Genome-wide association study to identify loci for sweetpotato root traits using dosage-sensitive models

Authors: Bowers Jr, Robert; SLONECKI, TYLER - Cornell University; OLUKOLU, BODE - University Of Tennessee; YENCHO, G - North Carolina State University; Wadl, Phillip

Submitted to: International Journal of Molecular Sciences
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/28/2024
Publication Date: 10/31/2024
Citation: Bowers Jr, R.R., Slonecki, T.J., Olukolu, B.A., Yencho, G.C., Wadl, P.A. 2024. Genome-wide association study to identify loci for sweetpotato root traits using dosage-sensitive models. International Journal of Molecular Sciences. 25(21):11727. https://doi.org/10.3390/ijms252111727.
DOI: https://doi.org/10.3390/ijms252111727

Interpretive Summary: Sweetpotato is essential for global food security, but breeding is challenging due to its large genome and cross compatibility issues. Genome-wide tools have enabled analysis and association studies to identify genetic regions impacting key root traits. We conducted a study on 384 sweetpotato individuals from the USDA germplasm collection and identified 33 molecular markers linked to traits like dry matter content and flesh color. Candidate genes linked to traits such as starch and beta-carotene synthesis were also identified. These findings support existing research on molecular markers for root traits and introduce new markers for breeders to develop improved sweetpotato varieties. These findings will be useful to public and private plant breeders and others working with sweetpotato.

Technical Abstract: Sweetpotato (Ipomoea batatas) is an important food crop that plays a pivotal role in preserving worldwide food security. Due to its polyploid genome, high heterogeneity, and phenotypic plasticity, sweetpotato genetic characterization and breeding is challenging. Genome wide association studies (GWAS) can provide important resources for breeders to improve breeding efficiency and effectiveness. GWASpoly was used here to identify 31 single nucleotide polymorphisms (SNPs) comprising 26 unique genetic loci associated with storage root traits including: dry matter (4 loci), subjective flesh color (6 loci), flesh hue angle (3 loci), subjective skin color and hue angle (10 loci), and shape (3 loci) in 384 accessions from the USDA sweetpotato germplasm collection. The I. batatas ‘Beauregard’ and I. trifida reference genomes were utilized to identify candidate genes located within 100 kb from the SNPs that may affect the key agronomic storage root traits of dry matter, color, and shape. These candidate genes include transcription factors (especially Myb, bHLH, and WRKY family members), metabolite transporters, and metabolic enzymes and associated proteins involved in starch, carotenoid, and anthocyanin synthesis. A greater understanding of the genetic loci underlying sweetpotato storage root traits will enable marker-assisted breeding of new varieties with desired traits. This study not only reinforces previous research findings on genetic loci associated with dry matter and 'beta-carotene content but also introduces novel genetic loci linked to these traits as well as other root characteristics.