Genotyping-by-sequencing data of 272 crested wheatgrass ( Agropyron cristatum ) genotypes

Molecular characterization of unsequenced plant species with complex genomes is now possible by genotyping-by-sequencing (GBS) using recent next generation sequencing technologies. This study represents the first use of GBS application to sample genome-wide variants of crested wheatgrass [Agropyron cristatum (L.) Gaertn.] and assess the genetic diversity present in 192 genotypes from 12 tetraploid lines. Bioinformatic analysis identified 45,507 single nucleotide polymorphism (SNP) markers in this outcrossing grass species. The model-based Bayesian analysis revealed four major clusters of the samples assayed. The diversity analysis revealed 15.8% of SNP variation residing among the 12 lines, and 12.1% SNP variation present among four genetic clusters identified by the Bayesian analysis. The principal coordinates analysis and dendrogram were able to distinguish four lines of Asian origin from Canadian cultivars and breeding lines. These results serve as a valuable resource for understanding genetic variability, and will aid in the genetic improvement of this outcrossing polyploid grass species for forage production. These findings illustrate the potential of GBS application in the characterization of non-model polyploid plants with complex genomes.

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Parentage Analysis in Giant Grouper (Epinephelus lanceolatus) Using Microsatellite and SNP Markers from Genotyping-by-Sequencing Data

Genes ◽

10.3390/genes12071042 ◽

2021 ◽

Vol 12 (7) ◽

pp. 1042

Author(s):

Zhuoying Weng ◽

Yang Yang ◽

Xi Wang ◽

Lina Wu ◽

Sijie Hua ◽

...

Keyword(s):

Fishery Management ◽

Genotyping By Sequencing ◽

Parentage Analysis ◽

Snp Markers ◽

Individual Identification ◽

Pedigree Information ◽

Nucleotide Polymorphisms ◽

Sequencing Data ◽

Polymorphic Snps ◽

Mixed Family

Pedigree information is necessary for the maintenance of diversity for wild and captive populations. Accurate pedigree is determined by molecular marker-based parentage analysis, which may be influenced by the polymorphism and number of markers, integrity of samples, relatedness of parents, or different analysis programs. Here, we described the first development of 208 single nucleotide polymorphisms (SNPs) and 11 microsatellites for giant grouper (Epinephelus lanceolatus) taking advantage of Genotyping-by-sequencing (GBS), and compared the power of SNPs and microsatellites for parentage and relatedness analysis, based on a mixed family composed of 4 candidate females, 4 candidate males and 289 offspring. CERVUS, PAPA and COLONY were used for mutually verification. We found that SNPs had a better potential for relatedness estimation, exclusion of non-parentage and individual identification than microsatellites, and > 98% accuracy of parentage assignment could be achieved by 100 polymorphic SNPs (MAF cut-off < 0.4) or 10 polymorphic microsatellites (mean Ho = 0.821, mean PIC = 0.651). This study provides a reference for the development of molecular markers for parentage analysis taking advantage of next-generation sequencing, and contributes to the molecular breeding, fishery management and population conservation.

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Cytology of 2n Pollen Formation in Diploid Crested Wheatgrass, Agropyron cristatum

Crop Science ◽

10.2135/cropsci1992.0011183x003200060011x ◽

1992 ◽

Vol 32 (6) ◽

pp. 1361-1365 ◽

Cited By ~ 7

Author(s):

Ian M. Ray ◽

Mary K. Tokach

Keyword(s):

Agropyron Cristatum ◽

2N Pollen ◽

Crested Wheatgrass ◽

Pollen Formation

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AFLAP: Assembly-Free Linkage Analysis Pipeline using k-mers from whole genome sequencing data

10.1101/2020.09.14.296525 ◽

2020 ◽

Author(s):

Kyle Fletcher ◽

Lin Zhang ◽

Juliana Gil ◽

Rongkui Han ◽

Keri Cavanaugh ◽

...

Keyword(s):

Linkage Analysis ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Genetic Map ◽

Genotyping By Sequencing ◽

Genetic Maps ◽

Whole Genome ◽

Sequencing Data ◽

Analysis Pipeline ◽

Genome Assemblies

AbstractBackgroundGenetic maps are an important resource for validation of genome assemblies, trait discovery, and breeding. Next generation sequencing has enabled production of high-density genetic maps constructed with 10,000s of markers. Most current approaches require a genome assembly to identify markers. Our Assembly Free Linkage Analysis Pipeline (AFLAP) removes this requirement by using uniquely segregating k-mers as markers to rapidly construct a genotype table and perform subsequent linkage analysis. This avoids potential biases including preferential read alignment and variant calling.ResultsThe performance of AFLAP was determined in simulations and contrasted to a conventional workflow. We tested AFLAP using 100 F2 individuals of Arabidopsis thaliana, sequenced to low coverage. Genetic maps generated using k-mers contained over 130,000 markers that were concordant with the genomic assembly. The utility of AFLAP was then demonstrated by generating an accurate genetic map using genotyping-by-sequencing data of 235 recombinant inbred lines of Lactuca spp. AFLAP was then applied to 83 F1 individuals of the oomycete Bremia lactucae, sequenced to >5x coverage. The genetic map contained over 90,000 markers ordered in 19 large linkage groups. This genetic map was used to fragment, order, orient, and scaffold the genome, resulting in a much-improved reference assembly.ConclusionsAFLAP can be used to generate high density linkage maps and improve genome assemblies of any organism when a mapping population is available using whole genome sequencing or genotyping-by-sequencing data. Genetic maps produced for B. lactucae were accurately aligned to the genome and guided significant improvements of the reference assembly.

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Fructan biosynthesis and fructosyltransferase evolution: Expression of the 6-SFT (sucrose : fructan 6-fructosyltransferase) gene in crested wheatgrass (Agropyron cristatum)

Journal of Plant Physiology ◽

10.1078/0176-1617-00241 ◽

2001 ◽

Vol 158 (9) ◽

pp. 1203-1213 ◽

Cited By ~ 41

Author(s):

Jun-Zhi Wei ◽

N. Jerry Chatterton

Keyword(s):

Agropyron Cristatum ◽

Crested Wheatgrass

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

Journal of Heredity ◽

10.1093/jhered/esab053 ◽

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.

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