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Folate profile diversity and associated SNPs using genome wide association study in pea

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Abstract

Folates are important metabolic cofactors essential for human growth and development. Eighty-five accessions from a pea genome wide association study (GWAS) panel were evaluated for folate profile using ultra-performance liquid chromatography coupled with mass spectrometry. A GWAS was conducted to identify SNP markers associated with the folate profile of pea. Five folates were quantified and the sum of folates ranged from 14 to 55 µg/100 g dry weight. Significant differences (P < 0.001) were observed among the accessions for all folates. The pea accessions were genotyped using genotyping-by-sequencing. After filtering for a read depth of five and minor allele frequency of 0.05, 14,391 SNPs were used for marker-trait association. Five SNP markers were significantly (P < 0.01) associated with the sum of folates. Fifteen, eight, and three SNP markers were associated with 5-methyltetrahydrofolate (5-MTHF), 5-formyltetrahydrofolate, and tetrahydrofolate, respectively. Based on associated SNP markers, an additional 24 accessions were evaluated for folate profile, and those predicted to have a relatively high folate concentration had a significantly greater concentration of 5-MTHF and the sum of folates than those predicted to have a lower concentration. In these accessions, Sc_6992_86348 and Sc_3060_11265 were significantly associated with 5-MTHF and the sum of folates in Saskatoon 2016. Six SNP markers were converted into KASP markers, and these can be used for marker-assisted selection in pea breeding.

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Acknowledgements

We gratefully acknowledge the financial support from the NSERC Industrial Research Chair in Lentil Genetic Improvement, the Saskatchewan Pulse Growers, and the Saskatchewan Ministry of Agriculture. We are thankful to Thermo Fisher for the use of the TSQ Vantage as part of a collaboration between the University of Saskatchewan and Thermo Fisher. We are also thankful to the pulse crop breeding staff at the University of Saskatchewan for their technical assistance.

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  1. Randy W. Purves

    Present address: Canadian Food Inspection Agency, 116 Veterinary Road, Saskatoon, SK, S7N 2R3, Canada

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  1. Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada

    Ambuj B. Jha, Krishna K. Gali, Haixia Zhang, Randy W. Purves, Bunyamin Tar’an, Albert Vandenberg & Thomas D. Warkentin

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Jha, A.B., Gali, K.K., Zhang, H. et al. Folate profile diversity and associated SNPs using genome wide association study in pea. Euphytica 216, 18 (2020). https://doi.org/10.1007/s10681-020-2553-8

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