水稻孤雌生殖诱导基因BBM1序列变异分析

doi:10.16819/j.1001-7216.2024.231210

摘要/Abstract

摘要：

【目的】在水稻卵细胞中异位表达BBM1能够诱导孤雌生殖，挖掘BBM1优异等位变异和功能类似基因对水稻杂种优势固定具有重要意义。【方法】利用383份水稻核心种质的三代测序数据，对BBM1基因进行结构变异分析、序列多态性分析、单倍型分析，并根据序列相似度以及表达模式相似度筛选BBM1功能类似基因。【结果】BBM1基因在3份种质中存在两个拷贝，在2份野生稻中存在微型颠倒重复转座元件（MITEs）插入变异；具有非常明显的籼粳分化，94.80%的粳稻和3.80%的籼稻中BBM1因单碱基变异造成翻译提前终止，缺少26个氨基酸残基；BBM1编码区序列十分保守，绝大多数材料中具有相同的单倍型；筛选到BBM1序列和表达模式相似基因LOC_Os06g44750，其可能具有BBM1诱导孤雌生殖的功能。【结论】明确了水稻中BBM1基因变异情况，挖掘出重要单倍型和功能类似候选基因，为进一步提高水稻孤雌生殖频率奠定基础。

关键词: 水稻, BBM1, 孤雌生殖, 序列变异

Abstract:

【Objective】Ectopic expression of BBM1 in rice egg cells can induce parthenogenesis. Exploring superior allelic variants of BBM1 and functionally similar genes is of great significance for heterosis fixation in rice.【Method】By utilizing third-generation sequencing data from 383 core rice accessions, we conducted an analysis of structural variations, sequence polymorphisms, and haplotypes of BBM1. Additionally, we screened for genes with similar sequences and expression patterns to identify functional analogues of BBM1.【Results】Our findings revealed the presence of two copies of the BBM1 gene in three rice accessions, along with MITEs insertion variants observed in two O. rufipogon accessions. The BBM1 sequence exhibited a clear indica-japonica differentiation, with 94.80% of japonica accessions and 3.80% of indica accessions experiencing premature termination due to single base mutations, resulting in the loss of 26 amino acid residues. Furthermore, the coding region of BBM1 is highly conserved, and most rice accessions share the same haplotype. We also identified LOC_Os06g44750 as a candidate gene with a similar sequence and expression pattern to BBM1, which may potentially contribute to inducing parthenogenesis.【Conclusion】This study provides insights into the variation present within the BBM1 gene in rice while also identifying important haplotypes and potential candidate genes with functional similarities. This foundational knowledge serves to enhance the frequency of parthenogenesis in rice.

Key words: rice, BBM1, parthenogenesis, sequence variation

汪晴, 王艳茹, 张秀丽, 吕启明. 水稻孤雌生殖诱导基因BBM1序列变异分析[J]. 中国水稻科学, 2024, 38(6): 627-637.

WANG Qing, WANG Yanru, ZHANG Xiuli, LÜ Qiming. Sequence Variation Analysis of the Parthenogeny-inducing Gene BBM1 in Rice[J]. Chinese Journal OF Rice Science, 2024, 38(6): 627-637.

图/表 10

图1 BBM1结构变异 A、B、C分别为TG12、wild12和NH190的BBM1结构变异示意图。其中蓝色代表BBM1侧翼大片段重复序列，红色代表BBM1基因序列。D: CW13和CW16中BBM1基因结构图。其中酒红色代表外显子，黄色代表内含子，▲代表MITE插入位点。

Fig. 1. Structural variation of BBM1 A, B, C show the BBM1 structural variants of TG12, wild12 and NH190, blue represents the BBM1 flanking large fragment repeat sequence and red represents the BBM1 gene sequence. D: Map of BBM1 gene structure of CW13 and CW16, burgundy represents exons, yellow represents introns, and ▲ represents MITE insertion sites.

图2 野生稻、籼稻和粳稻中BBM1序列核苷酸多态性 A、B、C分别表示野生稻、籼稻和粳稻中BBM1序列核苷酸多性。酒红色表示BBM1外显子，橙色表示BBM1内含子。

Fig. 2. Nucleotide diversity of BBM1 sequences in different rice accessions A, B and C show the nucleotide polymorphisms of BBM1 sequence in wild rice, indica and japonica rice, respectively. The BBM1 exon is shown in burgundy and the BBM1 intron in orange.

表1 不同水稻材料中BBM1序列多态性分析

Table 1. Analysis of BBM1 sequence polymorphism in different rice accessions

水稻类型 Rice type	对比序列数Number of sequences used	多态性位点Number of polymorphic (segregating) sites	突变总数 Total number of mutations	单倍体数Number of haplotypes	单倍型多样性Haplotype (gene) diversity	单倍型多态性方差 Variance of haplotype diversity	单倍型多态性标准差 Standard deviation of haplotype diversity	核苷酸多态性Nucleotide diversity
核心种质 Core collections	383	268	285	69	0.868	0.0001	0.010	0.00506
野生稻 Wild rice	30	196	200	29	0.998	0.00009	0.009	0.00623
籼稻 indica	204	91	94	22	0.786	0.00045	0.021	0.00333
粳稻 japonica	103	77	79	11	0.318	0.00359	0.060	0.00131

图3 383份水稻材料中BBM1序列进化关系分析

Fig. 3. Evolutionary relationship analysis of BBM1 sequences in 383 rice accessions

图4 单倍型分析

Fig. 4. Haplotype analysis

图5 BBM1结构域示意图 BBM1含有两个AP2结构域，红色代表AP2结构域，蓝色代表氨基酸序列，数字代表氨基酸位置。

Fig. 5. Schematic representation of the BBM1 domain BBM1 contains two AP2 domains, the AP2 domain in red, the amino acid sequence in blue, and the amino acid position in numbers.

表2 不同单倍型中非同义突变位点

Table 2. Nonsynonymous mutation sites in different haplotypes

单倍型 Haplotype	数量 Number	16	67	69	107	124	142	146	147	147.1	258	351	445	493	521	537	561
Hap-1	109	S	T	A	M	V	G	A	A	-	R	T	T	P	D	L	stop
Hap-36	92	S	T	A	M	A	D	A	A	-	R	I	T	P	D	V	+26AA
Hap-37	51	S	M	A	M	A	G	A	A	-	R	T	T	P	D	V	+26AA
Hap-22	29	S	T	A	M	A	G	A	A	-	R	T	T	Q	D	V	+26AA
Hap-17	17	S	T	A	M	A	G	A	A	-	R	T	T	P	D	V	+26AA
Hap-40	12	S	T	A	M	A	D	A	A	-	R	I	I	P	D	V	+26AA
Hap-4	10	S	T	A	M	A	G	-	-	-	R	T	T	P	N	V	+26AA
Hap-6	5	S	T	A	M	A	G	-	-	-	R	T	T	P	D	V	+26AA
Hap-43	4	Y	T	D	M	V	G	A	A	A	R	T	T	P	D	L	stop
Hap-23	3	S	T	A	M	A	G	A	A	-	R	T	T	P	D	V	+26AA
Hap-8	2	S	T	A	M	A	G	-	-	-	\	\	\	\	\	\	\
Hap-44	2	S	T	A	T	A	G	A	A	-	R	T	T	P	D	V	+26AA

图6 不同类型BBM1序列验证 A: 2941份水稻材料中不同BBM1类型分布，青色表示发生提前终止BBM1，绿色表示正常的BBM1；B: NIPP和R498中BBM1编码区序列全长扩增琼脂糖电泳结果；C: NIPP中BBM1编码区测序峰图；D: R498中BBM1序列编码区测序峰图。

Fig. 6. Validation of different types of BBM1 sequences A, Distribution map of different BBM1 types in 2941 rice accessions, cyan indicates the occurrence of premature termination of BBM1, and green indicates normal BBM1; B, Results of agarose electrophoresis of full-length amplified BBM1 coding region sequences in NIPP and R498; C, Sequencing peak map of BBM1 coding region in NIPP; D, Sequencing peak map of BBM1 coding region in R498.

图7 水稻AP2/ERF家族系统进化树

Fig. 7. Phylogenetic tree of the AP2/ERF family in rice

图8 候选基因组织表达谱

Fig. 8. Tissue expression profiles of candidate genes

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