Whole-genome 50KSNP chip for apostichopus japonicus breeding and application

A whole-genome, japonicus imitation technology, applied in the fields of bioinformatics, molecular breeding, functional genomics, and molecular biology, can solve the problems of lack of liquid-phase chips, etc., and achieve good typing effect, good targeting, and accuracy sex high effect

Pending Publication Date: 2021-12-14
OCEAN UNIV OF CHINA +1
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

However, there is still a lack of stable and efficient liquid-phase chips in the current research on the molecular breeding of sea cucumbers. The liquid-phase chips designed based on HD-Marker technology in the present invention can provide important information for the research on economic traits of sea cucumbers, species identification and marker-assisted breeding. Technical means that can meet the needs of large-scale commercial breeding of sea cucumbers

Method used

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  • Whole-genome 50KSNP chip for apostichopus japonicus breeding and application
  • Whole-genome 50KSNP chip for apostichopus japonicus breeding and application
  • Whole-genome 50KSNP chip for apostichopus japonicus breeding and application

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0085] Example 1: Development of a genome-wide 50kSNP chip of imitation sea cucumber

[0086] 1. Construction of imitation japonicus sample population

[0087] In different sea areas of Liaoning and Shandong, 500 imitation sea cucumber samples were randomly selected, and the tissues were taken and placed in 95% ethanol and brought back to the laboratory for preservation.

[0088] 2. Genome-wide SNP typing of sea cucumber

[0089] 2.1 DNA extraction

[0090] ①Add 500ul STE lysis buffer (100mM NaCl; 10mM Tris-Cl, pH8.0; 1mM EDTA, pH8.0), 50ul 10% SDS, 3.5ul proteinase K (20mg / ml), 16ul to a 1.5ml tube RNase A (100mg / ml), add about 0.1g of scallop adductor muscle, chop it up, grind it with a grinding rod, grind it until flocculent, treat it at 56°C for about 2 hours, during this period, mix it upside down every 30mins, and finally clarify the lysate state.

[0091] ②Add 500ul Tris saturated phenol, 100ul chloroform / isoamyl alcohol (24:1), shake gently for 20min, and centrifug...

Embodiment 2

[0149] Example 2: Application of 50K SNP chip of japonicus japonicus in molecular breeding

[0150] In order to verify the application effect of japonicus japonicus chips in imitation japonicus japonicus molecular breeding, we used 50K chips to detect samples from Russia (30), Dalian (100), and Shandong (100), and carried out molecular breeding:

[0151] (1) Genetic background analysis of different geographical populations; (2) Genome-wide association analysis (GWAS) of the growth-related number of japonicus japonicus spines

[0152] 1. The role of whole-genome breeding chip of sea cucumber in the analysis of genetic background of different populations of sea cucumber:

[0153] Screen the loci with a population typing rate greater than 90% and a minimum allele frequency greater than 0.05, and obtain 46,232 genotype information of 46,232 high-quality loci, and use the typing data to perform individual cluster analysis of A. japonicus, such as figure 1 It shows that the positio...

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Abstract

The invention discloses a whole-genome 50KSNP chip for apostichopus japonicus breeding and application. The method comprises the following steps: (1) development of the 50KSNP chip in a whole-genome range of apostichopus japonicus: constructing an apostichopus japonicus sample group, performing SNP typing in the whole-genome range, screening 50KSNP markers of the apostichopus japonicus, designing an HD-marker high-density chip and designing development probes to obtain a liquid-phase chip pool of 48K loci; (2) testing the accuracy and the typing effect of the chip, and ensuring the high accuracy and the good typing effect through DNA sample quality detection, HD-Marker chip detection and result analysis. The chip can be applied to genetic background analysis and character association analysis of the whole genome breeding chip of the apostichopus japonicus in different groups of the apostichopus japonicus.

Description

Technical field: [0001] It involves the fields of molecular biology, functional genomics, bioinformatics and molecular breeding, specifically involves a screening of SNP sites related to growth traits, and the genome SNP chip and preparation method of imitation sea cucumber, and also relates to this imitation sea cucumber See the usage of SNP chip. Background technique: [0002] Molecular markers are genetic markers based on nucleotide sequence variation in genetic material between individuals, and are a direct reflection of genetic polymorphism at the DNA level. Compared with several other genetic markers - morphological markers, biochemical markers, and cytological markers, DNA molecular markers have the following advantages: most molecular markers are co-dominant, which is very convenient for the selection of recessive traits; The genome variation is extremely rich, and the number of molecular markers is almost unlimited; the detection method is simple and rapid. With t...

Claims

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Application Information

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IPC IPC(8): C12Q1/6888C12Q1/6806G16B20/20
CPCC12Q1/6888C12Q1/6806G16B20/20C12Q2600/156C12Q2600/124C12Q2521/537C12Q2521/327C12Q2527/125C12Q2525/191
Inventor 王杨帆王孟秋倪萍吕佳王师胡景杰包振民
Owner OCEAN UNIV OF CHINA
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