scholarly journals Genetic Differentiation of Verticillium dahliae Populations Recovered from Symptomatic and Asymptomatic Hosts

2020 ◽  
pp. PHYTO-06-20-023
Author(s):  
Laura S. Bautista-Jalón ◽  
Omer Frenkel ◽  
Leah Tsror (Lahkim) ◽  
Glenna M. Malcolm ◽  
Beth K. Gugino ◽  
...  
Keyword(s):  
Genetic Differentiation ◽  
Verticillium Dahliae ◽  
Geographic Origin ◽  
Genotyping By Sequencing ◽  
Nucleotide Polymorphisms ◽  
Weed Species ◽  
Single Nucleotide ◽  
Vegetative Compatibility Groups ◽  
Main Research ◽  
Research Goal

Verticillium dahliae is a soilborne fungal pathogen affecting many economically important crops that can also infect weeds and rotational crops with no apparent disease symptoms. The main research goal was to test the hypothesis that V. dahliae populations recovered from asymptomatic rotational crops and weed species are evolutionarily and genetically distinct from symptomatic hosts. We collected V. dahliae isolates from symptomatic and asymptomatic hosts growing in fields with histories of Verticillium wilt of potato in Israel and Pennsylvania (United States), and used genotyping-by-sequencing to analyze the evolutionary history and genetic differentiation between populations of different hosts. A phylogeny inferred from 26,934 single-nucleotide polymorphisms (SNPs) in 126 V. dahliae isolates displayed a highly clonal structure correlated with vegetative compatibility groups, and isolates grouped in lineages 2A, 2B824, 4A, and 4B, with 77% of the isolates in lineage 4B. The lineages identified in this study were differentiated by host of origin; we found 2A, 2B824, and 4A only in symptomatic hosts but isolates from asymptomatic hosts (weeds, oat, and sorghum) grouped exclusively within lineage 4B, and were genetically indistinguishable from 4B isolates sampled from symptomatic hosts (potato, eggplant, and avocado). Using coalescent analysis of 158 SNPs of lineage 4B, we inferred a genealogy with clades that correlated with geographic origin. In contrast, isolates from asymptomatic and symptomatic hosts shared some of the same haplotypes and were not differentiated. We conclude that asymptomatic weeds and rotational hosts may be potential reservoirs for V. dahliae populations of lineage 4B, which are pathogenic to many cultivated hosts.

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 Population Genetics of Verticillium dahliae in Iran Based on Microsatellite and Single Nucleotide Polymorphism Markers

2018 ◽  
Vol 108 (6) ◽  
pp. 780-788 ◽  
Author(s):  
Vahideh Rafiei ◽  
Ziaeddin Banihashemi ◽  
Laura S. Bautista-Jalon ◽  
Maria del Mar Jiménez-Gasco ◽  
B. Gillian Turgeon ◽  
...  
Keyword(s):  
Mating Type ◽  
Verticillium Wilt ◽  
Verticillium Dahliae ◽  
Pathogenic Fungus ◽  
Geographic Origin ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
History Of ◽  
Northwestern Iran ◽  
Prunus Spp

Verticillium dahliae is a plant pathogenic fungus that reproduces asexually and its population structure is highly clonal. In the present study, 78 V. dahliae isolates from Iran were genotyped for mating type, single nucleotide polymorphisms (SNPs), and microsatellites to assign them to clonal lineages and to determine population genetic structure in Iran. The mating type of all isolates was MAT1-2. Based on neighbor-joining analysis and minimum spanning networks constructed from SNPs and microsatellite genotypes, respectively, all but four isolates were assigned to lineage 2B824; four isolates were assigned to lineage 4B. The inferred coalescent genealogy of isolates in lineage 2B824 showed a clear divergence into two clades that corresponded to geographic origin and host. Haplotypes of cotton and pistachio isolates sampled from central Iran were in one clade, and those of isolates from Prunus spp. sampled from northwestern Iran were in the other. The strong divergence in haplotypes between the two clades suggests that there were at least two separate introductions of lineage 2B824 to different parts of Iran. Given the history of cotton and pistachio cultivation and Verticillium wilt in Iran, these results are consistent with the hypothesis that cotton was historically a likely source inoculum causing Verticillium wilt in pistachio.

scholarly journals Single Nucleotide Polymorphism Discovery and Genetic Differentiation Analysis of Geese Bred in Poland, Using Genotyping-by-Sequencing (GBS)

Genes ◽  
2021 ◽  
Vol 12 (7) ◽  
pp. 1074
Author(s):  
Joanna Grzegorczyk ◽  
Artur Gurgul ◽  
Maria Oczkowicz ◽  
Tomasz Szmatoła ◽  
Agnieszka Fornal ◽  
...  
Keyword(s):  
Genotyping By Sequencing ◽  
Read Depth ◽  
Model Organisms ◽  
Single Nucleotide Polymorphism Discovery ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Polymorphism Discovery ◽  
Genome Wide ◽  
Plumage Development ◽  
Edar Gene

Poland is the largest European producer of goose, while goose breeding has become an essential and still increasing branch of the poultry industry. The most frequently bred goose is the White Kołuda® breed, constituting 95% of the country’s population, whereas geese of regional varieties are bred in smaller, conservation flocks. However, a goose’s genetic diversity is inaccurately explored, mainly because the advantages of the most commonly used tools are strongly limited in non-model organisms. One of the most accurate used markers for population genetics is single nucleotide polymorphisms (SNP). A highly efficient strategy for genome-wide SNP detection is genotyping-by-sequencing (GBS), which has been already widely applied in many organisms. This study attempts to use GBS in 12 conservative goose breeds and the White Kołuda® breed maintained in Poland. The GBS method allowed for the detection of 3833 common raw SNPs. Nevertheless, after filtering for read depth and alleles characters, we obtained the final markers panel used for a differentiation analysis that comprised 791 SNPs. These variants were located within 11 different genes, and one of the most diversified variants was associated with the EDAR gene, which is especially interesting as it participates in the plumage development, which plays a crucial role in goose breeding.

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 Differences in mate pairings of hatchery and natural origin coho salmon inferred from offspring genotypes

2021 ◽  
Author(s):  
H L Auld ◽  
D P Jacobson ◽  
A C Rhodes ◽  
M A Banks
Keyword(s):  
Mate Choice ◽  
Captive Breeding ◽  
Population Genomics ◽  
Coho Salmon ◽  
Genotyping By Sequencing ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Natural Origin ◽  
In Captivity ◽  
Genetic Level

Abstract Captive breeding can affect how sexual selection acts on subsequent generations. One context where this is important is in fish hatcheries. In many salmon hatcheries, spawning is controlled artificially and offspring are reared in captivity before release into the wild. While previous studies have suggested that hatchery and natural origin fish may make different mate choice decisions, it remains to be determined how hatchery fish may be making different mate choice decisions compared to natural origin fish at a genetic level. Using genotyping-by-sequencing (GBS), we identify single nucleotide polymorphisms (SNPs) associated with variation in mate pairings from a natural context involving hatchery and natural origin coho salmon (Oncorhynchus kisutch). In both natural origin and hatchery mate pairs, we observed more SNPs with negative assortment, than positive assortment. However, only 3% of the negative assortment SNPs were shared between the two mating groups, and 1% of the positive assortment SNPs were shared between the two mating groups, indicating divergence in mating cues between wild and hatchery raised salmon. These findings shed light on mate choice in general and may have important implications in the conservation management of species as well as for improving other captive breeding scenarios. There remains much to discover about mate choice in salmon and research described here reflects our intent to test the potential of ongoing advances in population genomics to develop new hatchery practices that may improve the performance of hatchery offspring, lessening the differences and thus potential impacts upon wild stocks.

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.

Ancient introgression between distantly related white oaks (Quercus sect Quercus) shows evidence of climate-associated asymmetric gene exchange

2021 ◽  
Author(s):  
Scott T O’Donnell ◽  
Sorel T Fitz-Gibbon ◽  
Victoria L Sork
Keyword(s):  
Gene Flow ◽  
Genotyping By Sequencing ◽  
Nucleotide Polymorphisms ◽  
Sequencing Data ◽  
Single Nucleotide ◽  
Scrub Oak ◽  
Population Genetic Inference ◽  
Genetic Inference ◽  
California Floristic Province ◽  
Python Package

Abstract Ancient introgression can be an important source of genetic variation that shapes the evolution and diversification of many taxa. Here, we estimate the timing, direction and extent of gene flow between two distantly related oak species in the same section (Quercus sect. Quercus). We estimated these demographic events using genotyping by sequencing data (GBS), which generated 25,702 single nucleotide polymorphisms (SNPs) for 24 individuals of California scrub oak (Quercus berberidifolia) and 23 individuals of Engelmann oak (Q. engelmannii). We tested several scenarios involving gene flow between these species using the diffusion approximation-based population genetic inference framework and model-testing approach of the Python package DaDi. We found that the most likely demographic scenario includes a bottleneck in Q. engelmannii that coincides with asymmetric gene flow from Q. berberidifolia into Q. engelmannii. Given that the timing of this gene flow coincides with the advent of a Mediterranean-type climate in the California Floristic Province, we propose that changing precipitation patterns and seasonality may have favored the introgression of climate-associated genes from the endemic into the non-endemic California oak.

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

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