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Open AccessArticle

RNA Sequencing-Based Bulked Segregant Analysis Facilitates Efficient D-genome Marker Development for a Specific Chromosomal Region of Synthetic Hexaploid Wheat

1
Graduate School of Agricultural Science, Kobe University, Rokkodai 1-1, Nada, Kobe 657-8501, Japan
2
Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama 710-0046, Japan
*
Authors to whom correspondence should be addressed.
Int. J. Mol. Sci. 2018, 19(12), 3749; https://doi.org/10.3390/ijms19123749
Received: 2 November 2018 / Revised: 20 November 2018 / Accepted: 22 November 2018 / Published: 26 November 2018
(This article belongs to the Special Issue Molecular Advances in Wheat and Barley)
Common wheat originated from interspecific hybridization between cultivated tetraploid wheat and its wild diploid relative Aegilops tauschii followed by amphidiploidization. This evolutionary process can be reproduced artificially, resulting in synthetic hexaploid wheat lines. Here we performed RNA sequencing (RNA-seq)-based bulked segregant analysis (BSA) using a bi-parental mapping population of two synthetic hexaploid wheat lines that shared identical A and B genomes but included with D-genomes of distinct origins. This analysis permitted identification of D-genome-specific polymorphisms around the Net2 gene, a causative locus to hybrid necrosis. The resulting single nucleotide polymorphisms (SNPs) were classified into homoeologous polymorphisms and D-genome allelic variations, based on the RNA-seq results of a parental tetraploid and two Ae. tauschii accessions. The difference in allele frequency at the D-genome-specific SNP sites between the contrasting bulks (ΔSNP-index) was higher on the target chromosome than on the other chromosomes. Several SNPs with the highest ΔSNP-indices were converted into molecular markers and assigned to the Net2 chromosomal region. These results indicated that RNA-seq-based BSA can be applied efficiently to a synthetic hexaploid wheat population to permit molecular marker development in a specific chromosomal region of the D genome. View Full-Text
Keywords: allohexaploid; homoeolog; hybrid necrosis; molecular marker; wheat allohexaploid; homoeolog; hybrid necrosis; molecular marker; wheat
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Nishijima, R.; Yoshida, K.; Sakaguchi, K.; Yoshimura, S.-I.; Sato, K.; Takumi, S. RNA Sequencing-Based Bulked Segregant Analysis Facilitates Efficient D-genome Marker Development for a Specific Chromosomal Region of Synthetic Hexaploid Wheat. Int. J. Mol. Sci. 2018, 19, 3749.

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