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Construction and evaluation of parting High Map on basis of high throughput

A genetic map, high-density technology, applied in biochemical equipment and methods, microbial measurement/inspection, instruments, etc.

Active Publication Date: 2014-12-31
BIOMARKER TECH
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

For highly heterozygous populations, there is no report on using HighMap to construct a high-density genetic linkage map

Method used

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  • Construction and evaluation of parting High Map on basis of high throughput
  • Construction and evaluation of parting High Map on basis of high throughput
  • Construction and evaluation of parting High Map on basis of high throughput

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0070] Example 1: Application of HighMap to the construction of genetic map of F1 population of 224 carp strains

[0071] Carp genetic map construction, including the following steps:

[0072] 1. Selection of carp colony (purchased from Heilongjiang Fisheries Research Institute): the colony is F1 colony with 224 strains and 2 parents. The high-throughput sequencing instrument is Illumina GA IIx.

[0073] 2. Use SLAFseq technology (the method of patent CN103088120A) to develop and type the whole genome markers of carp populations, and perform data identification processing on the original sequencing data. After cluster analysis and error correction, 185,014 SLAF tags were obtained; as shown in Table 1 Shown as the number of SLAF tags and sequencing depth statistics.

[0074] Table 1 Statistics on the number of total sequencing tags and sequencing depth

[0075]

[0076] 3. As shown in Table 2, the marker coding rules for the F1 population were selected. The above-mentione...

Embodiment 2

[0092] Example 2 HighMap is used to simulate genetic map construction and map quality assessment of simulating typing data

[0093] Genetic map construction and map quality assessment based on simulation data, including the following steps:

[0094] 1. Use the Monte Carlo method to simulate the missing typing and errors that may be caused by different sequencing depths. The results show that using the sequencing method for genotyping, the missing typing and typing errors related to the sequencing depth are inevitable. For high heterozygous In terms of species, the problem of typing quality caused by sequencing depth is particularly prominent. Table 6 shows the proportion of typing errors and typing deletions that may occur when sequencing and typing sites with different separation patterns at different sequencing depths. When the average sequencing depth is 1x, the sites with abxcd separation patterns, The typing error was as high as 34%. As the sequencing depth gradually inc...

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Abstract

The invention provides a construction method of a parting High Map on the basis of high throughput. The construction method comprises the steps as follows: 1), genetic segregation population markers subjected to development and parting with a high-throughput sequencing method; 2), every two markers are subjected to genetic linkage test, and linkage groups are divided; 3), linear ordering is performed and the genetic distance is calculated with an SGS algorithm, and parting errors and parting loss in sample parting data are subjected to error correction and loss compensation with a KNN algorithm; and 4), the constructed map is subjected to accuracy evaluation, and the map quality is directly displayed with a visual method. According to the construction method of the parting High Map, the parting errors and the parting loss caused by high-throughput sequencing parting are effectively eliminated through parting error correction, and the accuracy of the constructed map is improved remarkably; the SGS sequencing algorithm is used, so that the sequencing speed is high, a High Map with more than one thousand markers in a single linkage group can be constructed, and the map drawing efficiency is improved remarkably; and the requirement for original parting data is reduced, and the parting error tolerance is improved greatly.

Description

technical field [0001] The invention belongs to the field of biochemistry, and in particular relates to a method for constructing a genetic engineering data map and a method for evaluating the map. Background technique [0002] With the development of next-generation sequencing technology and bioinformatics featuring high throughput, low cost, low sequencing error rate, and short read length, high-throughput marker development has gradually become the most cost-effective molecular marker development method. Simplified genome technologies such as SLAF-seq, RAD-seq, and GBS can perform molecular marker development and large-scale typing on a genome-wide scale. The application of these technologies in different species has generated massive marker typing data, making it possible to construct high-density genetic maps. At the same time, new requirements are placed on the methods and software required for map construction, while traditional mapping software and methods are weak i...

Claims

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): C12Q1/68G06F19/26G16B45/00
CPCC12Q1/6881C12Q2600/156
Inventor 郑洪坤
Owner BIOMARKER TECH
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