番茄果重基因功能型分子标记的开发及群体基因型分析

doi:10.13560/j.cnki.biotech.bull.1985.2025-0101

摘要/Abstract

摘要：

目的开发并利用分子标记技术进行群体基因型分析，解析番茄（Solanum lycopersicum）果重调控关键基因Fruit weight 3.2（Fw3.2）和Fruit weight 11.3（Fw11.3）在不同驯化阶段的遗传变异规律，为番茄遗传资源的精准鉴定、高效利用和野生种质快速驯化提供有效工具。方法基于基因组序列比对，针对Fw3.2基因的拷贝数变异以及Fw11.3基因3′端1.4 kb的大片段插入缺失变异，分别设计了片段长度多态性分子标记。并利用上述分子标记对259份番茄材料［79份野生种醋栗番茄（S. pimpinellifolium, PIM），95份过渡种樱桃番茄（S. lycopersicum var. cerasiforme, CER），以及85份栽培种大果番茄（big-fruited S. lycopersicum, BIG）］进行基因型分析，以确定Fw3.2和Fw11.3的变异形式及其在不同番茄群体中的分布。结果开发的分子标记能够精准区分Fw3.2基因的拷贝数变异（fw3.2^WT 和fw3.2^dup ）以及Fw11.3基因的大片段插入缺失变异（fw11.3-WT和fw11.3-D）。在起源种醋栗番茄群体中，大果等位基因型fw3.2^dup 和fw11.3-WT的频率分别为0%和2.53%；在过渡种樱桃番茄群体中，这2个等位基因型的比例分别上升至10.53%和8.42%；而在栽培种大果番茄群体中，fw3.2^dup 和fw11.3-WT的比例分别达到了69.41%和92.94%。结论 fw3.2^dup 和fw11.3-D等位基因可以显著提高番茄果重，且二者能够以协同增效的方式发挥作用，从而更大幅度地提高番茄果重。在番茄驯化和改良的过程中，fw3.2^dup 和fw11.3-D大果等位基因的频率呈现出递增的趋势，表现出与果重增大的演化模式相一致的特点。

关键词: 番茄, 果重, 分子标记, Fw3.2, Fw11.3, 拷贝数变异, 插入缺失变异, 驯化

Abstract:

Objective This study is aimed to develop and apply molecular markers to identify and analyze the patterns of genetic variation in Fruit weight 3.2 (Fw3.2) and Fruit weight 11.3 (Fw11.3), two pivotal genes involved in the regulation of tomato (Solanum lycopersicum) fruit weight, at different domestication stages. It is expected to provide effective tools for the precise identification and utilization of tomato genetic resources, as well as the rapid domestication of wild germplasm. Method Fragment length polymorphism molecular markers were designed specifically based on the copy number variation (CNV) of Fw3.2 and the 1.4 kb large fragment insertion/deletion (Indel) variation at the 3′ end of Fw11.3. These markers were used to conduct genotype analysis on a collection of 259 tomato germplasms (including 79 Solanum pimpinellifolium (PIM) accessions, 95 Solanum lycopersicum var. cerasiforme (CER) accessions and 85 big-fruited S. lycopersicum accessions (BIG)), determining variation of Fw3.2 and Fw11.3 and their distribution within different tomato populations. Result By the molecular markers developed in this study, the CNVs (fw3.2^WT and fw3.2^dup ) of the Fw3.2 gene and the large fragment Indel variants of the Fw11.3 gene (fw11.3-WT and fw11.3-D) were successfully identified. Within PIM population, the frequencies of the large-fruit alleles fw3.2^dup and fw11.3-D were 0 and 2.53%, respectively. In the CER population, these allele frequencies increased to 10.53% for fw3.2^dup and 8.42% for fw11.3-D. Notably, in the BIG population, the prevalence of fw3.2^dup and fw11.3-D alleles rose significantly to 69.41% and 92.94%, respectively. Conclusion Both fw3.2^dup and fw11.3-D alleles significantly increase tomato fruit weight. Furthermore, these alleles lead to a synergistic effect that further enhances fruit weight in tomatoes. During the domestication and genetic improvement of tomatoes, the frequency of these large-fruit alleles has progressively increased, mirroring the evolutionary trajectory toward larger fruit size.

Key words: tomato, fruit weight, molecular marker, Fw3.2, Fw11.3, copy number variation, insertion/deletion variation, domestication

侯亚涛, 李迎辉, 邓磊, 李常保, 李传友, 孙传龙. 番茄果重基因功能型分子标记的开发及群体基因型分析[J]. 生物技术通报, 2025, 41(4): 98-105.

HOU Ya-tao, LI Ying-hui, DENG Lei, LI Chang-bao, LI Chuan-you, SUN Chuan-long. Development of Functional Molecular Markers for Tomato Fruit Weight Gene and Population Genotyping Analysis[J]. Biotechnology Bulletin, 2025, 41(4): 98-105.

图/表 7

表1 Fw3.2和Fw11.3 基因分子标记引物序列

Table 1 Primer sequences for molecular markers of the Fw3.2 and Fw11.3 gene

引物名称 Primer name	引物序列 Primer sequence （5′‒3′）
Fw3.2-pol-F	GTATAAGACTGTTCACTACG
Fw3.2-pol-R1	CGAATCAGCAGTATACACTG
Fw3.2-pol-R2	GTGGATGTGATGCATCAACT
Fw11.3-polF	TCACCGTCATCAATCAAAAT
Fw11.3-polR1	CAATTAATTACTATCGAAACGC
Fw11.3-polR2	CATATGCATTTAGTGAGGTTG

图1 Fw3.2（A）和Fw11.3（B）基因结构及引物位置示意图fw3.2WT 代表Fw3.2基因单拷贝等位基因型，fw3.2dup 代表Fw3.2基因双拷贝等位基因型；fw11.3-WT代表Fw11.3基因的野生型等位基因型；fw11.3-D代表Fw11.3基因3′基因区存在大片段缺失的等位基因型。下同

Fig. 1 Schematic diagram of the Fw3.2 (A) and Fw11.3 (B) gene structures and primer locationsfw3.2WT refers to the single-copy allele of the Fw3.2 gene, while fw3.2dup refers to the duplicated allele of the Fw3.2 gene. fw11.3-WT refers to the wild-type allele ofthe Fw11.3 gene, and fw11.3-D indicates the allele with a large fragment deletion in the 3′ region of the Fw11.3 gene. The same below

图2 不同番茄材料Fw3.2（A）和Fw11.3（B）多态性引物检测M：Marker；LA1589和LA1375为起源种醋栗番茄，Brandywine和M82为栽培种大果番茄

Fig. 2 Polymorphic primer detection for Fw3.2 (A) and Fw11.3 (B) in different tomato materialsM: Marker. LA1589 and LA1375 are S. pimpinellifolium (PIM) accessions, while Brandywine and M82 are big-fruited S. lycopersicum (BIG) accessions

图3 Fw3.2（A）和Fw11.3（B）等位基因型频率分析PIM：醋栗番茄；CER：樱桃番茄；BIG：大果栽培番茄。下同

Fig. 3 Allele frequency analysis of Fw3.2 (A) and Fw11.3 (B)A: PIM: S. pimpinellifolium. CER: S. lycopersicum var. cerasiforme. BIG: Big-fruited S. lycopersicum. The same below

表2 不同地理来源的番茄材料基因型分析结果 (accessions)

Table 2 Genotype analysis of tomato accessions collected from different geographic origins

地理来源 Geographic origin	类别 Category	fw3.2^WT	fw3.2^dup	fw11.3-WT	fw11.3-D
美洲 the Americas	PIM	76	0	74	2
	CER	83	10	85	8
	BIG	16	3	5	14
亚洲 Asia	BIG	2	48	1	49

图4 不同番茄群体中Fw3.2和Fw11.3单倍型分析结果fw3.2WTfw11.3-WT：单倍型1；fw3.2WTfw11.3-D：单型2；fw3.2dupfw11.3-WT：单倍型3；fw3.2dup fw11.3-D：单倍型4。下同

Fig. 4 Haplotype analysis of Fw3.2 and Fw11.3 in different tomato populationsfw3.2WTfw11.3-WT: Haplotype 1; fw3.2WTfw11.3-D: haplotype 2; fw3.2dupfw11.3-WT: haplotype 3; fw3.2dup fw11.3-D: haplotype 4. The same below

图5 不同番茄群体果重表型分析A：醋栗番茄、樱桃番茄和大果栽培番茄代表性图片，Bar = 1 cm；B：醋栗番茄、樱桃番茄和大果栽培番茄果重；C‒D：樱桃番茄（C）和大果栽培番茄（D）群体中Fw3.2不同基因型材料的果重表型差异；E‒F：樱桃番茄（E）和大果栽培番茄（F）群体中Fw11.3不同基因型材料的果重表型差异；G：大果栽培番茄群体中不同单倍型材料的果重表型差异。图B和图G采用单因素方差分析检验差异显著性，图C‒F采用双尾t-test检验差异显著性，不同字母代表差异显著（P<0.05）

Fig. 5 Phenotypic analysis of fruit weight in different tomato populationsA: Representative images of PIM, CER and BIG varieties. Bar = 1 cm. B: Fruit weight of PIM, CER, and BIG tomatoes. C‒D: Phenotypic variation in fruit weight among distinct Fw3.2 genotypes within CER (C) and BIG (D) populations. E‒F: Phenotypic variation in fruit weight among distinct Fw11.3 genotypes within CER (E) and BIG (F) populations. G: Phenotypic variation in fruit weight among distinct Fw3.2 and Fw11.3 haplotypes within the BIG. Significance of differences was tested using one-way ANOVA for panels B and G, and two-tailed t-tests for panels C‒F. Different letters indicate significant differences (P < 0.05)

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