High resolution mapping and candidate gene identification of downy mildew race 16 resistance in spinach

Authors: BHATTARAI, GEHENDRA - University Of Arkansas; YANG, WEI - University Of Arkansas; SHI, AINONG - University Of Arkansas; FENG, CHUNDA - University Of Arkansas; DHILLON, BRAHAM - University Of Florida; CORRELL, JAMES - University Of Arkansas; Mou, Beiquan

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/10/2021
Publication Date: 6/26/2021
Citation: Bhattarai, G., Yang, W., Shi, A., Feng, C., Dhillon, B., Correll, J.C., Mou, B. 2021. High resolution mapping and candidate gene identification of downy mildew race 16 resistance in spinach. BMC Genomics. 22. Article 478. https://doi.org/10.1186/s12864-021-07788-8.
DOI: https://doi.org/10.1186/s12864-021-07788-8

Interpretive Summary: Downy mildew, caused by a fungus (scientific name Peronospora effusa [=P. farinosa f. sp. spinaciae]), is the most devastating disease in spinach. Seventeen races of the pathogen have been reported to date. More than 10 new races were identified in the last three decades, overcoming resistance genes deployed in newly released spinach cultivars. The main objectives of this research were to find the location of a resistant gene RPF3 on the chromosomes of the spinach cultivar Whale inoculated with downy mildew race 16, and to identify associated DNA markers and other candidate genes. A spinach breeding population derived from the cross of cultivars Whale and Lazio were inoculated with race 16 in a growth chamber and dew chamber, and disease responses were recorded. Genotyping by sequencing (GBS) techniques identified six significant DNA markers associated with the resistance gene. The downy mildew resistance RPF3 gene was located on chromosome 3, which includes four disease resistance candidate genesclose to the identified DNA markers. These results are valuable for understanding the genetic basis of downy mildew resistance, and the DNA marker will be useful in spinach breeding for selection of downy mildew race 16-resistant plants.

Technical Abstract: Downy mildew, caused by the oomycete Peronospora effusa [=P. farinosa f. sp. spinaciae], is the most devastating disease in spinach. The P. effusa shows race specificities to the resistant host and a total of 17 races have been reported. Over ten new P. effusa races were identified in the last three decades, and the new races are overcoming the resistance genes deployed in the newly released commercial cultivars. The main objectives of this research were to map the RPF3 locus from spinach cultivar Whale inoculated with P. effusa race 16 and to identify associated SNP markers and candidate genes. A spinach breeding population derived from a cross of cultivars Whale and Lazio were inoculated with P. effusa race 16 in a growth chamber and dew chamber facility, and disease responses were recorded. Association analysis conducted in multiple programs using Genotyping by sequencing (GBS) markers identified six significant SNPs. The downy mildew resistance RPF3 locus was mapped to a 0.57 Mb region on chromosome 3 that includes four disease resistance candidate genes (Spo12736, Spo12784, Spo12908, and Spo1282) within 2.69-11.28 kb of the peak SNP. Genome-wide association analysis approach was used to map the resistant locus and identify associated SNP markers and the candidate genes. The results from this study could be valuable in understanding the genetic basis of downy mildew resistance, and the SNP marker will be useful in spinach breeding to select for spinach lines resistant to race 16.