SNP locus combination for detecting resistance of tomato yellow leaf curl virus disease and application thereof

A technology for tomato yellowing and curving leaves and viral diseases, applied in the field of plant biology, can solve the problems of linkage redundancy, insufficient versatility of SNP sites, and invalid selection of target genes, etc., achieve accurate detection, reduce manual inoculation identification and field transplanting The workload and the effect of improving breeding efficiency

Active Publication Date: 2021-12-03
AGRI GENOMICS INST CHINESE ACADEMY OF AGRI SCI +1
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

Through the analysis and identification of a large number of variant group data directly in the upstream and downstream adjacent regions of the known Ty-1 / Ty-3 and Ty-2 genes and within the genes, multiple genes that can quickly and effectively detect the resistance to tomato yellow leaf curl virus disease were obtained. SNP loci can realize accurate identification and selection of target gene regions, thereby solving the lack of versatility of SNP loci in the prior art, or functional molecular markers that are not directly related to target traits / genes (only linkage markers), causing target gene Selection is invalid, or linkage drag brings other non-target unfavorable gene fragments and other problems

Method used

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  • SNP locus combination for detecting resistance of tomato yellow leaf curl virus disease and application thereof
  • SNP locus combination for detecting resistance of tomato yellow leaf curl virus disease and application thereof
  • SNP locus combination for detecting resistance of tomato yellow leaf curl virus disease and application thereof

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0080] Example 1 Screening of SNP site combinations

[0081] 1. Experimental materials

[0082] The variant group data of 660 representative tomato germplasm resources from different sources worldwide were selected for SNP site screening in this embodiment. The source of the tomato variant group data is mainly based on the previous work of the project team where the inventor belongs. (Lin,T.,Zhu,G.,Zhang,J.et al.Genomic analyzes provide insights into the history of tomato breeding[J].Nat Genet,2014,46:1220~1226; Tieman D,Zhu G,Resende M F R , et al. A chemical genetic roadmap to improved tomato flavor [J]. Science, 2017, 355(6323): 391). Among them, the genotype data of some tomato germplasm resources and the resistance phenotype data of Ty-1 / Ty-3 and Ty-2 genes come from the existing public database (https: / / solgenomics.net / ).

[0083] 2. Screening of SNP site combinations

[0084] Using the target gene Ty-1 / Ty-3 gene (Solyc06g051170, Solyc06g051180, Solyc06g051190, databa...

Embodiment 2

[0088] Example 2 Primer Synthesis and Kit Preparation

[0089] 1. Primer design and screening

[0090] According to the flanking sequences of the Ty1-SNP01 site ~ Ty1-SNP08 site and the Ty2-SNP01 site ~ Ty2-SNP08 site provided in Example 1, for each SNP site, the principle of design and development according to the KASP marker (target product 80-150bp, the primers specifically match the target region on the reference genome and are located in non-SNP dense regions, avoiding complex sequence regions with high A\T or G\C content, etc.), use Primer3.0 software to design two upstream SNP sites A forward primer and a reverse primer were designed downstream.

[0091] Tomato samples to be tested include some germplasm resources of known genotypes and yellow leaf curl virus disease resistance phenotypes and 21 samples randomly selected from breeding materials as resistant, susceptible or heterozygous controls, and finally added 3 ddH 2 O is used as the NTC blank control, a total of ...

Embodiment 3

[0109] Example 3 Verification and Breeding Application of Tomato Yellow Leaf Curl Virus Resistance Genes Ty-1 / Ty-3 and Ty-2 High Efficiency KASP Markers

[0110] This example is based on the SNP site provided in Example 1, using the kit provided in Example 2 (including primer combinations) to carry out tomato anti-yellow leaf curl virus disease gene Ty-1 / Ty-3 and Ty-2 high-efficiency KASP Validation of markers and breeding application work.

[0111] Select 381 representative tomato samples including mainstream commercial varieties, core public germplasm of the National Resource Bank, breeding intermediate materials, new hybrid combinations, etc., involving large fruit tomatoes, cherry tomatoes, cluster tomatoes, fresh tomatoes, processed tomatoes and Various types of cultivated tomatoes such as farm species (local varieties), 154 of which obtained Ty-1 / Ty-3 and Ty-2 genotype data through third-party commercial institutions using closely linked SCAR markers (including 41 yellow...

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Abstract

The invention relates to the technical field of plant biology, and particularly relates to an SNP locus combination for detecting resistance of a tomato yellow leaf curl virus disease and application thereof. Based on this, the invention develops a primer combination, a kit and a detection method capable of quickly, intuitively and effectively identifying the genotype state of a target SNP locus. The SNP locus combination can realize quick, accurate and high-throughput detection of haplotypes of sections Ty-1/Ty-3 and Ty-2 of resistance genes of the tomato yellow leaf curl virus disease, has the advantages of simple operation, low cost, automation, high throughput efficiency, stable marking, safety, no toxicity, harmlessness and the like, can quickly and accurately identify the resistance of the tomato yellow leaf curl virus disease at high throughput in the seedling stage of tomatoes, reduces the workload of artificial inoculation identification and field transplantation, improves the breeding efficiency, reduces the breeding cost, accelerates the breeding process, and is very suitable for modern commercial breeding application and large-scale genetic improvement research.

Description

technical field [0001] The invention relates to the field of plant biotechnology, in particular to a combination of SNP sites for detecting tomato yellow leaf curl virus disease resistance and an application thereof. Background technique [0002] Tomato is an important vegetable economic crop in the world, which has important production application and basic research value. With the gradual expansion of tomato planting area around the world, the impact of tomato diseases and insect pests is increasing day by day. Among them, tomato yellow leaf curl virus (TYLCV) is a virus disease of Solanaceae crops widely distributed in tropical and subtropical regions. It is mainly carried and spread by Bemisia tabaci. After the tomato is infected, the plant will be obviously dwarfed, the leaf margins will turn yellow, and the leaves will become smaller and curled. This will seriously endanger the growth, flowering and fruit setting, and the fruit will not change color normally, and even...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): C12Q1/6858C12Q1/6895C12N15/11
CPCC12Q1/6858C12Q1/6895C12Q2600/156C12Q2600/13C12Q2600/172C12Q2563/107C12Q2531/113
Inventor 黄三文吴坤张金喆练群胡勇
Owner AGRI GENOMICS INST CHINESE ACADEMY OF AGRI SCI
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