scholarly journals Spontaneous hybridization and introgression between walleye ( Sander vitreus ) and sauger ( Sander canadensis ) in two large reservoirs: Insights from genotyping by sequencing

2020 ◽  
Author(s):  
Carly F. Graham ◽  
Rebecca L. Eberts ◽  
Una Goncin ◽  
Christopher M. Somers
Keyword(s):  
Genotyping By Sequencing ◽  
Sander Vitreus ◽  
Hybridization And Introgression

Loss of SNP genetic diversity following population collapse in a recreational walleye (Sander vitreus) fishery

2018 ◽  
Vol 75 (10) ◽  
pp. 1644-1651 ◽  
Author(s):  
Brandon E. Allen ◽  
Ella Bowles ◽  
Matthew R.J. Morris ◽  
Sean M. Rogers
Keyword(s):  
Genetic Diversity ◽  
Genotyping By Sequencing ◽  
Sander Vitreus ◽  
Nucleotide Polymorphisms ◽  
Tissue Samples ◽  
Recreational Angling ◽  
Genotype By Sequencing ◽  
Genetic Clustering ◽  
Genetic Signatures ◽  
Population Collapses

Walleye (Sander vitreus) are in demand as a commercially and recreationally harvested freshwater fish in Canada. Managed populations may exhibit different phenotypic and genetic signatures from their natural counterparts. In Alberta, Canada, this fishery is recovering from population collapses attributed to intensive recreational angling. We hypothesized that historical population collapses would be associated with signatures of reduced genetic diversity. To address this question, we sampled six walleye lakes in northern Alberta, including historical tissue samples for one population, and used genotyping-by-sequencing to characterize 1081 single nucleotide polymorphisms (SNPs). Lakes were identified as unique genetic clusters except for two lakes that unexpectedly exhibited signs of genetic clustering. Using historical DNA samples, 428 homologous SNPs characterized in walleye between pre- and postpopulation collapse exhibited significant reductions in multiple estimates of genetic diversity. Collectively, our results illustrate that genotype-by-sequencing methods that integrate historical and contemporary samples in association with managed populations provide insight into the consequences of harvest pressure causing collapse.

scholarly journals Genetic Diversity of Purple Passion Fruit, Passiflora edulis f. edulis, Based on Single-Nucleotide Polymorphism Markers Discovered through Genotyping by Sequencing

Diversity ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 144
Author(s):  
Nohra Castillo Rodríguez ◽  
Xingbo Wu ◽  
María Isabel Chacón ◽  
Luz Marina Melgarejo ◽  
Matthew Wohlgemuth Blair
Keyword(s):  
Genetic Diversity ◽  
Single Nucleotide Polymorphism ◽  
Genotyping By Sequencing ◽  
Passion Fruit ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Passiflora Edulis ◽  
Tropical Fruit ◽  
Commercial Cultivars ◽  
Purple Passion Fruit

Orphan crops, which include many of the tropical fruit species used in the juice industry, lack genomic resources and breeding efforts. Typical of this dilemma is the lack of commercial cultivars of purple passion fruit, Passiflora edulis f. edulis, and of information on the genetic resources of its substantial semiwild gene pool. In this study, we develop single-nucleotide polymorphism (SNP) markers for the species and show that the genetic diversity of this fruit crop has been reduced because of selection for cultivated genotypes compared to the semiwild landraces in its center of diversity. A specific objective of the present study was to determine the genetic diversity of cultivars, genebank accession, and landraces through genotyping by sequencing (GBS) and to conduct molecular evaluation of a broad collection for the species P. edulis from a source country, Colombia. We included control genotypes of yellow passion fruit, P. edulis f. flavicarpa. The goal was to evaluate differences between fruit types and compare landraces and genebank accessions from in situ accessions collected from farmers. In total, 3820 SNPs were identified as informative for this diversity study. However, the majority distinguished yellow and purple passion fruit, with 966 SNPs useful in purple passion fruits alone. In the population structure analysis, purple passion fruits were very distinct from the yellow ones. The results for purple passion fruits alone showed reduced diversity for the commercial cultivars while highlighting the higher diversity found among landraces from wild or semi-wild conditions. These landraces had higher heterozygosity, polymorphism, and overall genetic diversity. The implications for genetics and breeding as well as evolution and ecology of purple passion fruits based on the extant landrace diversity are discussed with consideration of manual or pollinator-assisted hybridization of this species.

scholarly journals High resolution mapping and candidate gene identification of downy mildew race 16 resistance in spinach

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Gehendra Bhattarai ◽  
Wei Yang ◽  
Ainong Shi ◽  
Chunda Feng ◽  
Braham Dhillon ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Downy Mildew ◽  
Association Analysis ◽  
Spinacia Oleracea ◽  
Genotyping By Sequencing ◽  
Significant Snps ◽  
Snp Markers ◽  
Resistance Locus ◽  
Downy Mildew Resistance ◽  
Mildew Resistance

Abstract Background Downy mildew, the most devastating disease of spinach (Spinacia oleracea L.), is caused by the oomycete Peronospora effusa [=P. farinosa f. sp. spinaciae]. The P. effusa shows race specificities to the resistant host and comprises 19 reported races and many novel isolates. Sixteen new P. effusa races were identified during the past three decades, and the new pathogen races are continually overcoming the genetic resistances used in commercial cultivars. A spinach breeding population derived from the cross between cultivars Whale and Lazio was inoculated with P. effusa race 16 in an environment-controlled facility; disease response was recorded and genotyped using genotyping by sequencing (GBS). The main objective of this study was to identify resistance-associated single nucleotide polymorphism (SNP) markers from the cultivar Whale against the P. effusa race 16. Results Association analysis conducted using GBS markers identified six significant SNPs (S3_658,306, S3_692697, S3_1050601, S3_1227787, S3_1227802, S3_1231197). The downy mildew resistance locus from cultivar Whale was mapped to a 0.57 Mb region on chromosome 3, including four disease resistance candidate genes (Spo12736, Spo12784, Spo12908, and Spo12821) within 2.69–11.28 Kb of the peak SNP. Conclusions Genomewide association analysis approach was used to map the P. effusa race 16 resistance loci and identify associated SNP markers and the candidate genes. The results from this study could be valuable in understanding the genetic basis of downy mildew resistance, and the SNP marker will be useful in spinach breeding to select resistant lines.

scholarly journals Fine-tuning the performance of ddRAD-seq in the peach genome

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Maximiliano Martín Aballay ◽  
Natalia Cristina Aguirre ◽  
Carla Valeria Filippi ◽  
Gabriel Hugo Valentini ◽  
Gerardo Sánchez
Keyword(s):  
Germplasm Collection ◽  
In Silico Analysis ◽  
Genotyping By Sequencing ◽  
Fine Tuning ◽  
The Novel ◽  
Peach Genome ◽  
Genome Complexity ◽  
Next Generation Sequencing Ngs ◽  
Sample Set ◽  
Silico Analysis

AbstractThe advance of Next Generation Sequencing (NGS) technologies allows high-throughput genotyping at a reasonable cost, although, in the case of peach, this technology has been scarcely developed. To date, only a standard Genotyping by Sequencing approach (GBS), based on a single restriction with ApeKI to reduce genome complexity, has been applied in peach. In this work, we assessed the performance of the double-digest RADseq approach (ddRADseq), by testing 6 double restrictions with the restriction profile generated with ApeKI. The enzyme pair PstI/MboI retained the highest number of loci in concordance with the in silico analysis. Under this condition, the analysis of a diverse germplasm collection (191 peach genotypes) yielded 200,759,000 paired-end (2 × 250 bp) reads that allowed the identification of 113,411 SNP, 13,661 InDel and 2133 SSR. We take advantage of a wide sample set to describe technical scope of the platform. The novel platform presented here represents a useful tool for genomic-based breeding for peach.

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