DOI: 10.5061/dryad.8sf7m0d0b
title: GBS sequence of wheat population from JagMut1095 x Jagger

description: Barley yellow dwarf (BYD) is one of the most serious viral diseases in
 cereal crops worldwide. Identification of quantitative trait loci (QTLs)
 underlining wheat resistance to barley yellow dwarf virus (BYDV) is
 essential for breeding BYDV tolerant wheat cultivars. In this study, a
 recombinant inbred line (RIL) population was developed from the cross
 between Jagger (PI 593688) and a Jagger mutant (JagMut1095). A linkage map
 of 3,106 cM consisting of 21 wheat chromosomes was developed using 1,003
 unique SNPs from the RIL population and was used to identify QTLs for BYDV
 resistance and yield-related traits including thousand kernel weight
 (TKW), kernel area (KA), kernel width (KW), and kernel length (KL).
 QByd.hwwg-2DL, a QTL on chromosome arm 2DL for BYDV resistance, was
 consistently identified in three field experiments, and explained 11.6% to
 44.5% of the phenotypic variation. For yield-related traits, six major and
 repeatable QTLs were identified on 1AS (QKa.hwwg-1AS), 2DL (QTkw.hwwg-2DL,
 QKa.hwwg-2DL, QKw.hwwg-2DL and QKl.hwwg-2DL) and 5AL (QKw.hwwg-5AL). The
 major QTLs on chromosome 2DL for TKW, KA, KW and KL were mapped between
 621 Mb and 643 Mb, overlapping with QByd.hwwg-2DL with all the favorable
 alleles from Jagger. This study reports the first native BYDV resistance
 QTL (QByd.hwwg-2DL) originating from common wheat and tightly linked
 markers to the QTL for improvement of wheat BYDV resistance in wheat
 breeding.
description: Leaf tissues were collected from a single plant of each F5 RIL
 and their parents at the three-leaf stage for DNA isolation using a
 modified cetyltrimethyl ammonium bromide (CTAB) method (Bai et al. 1999).
 DNA concentration was estimated and normalized to 20 ng/µL for
 construction of GBS library (Poland and Rife 2012) that was sequenced in
 an Ion Torrent Proton sequencer (ThermoFisher Scientific, Carlsbad, CA).
 The SNPs were called from GBS reads using a reference-based pipeline in
 TASSEL 5.0 (Bradbury et al. 2007) and the IWGSC reference genome RefSeq
 v2.1 (IWGSC, 2018). The raw data were filtered by removing SNPs with
 &gt;20% missing data, &gt;10% heterozygotes or &lt; 20% minor
 allele frequency. Additionally, previously generated exome-capture data of
 JagMut1095 and Jagger (Jordan et al. 2015) were used to increase marker
 density in the target QTL regions.
description: # `#GBS sequence of wheat population from JagMut1095 x Jagger ` We have
 submit our raw data
 on [https://doi.org/10.5061/dryad.8sf7m0d0b](https://doi.org/10.5061/dryad.8sf7m0d0b) \## Descriptions \### 1095xJagger_markerSeqs.fa\\_Data *&gt;chr1A_635964 is the chromosome name and the SNP position based on reference CS v2.1. *The sequence is a 400 bp reference sequence based on CS v2.1 with the SNP position at the 200 bp. \### GBS_SNPs_of_RIL_JagMut1095_x_Jagger.xlsx\\_Data *chrom: chrmosome name *position: position of the SNP based on CS v2.1 *S1A_635964: the SNP name *"A": the SNP of the parent (JagMut1095") *"B": the SNP of the parent (Jagger") *L61: the SNP of RIL line 61. *"A" present in the variables "L1095_8 to L59": Adenine *"T" present in the variables "L1095_8 to L59": Thymine *"C" present in the variables "L1095_8 to L59": Cytosine *"G" present in the variables "L1095_8 to L59": Guanine *"K" present in the variables "L1095_8 to L59": Guanine/Thymine *"M" present in the variables "L1095_8 to L59": Adenine/Cytosine *"N" present in the variables "L1095_8 to L59": unknown *"R" present in the variables "L1095_8 to L59": Guanine/Adenine *"S" present in the variables "L1095_8 to L59": Guanine/Cytosine *"W" present in the variables "L1095_8 to L59": Adenine/Thymine *"Y" present in the variables "L1095_8 to L59": Cytosine/Thymine