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

Abstract

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 KNOXs 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.

Keywords: I. trifida; I. triloba; KNOX; Abiotic stress; Hormone treatment; Sweet potato; Tissue-specific expression.

Fig. 1

Chromosomal localization and distribution of IbKNOXs (a), ItfKNOXs (b) and ItbKNOXs (c). The bars represented chromosomes, the chromosome numbers were displayed on the left side, and the gene names were displayed on the right side

Fig. 2

Phylogenetic analysis of the KNOXs in I. batatas, I. trifida, I. triloba, and A. thaliana. The green pentagram, blue circles, yellow squares, pink triangles respectively represented the 17 IbKNOXs in I. batatas, 12 ItfKNOXs in I. trifida, 11 ItbKNOXs in I. triloba, and 9 AtKNATs in Arabidopsis thaliana. The red line represented the Class I, the dark blue line represented the Class II, and the black line represented the Class M

Fig. 3

Conserved domains and exon-intron structure of KNOXs in I. batatas, I. trifida, and, I. triloba. (a) Phylogenetic tree and conserved domain structures of KNOXs. The red box represented the KNOX1 domain. The blue box represented the KNOX2 domain. The green box represented the ELK domain. The brown box represented the Homeobox-KN domain. The purple box represented the PLN02617 domain. (b) Exon-intron structures of KNOXs. The yellow boxes, green boxes, and black lines represented the UTRs, exons, and introns, respectively

Fig. 4

Cis-elements analysis of IbKNOXs in I. batatas. The cis-elements were divided into five categories. The depth of different colors represented the number of cis-elements in the IbKNOXs promoter

Fig. 5

Functional interaction networks of IbKNOXs in I. batatas according to orthologues in Arabidopsis. Network nodes represented proteins, and lines represented protein-protein associations. The size of the nodes indicated the number of interacting proteins. Dark blue IbKNOXs represented homologous proteins of Arabidopsis in I. batatas

Fig. 6

Gene expression patterns of IbKNOXs in different tissues. The gene expression patterns of IbKNOXs in leaf, petiole, stem, stem tip, pencil root, fibrous root, and storage root of Longshu 9 (a) and Xushu 18 (b) were determined by RNA-seq. Log2 (FPKM) was shown in the boxes

Fig. 7

Gene expression patterns of ItfKNOXs and ItbKNOXs in different tissues. The gene expression patterns of KNOXs in flowers, buds, leaf, stem, root 1, root 2 of I. trifida (a) and I. triloba (b) were determined by RNA-seq. Log2 (FPKM) was shown in the boxes

Fig. 8

Gene expression patterns of IbKNOXs in storage roots in Xu 22 at different periods. F represented fibrous root (diameter of approximately 1 mm), D1 represented initial storage root (diameter of approximately 1 cm), D3 represented storage root (diameter of approximately 3 cm), D5 represented storage root (diameter of approximately 5 cm) and D10 represented storage root (diameter of approximately 10 cm)

Fig. 9

Gene expression patterns of ItfKNOXs and ItbKNOXs under different hormones treatments. The gene expression patterns of KNOXs under ABA, GA3, and IAA treatments in I. trifida (a) and I. triloba (b) were determined by RNA-seq. CK: Hormone control. Log2 (FPKM) was shown in the boxes

Fig. 10

Gene expression patterns of IbKNOXs under PEG and NaCl treatments. (a) Expression analysis of IbKNOXs under PEG treatment in a drought-tolerant line Xu55-2. (b) Expression analysis of IbKNOXs under NaCl treatment in a salt-sensitive variety lzx and a salt-tolerant line ND98. Gene expression level data were determined by RNA-seq. Log2 (FPKM) was shown in the boxes

Fig. 11

Gene expression patterns of ItfKNOXs and ItbKNOXs under abiotic stresses. (a) Expression analysis of ItfKNOXs under 10/4 ℃ (day/night), mannitol and NaCl treatments in I. trifida. (b) Expression analysis of ItbKNOXs under 10/4 ℃ (day/night), mannitol and NaCl treatments in I. triloba. CK1: Cold control, CK2: Mannitol and NaCl control. Gene expression level data were determined by RNA-seq. Log2 (FPKM) was shown in the boxes