Current Research

My main research focus is to conduct research on the USDA Specialty Crop Research Initiative (SCRI) and the USDA Agricultural Marketing Service for a multi-state project to evaluate and develop disease resistance to downy mildew, white rust, and Fusarium wilt, develop genomic resources and identify SNP markers associated with the three main diseases in spinach. In addition, I am also involved in genetic studies of abiotic and biotic stress tolerances in other crops.

 

Downy mildew, caused by the obligate oomycete Peronospora effusa [P. farinosa f. sp. spinaciae (Pfs)], is the most economically important disease of spinach. New Pfs races are emerging and are overcoming newly deployed genetic resistances making downy mildew a major challenge for the sustainability of the spinach industry. White rust, caused by an obligate fungal pathogen Albugo occidentalis, is a serious disease of spinach in the United States, mainly in southern Texas. Utilization of host genetic resistance is an optimal breeding practice from both economic and ecologic viewpoints to limit disease occurrence and minimize crop loss. The spinach collection has been screened for resistance to downy mildew, white rust, and important traits. A varying level of resistance has been reported across the evaluated panels. Identifying additional resistance sources against the known races of Pfs and understanding the mechanism of genetic resistance could increase genetic resources to improve resistance durability. However, a challenge remains in the gaps in our knowledge of genetics and molecular aspects of qualitative and quantitative host resistance, pathogen virulence factors, and the mechanism of pathogen evolution. Our current aims include genetic characterization of the resistance sources to identify gene-based markers to facilitate R-gene pyramiding, plus a comprehensive and systematic understanding of the complex genetic mechanism of the disease resistances in spinach. 

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Research activities in the UofA vegetable breeding program

• Breeding activities in vegetable crops (spinach, cowpea, arugula).

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• Genetic investigations of tolerances to biotic and abiotic stress in spinach, cowpea, tomato, common bean, arugula. 

 

My recent accomplishments and ongoing activities:​

• I led the whole genome resequencing (WGR) at ~10x coverage of 480 USDA spinach germplasm accessions.

  • More than thirty million SNPs were identified following WGR based on the Monoe-Viroflay assembly​. 

  • We are using these new genomic datasets to perform identify genetic association to commercially import traits and standardizing genomic selection models.

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• Phenotypic evaluation of targeted traits in spinach germplasm panel.

  • Field tolerances to downy mildew in Salinas, California and Yuma, Arizona.

  • Resistance to white rust in Southern Texas.

  • Greenhouse screening for resistance to Stemphylium leaf spot.

  • Greenhouse screening for tolerance to Pythium aphanidermatum.

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• GWAS and GS of the phenotyped traits using WGR generated SNPs based on new genome assembly.

  • Preliminary reports were presented in the past using GBS-generated SNPs and the WGR generated SNPs using the Sp75 assembly.

  • SNPs identified using the new Monoe-Viroflay are now used for GWAS and GS. 

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• Genetic diversity studies of wild and cultivated spinach germplasm.

  • Wild and cultivated accessions at the CGN and USDA are added to this effort.

  • All accessions from the CGN spinach collection have been genotyped. We are now pursuing population genetics studies and characterizing the genetic basis of important traits using the GWAS approach..

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• QTL mapping of multiple spinach populations segregating for downy mildew and other important traits.

  • SNPs generated via low-coverage genome resequencing. 

  • Map the targeted traits at high-resolution.

  • Generate consensus maps. 

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• Characterize the molecular mechanism of downy mildew resistance in spinach using transcriptomics and proteomics approaches.

  • ​RNAseq and proteomics data from resistant (NIL3) and susceptible (Viroflay) genotypes inoculated with race 5 of downy mildew pathogen during the infection period have been generated. We are characterizing the host-pathogen interactions. 

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• I am engaged and involved in abiotic and biotic stress tolerances studies in other cowpea, common beans, arugula.

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• Bacterial wilt, salt, drought, and heat tolerances evaluation of tomato germplasm panel. Genotyping and diversity studies, GWAS, and GS.

  • I supervise and mentor graduate students (1 PhD, 2 MS) in Dr. Shi’s lab to perform tomato genetics research.