Genome-wide identification and expression analysis of the KNOX family and its diverse roles in response to growth and abiotic tolerance in sweet potato and its two diploid relatives

• Published in: BMC genomics Vol. 25; no. 1; pp. 572 - 18
• Main Authors: Jia, Li-Cong, Yang, Zi-Tong, Shang, Li-Li, He, Shao-Zhen, Zhang, Huan, Li, Xu, Xin, Guo-Sheng
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 06.06.2024; BioMed Central; BMC
• Subjects: Abiotic stress; Chromosomes; Diploids; Diploidy; Drought; Ecosystem components; Environmental aspects; Gene expression; Gene Expression Profiling; Gene Expression Regulation, Plant; Genes; Genetic aspects; Genetic research; Genome, Plant; Genomes; Genomic analysis; Genomics; Grain size; Growth; Homeobox; Homeobox genes; Homeodomain Proteins - genetics; Homeodomain Proteins - metabolism; Homeotic genes; Hormone treatment; I. trifida; I. triloba; Ipomoea batatas; Ipomoea batatas - genetics; Ipomoea batatas - growth & development; Ipomoea batatas - metabolism; KNOX; KNOX gene; Localization; Mannitol; Maximum likelihood method; Molecular weight; Morphogenesis; Multigene Family; Nucleotide sequence; Pesticides; Phylogenetics; Phylogeny; Physicochemical properties; Physiological aspects; Plant Proteins - genetics; Plant Proteins - metabolism; Potatoes; Promoter Regions, Genetic; Protein structure; Proteins; Roots; Sodium chloride; Software; Stress, Physiological - genetics; Structural analysis; Sweet potato; Sweet potatoes; Tissue-specific expression; Vegetables; China; Tissue-specific expression; I. trifida; Abiotic stress; Sweet potato; I. triloba; Hormone treatment; KNOX
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/s12864-024-10470-4

KNOXs , a type of homeobox genes that encode atypical homeobox proteins, play an essential role in the regulation of growth and development, hormonal response, and abiotic stress in plants. However, the KNOX gene family has not been explored in sweet potato. In this study, through sequence alignment, genomic structure analysis, and phylogenetic characterization, 17, 12 and 11 KNOX s in sweet potato ( I. batatas , 2n = 6x = 90) and its two diploid relatives I. trifida (2n = 2x = 30) and I. triloba (2n = 2x = 30) were identified. The protein physicochemical properties, chromosome localization, phylogenetic relationships, gene structure, protein interaction network, cis -elements of promoters, tissue-specific expression and expression patterns under hormone treatment and abiotic stresses of these 40 KNOX genes were systematically studied. IbKNOX4, -5 , and − 6 were highly expressed in the leaves of the high-yield varieties Longshu9 and Xushu18. IbKNOX3 and IbKNOX8 in Class I were upregulated in initial storage roots compared to fibrous roots. IbKNOXs in Class M were specifically expressed in the stem tip and hardly expressed in other tissues. Moreover, IbKNOX2 and − 6 , and their homologous genes were induced by PEG/mannitol and NaCl treatments. The results showed that KNOXs were involved in regulating growth and development, hormone crosstalk and abiotic stress responses between sweet potato and its two diploid relatives. This study provides a comparison of these KNOX genes in sweet potato and its two diploid relatives and a theoretical basis for functional studies.