Maize whole-genome InDel (insertion-deletion) chip and application thereof

A whole-genome and corn technology, applied in genomics, recombinant DNA technology, DNA/RNA fragments, etc., can solve the problem of expensive chip detection platform, difficult to scale and automate, and can not take into account high-throughput of sites and high-throughput of samples Quantity and other issues

Active Publication Date: 2020-02-28
BEIJING ACADEMY OF AGRICULTURE & FORESTRY SCIENCES
View PDF5 Cites 4 Cited by
  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

In particular, SSR markers, with their advantages of high polymorphism, multiple alleles and convenient detection, have been the mainstream markers for molecular identification of crops in my country in the past; however, due to the low distribution density of SSR markers, data sharing is difficult and difficult Realization of scale and automation limits its large-scale application in crop molecular breeding
[0004] SNP (Single Nucleotide Polymorphism, sing

Method used

the structure of the environmentally friendly knitted fabric provided by the present invention; figure 2 Flow chart of the yarn wrapping machine for environmentally friendly knitted fabrics and storage devices; image 3 Is the parameter map of the yarn covering machine
View more

Image

Smart Image Click on the blue labels to locate them in the text.
Viewing Examples
Smart Image
  • Maize whole-genome InDel (insertion-deletion) chip and application thereof
  • Maize whole-genome InDel (insertion-deletion) chip and application thereof
  • Maize whole-genome InDel (insertion-deletion) chip and application thereof

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 3

Embodiment 1

[0089] Example 1 Obtaining the InDel polymorphic site of the whole genome of maize and the synthesis of the whole genome chip

[0090] (1) Selection of InDel sites in 40K InDel chips

[0091] (1) Resequence 100 corn materials, each corn material has a sequencing data of about 10Gb, use bwa software (0.7.0) to compare the resequenced sequences of corn materials to the corn reference gene sequence, use Samtools and GATK software Mining small InDel variants were carried out. The length of the InDel sequence ranged from 1 to 20 bp, and a total of 7,843,126 InDel variant sites were excavated.

[0092] (2) In order to make InDel sites have the potential to adapt to electrophoretic analysis, InDel sites with a length of 3-10 bp were selected, and there were 1,705,519 InDel sites in total. These InDel sites were screened using the following conditions:

[0093] a, InDel locus with 2 alleles retained;

[0094] b, filter out InDel sites with MAF values ​​less than 0.1;

[0095] c, r...

Embodiment 2

[0105] Example 2 Application of corn 40K InDel chips in the analysis of corn germplasm resources

[0106] Using the MaizeIDP40K InDel chip synthesized in Example 1, 335 maize inbred lines from a wide range of sources were used for InDel marker genotyping analysis. The chip detected 335 corn inbred lines. The chip detection results passed the quality control test of the data analysis software Axiom analysis suite, and the sample pass rate was 99%. The missing rate and MAF value of the genotyping data of each InDel marker were calculated, and the data were filtered out. 24968 high-quality InDel markers ( figure 1 ), accounting for 61.2%. Using FAST STRUCTURE to analyze the population genetic structure of 335 maize inbred lines using the genotyping data of InDel markers. Population genetic structure analysis shows that when K=10, the ΔK value is the largest, that is, the analyzed inbred line population of the present invention can be divided into 10 groups, which are respective...

the structure of the environmentally friendly knitted fabric provided by the present invention; figure 2 Flow chart of the yarn wrapping machine for environmentally friendly knitted fabrics and storage devices; image 3 Is the parameter map of the yarn covering machine
Login to view more

PUM

No PUM Login to view more

Abstract

The invention discloses a maize whole-genome InDel (insertion-deletion) chip and application thereof. By large-scale sequencing mining, InDel sites of maize gene expression regions and whole-genome uniformly distributed InDel sites are determined, and the Affimatrix Axiom based high-flux InDel chip is designed and comprises probes aiming at 1536 InDel sites. The maize whole-genome InDel chip can be used for creating a maize DNA fingerprint database to perform maize variety authenticity identification, maize variety identification or authentication, maize clustering analysis, maize genetic relationship analysis and germplasm resource analysis and can also be used for maize linkage map construction, gene mapping analysis and maize molecular breeding material background selection, and a wideapplication range and remarkable benefits are realized.

Description

technical field [0001] The invention belongs to the technical field of crop breeding and molecular biology, and in particular relates to a corn whole genome InDel chip and its application. Background technique [0002] Insertion / deletion (insertion-deletion, InDel) refers to the insertion or deletion of nucleotide fragments of different sizes in the sequence of the same site in the genome between close relatives or different individuals of the same species, that is, a certain site in a sequence One or more bases are inserted or deleted compared to another sequence of homology. InDel is a phenomenon in which a homologous sequence alignment produces a gap (gap), but in most cases the ancestral sequence cannot be known, and it is difficult to determine which sequence has an insertion mutation at the gap site, or which sequence has a deletion mutation, so it is generally referred to as They are insertion / deletion mutations. [0003] Molecular markers refer to heritable and det...

Claims

the structure of the environmentally friendly knitted fabric provided by the present invention; figure 2 Flow chart of the yarn wrapping machine for environmentally friendly knitted fabrics and storage devices; image 3 Is the parameter map of the yarn covering machine
Login to view more

Application Information

Patent Timeline
no application Login to view more
IPC IPC(8): C12Q1/6895C12Q1/6837C12N15/11G16B20/20G16B30/10
CPCC12Q1/6895C12Q1/6837G16B20/20G16B30/10C12Q2600/156C12Q2537/165
Inventor 许理文王凤格田红丽赵久然
Owner BEIJING ACADEMY OF AGRICULTURE & FORESTRY SCIENCES
Who we serve
  • R&D Engineer
  • R&D Manager
  • IP Professional
Why Eureka
  • Industry Leading Data Capabilities
  • Powerful AI technology
  • Patent DNA Extraction
Social media
Try Eureka
PatSnap group products

Browse by: Latest US Patents, China's latest patents, Technical Efficacy Thesaurus, Application Domain, Technology Topic.

© 2024 PatSnap. All rights reserved.Legal|Privacy policy|Modern Slavery Act Transparency Statement|Sitemap