scholarly journals Developing and Testing Molecular Markers in Cannabis sativa (Hemp) for Their Use in Variety and Dioecy Assessments

Plants ◽  
2021 ◽  
Vol 10 (10) ◽  
pp. 2174
Author(s):  
Marcello Borin ◽  
Fabio Palumbo ◽  
Alessandro Vannozzi ◽  
Francesco Scariolo ◽  
Gio Batta Sacilotto ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Sexual Behaviors ◽  
Cannabis Sativa ◽  
Genetic Research ◽  
Breeding Value ◽  
Germplasm Management ◽  
Genetic Groups ◽  
Legal Implications ◽  
Population Structure Analysis ◽  
Nuclear Ssr

Cannabis sativa (2n = 2x = 20) is a popular species belonging to the Cannabaceae family. Despite its use for medical, recreational, and industrial purposes as well as its long history, the genetic research on this species is in its infancy due to the legal implications and the prohibition campaigns. The recent legalization of Cannabis in many countries along with the use of genomics boosted the approaches aimed at marker-assisted selection, germplasm management, genetic discrimination, and authentication of cultivars. Nonetheless, the exploitation of molecular markers for the development of commercial varieties through marker-assisted breeding schemes is still rare. The present study aimed to develop an informative panel of simple sequence repeat markers to be used for the genotyping of high breeding value C. sativa lines. Starting from 41 nuclear SSR designated by in silico analyses, we selected 20 highly polymorphic and discriminant loci that were tested in 104 individuals belonging to 11 distinct hemp varieties. The selected markers were successful in accessing homozygosity, genetic uniformity, and genetic variation within and among varieties. Population structure analysis identified eight genetic groups, clustering individuals based on sexual behaviors (dioecious and monoecious) and geographical origins. Overall, this study provides important tools for the genetic characterization, authentication, conservation of biodiversity, genetic improvement and traceability of this increasingly important plant species.

scholarly journals Grapevine Diversity and Genetic Relationships in Northeast Portugal Old Vineyards

Plants ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 2755
Author(s):  
Diana Augusto ◽  
Javier Ibáñez ◽  
Ana Lúcia Pinto-Sintra ◽  
Virgílio Falco ◽  
Fernanda Leal ◽  
...  
Keyword(s):  
Population Structure ◽  
Molecular Markers ◽  
Genetic Relationships ◽  
Product Diversification ◽  
Wine Production ◽  
Genetic Groups ◽  
Nuclear Ssr ◽  
The Mean ◽  
Genetic Profiles ◽  
Protected Designations Of Origin

More than 100 grapevine varieties are registered as suitable for wine production in “Douro” and “Trás-os-Montes” Protected Designations of Origin regions; however, only a few are actually used for winemaking. The identification of varieties cultivated in past times can be an important step to take advantage of all the potential of these regions grape biodiversity. The conservation of the vanishing genetic resources boosts greater product diversification, and it can be considered strategic in the valorisation of these wine regions. Hence, one goal of the present study was to prospect and characterise, through molecular markers, 310 plants of 11 old vineyards that constitute a broad representation of the grape genetic patrimony of “Douro” and “Trás-os-Montes” wine regions; 280 samples, grouped into 52 distinct known varieties, were identified through comparison of their genetic profiles generated via 6 nuclear SSR and 43 informative SNP loci amplification; the remaining 30 samples, accounting for 13 different genotypes, did not match with any profile in the consulted databases and were considered as new genotypes. This study also aimed at evaluating the population structure among the 65 non-redundant genotypes identified, which were grouped into two ancestral genetic groups. The mean probability of identity values of 0.072 and 0.510 (for the 6 SSR and 226 SNP sets, respectively) were determined. Minor differences were observed between frequencies of chlorotypes A and D within the non-redundant genotypes studied. Twenty-seven pedigrees were confirmed and nine new trios were established. Ancestors of eight genotypes remain unknown.

scholarly journals Comprehensive genotyping of a Brazilian cassava (Manihot esculenta Crantz) germplasm bank: insights into diversification and domestication

2021 ◽  
Vol 134 (5) ◽  
pp. 1343-1362
Author(s):  
Alex C. Ogbonna ◽  
Luciano Rogerio Braatz de Andrade ◽  
Lukas A. Mueller ◽  
Eder Jorge de Oliveira ◽  
Guillaume J. Bauchet
Keyword(s):  
Population Genetics ◽  
Population Structure ◽  
Manihot Esculenta ◽  
Ex Situ ◽  
Germplasm Bank ◽  
Effective Population ◽  
Manihot Esculenta Crantz ◽  
Genetic Groups ◽  
Population Structure Analysis ◽  
Modern Breeding

Abstract Key message Brazilian cassava diversity was characterized through population genetics and clustering approaches, highlighting contrasted genetic groups and spatial genetic differentiation. Abstract Cassava (Manihot esculenta Crantz) is a major staple root crop of the tropics, originating from the Amazonian region. In this study, 3354 cassava landraces and modern breeding lines from the Embrapa Cassava Germplasm Bank (CGB) were characterized. All individuals were subjected to genotyping-by-sequencing (GBS), identifying 27,045 single-nucleotide polymorphisms (SNPs). Identity-by-state and population structure analyses revealed a unique set of 1536 individuals and 10 distinct genetic groups with heterogeneous linkage disequilibrium (LD). On this basis, a density of 1300–4700 SNP markers were selected for large-effect quantitative trait loci (QTL) detection. Identified genetic groups were further characterized for population genetics parameters including minor allele frequency (MAF), observed heterozygosity $$({H}_{o})$$ ( H o ) , effective population size estimate $$\widehat{{(N}_{e}}$$ ( N e ^ ) and polymorphism information content (PIC). Selection footprints and introgressions of M. glaziovii were detected. Spatial population structure analysis revealed five ancestral populations related to distinct Brazilian ecoregions. Estimation of historical relationships among identified populations suggests an early population split from Amazonian to Atlantic forest and Caatinga ecoregions and active gene flows. This study provides a thorough genetic characterization of ex situ germplasm resources from cassava’s center of origin, South America, with results shedding light on Brazilian cassava characteristics and its biogeographical landscape. These findings support and facilitate the use of genetic resources in modern breeding programs including implementation of association mapping and genomic selection strategies.

scholarly journals Molecular markers and their applications in cattle genetic research: A review

2014 ◽  
Vol 6 (2) ◽  
pp. 49-58 ◽  
Author(s):  
Umesh Singh ◽  
Rajib Deb ◽  
Rafeeque Rahman Alyethodi ◽  
Rani Alex ◽  
Sushil Kumar ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Genetic Research

scholarly journals Assembly of chromosome-scale and allele-aware autotetraploid genome of the Chinese alfalfa cultivar Zhongmu-4 and identification of SNP loci associated with 27 agronomic traits

2021 ◽  
Author(s):  
Ruicai Long ◽  
Fan Zhang ◽  
Zhiwu Zhang ◽  
Mingna Li ◽  
Lin Chen ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Single Molecule ◽  
Agronomic Traits ◽  
Association Studies ◽  
Genetic Research ◽  
Chromosome 1 ◽  
Genome Wide Association Studies ◽  
Forage Crops ◽  
Legume Crop ◽  
Population Structure Analysis

AbstractAlfalfa (Medicago sativaL.), the most valuable perennial legume crop, referred to as “Queen of the Forages” for its high nutritional value and yield production among forage crops. Comprehensive genomic information of germplasm resources from different ecological regions and modern breeding strategies, such as molecular-marker assisted breeding are of great importance to breed new alfalfa varieties with environmental resilience. Here, we report assembly of the genome sequence of Zhongmu-4 (ZM-4), one of the most planted cultivars in China, and identification of SNPs associated with alfalfa agronomic traits by Genome-wide Association Studies (GWAS). Sequence of 32 allelic chromosomes was assembled successfully by single molecule real time sequencing and Hi-C technique with ALLHiC algorithm. About 2.74 Gbp contigs, accounting for 88.39% of the estimated genome, were assembled with 2.56 Gbp contigs anchored to 32 pseudo-chromosomes. In comparison withM. truncatulaA17, distinctive inversion and translocation on chromosome 1, and between chromosome 4 and 8, respectively, were detected. Moreover, we conducted resequencing of 220 alfalfa accessions collected globally and performed GWAS analysis based on our assembled genome. Population structure analysis demonstrated that alfalfa has a complex genetic relationship among germplasm with different geographic origins. GWAS identified 101 SNPs associated with 27 out of 93 agronomic traits. The updated chromosome-scale and allele-aware genome sequence, coupled with the resequencing data of most global alfalfa germplasm, provides valuable information for alfalfa genetic research, and further analysis of major SNP loci will accelerate unravelling the molecular basis of important agronomic traits and facilitate genetic improvement of alfalfa.

scholarly journals The Development of New Species-Specific Molecular Markers Based on 5S rDNA in Elaeagnus L. Species

Plants ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 2713
Author(s):  
Oleg S. Alexandrov ◽  
Gennady I. Karlov
Keyword(s):  
Molecular Markers ◽  
New Species ◽  
Western Europe ◽  
Economic Value ◽  
Ornamental Plants ◽  
Far East ◽  
Genetic Research ◽  
5S Rdna ◽  
Identification Of Species ◽  
Species Specific

The Elaeagnus L. species are trees and bushes that mainly grow in temperate zones of Western Europe; Minor, Central, and Southeast Asia; the Far East; and North America. Some species are used as fruit or ornamental plants and have economic value. Problems with the identification of species in the Elaeagnus genus by molecular genetical methods arise in the study of populations, systematics, breeding, and other areas of plant science and practice. Recently, the polymorphism of 5S ribosomal DNA non-transcribed spacers (5S rDNA NTSs) in Elaeagnaceae Adans. has been described. The results were used in our study as a basis for development of new species-specific molecular markers for some members of the Elaeagnus genus. The author’s method was applied for finding regions that were potentially applicable for species-specific primer design. As a result, some species-specific molecular markers were developed for Elaeagnus angustifolia L., E. commutata Bernh., E. pungens Thunb., and E. multiflora Thunb. These markers were tested in a range of samples and showed the presence of amplified fragments in lanes of the marked species only. Samples of other species showed no amplifications. Thus, the developed markers may be useful for the species identification of the studied Elaeagnus plants in botanical, dendrological, and genetic research (especially in a leafless period of year), as well as in breeding and hybridization experiments.

scholarly journals Genetic Diversity and Population Structure of Traditional Chinese Herb “Chai-Hu” Resources Using Genome-Wide SNPs Through Genotyping-By-Sequencing

2022 ◽  
Author(s):  
Ming Jiang ◽  
Song Yan ◽  
Weichao Ren ◽  
Nannan Xing ◽  
Hongyuan Li ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Chinese Herb ◽  
Genetic Research ◽  
Principal Component ◽  
Genotyping By Sequencing ◽  
Intrapopulation Variation ◽  
Traditional Chinese Herb ◽  
High Quality Snps ◽  
Population Structure Analysis

Abstract Bupleurum (named “Chai-hu”) is an important traditional Chinese medicine resource in China. It has been widely used since ancient times and has antipyretic, analgesic and cholagogic functions, but there is little research on its genetic diversity. In this study, genotyping-by-sequencing (GBS) was used to detect SNP loci in 39 Bupleurum germplasm resources from different regions in China and analyse their genetic diversity. A total of 25.1 Gb of data was obtained by sequencing, with an average of 0.64 Gb per sample. After screening, 83898 high-quality SNPs were obtained. The results of genetic research were obtained by phylogenetic tree, principal component analysis and population structure analysis, and the 39 experimental materials were divided into three groups. The average observed heterozygosity and expected heterozygosity of Bupleurum populations were 0.24 and 0.17, respectively, indicating that Bupleurum populations from five different provinces had a low level of genetic diversity. Population nucleotide diversity analysis and analysis of molecular variance showed that the percentage of intrapopulation variation was 120.88%, while the percentage of interpopulation variation was only 2.46%. There was relative aggregation of Bupleurum samples with the same geographical origin, but the division of population structure was not completely correlated with sample origin. The results showed that the genetic diversity of the materials was low and that the genetic variation was narrow. This provides a good basis for the genetic breeding and protection of species diversity of Bupleurum.

scholarly journals Pengelolaan Plasma Nutfah Tanaman Terintegrasi dengan Program Pemuliaan

2016 ◽  
Vol 14 (2) ◽  
pp. 57 ◽  
Author(s):  
NFN Sumarno ◽  
Nani Zuraida
Keyword(s):  
Plant Breeding ◽  
Genetic Research ◽  
Germplasm Collection ◽  
Breeding Population ◽  
Breeding Program ◽  
Team Work ◽  
Germplasm Management ◽  
Plant Germplasm ◽  
Plant Breeding Program ◽  
Donor Gene

<p>Plant breeding, as an applied of plant genetics, is based and is supported by various subdisciplines of genetic sciences, includeing plant germplasm, classical genetics, molecular genetics, cytogenetics, gene-transformation techniques, etc. Linkage and team work system between plant germplasm management and plant breeding program is most required, since the success of plant breeding maybe obtained from the contribution of gene donor parents, derived from the germplasm management. Without the flow of genes from the germplasm collection, varieties produced by the plant breeder would suffer a narrow genetical based or a bottle-necking genetic based. Plant germplasm research is an integral part of the germplasm management, aimed to (1) evaluate the genetic variation of the germplasm collection, to be readily available for the breeding program and to be used for scientific publications, (2) tracing the origin of plant species, and (3) officially release a selected germplasm, containing new economic gene (s). The linkage between germplasm management and plant breeding research program could be facilitated through the following activities (1) identifying an elit germplasm for varietal release, (2) selection and stabilization of a promising germplasm accession for possible varietal releases, (3) use of germplasm accession as a gene donor parent to incorporate adaptive genes into improved variety, (4) use of germplasm accession for a specific donor gene, (5) use of germplasm to broaden the genetical base of varieties through an introgression and nobilization, (6) use of germplasm to improve the genetic value of the breeding population, and (7) to develop multiple crossess involving many parents to broaden the genetical base of the breeding population. Another important function of the germplasm management is to conserve accessions carrying genes which may be useful in the future, to anticipate the dynamic changing of biological and environmental stresses on crop. Germplasm management is considered successfully conducted when it is continously supplying donor gene parents to breeders for parental crosses on their breeding program, conversely, breeding program in considered successfully managed, when it uses the rich genetic variability available on the germplasm collection. Separating the organizational units among the breeding program, germplasm management and molecular genetic research, is only for enhancing the intensity of the research, but should not separate the linkage program of the research.</p><p> </p><p><strong>Abstrak</strong></p><p>Pemuliaan tanaman merupakan ilmu genetika terapan yang didukung oleh berbagai cabang ilmu kegenetikaan, termasuk plasma nutfah, genetika klasik, genetika molekuler, sitogenetika, dan genetika transformasi. Keterpaduan antara pengelolaan plasma nutfah dengan pemuliaan tanaman tidak dapat ditawar, karena keberhasilan pemuliaan sangat tergantung dari ketersediaan sumber gen yang disediakan oleh pengelola plasma nutfah. Tanpa kontribusi sumber gen dari pengelola plasma nutfah, hasil pemuliaan tanaman mengalami penyempitan kandungan genetik, atau terjadi gejala leher botol genetik. Penelitian plasma nutfah merupakan bagian integral dari pengelolaan materi plasma nutfah, bertujuan untuk (1) menggali kekayaan sifat genetik plasma nutfah guna penyediaan tetua persilangan dan bahan publikasi ilmiah, (2) menelusuri asal-usul spesies tanaman, (3) melepas secara resmi plasma nutfah sebagai sumber gen yang diakui kepemilikannya. Keterkaitan pengelolaan plasma nutfah dengan program pemuliaan dapat dilaksanakan melalui (1) pemanfaatan langsung aksesi plasma nutfah elit untuk dilepas sebagai varietas unggul, (2) pemurnian dan pemantapan populasi aksesi plasma nutfah sebagai calon varietas, (3) pemanfaatan aksesi plasma nutfah sebagai donor gen untuk rekombinasi gen-gen unggul adaptif, (4) plasma nutfah sebagai donor gen spesifik, (5) plasma nutfah sebagai bahan perluasan latar belakang genetik varietas melalui proses introgresi dan nobilisasi, (6) pemanfaatan plasma nutfah untuk perbaikan genetik populasi seleksi, dan (7) pembentukan populasi dasar yang mengandung keragaman genetik luas melalui persilangan banyak tetua. Fungsi pengelolaan plasma nutfah lainnya adalah melestarikan sumber daya genetik untuk kebutuhan gen di masa depan, agar dapat menyediakan gen-gen untuk mengantisipasi perubahan ras patogen dan tipe baru serangga hama yang bersifat dinamis, serta penyediaan gen guna mengatasi cekaman abiotik alamiah. Pengelolaan plasma nutfah dinilai berhasil apabila telah mampu menyediakan aksesi plasma nutfah sebagai sumber gen donor dalam program pemuliaan. Pemuliaan tanaman berhasil secara optimal apabila telah memanfaatkan keragaman genetik sifat yang diinginkan, yang tersedia dalam koleksi plasma nutfah. Keterpisahan kelembagaan antara unit kerja pengelolaan plasma nutfah dengan program pemuliaan tidak boleh membatasi keterpaduan program penelitian antara kedua cabang disiplin keilmuan tersebut.</p>

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