Maize (Zea mays L.) Genome Diversity as Revealed by RNA-Sequencing

doi:10.1201/b16568-18

Cited by 49 publications

(55 citation statements)

References 39 publications

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“…SNPs and INDELs are powerful molecular markers, due in part to their abundance and relative ease of detection in a genome-wide high-throughput experiment (44). Quantitation of SNP and INDEL abundance allows construction of genetic maps and functional markers (44)(45)(46)(47). We identified polymorphisms and explored sequence diversity among seven hazelnut cultivars representing four major geo-graphical regions (2,48) of hazelnut production ( Table 4).…”

Section: Resequencing and Polymorphism Detection In Additional Hazelnmentioning

confidence: 99%

A Draft Genome and High-Density Genetic Map of European Hazelnut (Corylus avellanaL.)

Rowley

VanBuren

Bryant

et al. 2018

Preprint

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European hazelnut (Corylus avellana L.) is of global agricultural and economic significance, with genetic diversity existing in hundreds of accessions. Breeding efforts have focused on maximizing nut yield and quality and reducing susceptibility to diseases such as Eastern filbert blight (EFB). Here we present the first sequenced genome among the order Fagales, the EFB-resistant diploid hazelnut accession 'Jefferson' (OSU 703.007). We assembled the highly heterozygous hazelnut genome using an Illumina only approach and the final assembly has a scaffold N50 of 21.5kb. We captured approximately 91 percent (345 Mb) of the flow-cytometry-determined genome size and identified 34,910 putative gene loci. In addition, we identified over 2 million polymorphisms across seven diverse hazelnut accessions and characterized t heir effect on coding sequences. We produced t wo high-density genetic maps with 3,209 markers from an F1 hazelnut population, representing a five-fold increase in marker density over previous maps. These genomic resources will aide in the discovery of molecular markers linked to genes of interest for hazelnut breeding efforts, and are available to the community at https://www.cavellanagenomeportal.com/.

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Section: Resequencing and Polymorphism Detection In Additional Hazelnmentioning

confidence: 99%

A Draft Genome and High-Density Genetic Map of European Hazelnut (Corylus avellanaL.)

Rowley

VanBuren

Bryant

et al. 2018

Preprint

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“…Advent of PCR technology in early 1990s led to the development of new generation of PCR-based markers such as random amplification of polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP) and simple sequence repeats (SSRs) (Mammadov et al 2012a). Among these low-and medium-throughput molecular markers, SSR markers were declared as ''markers of choice'' as they were highly polymorphic, reproducible and amenable to automation (Powell et al 1996).…”

Section: Introductionmentioning

confidence: 99%

Discovery of large-scale SNP markers and construction of linkage map in a RIL population of jute (Corchorus capsularis)

et al. 2015

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Jute is the most important bast fibre crop of the world. Stem rot disease caused by Macrophomina phaseolina is a major constraint of jute cultivation. Recent advances in genomics and bioinformatics have enabled the development of highthroughput genotyping, allowing the construction of saturated linkage maps for identification of resistant lines. In the present study, single nucleotide polymorphism (SNP) markers associated with expressed sequence tags (ESTs) were developed and were used to generate comprehensive linkage maps for Corchorus capsularis. From a set of 43,335 variant nucleotide positions detected through in silico analysis, 768 SNPs were selected for genotyping of a recombinant inbred line population. A total of 705 SNPs (91.7 %) successfully detected segregating polymorphisms. In addition to EST-SNPs, genomic simple sequence repeats were assigned to the genetic map in order to obtain an evenly distributed genome-wide coverage. Nine linkage groups were constructed from genetic maps with estimated cumulative total map length of 2016 cM and average inter-locus interval of 4.2 cM. SNP assay and linkage mapping are important set of tools for marker-assisted selection, and it could be used for identifying resistance to M. phaseolina in jute cultivars. This is the first report of developing SNP markers and SNP-based linkage map in jute.

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“…Genomic approaches resulting in fast diagnostic tools represent a unique opportunity to hasten the delivery of these programmes (e.g. Mammadov et al 2012;Beaulieu et al 2014). For similar purposes, high-throughput SNP genotyping assays were designed for Picea glauca (Pavy et al 2013a), a sympatric but nonhybridizing boreal spruce species that diverged from P. mariana between 13 and 20 Ma (Bouill e & Bousquet 2005).…”

Section: Introductionmentioning

confidence: 99%

Development of highly reliable in silico SNP resource and genotyping assay from exome capture and sequencing: an example from black spruce (Picea mariana)

Pavy

Deschênes

Boyle

et al. 2015

Molecular Ecology Resources

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Picea mariana is a widely distributed boreal conifer across Canada and the subject of advanced breeding programmes for which population genomics and genomic selection approaches are being developed. Targeted sequencing was achieved after capturing P. mariana exome with probes designed from the sequenced transcriptome of Picea glauca, a distant relative. A high capture efficiency of 75.9% was reached although spruce has a complex and large genome including gene sequences interspersed by some long introns. The results confirmed the relevance of using probes from congeneric species to perform successfully interspecific exome capture in the genus Picea. A bioinformatics pipeline was developed including stringent criteria that helped detect a set of 97,075 highly reliable in silico SNPs. These SNPs were distributed across 14,909 genes. Part of an Infinium iSelect array was used to estimate the rate of true positives by validating 4267 of the predicted in silico SNPs by genotyping trees from P. mariana populations. The true positive rate was 96.2% for in silico SNPs, compared to a genotyping success rate of 96.7% for a set 1115 P. mariana control SNPs recycled from previous genotyping arrays. These results indicate the high success rate of the genotyping array and the relevance of the selection criteria used to delineate the new P. mariana in silico SNP resource. Furthermore, in silico SNPs were generally of medium to high frequency in natural populations, thus providing high informative value for future population genomics applications.

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Maize (Zea mays L.) Genome Diversity as Revealed by RNA-Sequencing

Cited by 49 publications

References 39 publications

A Draft Genome and High-Density Genetic Map of European Hazelnut (Corylus avellanaL.)

A Draft Genome and High-Density Genetic Map of European Hazelnut (Corylus avellanaL.)

Discovery of large-scale SNP markers and construction of linkage map in a RIL population of jute (Corchorus capsularis)

Development of highly reliable in silico SNP resource and genotyping assay from exome capture and sequencing: an example from black spruce (Picea mariana)

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