Wild grape drought-resistant key gene and genome variation map

Abstract

The invention discloses a vitis amurensis drought-resistant key gene and genome variation map, and relates to the technical field of plant genetics and breeding, and the method comprises the following steps: collecting a wild vitis amurensis resource, carrying out whole genome sequencing on a wild vitis amurensis sample, obtaining genetic marker information of each individual, and the precipitation variation coefficient and the warmth quarter precipitation environmental data are recorded through a website. According to the amur grape drought-resistant key gene and genome variation map, through correlation analysis of environmental factors and genotypes, nine drought-resistant related genes are determined, a precise molecular basis is provided for drought-resistant breeding, the amur grape drought-resistant key gene and genome variation map has high popularization and application values, and the efficiency and accuracy of grape drought-resistant breeding are remarkably improved.

Description

Technical Field

[0001] The present invention relates to the technical field of plant genetics and breeding, specifically to the key genes for drought resistance of Vitis amurensis and the genomic variation map. Background Art

[0002] As one of the important fruit trees in the world, grapes have extremely high cultivation value. According to the statistics of the International Organization of Vine and Wine (OIV), the global grape planting area reached 7.3 million hm2 in 2021. China is a major grape-producing country, with a planting area of about 0.783 million hm2, accounting for 10.73% of the global total area. In the northwestern region of China, grapes are widely planted. Due to the lack of fresh water resources and low precipitation in these areas, it directly affects the yield and quality of grapes. With global climate change, the frequency and intensity of extreme weather events (such as drought and high temperature) have increased, posing a major challenge to grape cultivation. Therefore, in order to reduce the losses caused by drought, it is urgent to cultivate new drought-resistant grape germplasms. Improving the drought resistance of grapes helps to enhance their adaptability to climate change; reduce the demand for irrigation water, lower production costs, and at the same time reduce water resource consumption, ensuring the sustainable development of the grape industry.

[0003] The current application of grape drought resistance technologies, such as a series of water and fertilizer regulation, in-row grass planting, shaping and pruning, spraying hormones, etc.; Although drought-resistant cultivation measures have alleviated the problem of water resource shortage to a certain extent, they still need to be continuously optimized and improved to reduce costs, improve effects, and reduce the impact on the environment. Therefore, strengthening the breeding work of drought-resistant grape varieties and improving the drought resistance of grapes from the source have important application prospects and promotion values in grape production.

[0004] Grapes have a long growth cycle and a complex genetic background. Traditional cross-breeding has limitations for the breeding of drought-resistant grape varieties: 1. Traditional cross-breeding requires multiple generations of selection and cultivation to obtain excellent varieties with stable inheritance. This process often takes several years or even decades.

[0005] 2. Traditional cross-breeding usually can only be carried out within a limited range of parents, which limits the genomic diversity and may not be able to fully utilize all potential excellent gene resources.

[0006] 3. Many excellent traits of grapes (such as disease resistance, yield, quality, etc.) may be distributed in different parents, and it is often difficult to concentrate these traits in a new variety through hybridization.

[0007] At present, modern biotechnology means (such as molecular marker-assisted breeding) have become efficient and feasible means in fruit tree genetic breeding. Molecular marker-assisted selection breeding is the combination point of modern molecular biology and traditional genetic breeding. With the help of molecular markers, accurate and stable selection of breeding materials can be carried out at the DNA level, so as to accelerate the breeding process, improve breeding efficiency, efficiently increase crop yield and improve comprehensive traits such as quality and resistance, and has gradually become a "conventional" technical means that breeders can generally apply. GWAS (Genome-Wide Association Study) technology can efficiently mine gene loci related to important traits of fruit trees. For the genetic improvement of fruit trees, this means that breeding and improvement work can be carried out more targeted. Through GWAS technology, genetic variations related to important agronomic traits can be quickly scanned and identified within the whole genome, greatly accelerating the process of crop improvement. However, there are significant differences in drought resistance among different grape varieties. Discovering SNP loci related to grape drought resistance and developing related molecular markers through GWAS technology can provide a theoretical basis for the genetic improvement of grape drought resistance traits and accelerate the breeding of new drought-resistant grape varieties in China.

[0008] Currently, grape drought resistance technologies and traditional breeding methods face multiple defects. Traditional drought-resistant cultivation measures such as water and fertilizer regulation, in-row grass planting, shaping and pruning, and hormone spraying, although alleviating the problem of water resource shortage, have high costs and limited effects, and may also have negative impacts on the environment. In addition, traditional cross-breeding has deficiencies in the selection of grape drought resistance traits, such as low efficiency, long cycle, and limited gene diversity. Due to the complex genetic background of grapes, it is difficult to concentrate multiple excellent traits such as disease resistance, yield increase, and high quality in the same variety by traditional methods, which often requires years or even decades of selection and cultivation. Facing the challenges of global climate change to grape cultivation, it is difficult to quickly obtain new drought-resistant varieties with strong adaptability only by traditional means. Therefore, there is an urgent need for modern molecular marker technology-assisted breeding to improve breeding efficiency, accelerate the cultivation of new varieties, and more effectively respond to climate pressure.

[0009] The present invention discloses a method for screening genes related to grape drought resistance traits based on genotype-environment association analysis. Aiming at the defects of long breeding cycle and low efficiency in traditional grape drought resistance breeding, the present invention conducts whole-genome sequencing on 330 wild Vitis amurensis samples and screens out molecular markers and 9 key drought resistance genes closely related to drought resistance based on genotype-environment association analysis. Summary of the Invention

[0010] To achieve the above object, the present invention is realized through the following technical solutions: The key genes and genomic variation maps of Vitis amurensis drought resistance, including the following steps: Step 1: Collect wild Vitis amurensis resources; Step 2: Conduct whole-genome sequencing on wild Vitis amurensis samples to obtain genetic marker information of each individual; Step 3. Record the environmental data of precipitation variation coefficient and precipitation in the warmest quarter through the website; Step 4. Use the R package LEA (v3.11.4) to conduct a correlation analysis between the genetic marker information of wild grape samples and environmental factors; Step 5. Identify the variation sites significantly associated with drought-resistant related environmental factors; Step 6. Conduct gene function annotation analysis on the variation sites.

[0011] The present invention provides a key gene for drought resistance of Vitis amurensis and a genomic variation map, having the following beneficial effects: 1. The key gene for drought resistance of Vitis amurensis and the genomic variation map screen out genes closely related to drought-resistant traits through genotype-environment association analysis. This method can screen out excellent drought-resistant individuals at the initial stage of breeding, reducing the dependence on environmental conditions and time in traditional breeding. Using this assisted breeding technology, the cultivation cycle of drought-resistant grape varieties can be shortened, and the breeding efficiency can be significantly improved. Through the association analysis of environmental factors and genotypes, the present invention has determined 9 drought-resistant related genes, providing an accurate molecular basis for drought-resistant breeding, having high promotion and application value, and significantly improving the efficiency and accuracy of grape drought-resistant breeding.

[0012] 2. The key gene for drought resistance of Vitis amurensis and the genomic variation map, through the whole-genome sequencing of 330 wild Vitis amurensis samples and combining environmental data, found the variation sites significantly associated with the precipitation variation coefficient and precipitation in the warmest quarter, and further analysis confirmed 9 genes related to drought resistance. This method can be used for the assisted breeding of grapes, improving the screening efficiency and shortening the breeding cycle, having important application prospects. Brief Description of the Drawings

[0013] Figure 1 It is the genomic screening flow chart of the drought-resistant trait gene of the present invention; Figure 2 It is the Manhattan plot of the genotype-environment association analysis of seasonal precipitation of the present invention; Figure 3 It is the Manhattan plot of the genotype-environment association analysis of precipitation in the warmest quarter of the present invention. Detailed Embodiments

[0014] The present invention will be further described in detail below in conjunction with the accompanying drawings and specific embodiments. The embodiments of the present invention are given for the purposes of illustration and description, and are not exhaustive or limit the present invention to the disclosed form. Many modifications and variations are obvious to those of ordinary skill in the art. The embodiments are selected and described to better illustrate the principles and practical applications of the present invention, and enable those of ordinary skill in the art to understand the present invention and thus design various embodiments with various modifications suitable for specific purposes.

[0015] The first embodiment is as Figures 1 to 3 shown. The present invention provides a technical solution: Key genes and genomic variation maps for drought resistance of Vitis amurensis Rupr., including the following steps: Step 1: 330 wild Vitis amurensis Rupr. resource samples were collected in China. Through population genomics analysis, they were mainly divided into 4 main populations: Northeast, Central, West, and South.

[0016] Step 2: In this experiment, we used the high-throughput sequencing technology of the Illumina NovaSeq 6000 platform to perform whole-genome sequencing on 330 wild Vitis amurensis Rupr. resource samples, with a depth exceeding 40X. In the data processing stage, we first performed quality control on the raw data, removing low-quality data and data contaminated with adapters, thus ensuring the accuracy of subsequent analysis and finally obtaining high-quality clean data. Through BWA (v0.7.17), the sequencing data was mapped to the Vitis amurensis Rupr. genome for variant typing. After variant typing analysis, 4,114,075 high-quality SNP variant sites were obtained.

[0017] Step 3: Environmental data was downloaded from the website http: / / www.worldclimate.com. Two environmental ecological factor data were obtained: Precipitation seasonality (Coefficient of Variation) and Precipitation of warmest quarter.

[0018] Step 4: The R package LEA (v3.11.4) was used to perform genotype-environment association analysis to determine molecular markers related to the two environmental ecological factors of Precipitation seasonality and Precipitation of warmest quarter. The Wald P-value test was used to statistically evaluate the correlation between SNP and phenotype data.

[0019] The Manhattan plot was generated using the GAP package from https: / / cran.r-project.org / web / packages / gap / .

[0020] Step 5: Based on the significantly correlated SNPs, we analyzed and identified 9 genes related to drought resistance, including 3 genes related to the coefficient of variation of precipitation (LAX5, TLP3, and Exo70B1) and 7 genes related to the precipitation in the warmest quarter (TLP3, MYB60, CLB, MYC2, JMJ27, ATHB6h, and NCED1).

[0021] Obviously, the described embodiments are only a part of the embodiments of the present invention, rather than all embodiments. All other embodiments obtained by those of ordinary skill in the art and related fields based on the embodiments of the present invention without creative efforts shall fall within the scope of protection of the present invention. Structures, devices, and operation methods not specifically described and explained in the present invention shall be implemented by conventional means in the art without special instructions and limitations.

Claims

1. A map of key drought-resistant genes and genomic variation in Vitis amurensis, characterized in that: The following steps are involved: Step 1: Collect wild wild grape resources; Step 2: Perform whole genome sequencing on wild grape samples to obtain genetic marker information for each individual; Step 3: Record the precipitation variation coefficient and quarterly precipitation environmental data through the website; Step 4: Use R package LEA (v3.11.4) to conduct association analysis between genetic marker information and environmental factors of wild grape samples; Step 5: Identify the variant sites associated with environmental factors related to drought resistance; Step 6: Perform gene function annotation analysis on the variant sites.

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