Submitted to: American Journal of Plant Sciences
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/19/2016
Publication Date: 8/22/2016
Citation: Shi, A., Mou, B., Correll, J., Koike, S., Motes, D., Qin, J., Weng, Y., Yang, W. 2016. Association analysis and identification of SNP markers for Stemphylium leaf spot (Stemphylium botryosum f. sp. spinacia) resistance in spinach (Spinacia oleracea). American Journal of Plant Sciences. 7:1600-1611.

Interpretive Summary: Stemphylium leaf spot, caused by a fungus Stemphylium botryosum, is an important disease in spinach. Use of genetic resistance is an efficient, economic and environment-friendly method to control this disease. The objective of this research was to conduct analysis and identify molecular markers associated with Stemphylium leaf spot resistance in spinach varieties. A total of 295 spinach varieties including 20 commercial cultivars were used for the analysis of leaf spot resistance. DNA of the varieties were sequenced to study the genetic diversity and association with the disease. The spinach varieties showed a wide range of disease incidence from 0 to 100%, suggesting that the Stemphylium leaf spot resistance in spinach is a complex trait, which may be controlled by many genes. Analysis indicated that seven molecular markers were associated with Stemphylium leaf spot resistance, which are located in four regions of the spinach chromosomes. The molecular markers identified may be useful for breeders to select plants for Stemphylium leaf spot resistance in spinach breeding programs.

Technical Abstract: Stemphylium leaf spot, caused by Stemphylium botryosum f. sp. spinacia is an important disease in spinach. Use of genetic resistance is an efficient, economic and environment-friendly method to control this disease. The objective of this research was to conduct association analysis and identify SNP markers associated with Stemphylium leaf spot resistance in spinach germplasm. A total of 295 spinach genotypes including 275 accessions of the USDA spinach germplasm collection and 20 commercial cultivars were used for the association analysis of leaf spot resistance. Genotyping by sequencing (GBS) was used as genotyping and 794 SNPs from GBS were used for genetic diversity and association analysis. The distribution of Stemphylium leaf spot resistance showed a near normal distribution with a wide range from 0 to 100% disease incidence, suggesting that the Stemphylium leaf spot resistance in spinach is a complex trait, which may be a quantitative trait controlled by minor genes. Association analysis indicated that seven SNP markers were associated with Stemphylium leaf spot resistance with a LOD greater than 2.5. Among the seven SNP markers, AYZV02031464_90, AYZV02031464_94, and AYZV02031464_95 were located at the same contig AYZV02031464 with only five bp distance; AYZV02076752_426 and AYZV02076752_431 at the same contig AYZV02076752 with only five bp distance; and other two SNPs, AYZV02124848_365 and AYZV02149880_108 at contig AYZV02124848 and AYZV02149880, respectively, indicating there are four genome regions (QTLs) for Stemphylium leaf spot resistance in spinach. The SNP markers may be useful for breeders to select plants and lines for Stemphylium leaf spot resistance in spinach breeding programs through marker-assisted selection.