A single nucleotide polymorphism in the "Fra" gene results in fractured starch granules in barley

TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik
Mika SaitoToshiki Nakamura

Abstract

We report here that the mutation causing fractured starch granules in the barley line "Franubet" results from a point mutation in the barley gene corresponding to the rice FLO6 gene. The "fra" mutation in barley, which was originally isolated and characterized over 30 years ago, results in fractured starch granules and an opaque phenotype. This mutation has been used in breeding programs, since it appears to be useful in the production of pearled barley for human consumption. However, selection for this phenotype is difficult, since wild-type and heterozygous kernels cannot be distinguished phenotypically, and until now, the gene involved in this mutation has not been determined. Here, we used a map-based cloning approach using nanopore sequencing to obtain long reads from a BAC clone carrying markers on either side of the fra locus. By fine mapping followed by aligning RNA-seq reads to four genes within the mapped region, we were able to determine that the fra mutation is caused by the introduction of a stop codon in the barley homologue of the rice FLOURY ENDOSPERM 6 (FLO6) gene. This gene has a CBM48 domain that binds to starch, and may act through interactions with isoamylase1 (ISA1), assisting in the binding of ISA1 to sta...Continue Reading

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Citations

Nov 20, 2018·Journal of Experimental Botany·David Seung, Alison M Smith
Feb 23, 2020·Annual Review of Plant Biology·Alison M Smith, Samuel C Zeeman
Nov 30, 2018·Frontiers in Plant Science·Casper WilkensMarie Sofie Møller
Nov 9, 2018·Journal of Experimental Botany·Yingxin ZhongKim Henrik Hebelstrup
Dec 17, 2019·Journal of Experimental Botany·James R Lloyd
Mar 8, 2021·Current Opinion in Plant Biology·Jiawen ChenDavid Seung
May 20, 2020·Current Opinion in Plant Biology·Melanie R Abt, Samuel C Zeeman

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Datasets Mentioned

BETA
LC318664
AK373583

Methods Mentioned

BETA
light microscopy
PCR
electrophoresis
Illumina sequencing
RNA-seq
genotyping
ISA

Software Mentioned

Ensemble
EnsemblPlants
BARLEX
Metrichor
BLAST
ChloroP
MEGANTE
CLC Genomics Workbench
Canu assembler
MapDisto

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