Location: Plant Introduction Research
Project Number: 5030-21000-064-01-S
Project Type: Non-Assistance Cooperative Agreement
Start Date: Jul 22, 2016
End Date: Sep 30, 2019
To develop molecular markers for genes coding for resistance to white rust of spinach, via genotyping by sequencing, field evaluation, and association analysis.
Leaves will be collected from each spinach accession growing in the field and DNA extracted from each germplasm using the CTAB (hexadecyltrimethyl ammonium bromide) method (Kisha et al., 1997). Genotyping for each accession will be done using GBS. GBS is done using HiSeq 2000 in Beijing Genome Institute (BGI). Sequence assemble, mapping and variant (SNP and Insert/Deletion) discovery of GBS data will be done using DNASTAR Lasergene Genomics Suite (http://www.dnastar.com/t-products-dnastar-lasergene-genomics.aspx). So far, about 300 USDA spinach accessions have been done for GBS. We will do GBS for another 100 accessions. Association analysis: Association tests are run with the mixed linear model method as described in TASSEL 5 (Bradbury et al., 2007) and the analysis will be also performed with compressed mixed linear model (Zhang et al., 2010) implemented in the GAPIT R package (Lipka et al., 2012). SNP marker identification and validation: for those SNPs associated with white rust resistance postulated from association analysis, we will conduct a validation through KASP SNP Genotyping. It is expected that 5-10 SNP markers will be identified for white rust resistance in the USDA spinach collection.