Genome-wide association analysis identifies candidate loci associated with hydroxycinnamic acid accumulation in sweetpotato

Hydroxycinnamic acid-related compounds are important phenolic bioactive constituents in sweetpotato storage roots and play important roles in quality formation and abiotic stress responses. In this study, the contents of 33 hydroxycinnamic acid-related compounds were determined in 229 sweetpotato germplasm accessions grown in three agroecological regions. Genome-wide association analysis (GWAS) was conducted to identify candidate genes, and the relationships of these genes with hydroxycinnamic acid-related compounds accumulation and abiotic stress responses were further investigated. The results showed that the 33 hydroxycinnamic acid-related compounds exhibited extensive natural variation within the population. Comprehensive evaluation identified several high-accumulation accessions, including BZ13, BZ31, BZ19, BZ20, and BZ30. GWAS identified 4,938 significant SNP-trait associations. Stable signals for FA-4-O-GlcA and isoFer-C1-GlcA were detected in the 19.71-21.09 Mb interval on Iba_chr05a, whereas recurrent signals on Iba_chr10a were concentrated in the 24.88-25.10 Mb and 25.54-26.14 Mb intervals. Candidate gene analysis identified genes encoding caffeoylshikimate esterase (CSE), UDP-glycosyltransferases (UGTs), ATP-binding cassette transporters (ABC transporters), and several transcription factors. Transcriptome analysis under stress conditions further showed that several candidate genes were differentially expressed under drought, heat, and cold stresses, indicating that they may also participate in abiotic stress responses in sweetpotato. Overall, this study revealed the natural variation and genetic basis of hydroxycinnamic acid-related compounds in sweetpotato and identified candidate loci and genes associated with both hydroxycinnamic acid-related compounds accumulation and abiotic stress responses, providing candidate loci for subsequent molecular marker development and useful genetic resources for functional quality improvement and stress-tolerant breeding in sweetpotato.