水稻BXL基因家族的全基因组鉴定及表达分析

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

生物技术通报 ›› 2025, Vol. 41 ›› Issue (6): 87-98.doi: 10.13560/j.cnki.biotech.bull.1985.2024-1215

水稻BXL基因家族的全基因组鉴定及表达分析

吴浩¹(), 董伟峰¹, 贺子天¹, 李艳肖¹, 谢辉², 孙明哲¹^,³, 沈阳¹^,⁴(), 孙晓丽¹()

^1.黑龙江八一农垦大学农学院作物逆境分子生物学实验室，大庆 163319
^2.国家粳稻工程技术研究中心，天津 300450
^3.北大荒垦丰种业股份有限公司，哈尔滨 150090
^4.黑龙江八尺禾科技有限公司，佳木斯 154000

收稿日期:2024-12-17 出版日期:2025-06-26 发布日期:2025-04-23
通讯作者: 沈阳，男，博士，研究方向：寒地作物逆境生理与分子调控；E-mail: shenyang2024@byau.edu.cn
孙晓丽，女，博士，教授，研究方向：寒地作物逆境生理与分子调控；E-mail: csmbl2016@126.com
作者简介:吴浩，男，硕士研究生，研究方向：寒地作物逆境生理与分子调控；E-mail: 2864288928@qq.com
基金资助:
中央引导地方科技发展专项项目(ZY24QY02);国家自然科学基金项目(U20A2025);中国博士后科学基金(2024MD763990);中国博士后科学基金(2021T140185);黑龙江省重点研发计划(2022ZX02B05);黑龙江省“双一流”学科协同创新成果孵化项目(LJGXCG2023-072);领航英才庆雁支持计划“新雁”团队项目(LJGXCG2024-F20);黑龙江八一农垦大学研究生创新科研项目(YJSCX2023-Y12)

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

WU Hao¹(), DONG Wei-feng¹, HE Zi-tian¹, LI Yan-xiao¹, XIE Hui², SUN Ming-zhe¹^,³, SHEN Yang¹^,⁴(), SUN Xiao-li¹()

^1.Crop Stress Molecular Biology Laboratory, College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing 163319
^2.National Japonica Rice Engineering and Technology Research Center, Tianjin 300450
^3.Beidahuang Kenfeng Seed Industry Co. , Ltd. , Harbin 150090
^4.Heilongjiang Bachihe Technology Co. , Ltd. , Jiamusi 154000

Received:2024-12-17 Published:2025-06-26 Online:2025-04-23

摘要/Abstract

摘要：

目的 BXL（β-D-xylosidase）属于β-木糖苷酶中第三族糖苷水解酶，负责催化细胞壁中木聚糖的降解，在植物生长发育及抵御非生物胁迫过程中发挥关键作用。鉴定和分析水稻OsBXL家族基因的进化及表达，为深入探究其功能奠定基础。方法通过生物信息学手段对OsBXL基因家族进行系统进化关系、复制事件、基因结构、保守基序及组织表达特征分析，并通过荧光定量PCR验证OsBXLs家族成员在非生物胁迫和激素处理下的表达变化情况。结果水稻BXL基因家族有10个成员，可划分为3个亚家族，其中Group III为单子叶植物特有；各亚族内的基因结构及保守结构域均表现出高度相似性；OsBXL基因分布在4条染色体上，其中4号染色体上的OsBXL5/6/7/8形成一个基因簇；转录组数据显示，OsBXL1/2/3/4/8在大多数组织中表现出较高的表达水平，而OsBXL5/6/7/10表达则相对较低；OsBXL7/10基因在特定发育阶段的幼穗和种子中高表达；OsBXL7在自然群体中存在3种不同单倍型，不同单倍型品种的籽粒长度、宽度和千粒重存在显著差异；荧光定量PCR结果显示，OsBXL家族成员对干旱、盐碱、脱落酸和茉莉酸甲酯处理的响应模式不同。结论水稻BXL基因家族具有高度的保守性，OsBXL7可能调控水稻籽粒大小，OsBXL1/3同时响应盐碱胁迫和茉莉酸甲酯处理。这些结果将为未来研究OsBXL基因功能提供重要参考。

关键词: 水稻, β-D-木糖苷酶, 籽粒大小, 非生物胁迫, 激素响应

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

吴浩, 董伟峰, 贺子天, 李艳肖, 谢辉, 孙明哲, 沈阳, 孙晓丽. 水稻BXL基因家族的全基因组鉴定及表达分析[J]. 生物技术通报, 2025, 41(6): 87-98.

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.

图/表 10

表1 荧光定量PCR引物信息

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

图1 OsBXLs蛋白保守结构域及序列比对A：蛋白结构域示意图；B：蛋白序列比对。SP：信号肽，Glyco_hydro_3 domain：糖苷水解酶N端催化结构域，Glyco_hydro_3_C domain：糖苷水解酶C端催化结构域，Fn 3 like domain：纤维连接蛋白Ⅲ型结构域；红色方框标注WGR和KH保守位点，蓝色三角形为亲核催化氨基酸残基位点Asp，黑色三角形为酸碱催化氨基酸残基位点Glu

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

表2 OsBXLs的基本信息

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

图2 水稻BXL家族系统进化关系分析绿色区域为Group Ⅰ、浅绿色区域为Group Ⅱ、橙色区域为Group Ⅲ

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

图3 OsBXLs基因结构和保守基序分析A：OsBXLs基因家族进化树；B：内含子-外显子结构组成，黄色方块代表CDS区、绿色方块代表UTR区域，实线代表内含子区域；C：保守基序，不同的motif对应关系位于图底部

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

图4 OsBXLs基因染色体分布和蛋白序列相似度A：染色体定位，浅绿色区域显示4个OsBXLs基因簇；B：OsBXLs蛋白序列相似度，图中展示的数字表示氨基酸相似度，单位为百分比（%）

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 (%)

图5 水稻、玉米和拟南芥BXL家族基因共线性分析背景中灰线代表水稻与玉米和拟南芥基因组中的共线性基因对，红线代表OsBXLs与ZmBXLs和AtBXLs具有共线性的基因对；蓝色、绿色和黄色线条分别表示拟南芥、水稻和玉米的染色体

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

图6 OsBXLs家族成员的组织表达模式Seedling root：幼苗根；Mature leaf：成熟叶；Young leaf：幼叶；SAM：叶芽顶端分生组织；Inflorescence花序（P1：花序原基阶段；P2-P4：枝梗分化阶段；P5-P6：小穗分化阶段）；Seed种子（S1：授粉后初期；S2-S3：胚发育阶段；S4-S5：籽粒成熟阶段）。红线区域对应Cluster I；绿线区域对应Cluster Ⅱ；将Log2FPKM >7定义为高表达；Log2FPKM <7定义为低表达

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

图7 OsBXL7基因CDS区单倍型分析A：OsBXL7不同单倍型碱基及氨基酸变化示意图，CDS：编码序列，AA：编码氨基酸，REF：参考单倍型；B：不同OsBXL7单倍型的品种分布图；GJ：粳稻，XI：籼稻，admix：混合类型，Bas：基础品种；C-F：分别为不同OsBXL7单倍型的水稻籽粒长度、宽度、长宽比和千粒重；P值采用单因素方差分析计算

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

图8 OsBXLs基因在非生物胁迫和激素处理下的表达分析A：干旱胁迫；B：盐碱胁迫；C：ABA处理；D：MeJA处理；*，**分别表示P <0.05，P <0.01

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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水稻BXL基因家族的全基因组鉴定及表达分析

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

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