Genotype by sequencing SNP dataset for Malus domestica x Malus sieversii F1 populations GMAL4591 and GMAL4592
Data files
Sep 29, 2023 version files 151.07 MB
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A1_SievQTL4591_Filt.vcf
83.04 MB
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A1_SievQTL4592_Filt.vcf
68.02 MB
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README.md
1.46 KB
Abstract
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 < 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 < 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.
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.
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 M. domestica 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 <0.1 (--geno), missing SNPs per individual <0.1 (--mind), and max heterozygosity of 0.7 (Purcell et al. 2007b).