(s):

Narinder P.S. Dhillon ◽

Supannika Sanguansil ◽

Roland Schafleitner ◽

Yen-Wei Wang ◽

James D. McCreight

Keyword(s):

Genetic Relationships ◽

Geographic Origin ◽

Bitter Gourd ◽

Breeding Lines ◽

Ssr Loci ◽

Geographical Group ◽

Dark Green ◽

High Level ◽

Simple Sequence

We report here the genetic characterization of bitter gourd (Momordica charantia) based on polymorphisms of 50 simple sequence repeat (SSR) loci in 114 accessions that included landraces, breeding lines, and commercial open-pollinated and F1 hybrid cultivars widely grown in Asia. Neighbor-joining tree analysis revealed a high level of genetic variability in the collection. The 114 accessions formed three subpopulations represented by five clusters. Distribution of accessions across the five clusters reflected their geographic origin to a large extent. South Asian accessions originating from India, Bangladesh, and Pakistan were more closely related to each other than to any other geographical group. Likewise, southeast Asian accessions that originated from Cambodia, Vietnam, Indonesia, and Philippines were grouped together. Accessions that originated from Taiwan were genetically distinct and grouped separately. A landrace from Laos was genetically close to the accessions from Thailand and genetically distinct from the rest of the accessions. White-fruited genotypes were genetically distinct from green- and dark green–fruited genotypes. Low- and medium-bitter accessions were more similar to each other than to the high-bitter genotypes. Accessions with cylindrical fruit were genetically distinct from those with spindle or elongated fruit. Commercial cultivars in each cluster were closely related, which indicated a narrowing of the bitter gourd genetic base in Asia in response to market demands for uniformity and yield. Use of diverse germplasm resources in bitter gourd breeding will help in sustainable breeding and production.

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Arawak Languages

Linguistics ◽

10.1093/obo/9780199772810-0119 ◽

2013 ◽

Author(s):

Alexandra Y. Aikhenvald

Keyword(s):

South America ◽

Central America ◽

French Guiana ◽

Genetic Relationships ◽

Caribbean Coast ◽

The Past ◽

Rio Negro ◽

The Family ◽

Linguistic Argument ◽

The Caribbean

The Arawak family is the largest in South America, with about forty extant languages. Arawak languages are spoken in lowland Amazonia and beyond, covering French Guiana, Suriname, Guiana, Venezuela, Colombia, Peru, Brazil, and Bolivia, and formerly in Paraguay and Argentina. Wayuunaiki (or Guajiro), spoken in the region of the Guajiro peninsula in Venezuela and Colombia, is the largest language of the family. Garifuna is the only Arawak language spoken in Belize, Honduras, Nicaragua, and Guatemala in Central America. Groups of Arawak speakers must have migrated from the Caribbean coast to the Antilles a few hundred years before the European conquest. At least several dozen Arawak languages have become extinct since the European conquest. The highest number of recorded Arawak languages is centered in the region between the Rio Negro and the Orinoco. This is potentially a strong linguistic argument in favor of the Arawak protohome having been located there. The diversity of Arawak languages south of the Amazon in central Peru around the Rivers Purús and Madeira must have been greater in the past than it is now. The settlements of Arawak-speaking peoples south of the Amazon are believed to be of considerable antiquity. The Arawak family is also known as Maipure or Maipuran (based on Maipure, formerly spoken in Venezuela). The family got its name “Arawak” from the language known as Lokono Arawak, Arawak, or Lokono Dian (spoken in French Guiana, Guiana, Suriname, and Venezuela by about 2,500 people). The genetic unity of Arawak languages was first recognized by Father Gilij as early as 1783. The recognition of the family was based on a comparison of pronominal cross-referencing prefixes in Maipure, a now-extinct language from the Orinoco Valley, and in Mojo (or Ignaciano) from Bolivia. Problems still exist concerning internal genetic relationships within the family and possible genetic relationships with other groups. North Arawak languages appear to constitute a separate subgroup; so do Campa languages and Arawak languages of the Xingu region. The legacy of Arawak languages survives in many common English words, including hammock, hurricane, barbecue, iguana, maize, papaya, savanna, guava, and possibly tobacco. This article focuses only on the major and most significant works. There are at least an equal number of more minor studies on the languages of the Arawak family.

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Comparative Transcriptomic Analysis Reveals the Effects of Drought on the Biosynthesis of Methyleugenol in Asarum sieboldii Miq.

Biomolecules ◽

10.3390/biom11081233 ◽

2021 ◽

Vol 11 (8) ◽

pp. 1233

Author(s):

Fawang Liu ◽

Tahir Ali ◽

Zhong Liu

Keyword(s):

Drought Stress ◽

Metabolic Pathways ◽

Molecular Genetic ◽

Volatile Oil ◽

Perennial Herb ◽

Rna Seq ◽

The Family ◽

Genetic Mechanisms ◽

Effects Of Drought ◽

Comparative Transcriptomic Analysis

Asarum sieboldii Miq., a perennial herb in the family Aristolochiaceae, is widely used to treat colds, fever, headache and toothache in China. However, little is known about the drought-tolerance characteristics of A. sieboldii. In this study, to elucidate the molecular–genetic mechanisms of drought-stress tolerance of A. sieboldii, RNA-seq was conducted. In total, 53,344 unigenes were assembled, and 28,715 unigenes were annotated. A total of 6444 differential-expression unigenes (DEGs) were found, which were mainly enriched in phenylpropanoid, starch and sucrose metabolic pathways. Drought stress revealed significant up-regulation of the unigenes encoding PAL, C4H, HCT, C3H, CCR and IGS in the methyleugenol-biosynthesis pathway. Under the condition of maintaining drought for 15 days and 30 days, drought stress reduced the biosynthesis of volatile oil by 24% and 38%, respectively, while the production of key medicinal ingredients (such as methyl eugenol) was increased. These results provide valuable information about the diverse mechanisms of drought resistance in the A. sieboldii, and the changes in the expression of the genes involved in methyleugenol biosynthesis in response to drought stress.

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Molecular genetics of the parasitic protozoan Leishmania

Biochemistry and Cell Biology ◽

10.1139/o95-028 ◽

1995 ◽

Vol 73 (5-6) ◽

pp. 235-240 ◽

Cited By ~ 4

Author(s):

Alexander Kin-Choi Wong

Keyword(s):

Genetic Analysis ◽

Molecular Genetics ◽

Molecular Genetic ◽

Molecular Genetic Analysis ◽

Parasitic Protozoan ◽

The Past ◽

The Family ◽

Recent Developments ◽

Genetic Techniques ◽

Higher Eukaryotes

Leishmania is a member of the family Trypanosomatidae, which causes debilitating diseases in humans. Over the past several years, researchers have applied molecular genetic techniques to study extensively the biology of this parasitic protozoan. Many aspects of Leishmania biology are found to be unique when compared with the higher eukaryotes. This minireview highlights some recent developments in the molecular genetic analysis of this fascinating organism.Key words: Leishmania, protozoan, molecular genetics, disease.

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Molecular identification and genetic relationships among Alcea (Malvaceae) species by ISSR Markers: A high value medicinal plant

Caryologia ◽

10.36253/caryologia-1330 ◽

2021 ◽

Vol 74 (3) ◽

pp. 65-75

Author(s):

Jinxin Cheng ◽

Dingyu Hu ◽

Yaran Liu ◽

Zetian Zhang ◽

Majid Khayatnezhad

Keyword(s):

Genetic Relationships ◽

Morphological Characteristics ◽

Molecular Data ◽

Issr Markers ◽

Great Capacity ◽

Inter Simple Sequence Repeats ◽

Plant Recognition ◽

The Family ◽

Simple Sequence ◽

Issr Primers

Alcea L. is one of the largest genera of Malvaceae family with nearly 70 species worldwide mainly distributed in SW Asia. According to the latest revision of the family, it is represented by 34 species in the Flora of Iran, among them, 15 species are endemic. It is tough to accurate germplasm/ plant recognition by using morphological characteristics because of its propagation, growing and using. We conducted a molecular data analysis on these plant species due to their importance. We examined 156 plants from 14 species in 16 regions that were selected randomly for this investigation. It has been 119 polymorphic bands (94.33%) were resulted from 128 bands of 10 primers in amplification of genomic DNA. ISSR primers have a great capacity to detect polymorphic loci among Alcea species, as evidenced by the high average PIC and MI values found. The genetic similarity of 14 species was calculated and ranged between 0.635 to 0.990. Inter-Simple sequence repeats (ISSR) markers research revealed that Alcea tarica Pakravan & Ghahreman and Alcea kopetdaghensis lljin had the least similarity, while Alcea semnanica Pakravan and Alcea mazandaranica Pakravan & Ghahreman had the most. The current study attempts to answer three questions: 1) can ISSR markers identify Alcea species? 2) what is the genetic structure of these taxa in Iran? and 3) what is the inter-relationship between these taxa? The current study discovered that ISSR markers can be used to identify species.

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Genetic diversity computation in sesame genotypes using morphological traits and genic SSR markers

Indian Journal of Genetics and Plant Breeding (The) ◽

10.31742/ijgpb.78.3.12 ◽

2018 ◽

Vol 78 (3) ◽

Author(s):

Adil Iqbal ◽

Udayan Bhattacharyya ◽

Rumana Akhtar ◽

Tapash Dasgupta

Keyword(s):

Genetic Diversity ◽

Morphological Traits ◽

Polymorphic Information Content ◽

Molecular Genetic ◽

Antioxidant Properties ◽

Geographic Origin ◽

Oilseed Crop ◽

Genic Ssr ◽

Molecular Genetic Diversity ◽

Geographical Regions

Sesame (Sesamum indicum L.), the most ancient and important oilseed crop, with rich source of protein, highquality seed oil and many antioxidant properties is extensively grown in India. In the present study, 235 genic markers developed through data mining of expressed sequence tags from the NCBI database were used to assess the molecular genetic diversity at molecular level of 70 genotypes, belonging to different eco-geographical regions of the world. Of the developed markers, 35 (15%) showed polymorphism with a total of 151 alleles identified across genotypes. The alleles detected by the markers varied from 3 to 6 with an average of 4.36 along with 69% of average genetic diversity. The polymorphic information content (PIC) ranged from 0.36 to 0.82, with an average of 0.61. Neighbor-Joining (NJ) analysis revealed the five major groups, and clustering was independent to geographic origin. By using UPGMA, 70 genotypes at 70% similarity coefficient among the morphological traits were classified into four distinct clusters and the clustering pattern was different than based on molecular markers.

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NUMERICAL COEFFICIENT FOR ENDOMETRIAL CANCER INDIVIDUAL RISK EVALUATION IN POSTMENOPAUSAL WOMEN

Problems in oncology ◽

10.37469/0507-3758-2017-63-3-461-465 ◽

2017 ◽

Vol 63 (3) ◽

pp. 461-465

Author(s):

Lev Bershteyn ◽

Dmitriy Vasilev ◽

Tatyana Poroshina ◽

Igor Berlev

Keyword(s):

Breast Cancer ◽

Endometrial Cancer ◽

Risk Evaluation ◽

Tumor Response ◽

Molecular Genetic ◽

Response To Treatment ◽

Individual Risk ◽

The Past ◽

Genetic Landscape ◽

Numerical Coefficient

Increased frequency of endometrial cancer (EC) since the beginning of this century exceeds that of breast cancer and to a large extent can be attributed to dynamics of parameters, which characterize hormonal and metabolic status of ill women and molecular genetic landscape of transforming endometrium. During the past few years there are suggested several options for a personalized assessment of the risk of EC. The aim of this article is to propose and justify own version of this score with the idea of its further not only retrospective but also prospective testing both in relation to the risk of developing endometrial cancer as well as an additional marker helping to predict tumor response to treatment.

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An Overview on Phytochemical and Pharmacological Profile of Morus alba Linn.

Current Bioactive Compounds ◽

10.2174/1573407216666201228114004 ◽

2020 ◽

Vol 16 ◽

Author(s):

Arpita Paul ◽

Monami Rajiung ◽

Kamaruz Zaman ◽

Sushil Kumar Chaudhary ◽

Hans Raj Bhat ◽

...

Keyword(s):

Traditional Medicine ◽

Morus Alba ◽

Biologically Active ◽

Pharmacological Profile ◽

Pharmacological Activities ◽

Significant Information ◽

The Past ◽

Comprehensive Information ◽

The Family ◽

White Mulberry

Background: Morus alba Linn. commonly known as white mulberry, belongs to the family Moraceae, is a promising traditional medicine. In Asia, besides its use in the preparation of delicacies, every part of this plant is utilized in traditional medicine. Over the past decade, studies related to identification and isolation of biologically active compounds, with flavonoids as the major class of phytoconstituents, from this plant has been reported. These phytoconstituents are not only found to be beneficial for the maintenance of general health but also are associated with a range of potential pharmacological activities such as antioxidant, anti-inflammatory, anti-diabetic, anticancer, hepatoprotective, cardioprotective, neuroprotective to name a few. Objective: This review aims to provide upgraded and comprehensive information regarding the phytochemical, ethnomedicinal use and pharmacological profile of the plant Morus alba Linn. Method: The significant information has been collected through various database viz. PubMed, Scopus, Web of Science, Science Direct based on the recent findings, using different terms of Morus alba. Results: The outcome of the study suggests that Morus alba is a multifunctional plant numerous phytochemicals, and possess a range of pharmacological activities. Conclusion: The data assembled on Morus alba will be beneficial to trigger research in various fields of pharmaceutical and allied science to explore the medicinal importance of this unique plant.

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