Resequencing worldwide spinach germplasm for identification of field resistance QTLs to downy mildew and assessment of genomic selection methods

Authors: BHATTARAI, GEHENDRA - University Of Arkansas; SHI, AINONG - University Of Arkansas; Mou, Beiquan; CORRELL, JAMES - University Of Arkansas

Submitted to: Horticulture Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/4/2022
Publication Date: 9/13/2022
Citation: Bhattarai, G., Shi, A., Mou, B., Correll, J. 2022. Resequencing worldwide spinach germplasm for identification of field resistance QTLs to downy mildew and assessment of genomic selection methods. Horticulture Research. 9. Article uhac205. https://doi.org/10.1093/hr/uhac205.
DOI: https://doi.org/10.1093/hr/uhac205

Interpretive Summary: Downy mildew, commercially the most important disease of spinach, is caused by a fungal pathogen, Peronospora effusa. Commercial spinach cultivars are bred with a few major resistance genes to impart resistance to downy mildew and are effective against some pathogen races. Over the past two decades, new pathogen races have repeatedly overcome the resistances used in newly released cultivars, indicating the need for more durable resistance. The objectives of this work include evaluation of the USDA spinach collection, which includes varieties collected from throughout the world, and commercial cultivars for downy mildew disease resistance in the field under natural disease pressure and identification of the genes associated with the resistance. Another objective was to evaluate the prediction accuracy (PA) using genetic analyses to improve spinach breeding for downy mildew field resistance. More than four hundred diverse spinach varieties from the USDA spinach collection and commercial cultivars were evaluated for downy mildew field resistance between 2017-2019 in the Salinas Valley, California and Yuma, Arizona. The DNA sequences of the varieties were analyzed, and 14, 12, 5, and 10 DNA markers (different nucleotides) were significantly associated with the downy mildew resistance from four locations, respectively; the resistance genes were detected at the previously reported region of resistance genes on chromosome 3 in three of the four experiments. In parallel, PA was assessed using six different methods and seven DNA marker datasets for downy mildew resistance across the four tested environments. The results suggest the ability of DNA analyses to predict the performance of downy mildew field resistances. The genes, DNA markers and PA of downy mildew disease resistance will provide information in spinach breeding to help select resistant plants and varieties, eventually leading to accumulation of beneficial genes for durable disease resistance.

Technical Abstract: Downy mildew, commercially the most important disease of spinach, is caused by the obligate oomycete, Peronospora effusa. In the past two decades, new pathogen races have repeatedly overcome the resistances used in newly released cultivars, indicating the need for more durable resistance. Commercial spinach cultivars are bred with major R genes to impart resistance to downy mildew and are effective against some pathogen races/isolates. The objectives of this work include evaluation of the USDA spinach germplasm collections and commercial cultivars for downy mildew disease resistance in the field under natural inoculum pressure, and genome wide association analysis (GWAS) to identify the genomic regions (alleles) associated with resistance. Another objective was to evaluate the prediction accuracy (PA) using several genomic prediction (GP) methods to assess the potential implementation of genomic selection (GS) to improve spinach breeding for downy mildew field resistance. More than four hundred diverse spinach genotypes comprising USDA germplasm accessions and commercial cultivars were evaluated for downy mildew field resistance between 2017-2019 in the Salinas Valley, California and Yuma, Arizona. GWAS was performed using single nucleotide polymorphism (SNP) markers identified via whole genome resequencing (WGR) with GAPIT and TASSEL programs. This detected 14, 12, 5, and 10 SNP markers significantly associated with the downy mildew resistance from four tested environments, respectively, and the QTL alleles were detected at the previously reported region of chromosome 3 in three of the four experiments. In parallel, PA was assessed using six different GP models and seven sets of marker datasets for downy mildew resistance across four tested environments. The results suggest the suitability of GS to improve downy mildew field resistances. The QTL, SNP markers and PA of downy mildew disease resistance will provide information in spinach breeding to select resistant plants and breeding lines through marker-assisted selection (MAS) and GS, eventually helping to accumulate beneficial alleles for durable disease resistance.