SNP Discovery via Genomic Reduction, Barcoding, and 454‐Pyrosequencing in Amaranth

By P. Maughan, Scott M. Yourstone, E. Jellen, Joshua Udall. 2009

103 citations recorded by the source corpus.

The grain amaranths are important pseudo‐cereals native to the New World. During the last decade they have garnered increased international attention for their nutritional quality, tolerance to abiotic stress, and importance as a symbol of indigenous cultures. We report the development of a novel genomic reduction protocol based on restriction‐site conservation and multiplex identifiers (MID) barcodes to discover single nucleotide polymorphisms (SNPs) from a pooled amaranth library of four mapping parents. The incorporation of MID barcodes allowed for DNA sample pooling, sequence deconvolution, and the identification of SNPs for specific mapping populations without additional genotyping. Approximately 1.3 million sequence‐reads with an average read length of 440 bp were collected from a single 454‐pyrosequencing run. Contigs specific to each of the four mapping populations were assembled. The assembled contigs had an average read‐length of 464 bp, and an average read‐depth of 16X. A total of 27,658 SNPs were observed across all populations. The average base coverage at all SNPs was 20X. Thirty‐four of 35 (97%) predicted SNPs were verified via resequencing and the random genomic distribution of the SNPs generated using this approach was shown in Arabidopsis. The method does not require a priori sequence information and should be readily adaptable to other species.

Subfields: Genetics, Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/5bd29f3c3cc1e0a05037de373139bb360b4039ce

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Citations in the corpus

Current knowledge on Amaranthus spp.: research avenues for improved nutritional value and yield in leafy amaranths in sub-Saharan Africa (2014, background): “A significant advance in the number of available markers occurred when Maughan et al. (2009) reported the utilization of a novel genomic reduction strategy linked with next-generation sequencing to identify 27,658 putative single nucleotide polymorphisms (SNPs) among four diverse amaranth…”
Genotyping-By-Sequencing for Plant Genetic Diversity Analysis: A Lab Guide for SNP Genotyping (2014, background): “[32], having no banding indicative of repetitive sequences in the target size range, but may not necessarily be the best option.”
Utilization of next-generation sequencing platforms in plant genomics and genetic variant discovery (2010, methodology): “…significant genomic or transcriptomic resources, to sequence indexed digested DNA fragments from four pooled mapping parents, followed by the de novo assembly of each indexed sequencing data sets and the detection of SNPs by way of comparing the resulting contig sequences (Maughan et al. 2009).”
Genomic Selection in Plant Breeding (2011, methodology): “Methods to identify SNPs from gene-enriched and complexity reduced portions of the genome have been developed with the de novo sequencing approach (Gore et al., 2009; Hyten et al., 2010; Maughan et al., 2009; Van Orsouw et al., 2007).”
Development, Characterization, and Linkage Mapping of Single Nucleotide Polymorphisms in the Grain Amaranths (Amaranthus sp.) (2011, methodology): “A signifi cant advance in the number of available markers occurred in 2009 when Maughan et al. (2009) reported the utilization of a novel genomic reduction strategy linked with next-generation sequencing to identify 27,658 putative single nucleotide polymorphisms (SNPs) among four diverse amaranth…”