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SNP molecular marker related to pod and seed size on peanut A06 chromosome and application thereof

A molecular marker, peanut technology, applied in the determination/inspection of microorganisms, biochemical equipment and methods, DNA/RNA fragments, etc. Effects of the breeding process

Active Publication Date: 2020-12-18
INST OF OIL CROPS RES CHINESE ACAD OF AGRI SCI
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

Linkage analysis, because the segregation population only involves two parents, the number of recombination in the population is limited, the accuracy of QTL mapping is generally between 10-30cM (Salvi and Tuberosa, 2005), and the subsequent work of QTL fine mapping is also quite time-consuming laborious

Method used

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  • SNP molecular marker related to pod and seed size on peanut A06 chromosome and application thereof
  • SNP molecular marker related to pod and seed size on peanut A06 chromosome and application thereof
  • SNP molecular marker related to pod and seed size on peanut A06 chromosome and application thereof

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0044] The character investigation of embodiment 1 natural population (250 parts of peanut materials)

[0045] In this example, 250 peanut materials were planted in the experimental bases in Nanchong, Sichuan and Wuhan, Hubei for two consecutive years in 2015 and 2016. After ripe harvesting and drying in the sun, the characteristics of pod length, pod width, seed length, seed width, 100-fruit weight and 100-kernel weight were investigated according to the Peanut Germplasm Resources Description Specification and Data Standard (Jiang Huifang et al., 2006) (Table 1). In the four environments (the four environments are: 2015 Wuhan base (2015WH), 2015 Nanchong base (2015NC), 2016 Wuhan base (2016WH), 2016 Nanchong base (2016NC)) the average frequency is continuous distribution (see figure 1 ), indicating the quantitative genetic characteristics of these traits.

[0046] Table 1 Investigation of pod and seed size traits under four environments

[0047]

Embodiment 2

[0048] Example 2 Library Construction and Sequencing

[0049] Leaf DNA of 250 materials was extracted by CTAB method. The purity and integrity of DNA were analyzed by agarose gel electrophoresis, the purity of DNA (OD260 / 280 ratio) was detected by Nanodrop, and the DNA concentration was accurately quantified by Qubit. For qualified DNA samples, TruSeq Library Construction Kit was used to construct a GBS library using MseI, HaeIII and NlaIII restriction endonucleases, and the reagents and consumables recommended in the instructions were strictly used. DNA fragments undergo end repair, polyA tailing, sequencing adapters, purification, PCR amplification and other steps to complete the entire library preparation. After the library construction is completed, use Qubit2.0 for preliminary quantification, dilute the library to 1ng / μl, and then use Agilent 2100 to detect the inserted fragments of the library. After the inserted fragments meet the expectations, use the Q-PCR method to ...

Embodiment 3

[0050] Example 3 Development of SNP markers

[0051] Perform quality control on the Raw data obtained after getting off the machine to obtain Clean data. The Clean data is compared to the reference genome, and the effective high-quality sequencing data is compared to the reference genome through the BWA software (with diploid A.duranensis (AA) and A.ipaensis (BB) as the reference genome, PeanutBase:http: https: / / peanutbase.org). GATK software was used to detect population SNPs. Use the Bayesian model to detect polymorphic sites in the population, and filter the detected 3,070,141 SNPs by retaining biallelic genes, miss≤0.83, and maf>0.05, and then infer by beagle, and then by GP value After filtering >0.6 and miss<0.2, 105,814 high-quality SNPs were obtained.

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Abstract

The invention relates to the technical field of molecular markers, and particularly relates to an SNP molecular marker related to pod and seed size on a peanut A06 chromosome and application thereof.The SNP molecular marker related to the pod and seed size on the peanut A06 chromosome is A06-107901527, and contains a nucleotide sequence with G / T polymorphism at the 12 site of the sequence shown in SEQ ID NO. 1. In the SNP molecular marker A06-107901527, the genotype of the site with the polymorphism is GG, the character value corresponding to the peanut pod and seed size is high, the genotype is TT, and the character value corresponding to the peanut pod and seed size is low. The SNP molecular marker is used for identifying the character phenotype of the peanut pod and seed size, theproduction cost can be greatly saved, and the selection efficiency can be improved.

Description

technical field [0001] The invention relates to the technical field of molecular markers, in particular to SNP molecular markers on peanut A06 chromosomes related to the size of pods and seeds and applications thereof. Background technique [0002] Peanut (Arachis hypogea L.) is an important oil and economic crop. It is of great significance to increase the yield of peanut. Although its yield has been significantly improved through continuous breeding and updating, there is still room for further improvement. [0003] Pod and seed size are important yield components. The pod size is composed of factors such as pod length, pod width, and 100-fruit weight, and the seed size is composed of seed length, seed width, and 100-kernel weight. It is generally believed that pod and seed size are quantitative traits (quantitative trait locus, QTL) controlled by multiple genes. These yield traits of peanut are relatively stable, and there is a significant positive correlation between...

Claims

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Application Information

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IPC IPC(8): C12Q1/6895C12Q1/6858C12N15/11G16B20/20G16B20/30
CPCC12Q1/6895C12Q1/6858G16B20/20G16B20/30C12Q2600/156C12Q2600/172C12Q2600/13C12Q2531/113C12Q2565/125
Inventor 周小静姜慧芳黄莉罗怀勇刘念陈伟刚
Owner INST OF OIL CROPS RES CHINESE ACAD OF AGRI SCI
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