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Corn whole genome SNP chip and application thereof

A whole genome, chip technology, applied in the fields of molecular biology and genome breeding, can solve the problems of limited application scope, high cost and difficult to meet the needs of large-scale breeding

Active Publication Date: 2018-05-08
INST OF CROP SCI CHINESE ACAD OF AGRI SCI
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

DNA resequencing of sample materials using sequencing technology can obtain high-density SNP maps, but the high cost of sequencing is difficult to meet the needs of large-scale breeding; and simplified genome sequencing, such as GBS (Genotyping by sequencing, genotyping sequencing), SNP analysis There are a large number of missing values ​​in the type results, which limits the application range of this type of technology

Method used

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  • Corn whole genome SNP chip and application thereof
  • Corn whole genome SNP chip and application thereof
  • Corn whole genome SNP chip and application thereof

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0092] Example 1 Application of corn SNP chips in molecular marker fingerprint analysis of corn germplasm resources

[0093] Using the corn SNP chip, the present invention conducts molecular marker fingerprint analysis on 368 corn inbred lines from a wide range of sources. Microarray detected 368 maize inbred lines. By calculating the deletion rate and MAF of each SNP marker, the sites with a deletion rate greater than 5% and a MAF less than 20% were deleted, leaving 3987 high-quality sites, accounting for 66.5% of the total number of sites ( 3987 / 6000). According to the genotyping results, the 368 maize inbred lines were clustered and analyzed, and it was found that all 150 tropical materials were clustered into one group, and the remaining 126 temperate materials were clustered into one group ( figure 2 a). The temperate materials were further clustered, and it was found that all 32 materials were clustered into the SS (Stiff Stalk) series, and the remaining 94 materials ...

Embodiment 2

[0095] Example 2 Application of Maize SNP Chip in Linkage Map Construction and QTL Mapping

[0096] In this study, the inbred lines Huangzaosi (HZS) and 1462 were used as parents to construct the F2 population, and the F2 population and its parents were genotyped using the maize SNP chip. After analysis, there are 1248 homozygous SNPs that are different and homozygous between the parents Huangzaosi (HZS) and 1462, 220 SNPs in the F2 population, and 1028 SNPs that were finally used for linkage map construction and QTL mapping. Accounting for 19.8% of effective loci (1028 / 5179). The total length of the constructed linkage map is 1596.94cM, including a total of 655 bins (bins are recombination units), and the average length of each bin is 2.4cM. Due to severe partial segregation on the 8th chromosome, most of the segment of the 8th chromosome is blank. The results show that the SNP typing of the population can be effectively carried out by the corn SNP chip.

[0097] The two p...

Embodiment 3

[0100] Example 3 Application of Corn SNP Chip in Mixed Pond Location

[0101] The object of this study is a maize mutant barren stalk with degenerated male and female spikes. The mutant shows that both male and female spikes are degenerated and do not differentiate into spikelets or florets. The mutant material was derived from a natural mutation of an inbred line, and the phenotype in the self-bred offspring showed a 3:1 segregation. The mutant material was used to construct a backcross population with maize inbred lines B73, Mo17, and Zheng58 to obtain a BC3F1 population. Mutants and wild-types in the population were pooled for every 10 individual plants, repeated 5 times, and the whole genome DNA was purified and quantified for microarray genotyping. According to the analysis of "Principle of Consistency between Phenotype and Genotyping", in theory, the marker closely linked to the target gene in the mutant should be a homozygous mutation site, while the corresponding site ...

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Abstract

The invention relates to the field of molecular biology and genome breeding, and particularly discloses a corn whole genome SNP chip and application thereof. SNP loci covering a genetic expression area and SNP loci which are uniformly distributed in the whole genome are collected, after sifting, a high-throughput Infinium SNP chip of Illumina is prepared, and the chip comprises 500 probes of SNP markers shown in a detection list 1. By means of the selected SNP loci based on a large-scale sequencing result, specific signals which have reasonable frequency distribution, a low miss rate and low false positives are obtained, wherein 2 / 3 SNP loci are distributed in all the corn warm zone and tropical zone materials, and can be effectively used for selecting and utilizing the tropical zone materials; 426 SNP loci are functional markers, and are obviously relevant to kernel substance accumulation gene expression; an Infinium platform of Illumina has the advantages of being high in SNP typingdetection rate, high in repetitive rate, simple in detection and high in accuracy. The corn whole genome SNP chip can be used for corn germplasm resource molecular marker fingerprint analysis, corn linkage map construction, QTL locating, corn breeding material background selection and the like.

Description

technical field [0001] The invention relates to the fields of molecular biology and genome breeding, in particular to a corn whole genome SNP chip. Background technique [0002] DNA molecular marker is a technology that uses genetic polymorphism at the DNA level to mark genetic variation among organisms. Traditional DNA molecular marker techniques, such as RFLP (Restriction Fragment Length Polymorphism, restriction length fragment polymorphism) and SSR (Simple Sequence Repeat, simple repeat sequence) have been widely used in the past few decades. In particular, SSR markers, with their advantages of high polymorphism and convenient detection, have been the mainstream technology for molecular identification of crops in my country for a long time in the past. However, due to the instability and low distribution density of SSR markers, it is difficult to realize large-scale automatic detection, which limits its large-scale application in crop molecular breeding. SNP (Single Nu...

Claims

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Application Information

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IPC IPC(8): C12Q1/6895C12N15/11
CPCC12Q1/6895C12Q2600/156
Inventor 付俊杰王国英何骋郝杨凡张红伟李莉
Owner INST OF CROP SCI CHINESE ACAD OF AGRI SCI
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