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ARS Home » Pacific West Area » Salinas, California » Crop Improvement and Protection Research » Research » Publications at this Location » Publication #342147
Title: Genetic diversity and association mapping of mineral element concentrations in spinach leaves

Author
item QIN, JUN - University Of Arkansas
item SHI, AINONG - University Of Arkansas
item Mou, Beiquan
item Grusak, Michael
item WENG, YUEJIN - University Of Arkansas
item RAVELOMBOLA, WALTRAM - University Of Arkansas
item BHATTARAI, GEHENDRA - University Of Arkansas
item DONG, LINGDI - University Of Arkansas
item YANG, WEI - University Of Arkansas

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/13/2017
Publication Date: 12/4/2017
Citation: Qin, J., Shi, A., Mou, B., Grusak, M.A., Weng, Y., Ravelombola, W., Bhattarai, G., Dong, L., Yang, W. 2017. Genetic diversity and association mapping of mineral element concentrations in spinach leaves. BMC Genomics. 18:941. https://doi.org/10.1186/s12864-017-4297-y.
DOI: https://doi.org/10.1186/s12864-017-4297-y

Interpretive Summary: Spinach is one of the healthiest vegetables in the human diet due to its high concentrations of nutrients and mineral elements. Breeding new spinach cultivars with high nutritional value is one of the main goals in spinach breeding programs worldwide, and identification of molecular markers for mineral elements is necessary to support spinach molecular breeding. The purpose of this study was to conduct genomic research and identify molecular markers associated with mineral elements in the USDA spinach germplasm collection. A total of 14 mineral elements: boron (B), calcium (Ca), cobalt (Co), copper (Cu), iron (Fe), potassium (K), magnesium (Mg), manganese (Mn), molybdenum (Mo), sodium (Na), nickel (Ni), phosphorus (P), sulfur (S), and zinc (Zn) were evaluated in 292 spinach accessions originally collected from 29 countries. Significant genetic variations among varieties as evidenced by the 2 – 42 times differences in mineral concentrations suggest that genetic improvement for mineral traits should be feasible. A total of 2,402 molecular markers were identified from DNA sequencing and were used for genetic diversity and association studies. Forty-five molecular markers were identified to be strongly associated with the concentrations of 13 mineral elements, except K which had two weak associated markers. Three molecular markers were associated with the accumulation of four mineral components, Co, Mn, S, and Zn, the concentrations of which were also highly correlated. This suggests that it is possible to pyramid high contents of multiple elements in a single spinach cultivar through breeding. Thirty-one spinach accessions, which rank in the top three highest content in each of the 14 mineral elements, were identified for spinach breeding programs in the future. The molecular markers underlying mineral elements could potentially be used in breeding programs to improve the spinach mineral elements.

Technical Abstract: Spinach is one of the healthiest vegetables in the human diet due to its high concentrations of nutrients and mineral elements. Breeding new spinach cultivars with high nutritional value is one of the main goals in spinach breeding programs worldwide, and identification of single nucleotide polymorphism (SNP) markers for mineral elements is necessary to support spinach molecular breeding. The purpose of this research was to conduct genome-wide association study (GWAS) and identify SNP markers associated with mineral elements in the USDA GRIN spinach germplasm collection. A total of 14 mineral elements: boron (B), calcium (Ca), cobalt (Co), copper (Cu), iron (Fe), potassium (K), magnesium (Mg), manganese (Mn), molybdenum (Mo), sodium (Na), nickel (Ni), phosphorus (P), sulfur (S), and zinc (Zn) were evaluated in 292 spinach accessions originally collected from 29 countries. Significant genetic variations among genotypes as evidenced by the 2 – 42 times differences in mineral concentrations suggest that genetic improvement for mineral traits should be feasible. A total of 2,402 SNPs identified from genotyping by sequencing (GBS) approach were used for genetic diversity and GWAS. Forty-five SNP markers were identified to be strongly associated with concentrations of 13 mineral elements, except K which had two weak associated SNP markers. The six statistic methods used were: single marker regression using Q-gene (SMR), single marker regression using Tassel (SMR), general linear model using Tassel (GLM), mixed linear model using Tassel (MLM), compressed mixed linear model using Gapit (cMLM), and enriched compressed mixed linear model using Gapit (EcMLM). Co-localization of SNPs for different element accumulations has been discovered in this research. Three SNP markers, AYZV02017731_40, AYZV02094133_57, and AYZV02094133_185 were identified to be associated with four mineral components, Co, Mn, S, and Zn. There is a high validating correlation coefficient with r > 0.7 among the four elements. This suggests that it is possible to pyramid high contents of multiple elements in a single spinach cultivar through breeding. Thirty-one spinach accessions, which rank in the top three highest content in each of the 14 mineral elements, were identified for spinach breeding programs in the future. The SNPs underlying mineral elements could potentially be used in breeding programs to improve the spinach mineral elements.