DOI: 10.5061/dryad.15dv41p3c
title: Genotype by sequencing SNP dataset for Malus domestica x Malus sieversii F1 populations GMAL4591 and GMAL4592

description: Fire blight, a bacterial disease caused by Erwinia amylovora, is the most
 devastating disease of apples and a major threat to apple production. Most
 commercial apple cultivars are susceptible to fire blight driving the need
 to develop fire blight resistant cultivars. Although several major fire
 blight resistance QTLs have been identified from wild species of Malus,
 the challenges of breeding apples due to long juvenile phase and
 heterozygosity greatly limit their use. M. sieversii, the primary
 progenitor of domesticated apples, is one of the wild Malus species that
 is sexually compatible with M. domestica and has some favorable fruit
 quality traits. In this study, we performed QTL analysis on two F1 apple
 populations of M. domestica cv. ‘Royal Gala’ × M. sieversii (GMAL4591 and
 GMAL4592) to identify fire blight resistance QTL. Parental linkage maps
 were constructed for each family using marker sets of approximately 20K
 GBS-SNPs. Phenotype data was collected from parents and progeny through
 controlled fire blight inoculations in the greenhouse for two subsequent
 years. A significant (P &lt; 0.0001) moderate-effect fire blight
 resistance QTL on linkage group 7 of GMAL4591 was identified from the
 paternal parent M. sieversii ‘KAZ 95 17-14’ (Msv_FB7). Msv_FB7 explains
 about 48–53% of the phenotyping variance across multiple years and time
 points. Additionally, a significant (P &lt; 0.001) minor effect QTL
 explaining 18% of the phenotypic variance was identified in population
 GMAL4592 on LG10 from ‘Royal Gala’. We developed diagnostic SSR markers
 flanking the Msv_FB7 QTL to use in apple breeding. These findings have the
 potential to accelerate the development of fire-blight-resistant
 cultivars.
description: Genotyping-by-sequencing and SNP Calling The
 DNeasy 96 Plant Kits (Qiagen, Valencia CA, USA) were used for DNA
 extraction of parents and progeny of GMAL4591 and GMAL4592.
 Genotyping-by-sequencing (GBS) library preparations were performed
 separately for each population as performed in Elshire et al. (2011) and
 processed with two different restriction enzymes (ApeKI, PstI-EcoT22I).
 Illumina Hi-Seq 2000 (96 samples per lane) was used to sequence the
 samples at Cornell University (Ithaca, New York, US) across 42 lanes
 generating 100-bp single-end reads. Read filtering and SNP calling
 procedures were done in accordance with Migicovsky et al. (2021). SNPs
 were called to the <em>M. domestica</em> GDDH13 v1.1 reference
 genome (Daccord et al. 2017a). The marker name includes information about
 the linkage group and the physical position (bp) in the GDDH13 v1.1
 genome. GBS Filtering The
 filtering process for genotypic data was conducted with a combination of
 PLINKv1.9 and TASSELv5 (Bradbury et al. 2007; Purcell et al. 2007a). The
 filtered genotypic data contained 19,295 SNPs for GMAL4591 and 16,440 SNPs
 for GMAL4592. Filtering was performed with PLINKv1.9 with parameters set
 to minor allele frequency of 0.05 (--maf), missing SNPs per marker site
 &lt;0.1 (--geno), missing SNPs per individual &lt;0.1 (--mind),
 and max heterozygosity of 0.7 (Purcell et al. 2007b).
description: # Genotype by sequence SNP datasets for *Malus domestica* x *Malus
 sieversii* populations GMAL4591 and GMAL4592 These GBS SNP datasets are
 related to the manuscript, Identification and marker development of a
 moderate-effect fire blight resistance QTL in *M. sieversii*, the primary
 progenitor of domesticated apples. This manuscript is in review with the
 journal Tree Genetics and Genomes. There are approximately 20K SNPs in
 each vcf file that were used for linkage map construction and QTL analysis
 to identify novel fire blight resistance alleles from *M. sieversii*. The
 populations used for QTL analysis are the two interspecific crosses with
 *M. domestica* cv. ‘Royal Gala’ (PI651008) as the common maternal parent.
 The paternal parent of population GMAL4591 KAZ 95 17-14 (PI613959). The
 paternal parent of population GMAL4592 is KAZ 95 10-04F (PI613978). The
 accessions used as the paternal parents were collected in 1995 from
 Kazakhstan during U.S. Department of Agriculture (USDA) led expeditions
 from 1989-1996. These F1 populations and their parents were developed and
 maintained in the orchards at the Plant Genetic Resources Unit (PGRU)
 USDA-ARS *Malus* collection in Geneva, NY. ## Description of the data and
 file structure These are standard variant call format (VCF) files that
 provide the SNP calls for each site and each progeny/parent. This data can
 be accessed with common software and bioinformatic tools such as TASSEL.
 ## <br>