Genetic diversity and population structure analysis of spinach by single-nucleotide polymorphisms identified through genotyping-by-sequencing

Authors: SHI, AINONG - University Of Arkansas; QIN, JUN - University Of Arkansas; Mou, Beiquan; CORRELL, JIM - University Of Arkansas; WENG, YUEJIN - University Of Arkansas; BRENNER, DAVID - Iowa State University; FENG, CHUNDA - University Of Arkansas; MOTES, DAVID - University Of Arkansas; YANG, WEI - University Of Arkansas; DONG, LINGDI - University Of Arkansas; BHATTARAI, GEHENDRA - University Of Arkansas; RAVELOMBOLA, WALTRAM - University Of Arkansas

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/17/2017
Publication Date: 11/30/2017
Citation: Shi, A., Qin, J., Mou, B., Correll, J., Weng, Y., Brenner, D., Feng, C., Motes, D., Yang, W., Dong, L., Bhattarai, G., Ravelombola, W. 2017. Genetic diversity and population structure analysis of spinach by single-nucleotide polymorphisms identified through genotyping-by-sequencing. PLoS One. 12(11):e0188745. https://doi.org/10.1371/journal.pone.0188745.
DOI: https://doi.org/10.1371/journal.pone.0188745

Interpretive Summary: Spinach (Spinacia oleracea L.) is an economically important vegetable crop worldwide and one of the healthiest vegetables due to its high concentrations of nutrients and mineral compounds. The objective of this research is to conduct genetic diversity and population structure analysis of world-wide spinach varieties using molecular markers. DNA sequencing was used to discover molecular markers in spinach varieties. Three types of spinach varieties were studied: (1) 268 USDA spinach germplasm accessions originally collected from 30 countries, (2) 45 commercial spinach F1 hybrid cultivars from 3 countries, and (3) 30 University of Arkansas spinach breeding lines. The results from this study indicated that (i) there were large variations existing in the all 343 spinach varieties tested, in the 45 commercial hybrid cultivars, or in the 30 Arkansas lines; (ii) the genetic backgrounds in commercial hybrid cultivars and in Arkansas cultivar/lines have been improved for cultivation and both have different genetic structures from the USDA germplasm accessions; (iii) genetic diversity and differences in genetic structures were associated with geography – region and country; and (iv) Arkansas spinach lines had special genetic background. This research will provide genetic diversity information for selecting parents and how to use spinach germplasm varieties in spinach breeding programs.

Technical Abstract: Spinach (Spinacia oleracea L., 2n=2x=12) is an economically important vegetable crop worldwide and one of the healthiest vegetables due to its high concentrations of nutrients and mineral compounds. The objective of this research is to conduct genetic diversity and population structure analysis of world-wide spinach genotypes using single nucleotide polymorphisms (SNP) markers. Genotyping by sequencing (GBS) was used to discover SNPs in spinach genotypes. Three types of spinach genotypes were used: (1) 268 USDA GRIN spinach germplasm accessions originally collected from 30 countries, (2) 45 commercial spinach F1 hybrids from 3 countries, and (3) 30 US Arkansas spinach breeding lines. The results from this study indicated that (i) there were large variations existing in the all 343 spinach genotypes tested as a panel, in the 45 commercial hybrids, or in the 30 Arkansas lines; (ii) the genetic backgrounds in commercial F1 hybrids and in Arkansas cultivar/lines have been improved for cultivation and both have different structured populations from the USDA germplasm; (iii) genetic diversity and population structures were associated with geography – region and country; and (iv) US Arkansas spinach lines had special genetic background. This research will provide genetic diversity information for selecting parents and how to use spinach germplasm in spinach breeding programs.