scholarly journals Genetic Diversity Assessed by Genotyping by Sequencing (GBS) in Watermelon Germplasm

Genes ◽  
2019 ◽  
Vol 10 (10) ◽  
pp. 822 ◽  
Author(s):  
Kyung Jun Lee ◽  
Jung-Ro Lee ◽  
Raveendar Sebastin ◽  
Myoung-Jae Shin ◽  
Seong-Hoon Kim ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Discriminant Analysis ◽  
Single Nucleotide Polymorphisms ◽  
Genetic Differentiation ◽  
Principal Components ◽  
Genotyping By Sequencing ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Breeding Programs

Watermelon is an economically important vegetable fruit worldwide. The objective of this study was to conduct a genetic diversity of 68 watermelon accessions using single nucleotide polymorphisms (SNPs). Genotyping by sequencing (GBS) was used to discover SNPs and assess genetic diversity and population structure using STRUCTURE and discriminant analysis of principal components (DAPC) in watermelon accessions. Two groups of watermelons were used: 1) highly utilized 41 watermelon accessions at the National Agrobiodiversity Center (NAC) at the Rural Development Administration in South Korea; and 2) 27 Korean commercial watermelons. Results revealed the presence of four clusters within the populations differentiated principally based on seed companies. In addition, there was higher genetic differentiation among commercial watermelons of each company. It is hypothesized that the results obtained from this study would contribute towards the expansion of this crop as well as providing data about genetic diversity, which would be useful for the preservation of genetic resources or for future breeding programs.

scholarly journals Genetic characterization of buckwheat accessions through genome-wide allele frequency fingerprints / Genetska karakterizacija vzorcev ajde z odtisi frekvence alelov v genomu

2020 ◽  
Vol 61 (1) ◽  
pp. 17-23
Author(s):  
Michelle M. Nay ◽  
Stephen L. Byrne ◽  
Eduardo A. Pérez ◽  
Achim Walter ◽  
Bruno Studer
Keyword(s):  
Genetic Diversity ◽  
Single Nucleotide Polymorphisms ◽  
Allele Frequency ◽  
Genotyping By Sequencing ◽  
Allele Frequencies ◽  
Fagopyrum Esculentum ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Fagopyrum Esculentum Moench

Genomics-assisted breeding of buckwheat (Fagopyrum esculentum Moench) depends on robust genotyping methods. Genotyping by sequencing (GBS) has evolved as a flexible and cost-effective technique frequently used in plant breeding. Several GBS pipelines are available to genetically characterize single genotypes but these are not able to represent the genetic diversity of buckwheat accessions that are maintained as genetically heterogeneous, open-pollinating populations. Here we report the development of a GBS pipeline which, rather than reporting the state of bi-allelic single nucleotide polymorphisms (SNPs), resolves allele frequencies within populations on a genome-wide scale. These genome-wide allele frequency fingerprints (GWAFFs) from 100 pooled individual plants per accession were found to be highly reproducible and revealed the genetic similarity of 20 different buckwheat accessions analysed in our study. The GWAFFs cannot only be used as an efficient tool to precisely describe buckwheat breeding material, they also offer new opportunities to investigate the genetic diversity between different buckwheat accessions and establish variant databases for key material. Furthermore, GWAFFs provide the opportunity to associate allele frequencies to phenotypic traits and quality parameters that are most reliably described on population level. This is the key to practically implement powerful genomics-assisted breeding concepts such as marker-assisted selection and genomic selection in future breeding schemes of allogamous buckwheat. Key words: Buckwheat (Fagopyrum esculentum Moench), genotyping by sequencing (GBS), population genomics, genome-wide allele frequency fingerprints (GWAFFs)   Izvleček Genomsko podprto žlahtnjenje ajde (Fagopyrum esculentum Moench) je odvisno od robustnih metod genotipiziranja. Genotipiziranje s spremljanjem sekvenc (genotyping by sequencing, GBS) se je razvilo kot fleksibilna in razmeroma poceni metoda, ki se jo uporablja pri žlahtnjenju rastlin. Uporabnih je več virov GBS za genetsko karakterizacijo posamičnih genotipov, toda te metode niso primerne za predstavitev genetske raznolikosti vzorcev ajde, ki jih vzdržujemo v heterozigotni obliki, kar velja za odprto oplodne populacije. Tu poročamo o razvoju GBS metode, ki, namesto prikazovanja bi-alelnega polimorfizma posameznih nukleotidov (single nucleotide polymorphisms, SNPs), pokaže frekvence alelov v populaciji na nivoju genoma. Ta prikaz frekvence alelov na nivoju genoma (genome-wide allele frequency fingerprints, GWAFFs) z združenimi sto posameznimi rastlinami vsakega vzorca se je pokazal kot visoko ponovljiv in je prikazal genetsko podobnost 20 različnih vzorcev ajde, ki smo jih analizirali v naši raziskavi. Metoda GWAFFs ni uporabna samo kot učinkovito orodje za natančen opis materiala za žlahtnjenje ajde, ponuja tudi možnosti raziskave  genetskih razlik med različnimi vzorci ajde in omogoča zbirke podatkov. Nadalje, metoda GWAFFs omogoča povezovanje frekvenc alelov s fenotipskimi lastnostmi in kvalitativnih parametrov, ki so najbolj zanesljivo opisani na nivoju populacij. To je ključ za praktično uporabo z genomiko podprtega žlahtnjenja, kot je z genskimi markerji podprta selekcija in genomska selekcija z GWAFFs. Ključne besede: ajda (Fagopyrum esculentum Moench), genotipizacija s sekvenciranjem (GBS), populacijska genomika, GWAFFs

scholarly journals Classification of cannabis strains in the Canadian market with discriminant analysis of principal components using genome-wide single nucleotide polymorphisms

PLoS ONE ◽  
2021 ◽  
Vol 16 (6) ◽  
pp. e0253387
Author(s):  
Dan Jin ◽  
Philippe Henry ◽  
Jacqueline Shan ◽  
Jie Chen
Keyword(s):  
Discriminant Analysis ◽  
Single Nucleotide Polymorphisms ◽  
Principal Components ◽  
Large Scale ◽  
Therapeutic Potential ◽  
Morphological Characteristics ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genome Wide

The cannabis community typically uses the terms “Sativa” and “Indica” to characterize drug strains with high tetrahydrocannabinol (THC) levels. Due to large scale, extensive, and unrecorded hybridization in the past 40 years, this vernacular naming convention has become unreliable and inadequate for identifying or selecting strains for clinical research and medicinal production. Additionally, cannabidiol (CBD) dominant strains and balanced strains (or intermediate strains, which have intermediate levels of THC and CBD), are not included in the current classification studies despite the increasing research interest in the therapeutic potential of CBD. This paper is the first in a series of studies proposing that a new classification system be established based on genome-wide variation and supplemented by data on secondary metabolites and morphological characteristics. This study performed a whole-genome sequencing of 23 cannabis strains marketed in Canada, aligned sequences to a reference genome, and, after filtering for minor allele frequency of 10%, identified 137,858 single nucleotide polymorphisms (SNPs). Discriminant analysis of principal components (DAPC) was applied to these SNPs and further identified 344 structural SNPs, which classified individual strains into five chemotype-aligned groups: one CBD dominant, one balanced, and three THC dominant clusters. These structural SNPs were all multiallelic and were predominantly tri-allelic (339/344). The largest portion of these SNPs (37%) occurred on the same chromosome containing genes for CBD acid synthases (CBDAS) and THC acid synthases (THCAS). The remainder (63%) were located on the other nine chromosomes. These results showed that the genetic differences between modern cannabis strains were at a whole-genome level and not limited to THC or CBD production. These SNPs contained enough genetic variation for classifying individual strains into corresponding chemotypes. In an effort to elucidate the confused genetic backgrounds of commercially available cannabis strains, this classification attempt investigated the utility of DAPC for classifying modern cannabis strains and for identifying structural SNPs.

Genome-Wide Single Nucleotide Polymorphisms are Robust in Resolving Fine-Scale Population Genetic Structure of the Small Brown Planthopper, Laodelphax striatellus (Fallén) (Hemiptera: Delphacidae)

2019 ◽  
Vol 112 (5) ◽  
pp. 2362-2368
Author(s):  
Yan Liu ◽  
Lei Chen ◽  
Xing-Zhi Duan ◽  
Dian-Shu Zhao ◽  
Jing-Tao Sun ◽  
...  
Keyword(s):  
Population Structure ◽  
Discriminant Analysis ◽  
Genetic Structure ◽  
Population Genetic ◽  
Brown Planthopper ◽  
Fine Scale ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Small Brown Planthopper ◽  
Scale Population

Abstract Deciphering genetic structure and inferring migration routes of insects with high migratory ability have been challenging, due to weak genetic differentiation and limited resolution offered by traditional genotyping methods. Here, we tested the ability of double digest restriction-site associated DNA sequencing (ddRADseq)-based single nucleotide polymorphisms (SNPs) in revealing the population structure relative to 13 microsatellite markers by using four small brown planthopper populations as subjects. Using ddRADseq, we identified 230,000 RAD loci and 5,535 SNP sites, which were present in at least 80% of individuals across the four populations with a minimum sequencing depth of 10. Our results show that this large SNP panel is more powerful than traditional microsatellite markers in revealing fine-scale population structure among the small brown planthopper populations. In contrast to the mixed population structure suggested by microsatellites, discriminant analysis of principal components (DAPC) of the SNP dataset clearly separated the individuals into four geographic populations. Our results also suggest the DAPC analysis is more powerful than the principal component analysis (PCA) in resolving population genetic structure of high migratory taxa, probably due to the advantages of DAPC in using more genetic variation and the discriminant analysis function. Together, these results point to ddRADseq being a promising approach for population genetic and migration studies of small brown planthopper.

scholarly journals Genotyping-by-Sequencing of Gossypium hirsutum Races and Cultivars Uncovers Novel Patterns of Genetic Relationships and Domestication Footprints

2019 ◽  
Vol 15 ◽  
pp. 117693431988994
Author(s):  
Shulin Zhang ◽  
Yaling Cai ◽  
Jinggong Guo ◽  
Kun Li ◽  
Renhai Peng ◽  
...  
Keyword(s):  
Gossypium Hirsutum ◽  
Genetic Relationships ◽  
Phylogenetic Analyses ◽  
Genotyping By Sequencing ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Breeding Programs ◽  
Association Analyses ◽  
Genome Wide ◽  
Candidate Gene Locus

Determining the genetic rearrangement and domestication footprints in Gossypium hirsutum cultivars and primitive race genotypes are essential for effective gene conservation efforts and the development of advanced breeding molecular markers for marker-assisted breeding. In this study, 94 accessions representing the 7 primitive races of G hirsutum, along with 9 G hirsutum and 12 Gossypium barbadense cultivated accessions were evaluated. The genotyping-by-sequencing (GBS) approach was employed and 146 558 single nucleotide polymorphisms (SNP) were generated. Distinct SNP signatures were identified through the combination of selection scans and association analyses. Phylogenetic analyses were also conducted, and we concluded that the Latifolium, Richmondi, and Marie-Galante race accessions were more genetically related to the G hirsutum cultivars and tend to cluster together. Fifty-four outlier SNP loci were identified by selection-scan analysis, and 3 SNPs were located in genes related to the processes of plant responding to stress conditions and confirmed through further genome-wide signals of marker-phenotype association analysis, which indicate a clear selection signature for such trait. These results identified useful candidate gene locus for cotton breeding programs.

scholarly journals DNA Variation in a Diversity Panel of Tomato Genetic Resources

2021 ◽  
pp. 1-7
Author(s):  
Joanne A. Labate
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Crop Improvement ◽  
Genotyping By Sequencing ◽  
Genetic Distances ◽  
Nucleotide Polymorphisms ◽  
Fresh Market ◽  
Single Nucleotide ◽  
Dna Variation ◽  
Diversity Panel ◽  
Home Gardening

A diversity panel of 190 National Plant Germplasm System (NPGS) tomato (Solanum lycopersicum) accessions was genotyped using genotyping by sequencing. These originated from 31 countries and included fresh market, ornamental, processing, breeders’ lines, landraces, and home gardening types, as well as six different accessions of the economically valuable cultivar San Marzano. Most of the 34,531 discovered single nucleotide polymorphisms were rare and therefore excluded from downstream analyses. A total of 3713 high-quality, mapped single nucleotide polymorphisms that were present in at least two accessions were used to estimate genetic distances and population structure. Results showed that these phenotypically and geographically diverse NPGS tomato accessions were closely related to each other. However, a subset of divergent genotypes was identified that included landraces from primary centers of diversity (South America), secondary centers of diversity (Italy, Taiwan, and France), and genotypes that originated from wild species through 20th century breeding for disease resistance (e.g., ‘VFNT Cherry’). Extreme variant accessions produce cultivated fruit traits in a background that contains many wild or primitive genes. These accessions are promising sources of novel genes for continued crop improvement.

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