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United States Department of Agriculture

Agricultural Research Service

Research Project: Genetic Enhancement of Lettuce, Spinach, Melon, and Related Species

Location: Crop Improvement and Protection Research

Title: SNP association analysis of resistance to Verticillium wilt (Verticillium dahliae Kleb.) in spinach

Author
item Shi, Ainong
item Mou, Beiquan
item Correll, James
item Motes, Dennis
item Weng, Yuejin
item Qin, Jun
item Yang, Wei

Submitted to: Australian Journal of Crop Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/7/2016
Publication Date: 8/1/2016
Citation: Shi, A., Mou, B., Correll, J., Motes, D., Weng, Y., Qin, J., Yang, W. 2016. SNP association analysis of resistance to Verticillium wilt (Verticillium dahliae Kleb.) in spinach. Australian Journal of Crop Science. 10(8):1188-1196.

Interpretive Summary: Spinach (Spinacia oleracea L.) is an economically important vegetable crop worldwide. Verticillium wilt, caused by the pathogen Verticillium dahliae Kleb. is one of important fungus diseases in spinach and the most economical method of control this disease is through the use of genetic resistance, especially for organic growers. The objective of this research is to evaluate resistance resources and to conduct association analysis for Verticillium wilt resistance in spinach. A total of 95 USDA spinach germplasm accessions were screened for resistance to Verticillium wilt in this study. Significant differences in Verticillium wilt disease resistance were observed among the 95 spinach accessions with a wide range of disease severity scores from 0.3 to 3. Eight varieties, NSL 81328, NSL 92513, PI 169675, PI 174960, PI 176774, PI 179588, PI 204732, and PI 204735, showed highest Verticillium wilt resistance with disease severity scores of 1 or less. Genotyping by sequencing (GBS) technique was used in this study and around half million molecular markers (SNPs) were discovered from the 95 spinach genotypes. After filtering, 2,878 SNPs were used for genetic diversity and association analysis. Seven SNP markers (AYZV01040555-2183, AYZV01049272-10266, AYZV01084682-14543, AYZV01092619-146, AYZV01108434-3277, AYZV01145092-156, and AYZV01203883-41) were identified to be strongly associated with Verticillium wilt. These markers can be utilized in molecular spinach breeding for Verticillium wilt resistance.

Technical Abstract: Verticillium wilt, caused by Verticillium dahliae Kleb. is one of important fungus diseases in spinach (Spinacia oleracea L.) and the most economical method of control this disease is through the use of genetic resistance, especially for organic growers. The objective of this research is to evaluate resistance resources and to conduct association analysis for Verticillium wilt resistance in spinach. A total of 95 USDA spinach germplasm accessions were screened for resistance to Verticillium wilt in this study. Significant genetic variance of Verticillium wilt disease resistance was observed among the 95 spinach accessions with a wide range of disease severity scores from 0.3 to 3. Eight genotypes, NSL 81328, NSL 92513, PI 169675, PI 174960, PI 176774, PI 179588, PI 204732, and PI 204735, showed highest Verticillium wilt resistance with disease severity rate 1 or less. Genotyping by sequencing (GBS) was conducted and around half million SNPs were discovered from the 95 spinach genotypes. After filtering, 2,878 SNPs were used for genetic diversity and association analysis. Two well-differentiated genetic populations and admixtures were postulated in the spinach panel by STRUCTURE 2.3.4 and MEGA 6. Association analysis for Verticillium wilt resistance was done using single marker regression (SMR), general linear mode (GLM), and mixed linear mode (MLM) by Tassel 5, GAPIT, and QGene 4. Seven SNP markers (AYZV01040555-2183, AYZV01049272-10266, AYZV01084682-14543, AYZV01092619-146, AYZV01108434-3277, AYZV01145092-156, and AYZV01203883-41) were identified to be strongly associated with Verticillium wilt resistance with LOD ranged from 2.53 to 4.69 and R-squared from 9.4 – 18.5% for these SNP markers. These markers can be utilized in molecular spinach breeding for Verticillium wilt resistance.

Last Modified: 10/17/2017
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