Genome-Wide Analysis of KNOX Transcription Factors and Expression Pattern of Dwarf-Related KNOX Genes in Pear

Abstract

KNOTTED1-like homeobox (KNOX) transcription factors (TFs) belonging to the homeobox TF family play important roles in plant growth, development, and responses to abiotic and biotic stress. However, little information is available on KNOX TF in pear (Pyrus). In this study, 19 PbKNOXs TFs were re-identified in pear (Pyrus bretschneideri Rehd.). Phylogenetic analysis revealed that the TFs were clustered into three groups with 10 conserved motifs, some of which were group- or subgroup-specific, implying that they are important for the functions of the KNOX in these clades. PbKNM1 and PbKNM2 are KNM (encodes a MEINOX domain but not a homeodomain) genes identified in pear for the first time. KNOX genes in Pyrus and Malus were closely related, and a collinear relationship among PbKNOX genes in Pyrus and Malus was observed. Analysis of the expression patterns of PbKNOX genes in different tissues, at various growth stages, and in response to abiotic and biotic stress revealed that PbKNOXs are involved in plant growth and development. Our comparative transcriptional analysis of dwarf mutant varieties revealed that genes belonging to class I are highly expressed compared with genes in other classes. Analysis of the expression of PbKNOX genes in the hybrid offspring of vigorous and dwarf varieties revealed that PbKNOX genes were highly expressed in the vigorous offspring and weakly expressed in the dwarf offspring. These findings provide new insight into the function of KNOX TFs in pear and will aid future studies of dwarf fruit trees.

Genome-wide identification of three-amino-acid-loop-extension gene family and their expression profile under hormone and abiotic stress treatments during stem development of Prunus mume

“…A later study found that the silencing of GhKNOX10 and GhKNOX14 in cotton reduced the tolerance of seedlings to salt stress, while the silencing of GhKNOX2 enhanced the salt tolerance of cotton seedlings (Zhang et al, 2021b). Members of the pear KNOX subfamily can respond to drought stress treatment, specifically, the expression of PbKNOX7/13 is increased under drought stress, while the expression of PbKNOX5/16 is inhibited under drought stress (Liu et al, 2022). In this study, the promoter analysis of TALE genes of P. mume revealed a variety of abiotic stress elements, including low temperature, drought, hypoxia induction, and trauma response.…”

“…The promoters of TALE gene family members in soybean contained cis-elements that responded to various stresses, and the expression level of GmTALE genes could change in response to salt stress and drought stress (Wang et al, 2021). Overexpression of the KNOX-like gene TaKNOX11-A of Triticum aestivum in A. thaliana can increase the content of proline and reduce the content of malondialdehyde, thereby enhancing the salt tolerance and drought resistance of the plant (Han et al, 2022). Cotton BELL-like gene GhBLH5-A05 plays an important role in combating drought stress.…”

“…Populus alba × P. glandulosa KNOX subfamily member PagKNAT2/6b can be significantly induced by drought treatment, and can mediate drought response by down-regulating PagGA20ox1 gene of GA pathway (Song et al, 2021). Members of the pear KNOX subfamily can respond to drought stress treatment, specifically, the expression of PbKNOX7/13 is increased under drought stress, while the expression of PbKNOX5/16 is inhibited under drought stress (Liu et al, 2022).…”

“…The members of the KNOX subfamily of pear have an important regulatory effect on the growth and development of pear. Specifically, they are highly expressed in robust hybrid progeny and weakly expressed in dwarf hybrid progeny (Liu et al, 2022). In addition, PbKNOX in pear can inhibit the level of lignin, thereby regulating the formation of stone cells in fruit (Cheng et al, 2019).…”

Genome-Wide Analysis of Anthocyanin Biosynthesis Regulatory WD40 Gene FcTTG1 and Related Family in Ficus carica L.

“…Genes with similar amino acid sequences usually have similar functions, and vice versa ( Liu et al, 2022 ). Eight TTG1 proteins from different plants were found to be 78.2%–99.12% homologous, indicating that the functions of TTG1s are conserved in different species.…”