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Method for researching corn southern rust group inheritance and transmission based on SNP (Single Nucleotide Polymorphism)

A technology of southern rust and population genetics, applied in the field of molecular biology, can solve the problems such as the absence of SNP markers of Puccinia multicumulus, and achieve the effect of reducing the use of pesticides and reducing yield loss

Pending Publication Date: 2022-04-01
CHINA AGRI UNIV
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Problems solved by technology

[0005] There is no report of SNP markers found in Puccinia multihexa

Method used

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  • Method for researching corn southern rust group inheritance and transmission based on SNP (Single Nucleotide Polymorphism)
  • Method for researching corn southern rust group inheritance and transmission based on SNP (Single Nucleotide Polymorphism)
  • Method for researching corn southern rust group inheritance and transmission based on SNP (Single Nucleotide Polymorphism)

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Experimental program
Comparison scheme
Effect test

Embodiment 1

[0029] The screening of embodiment 1 restriction endonuclease

[0030] Sampling of Puccinia spp. in Hainan, Guangdong and Guangxi of my country, and bringing the collected samples of Puccinia back to the laboratory. Single spore piles were picked for single spore isolation and culture to obtain single spore lines (strains). For the specific method, refer to the invention patent applied by our research group (a method for single spore propagation of Puccinia multicumulus corn, patent number: ZL201510765142. 1), through multiplication, each monospore line obtains a large number of uredospores. Extract DNA from a single spore. The quality of DNA extraction was detected by 0.8% agarose gel electrophoresis, and DNA was quantified by UV spectrophotometer. Use a combination of restriction endonucleases to digest the DNA. After digestion, take 5ul of each sample for gel run detection. The DNA digestion is required to be complete, that is, there is no main band after the digestion; t...

Embodiment 2

[0035] Example 2 SNP marker mining

[0036] The DNA of different strains was digested with a combination of EcoRI and MspI restriction endonucleases, and the digested sequence fragments were subjected to pair-end sequencing on the NovaSeq 6000 platform through simplified genome technology, and the length of the sequenced fragments was 150 bp. Using stacks software, the simplified genome sequences of 106 strains collected from Hainan, Guangdong and Guangxi were compared to detect mutation sites and obtain SNP data of different strains.

Embodiment 3

[0037] Example 3 Population Genetics Analysis and Path Inference

[0038] Genetic Diversity Analysis

[0039] Based on the SNP data, using the poppr data package of R software (Kamvar et al., 2014), the genetic diversity of a total of 106 Puccinia strains in Hainan, Guangdong and Guangxi was analyzed, including the average individual at each site in the population The number (NumIndv), the average observed heterozygosity of all loci (Obs Het), the average observed homozygosity of all loci (Obs Hom), and the average expected heterozygosity of all stable points in the population (Exp Het ). The strains in Guangdong and Guangxi were found to have higher genetic diversity, while the strains in Hainan had lower genetic diversity (Table 2).

[0040] Table 2 Genetic diversity results of different populations

[0041]

[0042] Note: HN represents the population of Puccinia multicumulus collected from Hainan Province, GX represents the population collected from Guangxi, and GD re...

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Abstract

The invention provides a method for researching genetic and propagation paths of a corn southern rust group based on an SNP (Single Nucleotide Polymorphism) marker. According to the method, DNA of different strains is subjected to enzyme digestion by using screened restriction enzymes EcoRI and MspI, so that a genome sequencing technology is simplified, SNP markers are mined by using Stacks software, and then the genetic structure and the propagation path of a puccinia multiflora population are researched; the restriction endonucleases EcoRI and MspI provided by the invention have a better cutting effect on the whole genome of puccinia multiflora, and compared with other combinations, more tags can be obtained under the condition of the same sequencing depth. At present, whole genome sequencing of puccinia multiflora is not performed yet, and the method for researching the population genetic structure and the propagation path of puccinia multiflora on the basis of the SNP sites obtained by simplifying genome sequencing and utilizing stacks software has important significance on comprehensive treatment and accurate prevention and control of diseases.

Description

technical field [0001] The invention belongs to the fields of molecular biology and genetic analysis. Specifically, the application provides a method for analyzing genetics and transmission paths of maize southern rust populations based on SNP markers and its application. Background technique [0002] Southern rust of maize is caused by Puccinia multicumulus and is a worldwide disease. The disease has caused major outbreaks in several countries, resulting in severe yield losses. Currently, the disease is widespread in Hainan, Guangdong, Guangxi, Hunan, Zhejiang, Fujian, Jiangxi, Yunnan, Guizhou, Chongqing, Sichuan, Anhui, Jiangsu, Henan, Hubei, Hebei, Tianjin, Beijing, Shanxi, Shaanxi and Liaoning provinces. have happened. The main maize varieties planted in my country, such as Zhengdan 958, Jundan 20 and Xianyu 335, all showed high susceptibility to the disease. The disease broke out in my country in 2015, causing a loss of 7.56 million tons of corn production. The dise...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): C12Q1/6895C12Q1/6806C12R1/645
Inventor 马占鸿孙秋玉高建孟黄莉群李磊福张克瑜董佳玉
Owner CHINA AGRI UNIV
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