Genome-wide association study identified candidate genes controlling continuous storage root formation and bulking in hexaploid sweetpotato
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Date
2020
Journal Title
Journal ISSN
Volume Title
Publisher
BMC plant biology
Abstract
Continuous storage root formation and bulking (CSRFAB) in sweetpotato is an important trait from
agronomic and biological perspectives. Information about the molecular mechanisms underlying CSRFAB traits is
lacking.
Results: Here, as a first step toward understanding the genetic basis of CSRFAB in sweetpotato, we performed a
genome-wide association study (GWAS) using phenotypic data from four distinct developmental stages and 33,068
single nucleotide polymorphism (SNP) and insertion-deletion (indel) markers. Based on Bonferroni threshold (pvalue
< 5 × 10− 7), we identified 34 unique SNPs that were significantly associated with the complex trait of CSRFAB
at 150 days after planting (DAP) and seven unique SNPs associated with discontinuous storage root formation and
bulking (DCSRFAB) at 90 DAP. Importantly, most of the loci associated with these identified SNPs were located
within genomic regions (using Ipomoea trifida reference genome) previously reported for quantitative trait loci
(QTL) controlling similar traits. Based on these trait-associated SNPs, 12 and seven candidate genes were
respectively annotated for CSRFAB and DCSRFAB traits. Congruent with the contrasting and inverse relationship
between discontinuous and continuous storage root formation and bulking, a DCSRFAB-associated candidate gene
regulates redox signaling, involved in auxin-mediated lateral root formation, while CSRFAB is enriched for genes
controlling growth and senescence.
Conclusion: Candidate genes identified in this study have potential roles in cell wall remodeling, plant growth,
senescence, stress, root development and redox signaling. These findings provide valuable insights into
understanding the functional networks to develop strategies for sweetpotato yield improvement. The markers as
well as candidate genes identified in this pioneering research for CSRFAB provide important genomic resources for
sweetpotato and other root crops.
Description
Keywords
DArTseq, Genotyping-by-sequencing, GWAS, CSRFAB, GBSapp, Polyploid, SNPs, Sweetpotato
Citation
Bararyenya, A., Olukolu, B. A., Tukamuhabwa, P., Grüneberg, W. J., Ekaya, W., Low, J., ... & Mwanga, R. O. (2020). Genome-wide association study identified candidate genes controlling continuous storage root formation and bulking in hexaploid sweetpotato. BMC plant biology, 20(1), 1-16. https://doi.org/10.1186/s12870-019-2217-9