InDel marker combination for identifying authenticity of tomato varieties and seed purity and application thereof

Abstract

The application belongs to the technical field of agricultural vegetable variety identification, and particularly relates to an InDel marker combination for identifying the authenticity of tomato varieties and the purity of seeds and application thereof. 84 InDel markers which are uniformly distributed in the whole genome of tomatoes and have good polymorphism are successfully developed. According to the polymorphism differences of the markers in different types of tomatoes, core identification marker combinations suitable for ordinary fresh tomatoes, taste tomatoes, processing tomatoes and cherry tomatoes are respectively screened, each of which contains 48, 36, 48 and 48 pairs of primers, and a variety DNA fingerprint is constructed accordingly, and the application is successfully applied to the construction of a variety fingerprint, authenticity identification and hybrid purity detection, thereby providing technical support for the management of tomato germplasm resources, molecular breeding and variety right protection.

Description

Technical Field

[0001] This invention belongs to the field of agricultural vegetable variety identification technology, specifically relating to an InDel marker combination for identifying the authenticity of tomato varieties and seed purity and its application. Background Technology

[0002] tomato( Solanum lycopersicum L.) belongs to the Solanaceae family ( Solanaceae Solanum genus ( Solanum Tomato (Tomato germplasm) is an annual or perennial herbaceous plant. Due to the rich nutritional value of its fruits, it has become a widely cultivated and important vegetable crop globally, occupying a significant position in vegetable production. With the rapid development of seed technology, tomato breeding levels have significantly improved, and the application rate of domestically bred varieties in production continues to rise. Against this backdrop, the scientific management and efficient utilization of tomato germplasm resources has become a core key to supporting the sustainable development of the industry.

[0003] Traditional methods of variety identification mainly rely on morphological traits such as plant structure, leaves, and fruits. However, these traits are easily affected by both environmental conditions and the subjectivity of human assessment, leading to significant phenotypic differences in the same variety under different growing environments, which seriously affects the stability and reliability of identification results. In contrast, DNA fingerprinting technology based on molecular markers has outstanding advantages such as high genetic stability, immunity to environmental interference, and high detection throughput, and has become an important auxiliary tool for modern variety identification.

[0004] With the continuous decline in the cost of high-throughput sequencing technology, novel molecular markers developed based on whole-genome resequencing, such as single nucleotide polymorphisms (SNPs) and insertion / deletion (InDel) markers, have been widely used. In the genome, the polymorphism frequency of InDel markers is second only to SNP markers, and they can be detected by polymerase chain reaction (PCR) combined with conventional agarose gel electrophoresis or polyacrylamide gel electrophoresis, offering significant advantages in terms of genotyping simplicity and experimental cost. Therefore, InDel markers are considered an ideal source for developing practical molecular markers across the entire genome and have played a crucial role in genetic research and variety identification of various vegetable crops such as tomato, cucumber, pepper, eggplant, cowpea, and Chinese cabbage. However, the number of InDel markers reported in tomatoes is currently limited, and most of the developed markers are based on minute fragment differences of a few to a dozen bases, typically requiring separation using higher-resolution non-denaturing polyacrylamide gel electrophoresis or high-concentration agarose gel electrophoresis. This, to some extent, limits their widespread adoption and application in conventional breeding laboratories. Therefore, developing an InDel marker system that covers the entire tomato genome, is highly polymorphic, and can be rapidly detected by conventional agarose gel electrophoresis is of great theoretical and practical significance for improving the efficiency and accuracy of tomato variety identification, deepening the genetic evaluation of germplasm resources, and supporting molecular marker-assisted breeding practices. Summary of the Invention

[0005] To address the shortcomings of the existing technology, the purpose of this invention is to provide an InDel marker combination for identifying the authenticity of tomato varieties and the purity of seeds, and its application.

[0006] This invention successfully developed 84 InDel markers that are evenly distributed throughout the tomato genome and exhibit good polymorphism. Based on the differences in polymorphism of these markers in different types of tomatoes, core identification marker combinations suitable for common fresh tomatoes, flavor tomatoes, processing tomatoes, and cherry tomatoes were selected, each containing 48, 36, 48, and 48 primer pairs, respectively. Based on these combinations, varietal DNA fingerprint maps were constructed and successfully applied to varietal fingerprint map construction, authenticity identification, and hybrid purity detection, providing technical support for tomato germplasm resource management, molecular breeding, and variety rights protection.

[0007] The tomato variety "Tainan Xibei" mentioned below refers to the variety that originated in Taiwan Province, China, and is simply referred to as "Tainan Xibei".

[0008] To achieve the above objectives, the present invention adopts the following technical solution: In a first aspect, the present invention provides an InDel marker combination for identifying the authenticity and seed purity of tomato varieties, wherein the chromosomal location of the InDel marker loci, primer pairs, primer sequences, and amplification product size of the InDel marker combination are shown below:

[0009] Preferably, the tomato varieties include common fresh tomatoes, flavor tomatoes, processed tomatoes, and cherry tomatoes; Preferably, the InDel marker primer pairs used to identify the authenticity and seed purity of common fresh tomatoes are 1-1, 1-3, 1-7, 1-8, 1-11, 2-6, 2-7, 2-8, 3-1, 3-3, 3-10, 4-1, 4-2, 4-10, 5-1, 5-2, 5-5, 5-7, 5-9, 6-1, 6-2, 6-6, 7-1, 7-2, 7-5, 7-6, 7-8, 7-11, 8-1, 8-9, 8-10, 9-1, 9-10, 10-1, 10-2, 10-7, 10-9, 10-10, 11-1, 11-2, 11-4, 11-5, 11-6, 12-1, 12-2, 12-4, 12-6, 12-10; Preferably, the InDel marker primer pairs used to identify the authenticity of the tomato flavor and the purity of the seeds are 1-1, 1-3, 1-6, 1-10, 2-6, 2-8, 3-1, 3-3, 3-7, 3-9, 3-10, 4-2, 4-6, 4-10, 5-5, 6-1, 6-2, 6-6, 7-6, 7-8, 7-11, 8-10, 9-1, 9-2, 9-3, 10-1, 10-7, 10-10, 11-4, 11-5, 11-9, 12-1, 12-2, 12-5, 12-6, 12-10; Preferably, the InDel marker primer pairs used to identify the authenticity and seed purity of processed tomatoes are 1-1, 1-3, 1-7, 1-9, 2-7, 2-10, 3-1, 3-8, 3-10, 4-2, 4-6, 4-10, 4-11, 4-12, 5-1, 5-2, 5-5, 5-7, 5-8, 5-9, 5-10, 6-1, 6-2, 7-1, 7-5, 7-6, 7-9, 7-11, 8-2, 8-10, 9-1, 9-2, 9-3, 9-10, 10-2, 10-6, 10-7, 10-9, 11-1, 11-2, 11-3, 11-4, 11-5, 11-6, 12-2, 12-4, 12-6, 12-10; Preferably, the InDel marker primer pairs used to identify the authenticity and seed purity of cherry tomatoes are 1-1, 1-2, 1-3, 1-6, 1-9, 1-10, 1-11, 2-5, 2-9, 2-10, 3-1, 3-7, 3-9, 3-10, 3-11, 4-9, 4-11, 5-1, 5-3, 5-4, 5-8, 6-1, 6-2, 6-6, 6-7, 6-9, 7-5, 7-6, 7-8, 7-10, 8-1, 8-2, 8-8, 8-10, 9-6, 9-8, 9-9, 9-10, 10-2, 10-7, 11-1, 11-3, 11-6, 11-11, 12-2, 12-3, 12-5, 12-10.

[0010] A second aspect of the present invention provides a method for identifying the authenticity of a common fresh tomato variety, comprising the following steps: Genomic DNA was extracted from two unknown common fresh tomato samples; Using the genomic DNA as a template, PCR amplification was performed using the InDel marker primer pair described in the first aspect for identifying the authenticity and seed purity of common fresh tomatoes, and PCR products were obtained. The PCR products were subjected to agarose gel electrophoresis to obtain electrophoretic images, and the tested varieties were genotyped based on the electrophoretic images. If the genotypes of two samples are compared, and the genotypes of two or more loci are different, the two samples are considered to be different; if all genotypes are the same, the two samples are considered to be of the same variety.

[0011] A third aspect of the present invention provides a method for identifying the purity of common fresh tomato seeds, comprising the following steps: N samples were obtained for testing; Determine the target primer set: If the parent variety of the sample to be tested is known, use the parent genomic DNA of the sample to be tested as a template, and perform PCR amplification using the InDel-labeled primer pairs described in the first aspect for identifying the authenticity and seed purity of common fresh tomatoes to obtain PCR products. Detect the PCR products by agarose gel electrophoresis, and select 1-3 InDel-labeled primer pairs that show differences between parents, have single bands, and are located on different chromosomes as the target primer set; If the parent variety of the sample to be tested is unknown, select the genomic DNA of at least 10 plants from the obtained N sample plants to be tested as a template, and perform PCR amplification using the InDel-labeled primer pairs described in the first aspect for identifying the authenticity and seed purity of common fresh tomatoes to obtain PCR products. Detect the PCR products by agarose gel electrophoresis, and select 1-3 InDel-labeled primer pairs that have a relatively large number of heterozygous bands and are clearly located on different chromosomes as the target primer set. Using the genomic DNA of the sample to be tested as a template, PCR amplification was performed using the target primer set to obtain PCR products of each sample under different target primer sets. The PCR products were detected by agarose gel electrophoresis. The sample to be tested with heterozygous bands was identified as a hybrid. The seed purity of the hybrid sample to be tested was obtained based on the number of plants with heterozygous bands under each target primer set. The identified target primer set can be one, two, or more. When multiple target primer sets exist, the purity of the hybrid obtained from multiple target primer sets can be used to determine the final purity of the tomato hybrid to be tested. Specifically: The number of plants showing heterozygous bands and the number of plants without bands for each target primer set were counted. The purity of the tomato hybrids obtained from each target primer set was calculated, and then the average value was calculated. Seed purity calculation formula: Seed purity = Number of plants showing heterozygous bands with a certain target primer set / (N - Number of plants not showing bands with a certain target primer set) × 100%.

[0012] A fourth aspect of the present invention provides a method for identifying the authenticity of a tomato variety based on its flavor, comprising the following steps: Genomic DNA was extracted from two tomato samples with unknown taste; Using the genomic DNA as a template, PCR amplification was performed using the InDel marker primer pair described in the first aspect for identifying the authenticity of the tomato flavor and the purity of the seeds, and PCR products were obtained. The PCR products were subjected to agarose gel electrophoresis to obtain electrophoretic images, and the tested varieties were genotyped based on the electrophoretic images. If the genotypes of two samples are compared, and the genotypes of two or more loci are different, the two samples are considered to be different; if all genotypes are the same, the two samples are considered to be of the same variety.

[0013] A fifth aspect of the present invention provides a method for identifying the purity of tomato seeds in terms of taste, comprising the following steps: N samples were obtained for testing; Determine the target primer set: If the parental variety of the sample to be tested is known, use the genomic DNA of the parental variety as a template, and perform PCR amplification using the InDel marker primer pairs described in the first aspect for identifying the authenticity of flavor tomatoes and seed purity to obtain PCR products. Detect the PCR products by agarose gel electrophoresis, and select 1-3 InDel marker pairs that show differences between parents, have single bands, and are located on different chromosomes as the target primer set. If the parental variety of the sample to be tested is unknown, select the genomic DNA of at least 10 plants from the obtained N sample plants to be tested as a template, and perform PCR amplification using the InDel marker primer pairs described in the first aspect for identifying the authenticity of flavor tomatoes and seed purity to obtain PCR products. Detect the PCR products by agarose gel electrophoresis, and select 1-3 InDel marker primer pairs that have a relatively large number of heterozygous bands and are clearly located on different chromosomes as the target primer set. Using the genomic DNA of the sample to be tested as a template, PCR amplification was performed using the target primer set to obtain PCR products of each sample under different target primer sets. The PCR products were detected by agarose gel electrophoresis. The sample to be tested with heterozygous bands was identified as a hybrid. The seed purity of the hybrid sample to be tested was obtained based on the number of plants with heterozygous bands under each target primer set. The identified target primer set can be one, two, or more. When multiple target primer sets exist, the purity of the hybrid obtained from multiple target primer sets can be used to determine the final purity of the tomato hybrid to be tested. Specifically: The number of plants showing heterozygous bands and the number of plants without bands for each target primer set were counted. The purity of the tomato hybrids obtained from each target primer set was calculated, and then the average value was calculated. Seed purity calculation formula: Seed purity = Number of plants showing heterozygous bands with a certain target primer set / (N - Number of plants not showing bands with a certain target primer set) × 100%.

[0014] A sixth aspect of the present invention provides a method for identifying the authenticity of processed tomato varieties, comprising the following steps: Genomic DNA was extracted from two unknown processed tomato samples; Using the genomic DNA as a template, PCR amplification was performed using the InDel marker primer pair described in the first aspect for identifying the authenticity and seed purity of processed tomatoes, and PCR products were obtained. The PCR products were subjected to agarose gel electrophoresis to obtain electrophoretic images, and the tested varieties were genotyped based on the electrophoretic images. If the genotypes of two samples are compared, and the genotypes of two or more loci are different, the two samples are considered to be different; if all genotypes are the same, the two samples are considered to be of the same variety.

[0015] A seventh aspect of the present invention provides a method for identifying the purity of processed tomato seeds, comprising the following steps: N samples were obtained for testing; Determine the target primer set: If the parental variety of the sample to be tested is known, use the parental genomic DNA of the sample to be tested as a template, and perform PCR amplification using the InDel marker primer pairs described in the first aspect for identifying the authenticity and seed purity of processed tomatoes to obtain PCR products. Detect the PCR products by agarose gel electrophoresis, and select 1-3 InDel marker pairs that show differences between parents, have single bands, and are located on different chromosomes as the target primer set; If the parental variety of the sample to be tested is unknown, select the genomic DNA of at least 10 plants from the obtained N sample plants to be tested as a template, and perform PCR amplification using the InDel marker primer pairs described in the first aspect for identifying the authenticity and seed purity of processed tomatoes to obtain PCR products. Detect the PCR products by agarose gel electrophoresis, and select 1-3 InDel marker primer pairs that have a relatively large number of heterozygous bands and are clearly located on different chromosomes as the target primer set. Using the genomic DNA of the sample to be tested as a template, PCR amplification was performed using the target primer set to obtain PCR products of each sample under different target primer sets. The PCR products were detected by agarose gel electrophoresis. The sample to be tested with heterozygous bands was identified as a hybrid. The seed purity of the hybrid sample to be tested was obtained based on the number of plants with heterozygous bands under each target primer set. The identified target primer set can be one, two, or more. When multiple target primer sets exist, the purity of the hybrid obtained from multiple target primer sets can be used to determine the final purity of the tomato hybrid to be tested. Specifically: The number of plants showing heterozygous bands and the number of plants without bands for each target primer set were counted. The purity of the tomato hybrids obtained from each target primer set was calculated, and then the average value was calculated. Seed purity = Number of plants showing heterozygous bands with a specific primer set / (N - Number of plants not showing bands with a specific primer set) × 100%.

[0016] An eighth aspect of the present invention provides a method for identifying the authenticity of a cherry tomato variety, comprising the following steps: Genomic DNA was extracted from two unknown cherry tomato samples; Using the genomic DNA as a template, PCR amplification was performed using the InDel marker primer pair described in the first aspect for identifying the authenticity and seed purity of cherry tomatoes, and PCR products were obtained. The PCR products were subjected to agarose gel electrophoresis to obtain electrophoretic images, and the tested varieties were genotyped based on the electrophoretic images. If the genotypes of two samples are compared, and the genotypes of two or more loci are different, the two samples are considered to be different; if all genotypes are the same, the two samples are considered to be of the same variety.

[0017] A ninth aspect of the present invention provides a method for identifying the purity of cherry tomato seeds, comprising the following steps: N samples were obtained for testing; Determine the target primer set: If the parental variety of the sample to be tested is known, use the parental genomic DNA of the sample to be tested as a template, and perform PCR amplification using the InDel marker primer pairs described in the first aspect for identifying the authenticity and seed purity of cherry tomatoes to obtain PCR products. Detect the PCR products by agarose gel electrophoresis, and select 1-3 InDel marker pairs that show differences between parents, have single bands, and are located on different chromosomes as the target primer set; If the parental variety of the sample to be tested is unknown, select the genomic DNA of at least 10 plants from the obtained N sample plants to be tested as a template, and perform PCR amplification using the InDel marker primer pairs described in the first aspect for identifying the authenticity and seed purity of cherry tomatoes to obtain PCR products. Detect the PCR products by agarose gel electrophoresis, and select 1-3 InDel marker primer pairs that have a relatively large number of heterozygous bands and are clearly located on different chromosomes as the target primer set. Using the genomic DNA of the sample to be tested as a template, PCR amplification was performed using the target primer set to obtain PCR products of each sample under different target primer sets. The PCR products were detected by agarose gel electrophoresis. The sample to be tested with heterozygous bands was identified as a hybrid. The seed purity of the hybrid sample to be tested was obtained based on the number of plants with heterozygous bands under each target primer set. The identified target primer set can be one, two, or more. When multiple target primer sets exist, the purity of the hybrid obtained from multiple target primer sets can be used to determine the final purity of the tomato hybrid to be tested. Specifically: The number of plants showing heterozygous bands and the number of plants without bands for each target primer set were counted. The purity of the tomato hybrids obtained from each target primer set was calculated, and then the average value was calculated. Seed purity calculation formula: Seed purity = Number of plants showing heterozygous bands with a certain target primer set / (N - Number of plants not showing bands with a certain target primer set) × 100%.

[0018] A tenth aspect of the invention provides the application of the InDel tag combination described in the first aspect in any of the following: (1) To identify or assist in the identification of the authenticity of tomato varieties and the purity of seeds; (2) To prepare products for identifying or assisting in the identification of tomato variety authenticity and seed purity; (3) Construction of InDel fingerprinting of specific tomato varieties, evaluation of genetic diversity of germplasm resources and analysis of phylogenetic relationships; (4) Tomato breeding; The tomato varieties mentioned include regular fresh tomatoes, flavor tomatoes, processed tomatoes, and cherry tomatoes.

[0019] In this invention, the common fresh tomato varieties include, but are not limited to, Huachen No. 1, Huafeng 56, Huaguan 36, Jingao No. 2, Zhongyan 460, Tianfei Eleven, Zhuofen No. 1, Tianbao 326, Tianci 595, Tianci No. 3, Guanqun No. 7, Jili No. 2, Xiwang No. 2, Fenkang No. 4, Pujin 901, Fengshou 128, Yibaifen-5, Wofen No. 2, Kaideyali 87360, Fendeli, Lola, Annecy, Toro, Saint Laurent, Ruila, Zidali, Ruifei, Dongnuan, Kelly No. 3, Sibeide, Antres, SV4224TH, Oudun, SVTH1366, Ouke, Jingfan 101. Jingfan 301, Jingfan 501, Jingfan 404, Jingfan 403, Qiangfeng, Zhongza 9, Zhongza 101, Zhongza 301, Zhongza 302, Xilaide 1, Ferrari, Fenyan 1, Baili, Mawa, Gray, Legend, Fentaro, Ruixing Dabao, Ruixing 5, Zheza 506, Zhefen 21066, Jinpeng 8, Qiusheng, Tiansheng 1, Tianzhen 1, Yashu 2203, Tianzheng 1567, Ouxiu 806, Zhuoqun 3, Kakuqi, Vienna 2, Hezuo 903, Wofen 1274, Ningfan 640, Xianke 8, Maofen 802, 1643, 1648 and Jingfen 1.

[0020] The tomato varieties mentioned include, but are not limited to, 56FE, Pinfan 2045, Pinfan 4027, Pinfan 4031, Pinfan 20311, Anlida, Xiuqing, Fuxing, Youkang SS28, Jiawen No. 1, Shengfan No. 2, Qingdaiyulang No. 3, Fanyu 2099, Xiantao No. 5, Tiancuicui-2, Zhewei No. 3, Wanmei, Strawberry No. 5, Yuanwei 128, Cuiyu No. 2, Chudai No. 6, Fengtian 126, Strawberry No. 15, Tianmei, Jingfan 309, XX45, Taomengxi, Diana, Xianmei No. 5, Provence, Strawberry No. 2, Beiweimei, Zhewei No. 2, Tiemei No. 6, Zhenyoumei, and Xinsheng 2301. Yun, Hongxiu, Huiwei 99, Fengtian A8, 23G666, Fantaro No. 8, Yashu No. 11, Yuxi, Zhongza 315, Lianji, Hefan No. 1, JPCQ6, Yibanzha, Tianzhu Latte, Gala Fruit, Beishi No. 3, Hangza 602, JSH46, Feini, Guanghui 101, Youyouguo, Boyan 68, Boyan 366, Jingfan H2205, Jingfan H2302, Jingcai No. 8, Jingfan 308, Yashu No. 12, Yuyi No. 6, Xiangbalang, Weimeijia, Alilang, Qingfantaro, Tianmi, Yuyi Suantianguo, Strawberry Fruit 168, Gaopin 1918, Gaopin 2718 and Pinfan 1933.

[0021] The processed tomato varieties include, but are not limited to, IVF398, IVF1305, IVF1678, IVF1893, IVF2088, IVF3535, IVF5200, IVF5212, IVF6193, H1015, DF8815, Hongza 10, Jinfan 3166, Jinfan 1266, Shifan 45, Jing Rx4-1806, Roma, San Marzano, Santa Cruz B, R996, R001, Peto95-43, SS809, ONT7710, Hunt100, E6203, E3259, 23TH-22, Campbell 31, Campbell 1327, BVS-22, BVS31, H3402, DM-31(A2), M82, JT1401, JT1402, XH2401, JT1904, Africa One, JSLS-1, JSLS-5, JSLS-9, JSLS-17, JSLS-19, JSLS-21, JSLS-23, JSLS-32, JSLS-36 JSLS-50, 1814, 1869, 2102-1, 2111-1, 2124, 2156, 18S-1, 18S-2, 18S-3, 786, JF9605, JF6366, XH71, JF2203, XH2405, XH62, JF3703, HY083, JF5108, JF1606, JF2110 and Heinz 1706.

[0022] The cherry tomato varieties mentioned include, but are not limited to, Flame, Kumquat, White Arrow, Bedouin, Cherry Pink 208, Cherry Pink 576, Yellow Agate 1015, Xiaguang No. 1, Golden Bean, Red Pearl, Red Cloud, Red Agate 2015, Red Beauty, Emerald Pearl, Wonderful 6453, Purple Fairy, Purple Bei, Jinyuan 216, Pink Princess, Winter Charm, Pink Dan, Golden Delight, Weite Red 1, Delicate Beauty 5, Aomei No. 2, Cun Mang, Cabernet Sauvignon, Tainan Xibei, C703, Jiaxina, Qiande Baiwa, Yellow Ball, Green Sweet No. 2, Dream Sweet, Cherry Blossom, Millennium, Golden Summer, Pink Baby, Busan 88 sapolo, Vitalin, Red Beauty, Jingfan Red String No. 1, Jingfan Yellow Star No. 1, Jingfan Rose Yellow, Yuekeda 102, Yuekeda 105, Ouxiu Yellow Cherry, Ouxiu Red Cherry, Venus, Xia Zhixing No. 17, Zhe Cherry Pink No. 1, Zhe Cherry Pink No. 8, Angel's Lips, Sweet Pearl, Bijiao, Green Cherry Jade, Pink Belle Ling 201, Golden Sun Honey Pearl, Yellow Diamond No. 1, Ning Cherry 479, Heavenly Pearl No. 1, Pink Belle 2006, Shanghai Red Cherry 201, Fragrant Honey, Princess, Fragrant Concubine No. 2, Ailong No. 2, Hua Cherry 746, 2203-117, Wanxi, White Angel and Pink Joy.

[0023] Compared with the prior art, the technical solution of the present invention has the following beneficial effects: This invention successfully developed 84 InDel markers that are evenly distributed throughout the tomato genome and exhibit good polymorphism. Based on the differences in polymorphism of these markers in different types of tomatoes, core identification marker combinations suitable for common fresh tomatoes, flavor tomatoes, processing tomatoes, and cherry tomatoes were selected, each containing 48, 36, 48, and 48 primer pairs, respectively. Based on these combinations, varietal DNA fingerprint maps were constructed and successfully applied to varietal fingerprint map construction, authenticity identification, and hybrid purity detection, providing technical support for tomato germplasm resource management, molecular breeding, and variety rights protection.

[0024] The whole-genome InDel marker system developed in this invention has high polymorphism and is easy to detect. It can effectively reveal the genetic diversity and population structure of commercial tomato varieties and has been successfully applied to variety fingerprinting, authenticity identification and hybrid purity detection. It can provide technical support for tomato germplasm resource management, molecular breeding and variety rights protection. Attached Figure Description

[0025] Figure 1 The locations of 84 InDel markers in the tomato reference genome, version SL4.0, were determined.

[0026] Figure 2 A UPGMA phylogenetic tree for 288 tomato varieties was constructed based on 84 InDel markers.

[0027] Figure 3Principal component analysis (PCA) of 288 tomato varieties based on 84 InDel markers. In the figure, PC1 and PC2 explained 21.54% and 11.57% of the genetic variation, respectively. Different colors represent different types of tomatoes.

[0028] Figure 4 Fingerprints of 72 common fresh tomato varieties based on 48 pairs of core InDel markers were obtained.

[0029] Figure 5 The results of authenticity identification of two common fresh tomato varieties, “1643” and “1648”, based on 48 core InDel markers.

[0030] Figure 6 The purity identification results of the hybrid of the common fresh tomato variety "Jingfen No. 1" are shown in Figure A, which represents the primer screening results. B, C and D represent the amplification results of F1 hybrid plants by primer groups 4-2, 5-1 and 9-1, respectively. P1 represents the maternal sample, P2 represents the paternal sample, and 1 to 94 represent F1 hybrid plants.

[0031] Figure 7 Fingerprints of 72 flavor tomato varieties based on 36 pairs of core InDel markers were obtained.

[0032] Figure 8 The results of the authenticity identification of two flavor tomato varieties, “Gaopin 1918” and “Gaopin 2718”, based on 36 core InDel markers.

[0033] Figure 9 The purity identification results of the hybrid of the flavorful tomato variety "Pinfan 1933" are shown in Figure A, which represents the primer screening results. Figures B, C, and D represent the amplification results of F1 hybrid plants using primer sets 1-10, 3-9, and 11-5, respectively. P1 represents the maternal sample, P2 represents the paternal sample, and 1 to 94 represent F1 hybrid plants.

[0034] Figure 10 Fingerprints of 72 processing tomato varieties based on 48 pairs of core InDel markers were obtained.

[0035] Figure 11 The results of the authenticity identification of two processing tomato varieties, “Jinfan 3166” and “Jinfan 1266”.

[0036] Figure 12 The purity identification results of the processing tomato variety “IVF5200” hybrid are shown in Figure A, which represents the primer screening results. Figures B, C, and D represent the amplification results of F1 hybrid plants using primer sets 2-7, 3-10, and 4-6, respectively. P1 represents the maternal sample, P2 represents the paternal sample, and 1 to 94 represent F1 hybrid plants.

[0037] Figure 13 Fingerprints of 72 cherry tomato varieties based on 48 pairs of core InDel markers were obtained.

[0038] Figure 14 The results of authenticity identification of two cherry tomato varieties, “Fen Dan” and “Fen Xi”, based on 48 core InDel markers.

[0039] Figure 15 The results of purity identification of the cherry tomato variety "Jinyuan 216" hybrid are shown in Figure A, which represents the primer screening results. Figures B, C, and D represent the amplification results of F1 hybrid plants using primer sets 3-9, 5-4, and 8-10, respectively. P1 represents the maternal sample, P2 represents the paternal sample, and 1 to 94 represent F1 hybrid plants. Detailed Implementation

[0040] It should be noted that the following detailed descriptions are exemplary and intended to provide further illustration of the invention. Unless otherwise specified, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention pertains.

[0041] It should be noted that the terminology used herein is for the purpose of describing particular embodiments only and is not intended to limit the exemplary embodiments of the present invention. As used herein, the singular form is intended to include the plural form as well, unless the context clearly indicates otherwise. Furthermore, it should be understood that when the terms "comprising" and / or "including" are used in this specification, they indicate the presence of features, steps, operations, and / or combinations thereof.

[0042] To enable those skilled in the art to better understand the technical solution of the present invention, the technical solution of the present invention will be described in detail below with reference to specific embodiments.

[0043] Example 1: Filtering Indel Tags 1. Experimental Materials: A total of 288 commercial tomato varieties were used in the experiment, sourced from different breeding units and seed companies both domestically and internationally. These included four types: common table tomatoes (B), flavor tomatoes (K), processing tomatoes (P), and cherry tomatoes (Y), with 72 varieties in each type. These varieties encompassed F1 hybrids and conventional varieties, widely used in commercial production, and thus possessed good representativeness. All materials were cultured in the indoor environment of the Vegetable Research Institute of Shandong Academy of Agricultural Sciences, with the seedling temperature controlled at 26-28℃. Detailed information on different varieties is shown in Table 1.

[0044] Table 1 Tomato varieties tested

[0045] 2. Experimental Methods Genomic DNA extraction: Five individual plants were randomly selected from each tomato variety. Young leaves were collected and mixed, and genomic DNA was extracted using the CTAB method. DNA quality and concentration were measured using a NanoDrop spectrophotometer to ensure A... 260 / A 280 When the value is between 1.8 and 2.0, the DNA concentration should be adjusted to 30-50 ng·μL. - ¹, Store at -20 ℃ for later use.

[0046] InDel marker development: Based on publicly available tomato resequencing data, variant sites meeting the target criteria were screened and primers were designed. The screening criteria were as follows: (1) Insertion / deletion base number 50-150 bp; (2) Minor allele frequency (MAF) > 0.2; (3) Polymorphism information content (PIC) > 0.25; (4) Genotype deletion rate of the site < 10%, and individual heterozygosity < 15%. Reference genome base sequences of 300 bp upstream and downstream of the variant site were extracted using a script written in Perl language, and primers were designed using Primer 5.0 software. The design parameters were: primer length 18-24 bp, GC content 40%-60%, annealing temperature 55-65℃, and expected amplification product size 100-300 bp. The primers were synthesized by Beijing Liuhe BGI Genomics Co., Ltd.

[0047] Based on the screening criteria, a total of 2268 InDel variant sites matching the target were detected across the entire genome, averaging 189 per chromosome. Chromosome 4 had the most (490), while chromosome 1 had the fewest (118). Ten to twelve relatively evenly distributed sites were selected from each chromosome to design InDel primers, and polymorphism verification and screening were performed using four different tomato varieties. After rigorous screening and supplementation, a total of 84 polymorphic InDel markers were obtained, averaging seven per chromosome. The distribution of these markers on the chromosomes is shown below. Figure 1 As shown, the tomato reference genome version is SL4.0.

[0048] 3. Tomato genetic diversity analysis and cluster analysis Twenty-four varieties of tomatoes were selected for each type, and the developed markers were validated and screened using tomato genomic DNA as a template.

[0049] The PCR amplification system consisted of 10 μL of DNA template, 5 μL of 2×Taq Master Mix, and upstream and downstream primers (10 μmol·L⁻¹). -1 0.25 μL of each of the following: 0.25 μL of ddH2O and 2.5 μL of ddH2O. The amplification program was as follows: 94℃ pre-denaturation for 3 min; 94℃ denaturation for 30 s, 55℃ annealing for 30 s, 72℃ extension for 30 s, for a total of 32 cycles; 72℃ extension for 5 min, and storage at 4℃. The amplified products were separated by 1.8% agarose gel electrophoresis, and images were acquired using a Bio-Rad gel imaging system. Genotypes were determined based on band size, coded as: a (homozygous reference type), h (heterozygous type), b (homozygous variant type), and NA (unknown). The observed heterozygosity (Ho), expected heterozygosity (He), polymorphism information content (PIC), and minor allele frequency (MAF) of each marker were calculated using R software. The genetic similarity coefficient between varieties was calculated using the Identity by State (IBS) method. Based on this, the genetic distance is further converted to genetic distance using the formula: Genetic distance = 1 - Genetic similarity coefficient. Based on the genetic distance matrix, a phylogenetic tree is constructed using the unweighted pair-group method with arithmetic means (UPGMA), and the tree is visualized using the ggtree package in R. Principal component analysis (PCA) is performed on the standardized genotype matrix, and the percentage of variation explained by each principal component is calculated using the prcomp function in R, and a scatter plot of PC1-PC2 is plotted. The mean genetic distance within and between each type is calculated, and nonparametric tests are used to evaluate the significance of differences. All statistical analyses and plotting are performed in the R 4.4.2 environment.

[0050] Genetic diversity information and genetic distance matrices for different types of tomatoes are shown in Tables 2 and 3.

[0051] Table 2 Genetic diversity information of different tomato types

[0052] Table 3 Genetic distance matrix among different types of tomatoes

[0053] As shown in the table above, the average expected heterozygosity (He) of the 288 tomato varieties was 0.3693, and the average observed heterozygosity (Ho) was 0.2536. Among the different types of tomatoes, cherry tomatoes had the highest genetic diversity, with an average He of 0.3606, an average Ho of 0.337, and an average polymorphism information content (PIC) of 0.2849, significantly higher than the other three types of tomatoes.

[0054] Cluster analysis results showed that the 288 tomato varieties were mainly divided into four major groups ( Figure 2 The genetic similarity coefficients among varieties basically correspond to the tomato types, ranging from 0.369 to 0.994, with an average of 0.667. The genetic similarity coefficients within each type are: B: 0.5893-0.9702; K: 0.6448-0.994; Y: 0.5-0.9643; P: 0.5119-0.994, indicating that some varieties are genetically very similar and may be highly similar varieties. Table 2 shows that the average genetic distances between cherry tomatoes and fresh tomatoes, flavor tomatoes, and processing tomatoes are 0.4122, 0.429, and 0.4208, respectively, all significantly higher than the genetic distances between other types. This is consistent with the results of PCA analysis (…). Figure 3 The results are consistent with those of cherry tomatoes, further confirming their unique genetic background. Furthermore, the genetic distance between fresh tomatoes and flavorful tomatoes is the smallest (0.2619), significantly lower than their genetic distances with cherry tomatoes or processed tomatoes. Moreover, there is significant overlap between the two in phylogenetic trees and PCA space, indicating a close genetic relationship between them.

[0055] 4. Screening of InDel identification combinations Given the inter-type differences in marker polymorphism, the core marker combinations were streamlined for different types of tomatoes based on the principles of high PIC values, uniform chromosome distribution, and non-tight linkage. Ultimately, 48 pairs of core markers were suitable for identifying common fresh tomatoes, 36 pairs for flavor tomatoes, 48 ​​pairs for processing tomatoes, and 48 pairs for cherry tomatoes. All marker information is shown in Table 4.

[0056] Table 4 InDel Marking Information

[0057] Note: In the table, B represents regular fresh tomatoes, K represents flavored tomatoes, P represents processed tomatoes, and Y represents cherry tomatoes.

[0058] Example 2: Application of InDel markers in identifying the authenticity of common fresh tomato varieties and the purity of hybrids Table 5 shows the 48 pairs of core marker information of common fresh tomatoes selected based on Example 1.

[0059] Table 5. InDel Marker Information for Identifying Common Fresh Tomatoes

[0060] The fingerprint map constructed based on 48 pairs of core markers is as follows: Figure 4 As shown, this method can effectively distinguish different common fresh tomato varieties.

[0061] Two common fresh tomato varieties, “1643” and “1648”, were used as experimental materials. Genomic DNA was extracted, and PCR amplification was performed using the 48 InDel-labeled primer pairs listed in Table 5. PCR amplification products were obtained, and the products were separated by 1.8% agarose gel electrophoresis. Electrophoresis images were obtained, and the results are shown below. Figure 5 As shown, 19 out of 48 InDel markers exhibited differences, indicating that "1643" and "1648" are two different tomato varieties. This demonstrates that the InDel core marker combinations in Table 5 can be used for the authenticity identification of common fresh tomato varieties.

[0062] Using the parental DNA of the tomato variety "Jingfen No. 1" as a template, amplification was performed using 48 pairs of InDel marker primers listed in Table 5. InDel markers showing differences between the parents were selected as the target primer set for hybrid identification. Figure 6 As indicated by A in the diagram, there are 23 pairs of polymorphic markers among the parents. Three markers with clear and stable bands located on different chromosomes were randomly selected: primer sets 4-2, 5-1, and 9-1. These primer sets were used to amplify the genomic DNA of 94 F1 hybrids. The PCR products were detected by agarose gel electrophoresis. Samples with heterozygous bands were identified as hybrids. The seed purity of the hybrids was determined based on the number of plants with heterozygous bands amplified by each target primer set. The identified target primer set can be one, two, or more. When multiple target primer sets exist, the purity of the hybrids obtained from multiple target primer sets can be used to determine the final purity of the tomato hybrids being tested. Specifically: The number of plants showing heterozygous bands and the number of plants without bands for each target primer set were counted. The purity of the tomato hybrids obtained from each target primer set was calculated, and then the average value was calculated. Seed purity calculation formula: Seed purity = Number of plants showing heterozygous bands with a certain target primer set / (N - Number of plants not showing bands with a certain target primer set) × 100%.

[0063] The results are as follows Figure 6 As shown in B, C, and D, each plant exhibits both parental bands, indicating a hybrid purity of 100%. These results demonstrate that the InDel marker in Table 5 can be used for the efficient detection of hybrid purity in common fresh tomato varieties.

[0064] Example 3: Application of InDel marker in identifying the authenticity of flavor-enhancing tomato varieties and the purity of hybrids Table 6 shows the 36 InDel marker information for identifying flavor tomatoes selected based on Example 1.

[0065] Table 6 InDel Marking Information for Identifying Tomato Taste

[0066] The fingerprint map constructed based on 36 pairs of core markers is as follows: Figure 7 As shown, this method can effectively distinguish between different tomato varieties with different tastes.

[0067] Two tomato varieties, “Gaopin 1918” and “Gaopin 2718”, were used as experimental materials. Genomic DNA was extracted, and PCR amplification was performed using 36 pairs of InDel-labeled primers listed in Table 6. PCR amplification products were obtained, and the products were separated by 1.8% agarose gel electrophoresis. Electrophoresis images were obtained, and the results are shown below. Figure 8 As shown, 7 out of 36 markers exhibited differences, indicating that "Gaopin 1918" and "Gaopin 2718" are two different tomato varieties. This demonstrates that the InDel core marker combination in Table 6 can be used for the authenticity identification of flavor tomato varieties.

[0068] Using the parental DNA of the new variety "Pinfan 1933" as a template, amplification was performed using 48 pairs of InDel marker primers listed in Table 5. InDel markers showing differences between the parents were selected as the target primer sets for hybrid identification. Figure 9 As indicated by A in the diagram, there are 14 pairs of polymorphic markers among the parents. Three markers with clear and stable bands located on different chromosomes were randomly selected: primer sets 1-10, 3-9, and 11-5. These primer sets were used to amplify the genomic DNA of 94 F1 hybrids. The PCR products were detected by agarose gel electrophoresis. Samples with heterozygous bands were identified as hybrids. The seed purity of the hybrids was determined based on the number of plants with heterozygous bands amplified by each target primer set. The identified target primer set can be one, two, or more. When multiple target primer sets exist, the purity of the hybrids obtained from multiple target primer sets can be used to determine the final purity of the tomato hybrids being tested. Specifically: The number of plants showing heterozygous bands and the number of plants without bands for each target primer set were counted. The purity of the tomato hybrids obtained from each target primer set was calculated, and then the average value was calculated. Seed purity calculation formula: Seed purity = Number of plants showing heterozygous bands with a certain target primer set / (N - Number of plants not showing bands with a certain target primer set) × 100%.

[0069] The results are as follows Figure 6 B, C, and D in Table 6 indicate that, except for plant number 62 which has the same genotype as the maternal parent, all other plants exhibit both parental banding, and the hybrid purity is 98.94%. These results demonstrate that the InDel marker in Table 6 can be used for efficient detection of the purity of flavor-enhancing tomato hybrids.

[0070] Example 4: Application of InDel markers in identifying the authenticity of processed tomato varieties and the purity of hybrids Table 7 shows the InDel marker information of 48 pairs of processed tomato varieties selected based on Example 1.

[0071] Table 7 InDel Marking Information for Identifying Processed Tomatoes

[0072] A fingerprint map constructed based on 48 pairs of core markers from processed tomatoes is shown below. Figure 10 As shown, this method can effectively distinguish different varieties of processed tomatoes.

[0073] Two processing tomato varieties, “Jinfan 3166” and “Jinfan 1266”, were used as experimental materials. Genomic DNA was extracted, and PCR amplification was performed using 48 InDel-labeled primer pairs listed in Table 7. PCR amplification products were obtained, and the products were separated by 1.8% agarose gel electrophoresis. Electrophoresis images were obtained, and the results are shown below. Figure 11 As shown, 30 out of 48 markers exhibited differences, indicating that "Jinfan 3166" and "Jinfan 1266" are two different tomato varieties. These results demonstrate that the InDel core marker combination in Table 7 can effectively identify the authenticity of processing tomato varieties.

[0074] Using the parental DNA of the processed tomato variety "IVF5200" as a template, amplification was performed using 48 pairs of InDel marker primers listed in Table 7. InDel markers showing differences between the parents were selected as the target primer set for hybrid identification. Figure 12As indicated by A, there are 14 pairs of polymorphic markers among the parents. Three markers with clear and stable bands located on different chromosomes were randomly selected: primer sets 2-7, 3-10, and 4-6. These primer sets were used to amplify the genomic DNA of 94 F1 hybrids. The PCR products were detected by agarose gel electrophoresis. Samples with heterozygous bands were identified as hybrids. The seed purity of the hybrids was determined based on the number of plants with heterozygous bands amplified by each target primer set. The identified target primer set can be one, two, or more. When multiple target primer sets exist, the purity of the hybrids obtained from multiple target primer sets can be used to determine the final purity of the tomato hybrids being tested. Specifically: The number of plants showing heterozygous bands and the number of plants without bands for each target primer set were counted. The purity of the tomato hybrids obtained from each target primer set was calculated, and then the average value was calculated. Seed purity calculation formula: Seed purity = Number of plants showing heterozygous bands with a certain target primer set / (N - Number of plants not showing bands with a certain target primer set) × 100%.

[0075] The results are as follows Figure 12 As shown in B, C, and D, the InDel markers in Table 7 can be used for efficient detection of the purity of processed tomato hybrids.

[0076] Example 5: Application of InDel markers in identifying the authenticity of cherry tomato varieties and the purity of hybrids The 48 InDel markers selected in Example 1 for identifying cherry tomato varieties are shown in Table 8.

[0077] Table 8. InDel Marking Information for Identifying Cherry Tomatoes

[0078] The fingerprint map constructed based on 48 pairs of core markers from cherry tomatoes is as follows: Figure 13 As shown, this method can effectively distinguish different cherry tomato varieties.

[0079] Using two cherry tomato varieties, 'Fen Dan' and 'Fen Xi', as experimental materials, genomic DNA was extracted. PCR amplification was performed using the 48 InDel-labeled primer pairs listed in Table 8. PCR amplification products were obtained, and the products were separated by 1.8% agarose gel electrophoresis. Electrophoresis images were obtained, and the results are shown below. Figure 14 As shown, 9 out of 48 InDel markers showed differences, indicating that "FenDan" and "FenXi" are two different tomato varieties. The InDel core marker combinations in Table 8 can effectively identify the authenticity of cherry tomato varieties.

[0080] Using the parental DNA of the cherry tomato variety "Jinyuan 216" as a template, amplification was performed using 48 pairs of InDel marker primers listed in Table 5. InDel markers showing differences between the parents were selected as the target primer sets for hybrid identification. Figure 15 As indicated by A in the diagram, there are 15 pairs of polymorphic markers among the parents. Three markers with clear and stable bands located on different chromosomes were randomly selected: primer sets 3-9, 5-4, and 8-10. These primer sets were used to amplify the genomic DNA of 94 F1 hybrids. The PCR products were detected by agarose gel electrophoresis. Samples with heterozygous bands were identified as hybrids. The seed purity of the hybrids was determined based on the number of plants with heterozygous bands amplified by each target primer set. The identified target primer set can be one, two, or more. When multiple target primer sets exist, the purity of the hybrids obtained from multiple target primer sets can be used to determine the final purity of the tomato hybrids being tested. Specifically: The number of plants showing heterozygous bands and the number of plants without bands for each target primer set were counted. The purity of the tomato hybrids obtained from each target primer set was calculated, and then the average value was calculated. Seed purity calculation formula: Seed purity = Number of plants showing heterozygous bands with a certain target primer set / (N - Number of plants not showing bands with a certain target primer set) × 100%.

[0081] The results are as follows Figure 15 As shown in B, C, and D, except for plant number 34 which has the same genotype as the maternal parent, all other plants exhibit both parental banding, and the hybrid purity is 98.94%. These results demonstrate that the InDel marker can be used for efficient detection of the purity of cherry tomato hybrids.

[0082] Finally, it should be noted that the above description is merely a preferred embodiment of the present invention and is not intended to limit the present invention. Although the present invention has been described in detail with reference to the foregoing embodiments, those skilled in the art can still modify the technical solutions described in the foregoing embodiments or make equivalent substitutions for some of them. Any modifications, equivalent substitutions, improvements, etc., made within the spirit and principles of the present invention should be included within the protection scope of the present invention.

Claims

1. An InDel marker combination for identifying the authenticity of tomato varieties and seed purity, characterized in that, The chromosomal location of the InDel marker site, primer pair, primer sequence, and amplification product size in the InDel marker combination are shown below: ； Preferably, the tomato varieties include common fresh tomatoes, flavor tomatoes, processed tomatoes, and cherry tomatoes; Preferably, the InDel marker primer pairs used to identify the authenticity and seed purity of common fresh tomatoes are 1-1, 1-3, 1-7, 1-8, 1-11, 2-6, 2-7, 2-8, 3-1, 3-3, 3-10, 4-1, 4-2, 4-10, 5-1, 5-2, 5-5, 5-7, 5-9, 6-1, 6-2, 6-6, 7-1, 7-2, 7-5, 7-6, 7-8, 7-11, 8-1, 8-9, 8-10, 9-1, 9-10, 10-1, 10-2, 10-7, 10-9, 10-10, 11-1, 11-2, 11-4, 11-5, 11-6, 12-1, 12-2, 12-4, 12-6, 12-10; Preferably, the InDel marker primer pairs used to identify the authenticity of the tomato flavor and the purity of the seeds are 1-1, 1-3, 1-6, 1-10, 2-6, 2-8, 3-1, 3-3, 3-7, 3-9, 3-10, 4-2, 4-6, 4-10, 5-5, 6-1, 6-2, 6-6, 7-6, 7-8, 7-11, 8-10, 9-1, 9-2, 9-3, 10-1, 10-7, 10-10, 11-4, 11-5, 11-9, 12-1, 12-2, 12-5, 12-6, 12-10; Preferably, the InDel marker primer pairs used to identify the authenticity and seed purity of processed tomatoes are 1-1, 1-3, 1-7, 1-9, 2-7, 2-10, 3-1, 3-8, 3-10, 4-2, 4-6, 4-10, 4-11, 4-12, 5-1, 5-2, 5-5, 5-7, 5-8, 5-9, 5-10, 6-1, 6-2, 7-1, 7-5, 7-6, 7-9, 7-11, 8-2, 8-10, 9-1, 9-2, 9-3, 9-10, 10-2, 10-6, 10-7, 10-9, 11-1, 11-2, 11-3, 11-4, 11-5, 11-6, 12-2, 12-4, 12-6, 12-10; Preferably, the InDel marker primer pairs used to identify the authenticity and seed purity of cherry tomatoes are 1-1, 1-2, 1-3, 1-6, 1-9, 1-10, 1-11, 2-5, 2-9, 2-10, 3-1, 3-7, 3-9, 3-10, 3-11, 4-9, 4-11, 5-1, 5-3, 5-4, 5-8, 6-1, 6-2, 6-6, 6-7, 6-9, 7-5, 7-6, 7-8, 7-10, 8-1, 8-2, 8-8, 8-10, 9-6, 9-8, 9-9, 9-10, 10-2, 10-7, 11-1, 11-3, 11-6, 11-11, 12-2, 12-3, 12-5, 12-10.

2. A method for identifying the authenticity of common fresh tomato varieties, characterized in that, Includes the following steps: Genomic DNA was extracted from two unknown common fresh tomato samples; Using the genomic DNA as a template, PCR amplification was performed using the InDel marker primer pair described in claim 1 for identifying the authenticity and seed purity of common fresh tomatoes, and PCR products were obtained. The PCR products were subjected to agarose gel electrophoresis to obtain electrophoretic images, and the tested varieties were genotyped based on the electrophoretic images. If the genotypes of two samples are compared, and the genotypes of two or more loci are different, the two samples are considered to be different; if all genotypes are the same, the two samples are considered to be of the same variety.

3. A method for identifying the purity of common fresh tomato seeds, characterized in that, Includes the following steps: N samples were obtained for testing; Determine the target primer set: If the parent variety of the sample to be tested is known, use the genomic DNA of the parent variety as a template, and perform PCR amplification using the InDel-labeled primer pair described in claim 1 for identifying the authenticity and seed purity of common fresh tomatoes to obtain PCR products. Detect the PCR products by agarose gel electrophoresis, and select 1-3 InDel-labeled primer pairs that show differences between parents, have single bands, and are located on different chromosomes as the target primer set. If the parent variety of the sample to be tested is unknown, select the genomic DNA of at least 10 plants from the obtained N sample plants to be tested as a template, and perform PCR amplification using the InDel-labeled primer pair described in claim 1 for identifying the authenticity and seed purity of common fresh tomatoes to obtain PCR products. Detect the PCR products by agarose gel electrophoresis, and select 1-3 InDel-labeled primer pairs that have a relatively large number of heterozygous bands and are clearly located on different chromosomes as the target primer set. Using the genomic DNA of the sample to be tested as a template, PCR amplification was performed using the target primer set to obtain PCR products of each sample under different target primer sets. The PCR products were detected by agarose gel electrophoresis. The sample to be tested with heterozygous bands was identified as a hybrid. The seed purity of the hybrid sample to be tested was obtained based on the number of plants with heterozygous bands under each target primer set. Seed purity calculation formula: Seed purity = Number of plants showing heterozygous bands with a certain target primer set / (N - Number of plants not showing bands with a certain target primer set) × 100%.

4. A method for identifying the authenticity of a tomato variety based on its taste, characterized in that, Includes the following steps: Genomic DNA was extracted from two tomato samples with unknown taste; Using the genomic DNA as a template, PCR amplification was performed using the InDel marker primer pair described in claim 1 for identifying the authenticity of the tomato flavor and the purity of the seeds, to obtain the PCR product; The PCR products were subjected to agarose gel electrophoresis to obtain electrophoretic images, and the tested varieties were genotyped based on the electrophoretic images. If the genotypes of two samples are compared, and the genotypes of two or more loci are different, the two samples are considered to be different; if all genotypes are the same, the two samples are considered to be of the same variety.

5. A method for identifying the purity of tomato seeds based on their taste, characterized in that, Includes the following steps: N samples were obtained for testing; Determine the target primer set: If the parent variety of the sample to be tested is known, use the genomic DNA of the parent variety as a template, and perform PCR amplification using the InDel marker primer pair described in claim 1 for identifying the authenticity of flavor tomatoes and seed purity to obtain PCR products. Detect the PCR products by agarose gel electrophoresis, and select 1-3 InDel marker pairs that show differences between parents, have single bands, and are located on different chromosomes as the target primer set. If the parent variety of the sample to be tested is unknown, select the genomic DNA of at least 10 plants from the obtained N sample plants to be tested as a template, and perform PCR amplification using the InDel marker primer pair described in claim 1 for identifying the authenticity of flavor tomatoes and seed purity to obtain PCR products. Detect the PCR products by agarose gel electrophoresis, and select 1-3 InDel marker primer pairs that have a relatively large number of heterozygous bands and are clearly located on different chromosomes as the target primer set. Using the genomic DNA of the sample to be tested as a template, PCR amplification was performed using the target primer set to obtain PCR products of each sample under different target primer sets. The PCR products were detected by agarose gel electrophoresis. The sample to be tested with heterozygous bands was identified as a hybrid. The seed purity of the hybrid sample to be tested was obtained based on the number of plants with heterozygous bands under each target primer set. Seed purity calculation formula: Seed purity = Number of plants showing heterozygous bands with a certain target primer set / (N - Number of plants not showing bands with a certain target primer set) × 100%.

6. A method for identifying the authenticity of processed tomato varieties, characterized in that, Includes the following steps: Genomic DNA was extracted from two unknown processed tomato samples; Using the genomic DNA as a template, PCR amplification was performed using the InDel marker primer pair described in claim 1 for identifying the authenticity and seed purity of processed tomatoes, and PCR products were obtained. The PCR products were subjected to agarose gel electrophoresis to obtain electrophoretic images, and the tested varieties were genotyped based on the electrophoretic images. If the genotypes of two samples are compared, and the genotypes of two or more loci are different, the two samples are considered to be different; if all genotypes are the same, the two samples are considered to be of the same variety.

7. A method for identifying the purity of processed tomato seeds, characterized in that, Includes the following steps: N samples were obtained for testing; Determine the target primer set: If the parental variety of the sample to be tested is known, use the parental genomic DNA of the sample to be tested as a template, and perform PCR amplification using the InDel marker primer pair described in claim 1 for identifying the authenticity and seed purity of processed tomatoes to obtain PCR products. Detect the PCR products by agarose gel electrophoresis, and select 1-3 InDel marker pairs that show differences between parents, have single bands, and are located on different chromosomes as the target primer set; If the parental variety of the sample to be tested is unknown, select the genomic DNA of at least 10 plants from the obtained N sample plants to be tested as a template, and perform PCR amplification using the InDel marker primer pair described in claim 1 for identifying the authenticity and seed purity of processed tomatoes to obtain PCR products. Detect the PCR products by agarose gel electrophoresis, and select 1-3 InDel marker primer pairs that have a relatively large number of heterozygous bands and are clearly located on different chromosomes as the target primer set; Using the genomic DNA of the sample to be tested as a template, PCR amplification was performed using the target primer set to obtain PCR products of each sample under different target primer sets. The PCR products were detected by agarose gel electrophoresis. The sample to be tested with heterozygous bands was identified as a hybrid. The seed purity of the hybrid sample to be tested was obtained based on the number of plants with heterozygous bands under each target primer set. Seed purity = Number of plants showing heterozygous bands with a specific primer set / (N - Number of plants not showing bands with a specific primer set) × 100%.

8. A method for identifying the authenticity of a cherry tomato variety, characterized in that, Includes the following steps: Genomic DNA was extracted from two unknown cherry tomato samples; Using the genomic DNA as a template, PCR amplification was performed using the InDel marker primer pair described in claim 1 for identifying the authenticity and seed purity of cherry tomatoes, and PCR products were obtained. The PCR products were subjected to agarose gel electrophoresis to obtain electrophoretic images, and the tested varieties were genotyped based on the electrophoretic images. If the genotypes of two samples are compared, and the genotypes of two or more loci are different, the two samples are considered to be different; if all genotypes are the same, the two samples are considered to be of the same variety.

9. A method for identifying the purity of cherry tomato seeds, characterized in that, Includes the following steps: N samples were obtained for testing; Determine the target primer set: If the parental variety of the sample to be tested is known, use the genomic DNA of the parental variety as a template, and perform PCR amplification using the InDel marker primer pair described in claim 1 for identifying the authenticity and seed purity of cherry tomatoes to obtain PCR products. Detect the PCR products by agarose gel electrophoresis, and select 1-3 InDel marker pairs that show differences between parents, have single bands, and are located on different chromosomes as the target primer set. If the parental variety of the sample to be tested is unknown, select the genomic DNA of at least 10 plants from the obtained N sample plants to be tested as a template, and perform PCR amplification using the InDel marker primer pair described in claim 1 for identifying the authenticity and seed purity of cherry tomatoes to obtain PCR products. Detect the PCR products by agarose gel electrophoresis, and select 1-3 InDel marker primer pairs that have a relatively large number of heterozygous bands and are clearly located on different chromosomes as the target primer set. Using the genomic DNA of the sample to be tested as a template, PCR amplification was performed using the target primer set to obtain PCR products of each sample under different target primer sets. The PCR products were detected by agarose gel electrophoresis. The sample to be tested with heterozygous bands was identified as a hybrid. The seed purity of the hybrid sample to be tested was obtained based on the number of plants with heterozygous bands under each target primer set. Seed purity calculation formula: Seed purity = Number of plants showing heterozygous bands with a certain target primer set / (N - Number of plants not showing bands with a certain target primer set) × 100%.

10. The use of the InDel marker combination of claim 1 in any of the following: (1) To identify or assist in the identification of the authenticity of tomato varieties and the purity of seeds; (2) To prepare products for identifying or assisting in the identification of the authenticity of tomato varieties and the purity of seeds; (3) Construction of InDel fingerprinting of specific tomato varieties, evaluation of genetic diversity of germplasm resources and analysis of phylogenetic relationships; (4) Tomato breeding; The tomato varieties mentioned include regular fresh tomatoes, flavor tomatoes, processed tomatoes, and cherry tomatoes.

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