Genome-wide Identification and Expression Analysis of the Rice BXL Gene Family

doi:10.13560/j.cnki.biotech.bull.1985.2024-1215

Abstract

Abstract:

Objective BXL (β-D-xylosidase) belongs to the third family of glycoside hydrolases, which catalyzes the degradation of xylan in the cell wall, and plays a key role in regulating plant growth and development as well as abiotic stress response. Evolutionary and expression analysis of the OsBXL gene family will facilitate further exploration of their functions in rice. Method Bioinformatic technologies were used for analyzing the phylogenetic relationships, replication events, gene structure, conserved motifs, and tissue expression profiles of OsBXLs, and fluorescence quantitative PCR was used to investigate the expression pattern of OsBXLs under abiotic stress and hormone treatments. Result There are 10 members in rice BXL gene family, which can be divided into three subfamilies, with Group III specific to monocots. The gene structures and structural domains of OsBXLs within each group showed a high similarity. Gene location analysis indicated that OsBXL family members were unevenly distributed on 4 chromosomes, with OsBXL5/6/7/8 on chromosome 4 in a gene cluster. Transcriptome data revealed that OsBXL1/2/3/4/8 showed high expressions in a majority of detected tissues/organs, while OsBXL5/6/7/10 were expressed at low levels. Notably, the expressions of OsBXL7/10 were significantly high at the certain stage during the maturation of young inflorescence and seed. Moreover, three haplotypes of OsBXL7 were identified in the natural population, and significant differences in grain length, width, and thousand-grain weight were observed among different haplotypes. Fluorescence quantitative PCR revealed different expression patterns of OsBXLs under drought, saline-alkali, abscisic acid and methyl jasmonate treatments. Conclusion The OsBXL gene family is highly conserved, OsBXL7 is possibly involved in regulating rice grain size, while OsBXL1/3 simultaneously respond to salt-alkali stress and methyl jasmonate treatment. Together, these results provide a key guide for future functional analyses of OsBXL genes in rice.

Key words: rice, β-D-xylosidase, grain size, abiotic stress, hormone response

WU Hao, DONG Wei-feng, HE Zi-tian, LI Yan-xiao, XIE Hui, SUN Ming-zhe, SHEN Yang, SUN Xiao-li. Genome-wide Identification and Expression Analysis of the Rice BXL Gene Family[J]. Biotechnology Bulletin, 2025, 41(6): 87-98.

Figures/Tables 10

Table 1 Primers for quantitative fluorescence PCR

基因名称 Gene name	上游引物 Forward primer （5'-3'）	下游引物 Reverse primer （5'-3'）
OsBXL1	GCTGACCAACCTCTACCTCAC	TGCCACCGAATTGACCTTCT
OsBXL2	CACGTACAACCCTCCGTTCA	CCTCCAATCTCCCCTTGCAG
OsBXL3	TACGGAGAGGAAGGCAGGAT	CTTGCACGACCTTCCTGGAT
OsBXL4	AGCACTACACCGCATACGAC	AGCACATAACACTGGCCACA
OsBXL8	AACGGTGTCCAACGCTACAA	GGCGCACATTATGCACGTAG
OsELf1-α	CATGATCACCGGTACCTCG	CCAGCATGTTGTCTCCGTG

Fig. 1 Functional domains and sequence alignment of OsBXL proteinsA: Schematic diagram of structural domains in proteins. B: Multiple sequence alignment of proteins; SP: signal peptide, Glyco_hydro_3 domain: N-terminal catalytic domain of glycoside hydrolase; Glyco_hydro_3_C domain: C-terminal catalytic domain of glycoside hydrolase; Fn 3-like domain: fibronectin type Ⅲ domain. red boxes mark the WGR and KH conserved sites, the blue triangle refers to the nucleophilic catalytic amino acid residue site Asp, the black triangle refers to the acid-base catalytic amino acid residue Glu

Table 2 Basic information of OsBXLs

基因名称 Gene name	基因登录号 Gene ID	蛋白长度 Length of protein sequences （aa）	分子量 Molecular weight （kD）	理论等电点 Theoretical pI	亲疏水性 GRAVY	亚细胞定位/置信度 Subcellular location/Probability	信号肽位置 Signal peptide position （aa）
OsBXL1	LOC_Os01g19220	771	82.60	6.61	-0.191	细胞壁/0.7852 Cell wall	1-24
OsBXL2	LOC_Os02g51620	818	87.12	5.21	0.030	细胞壁/0.7618 Cell wall	1-27
OsBXL3	LOC_Os04g44840	782	83.43	5.77	-0.110	细胞壁/0.753 Cell wall	1-20
OsBXL4	LOC_Os04g54810	770	83.65	5.84	-0.111	细胞壁/0.8309 Cell wall	1-26
OsBXL5	LOC_Os11g18690	793	85.03	6.33	-0.103	细胞壁/0.5974 Cell wall	1-26
OsBXL6	LOC_Os11g18730	780	84.30	6.32	-0.146	细胞壁/0.8285 Cell wall	1-22
OsBXL7	LOC_Os11g19160	853	91.66	9.10	-0.130	细胞壁/0.7545 Cell wall	1-21
OsBXL8	LOC_Os11g19210	816	88.75	6.19	-0.150	细胞壁/0.6741 Cell wall	1-31
OsBXL9	LOC_Os11g44950	765	80.92	6.42	0.022	细胞壁/0.8602 Cell wall	1-18
OsBXL10	LOC_Os11g47350	664	70.19	7.92	-0.069	细胞壁/0.7416 Cell wall	1-24

Fig. 2 Phylogenetic relation analysis of rice BXL familyThe green area indicates Group I, the light green area indicates Group II, and the orange area indicates Group Ⅲ

Fig. 3 Gene structures and conserved motifs of OsBXLsA: Phylogenetic tree of the OsBXL genefamily. B: The intron-exon architecture, yellow boxes indicate CDS, green boxes indicate UTR, and solid lines indicate intron. C: Conserved motifs, different colored boxes at the bottom indicate different motifs

Fig. 4 Chromosomal location and protein sequence similarity of OsBXLsA: Chromosomal location, with the light green areas highlighting gene cluster containing four members. B: Protein sequence similarity of OsBXLs, with the numbers shown in the figure indicating amino acid similarity expressed as a percentage (%)

Fig. 5 Co-linearity analysis of BXL family genes in rice, maize, and ArabidopsisThe background gray lines indicate synteny in the genomes of rice with maize and Arabidopsis. The red lines indicate the synteny of OsBXLs with ZmBXLs and AtBXLs. The blue, green, and yellow bars indicate the chromosomes of Arabidopsis, rice, and maize, respectively

Fig. 6 Tissue expression pattern of OsBXLs genes family membersThe red line area corresponds to Cluster I, while the green line area corresponds to Cluster II; Log2FPKM >7 is defined as high expression, and Log2FPKM <7 is defined as low expression

Fig. 7 Haplotype analysis of OsBXL7 based on the coding sequenceA: Schematic of the base and amino acid variations in different haplotypes of OsBXL7, CDS: coding sequence; AA: amino acids; REF: reference haplotype. B: Distribution of varieties with different haplotypes of OsBXL7. C-F: The grain length, grain width, length/width ratio and thousand-grain weight of rice varieties with different haplotypes of OsBXL7, respectively. P values were calculated by one-way ANOVA analysis

Fig. 8 Expression analysis of OsBXLs under abiotic stress and hormone treatmentA: Drought stress. B: Salt-alkali stress. C: ABA treatment. D: MeJA treatment; * and ** indicate P <0.05, P <0.01, respectively

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