A Large-scale Chromosome-specific SNP Discovery Guideline

Overview

Journal Funct Integr Genomics

Publisher Springer

Specialties Genetics
Molecular Biology

Date 2016 Dec 1

PMID 27900504

Citations 13

Authors

Bala Ani Akpinar

Stuart Lucas

Hikmet Budak

Affiliations

Soon will be listed here.

Abstract

Single-nucleotide polymorphisms (SNPs) are the most prevalent type of variation in genomes that are increasingly being used as molecular markers in diversity analyses, mapping and cloning of genes, and germplasm characterization. However, only a few studies reported large-scale SNP discovery in Aegilops tauschii, restricting their potential use as markers for the low-polymorphic D genome. Here, we report 68,592 SNPs found on the gene-related sequences of the 5D chromosome of Ae. tauschii genotype MvGB589 using genomic and transcriptomic sequences from seven Ae. tauschii accessions, including AL8/78, the only genotype for which a draft genome sequence is available at present. We also suggest a workflow to compare SNP positions in homologous regions on the 5D chromosome of Triticum aestivum, bread wheat, to mark single nucleotide variations between these closely related species. Overall, the identified SNPs define a density of 4.49 SNPs per kilobyte, among the highest reported for the genic regions of Ae. tauschii so far. To our knowledge, this study also presents the first chromosome-specific SNP catalog in Ae. tauschii that should facilitate the association of these SNPs with morphological traits on chromosome 5D to be ultimately targeted for wheat improvement.

Citing Articles

Genetic dissection of grain iron concentration in hexaploid wheat ( L.) using a genome-wide association analysis method.

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Omics Approaches for Engineering Wheat Production under Abiotic Stresses.

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Exploiting the Genomic Diversity of Rice ( L.): SNP-Typing in 11 Early-Backcross Introgression-Breeding Populations.

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PMID: 29988489 PMC: 6024854. DOI: 10.3389/fpls.2018.00849.

Chromosome-based survey sequencing reveals the genome organization of wild wheat progenitor Triticum dicoccoides.

Akpinar B, Biyiklioglu S, Alptekin B, Havrankova M, Vrana J, Dolezel J Plant Biotechnol J. 2018; 16(12):2077-2087.

PMID: 29729062 PMC: 6230948. DOI: 10.1111/pbi.12940.

Mapping QTLs conferring salt tolerance and micronutrient concentrations at seedling stagein wheat.

Hussain B, Lucas S, Ozturk L, Budak H Sci Rep. 2017; 7(1):15662.

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