Genome-wide association study to identify novel loci and genes for Fusarium root rot resistance in sweet potato using genotyping-by-sequencing

Tae Hwa Kim; Sujung Kim; Won Park; Koan Sik Woo; Keunpyo Lee; Mi Nam Chung; Young Hoon Lee; Hyeong-Un Lee; Kyo Hwui Lee; Sang-Sik Nam; Hyun Jo; Jeong-Dong Lee

doi:10.3389/fpls.2023.1251157

Genome-wide association study to identify novel loci and genes for Fusarium root rot resistance in sweet potato using genotyping-by-sequencing

Front Plant Sci. 2023 Oct 4:14:1251157. doi: 10.3389/fpls.2023.1251157. eCollection 2023.

Authors

Affiliations

¹ Bioenergy Crop Research Institute, National Institute of Crop Science, Rural Development Administration, Muan, Republic of Korea.
² International Technology Cooperation Center, Technology Cooperation Bureau, Rural Development Administration, Jeonju, Republic of Korea.
³ Planning and Coordination Division, National Institute of Crop Science, Rural Development Administration, Jeonju, Republic of Korea.
⁴ Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea.

Abstract

Fusarium root rot, caused by Fusarium solani, is a major post-harvest disease in sweet potatoes (Ipomoea batatas (L.) Lam.). An effective strategy for controlling this disease is the development of resistant varieties. In this study, a genome-wide association study (GWAS) was conducted on 96 sweet potato genotypes to identify novel candidate loci and dissect the genetic basis of Fusarium root rot resistance. Genotyping was performed using genotyping-by-sequencing (GBS), and 44,255 SNPs were identified after filtering. The genotypes (n = 96) were evaluated through resistance tests in 2021 and 2022, separately and combined. The GWAS identified two significant SNP markers (LG3_22903756 and LG4_2449919) on chromosomes 3 and 4 associated with Fusarium root rot resistance, respectively. Lesion length showed significant differences between homozygous A and G alleles of LG3_22903756, which can potentially be used to develop molecular markers for selecting accessions resistant to Fusarium root rot. Expression analysis of 11 putative genes flanking the significant SNPs revealed the alteration in the expression of nine genes, indicating their possible involvement in Fusarium root rot resistance. The results of this study will aid in the marker-assisted selection and functional analysis of candidate genes for Fusarium root rot resistance in sweet potatoes.

Keywords: Fusarium root rot; genome-wide association study; genotyping-by-sequencing; resistance; sweet potato.

Grants and funding

The authors declare financial support was received for the research, authorship, and/or publication of this article. This study was supported by a grant from the National Institute of Crop Science (NICS), Rural Development Administration, Republic of Korea (Agenda Project No. PJ01605802).