scholarly journals Novel design of imputation-enabled SNP arrays for breeding and research applications supporting multi-species hybridisation

2021 ◽  
Author(s):  
Gabriel Keeble-Gagnère ◽  
Raj Pasam ◽  
Kerrie L Forrest ◽  
Debbie Wong ◽  
Hannah Robinson ◽  
...  
Keyword(s):  
Statistical Power ◽  
Snp Array ◽  
Tetraploid Wheat ◽  
Genotyping By Sequencing ◽  
Cost Effective ◽  
Single Copy ◽  
Snp Genotyping ◽  
D Genome ◽  
High Resolution Data ◽  
Haplotypic Diversity

Array-based SNP genotyping platforms have low genotype error and missing data rates compared to genotyping-by-sequencing technologies. However, design decisions used to create array-based SNP genotyping assays for both research and breeding applications are critical to their success. We describe a novel approach applicable to any animal or plant species for the design of cost-effective imputation-enabled SNP genotyping arrays with broad utility and demonstrate its application through the development of the Infinium Wheat Barley 40K SNP array. We show the approach delivers high-quality and high-resolution data for wheat and barley, including when samples are jointly hybridised. The new array aims to maximally capture haplotypic diversity in globally diverse wheat and barley germplasm while minimising ascertainment bias. Comprising mostly biallelic markers designed to be species-specific and single-copy, it permits highly accurate imputation in diverse germplasm to improve statistical power for GWAS and genomic selection. The SNP content captures tetraploid wheat (A- and B-genome) and Ae. tauschii (D-genome) diversity and delineates synthetic and tetraploid wheat from other wheats, as well as tetraploid species and subgroups. The content includes SNP tagging key trait loci in wheat and barley and that directly connect to other genotyping platforms and legacy datasets. The utility of the array is enhanced through the web-based tool Pretzel (https://plantinformatics.io/) which enables the array's content to be visualised and interrogated interactively in the context of numerous genetic and genomic resources to more seamlessly connect research and breeding. The array is available for use by the international wheat and barley community.

scholarly journals Novel Design of Imputation-Enabled SNP Arrays for Breeding and Research Applications Supporting Multi-Species Hybridization

2021 ◽  
Vol 12 ◽  
Author(s):  
Gabriel Keeble-Gagnère ◽  
Raj Pasam ◽  
Kerrie L. Forrest ◽  
Debbie Wong ◽  
Hannah Robinson ◽  
...  
Keyword(s):  
Statistical Power ◽  
Association Studies ◽  
Aegilops Tauschii ◽  
Snp Array ◽  
Tetraploid Wheat ◽  
Snp Genotyping ◽  
Genome Wide Association Studies ◽  
D Genome ◽  
High Resolution Data ◽  
Haplotypic Diversity

Array-based single nucleotide polymorphism (SNP) genotyping platforms have low genotype error and missing data rates compared to genotyping-by-sequencing technologies. However, design decisions used to create array-based SNP genotyping assays for both research and breeding applications are critical to their success. We describe a novel approach applicable to any animal or plant species for the design of cost-effective imputation-enabled SNP genotyping arrays with broad utility and demonstrate its application through the development of the Illumina Infinium Wheat Barley 40K SNP array Version 1.0. We show that the approach delivers high quality and high resolution data for wheat and barley, including when samples are jointly hybridised. The new array aims to maximally capture haplotypic diversity in globally diverse wheat and barley germplasm while minimizing ascertainment bias. Comprising mostly biallelic markers that were designed to be species-specific and single-copy, the array permits highly accurate imputation in diverse germplasm to improve the statistical power of genome-wide association studies (GWAS) and genomic selection. The SNP content captures tetraploid wheat (A- and B-genome) and Aegilops tauschii Coss. (D-genome) diversity and delineates synthetic and tetraploid wheat from other wheat, as well as tetraploid species and subgroups. The content includes SNP tagging key trait loci in wheat and barley, as well as direct connections to other genotyping platforms and legacy datasets. The utility of the array is enhanced through the web-based tool, Pretzel (https://plantinformatics.io/) which enables the content of the array to be visualized and interrogated interactively in the context of numerous genetic and genomic resources to be connected more seamlessly to research and breeding. The array is available for use by the international wheat and barley community.

Molecular characterization and chromosome-specific TRAP-marker development for Langdon durum D-genome disomic substitution lines

Genome ◽  
2006 ◽  
Vol 49 (12) ◽  
pp. 1545-1554 ◽  
Author(s):  
J. Li ◽  
D.L. Klindworth ◽  
F. Shireen ◽  
X. Cai ◽  
J. Hu ◽  
...  
Keyword(s):  
Triticum Turgidum ◽  
Tetraploid Wheat ◽  
Substitution Lines ◽  
Genome Chromosome ◽  
D Genome ◽  
Single Chromosome ◽  
B Genome ◽  
The Individual ◽  
Trap Marker

The aneuploid stocks of durum wheat ( Triticum turgidum L. subsp. durum (Desf.) Husnot) and common wheat ( T. aestivum L.) have been developed mainly in ‘Langdon’ (LDN) and ‘Chinese Spring’ (CS) cultivars, respectively. The LDN-CS D-genome chromosome disomic substitution (LDN-DS) lines, where a pair of CS D-genome chromosomes substitute for a corresponding homoeologous A- or B-genome chromosome pair of LDN, have been widely used to determine the chromosomal locations of genes in tetraploid wheat. The LDN-DS lines were originally developed by crossing CS nulli-tetrasomics with LDN, followed by 6 backcrosses with LDN. They have subsequently been improved with 5 additional backcrosses with LDN. The objectives of this study were to characterize a set of the 14 most recent LDN-DS lines and to develop chromosome-specific markers, using the newly developed TRAP (target region amplification polymorphism)-marker technique. A total of 307 polymorphic DNA fragments were amplified from LDN and CS, and 302 of them were assigned to individual chromosomes. Most of the markers (95.5%) were present on a single chromosome as chromosome-specific markers, but 4.5% of the markers mapped to 2 or more chromosomes. The number of markers per chromosome varied, from a low of 10 (chromosomes 1A and 6D) to a high of 24 (chromosome 3A). There was an average of 16.6, 16.6, and 15.9 markers per chromosome assigned to the A-, B-, and D-genome chromosomes, respectively, suggesting that TRAP markers were detected at a nearly equal frequency on the 3 genomes. A comparison of the source of the expressed sequence tags (ESTs), used to derive the fixed primers, with the chromosomal location of markers revealed that 15.5% of the TRAP markers were located on the same chromosomes as the ESTs used to generate the fixed primers. A fixed primer designed from an EST mapped on a chromosome or a homoeologous group amplified at least 1 fragment specific to that chromosome or group, suggesting that the fixed primers might generate markers from target regions. TRAP-marker analysis verified the retention of at least 13 pairs of A- or B-genome chromosomes from LDN and 1 pair of D-genome chromosomes from CS in each of the LDN-DS lines. The chromosome-specific markers developed in this study provide an identity for each of the chromosomes, and they will facilitate molecular and genetic characterization of the individual chromosomes, including genetic mapping and gene identification.

A cytological and molecular analysis of D-genome chromosome retention following F2–F6 generations of hexaploid×tetraploid wheat crosses

2018 ◽  
Vol 69 (2) ◽  
pp. 121 ◽  
Author(s):  
Sriram Padmanaban ◽  
Peng Zhang ◽  
Mark W. Sutherland ◽  
Noel L. Knight ◽  
Anke Martin
Keyword(s):  
Durum Wheat ◽  
Tetraploid Wheat ◽  
Triticum Aestivum L ◽  
Food Crops ◽  
Cytological Analysis ◽  
Genome Chromosome ◽  
D Genome ◽  
Ploidy Levels ◽  
F2 Generation ◽  
Global Food

Both hexaploid bread wheat (AABBDD) (Triticum aestivum L.) and tetraploid durum wheat (AABB) (T. turgidum spp. durum) are highly significant global food crops. Crossing these two wheats with different ploidy levels results in pentaploid (AABBD) F1 lines. This study investigated the differences in the retention of D chromosomes between different hexaploid × tetraploid crosses in subsequent generations by using molecular and cytological techniques. Significant differences (P < 0.05) were observed in the retention of D chromosomes in the F2 generation depending on the parents of the original cross. One of the crosses, 2WE25 × 950329, retained at least one copy of each D chromosome in 48% of its F2 lines. For this cross, the retention or elimination of D chromosomes was determined through several subsequent self-fertilised generations. Cytological analysis indicated that D chromosomes were still being eliminated at the F5 generation, suggesting that in some hexaploid × tetraploid crosses, D chromosomes are unstable for many generations. This study provides information on the variation in D chromosome retention in different hexaploid × tetraploid wheat crosses and suggests efficient strategies for utilising D genome retention or elimination to improve bread and durum wheat, respectively.

scholarly journals Prim-SNPing: a primer designer for cost-effective SNP genotyping

BioTechniques ◽  
2009 ◽  
Vol 46 (6) ◽  
pp. 421-431 ◽  
Author(s):  
Hsueh-Wei Chang ◽  
Li-Yeh Chuang ◽  
Yu-Huei Cheng ◽  
Yu-Chen Hung ◽  
Cheng-Hao Wen ◽  
...  
Keyword(s):  
Cost Effective ◽  
Snp Genotyping

Employing Space-Based Hyperspectral Imagery for Pipeline Leak Prevention, Detection and Compliance

2020 ◽  
Author(s):  
R. Peter Weaver ◽  
Dan Katz ◽  
Tushar Prabahakar ◽  
Katie A. Corcoran
Keyword(s):  
Environmental Protection Agency ◽  
Oil And Gas ◽  
State Of The Art ◽  
Hyperspectral Imagery ◽  
Cost Effective ◽  
Protection Agency ◽  
High Resolution Data ◽  
Hydrocarbon Detection ◽  
Detection Capabilities ◽  
Vapor Emissions

Abstract We are now living in what has been described as the Experience Era, where lines between the digital and physical are increasingly blurred. As such, we are just beginning to see how customized access to space will improve asset stewardship in ways that are still evolving, as customization of on-orbit technology pushes the bounds of how we receive and process information. Specific to oil and gas operators, one technology being launched by microsatellite, hyperspectral imagery (HSI), is poised to enable unparalleled daily global pipeline leak prevention, detection and speciation, intrusion and change detection capabilities. This will replace conventional DOT pipeline patrol for compliance while contributing to our understanding of vapor emissions as regulated by the Environmental Protection Agency. This paper discusses both the evolving space marketplace and the state of the art for HSI, including current examples of hyperspectral findings regarding pipeline and terminal leaks. Successful deployment of HSI will drive a decrease in the number and magnitude of pipeline leaks using persistent, global, high-resolution data collection, rapid and reliable analysis, and immediate reporting of actionable information. For decades, satellite HSI technology has offered a promise of remote hydrocarbon detection and other features of interest. It is only now becoming scalable, accessible to, and cost-effective for the pipeline industry, and thus a reality for cost-effective pipeline stewardship.

DNA-DNA Hybridization, Phylogenetic Reconstruction and the Fossil Record

1988 ◽  
Vol 1 ◽  
pp. 75-88 ◽  
Author(s):  
Charles R. Marshall
Keyword(s):  
Dna Hybridization ◽  
Nuclear Dna ◽  
Phylogenetic Reconstruction ◽  
Cost Effective ◽  
Single Copy ◽  
Molecular Techniques ◽  
Phylogenetic Information ◽  
Molecular Approaches ◽  
Molecular Characters ◽  
Rates Of Molecular Evolution

In 1962 Zuckerkandl & Pauling suggested that the amino acid sequence of proteins might evolve in a clock-like fashion and thus may be useful for phylogenetic reconstruction. Since then, many different molecular approaches to phylogenetic reconstruction have been proposed (Wilson et al., 1977). Enthusiasm for the clock hypothesis was dampened by the discovery that rates of molecular evolution for many macromolecules have been highly variable through time (Romero-Herrera et al., 1979). However, the contribution of molecular characters to the study of phylogeny is not necessarily dependent on the notion of a molecular clock and molecular approaches continue to be an important source of phylogenetic information. One of the more powerful and cost-effective molecular techniques for phylogenetic purposes is DNA-DNA hybridization, which measures the single-copy nuclear DNA sequence divergences between species.

COLD HARDINESS IN HEXAPLOID TRITICALE

1985 ◽  
Vol 65 (3) ◽  
pp. 487-490 ◽  
Author(s):  
A. E. LIMIN ◽  
J. DVORAK ◽  
D. B. FOWLER
Keyword(s):  
Cold Hardiness ◽  
Tetraploid Wheat ◽  
Triticum Aestivum L ◽  
Hexaploid Triticale ◽  
D Genome ◽  
Potential Source ◽  
Secale Cereale L ◽  
Cold Hardy ◽  
Triticosecale Wittmack ◽  
X Triticosecale Wittmack

The excellent cold hardiness of rye (Secale cereale L.) makes it a potential source of genetic variability for the improvement of this character in related species. However, when rye is combined with common wheat (Triticum aestivum L.) to produce octaploid triticale (X Triticosecale Wittmack, ABDR genomes), the superior rye cold hardiness is not expressed. To determine if the D genome of hexaploid wheat might be responsible for this lack of expression, hexaploid triticales (ABR genomes) were produced and evaluated for cold hardiness. All hexaploid triticales had cold hardiness levels similar to their tetraploid wheat parents. Small gains in cold hardiness of less than 2 °C were found when very non-hardy wheats were used as parents. This similarity in expression of cold hardiness in both octaploid and hexaploid triticales indicates that the D genome of wheat is not solely, if at all, responsible for the suppression of rye cold hardiness genes. There appears to be either a suppressor(s) of the rye cold hardiness genes on the AB genomes of wheat, or the expression of diploid rye genes is reduced to a uniform level by polyploidy in triticale. The suppression, or lack of expression, of rye cold hardiness genes in a wheat background make it imperative that cold-hardy wheats be selected as parents for the production of hardy triticales.Key words: Triticale, Secale, winter wheat, cold hardiness, gene expression

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