SSR (simple sequence repeat) molecular marker L10 closely linked with rice high stalk QTL as well as application thereof

A molecular marker, rice technology, applied in the field of DNA molecular marker technology and molecular biology, can solve the problem of under-saturation of rice SSR marker development

Inactive Publication Date: 2018-11-20
BIOTECH RES CENT SHANDONG ACADEMY OF AGRI SCI
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

Currently, a large number of SSR markers have been developed based on the rice genome sequencing results (McCouch et al., 2002; Saini et al., 2004; Nonoue et al., 2008; Matsubara et al., 2008; Maas et al., 2010), However, the development of rice SSR markers is still not saturated

Method used

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  • SSR (simple sequence repeat) molecular marker L10 closely linked with rice high stalk QTL as well as application thereof
  • SSR (simple sequence repeat) molecular marker L10 closely linked with rice high stalk QTL as well as application thereof
  • SSR (simple sequence repeat) molecular marker L10 closely linked with rice high stalk QTL as well as application thereof

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0029] Example 1 Design of SSR Molecular Markers Tightly Linked to Rice Tall Stalk QTL

[0030] 1.1 Primer design method:

[0031] Molecular marker design is carried out on the chromosome segments where microsatellite markers need to be developed. The sequences of PAC / BAC clones in this region were downloaded from the TIGR website (The Institute of Genome Research) (http: / / www.tigr.org / tdb / rice). TIGR has integrated PAC / BAC clones sequenced by IRGSP (International Rice Genome Sequencing Project, IRGSP) into the genetic map. The sequences of PAC / BAC clones downloaded from the target region first need to use the repetitive sequence search software SSRIT (http: / / www .gramene.org / microsat / ) to search the microsatellite sequence, and then select the appropriate microsatellite sequence (generally require the number of repeats to be more than 8, and avoid the motif being AT), and download a small segment containing the microsatellite sequence Genome sequence (350-500bp), and finall...

Embodiment approach

[0039] Polymorphic screening was carried out by published SSR markers, and the gene controlling rice tall stem was located in the region between the two markers PSM331 and RM1068 on the short and long arm of rice chromosome 1 ( figure 1 , figure 2 ), the specific implementation is as follows:

[0040] According to the polymorphic screening of the published SSR markers (as shown in Table 1), it was found that RM315, PSM331, PSM423, RM104, and RM529, a total of five SSR markers, were polymorphic between the two parents.

[0041] According to the results of molecular marker analysis, the software MAPMAKER (EXP3.0b) was used to analyze the molecular data and calculate the genetic distance between the markers. The plant height gene PH-1(t) was located on the first chromosome, and the genetic distances between the microsatellite markers RM1068, PSM423, RM104 and PH-1(t) on the side of the long arm were 0.5cM, 0.9cM, 8.9cM, and the genetic distances between the microsatellite mark...

Embodiment 2

[0052] Example 2 Application of Rice SSR Molecular Marker L06, SSR Molecular Marker L08, and SSR Molecular Marker L10

[0053] 2.1 Rice genomic DNA extraction

[0054] The total DNA of rice genome was extracted by the improved TPS simple method, and the specific steps were as follows:

[0055] 1. At the peak tillering stage, take 1 to 2 young leaves from the upper part of each plant, and store them in a -80°C refrigerator for later use;

[0056] 2. When extracting DNA, take 2-4cm long rice leaves and put them into a 1.5ml centrifuge tube, put them in liquid nitrogen, grind them, add 900ml of TPS extract solution, and bathe in 75°C water bath for 30-60min;

[0057] 3. Centrifuge at 12000rpm for 10min, absorb about 500ml of the supernatant and transfer to a new 1.5ml centrifuge tube;

[0058] 4. Add pre-cooled isopropanol or absolute ethanol to top up. Overnight at 4°C, centrifuge at 12000rpm for 10min;

[0059] 5. Discard the supernatant, dry the precipitate, add 150 μl ste...

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Abstract

The invention relates to an SSR (simple sequence repeat) molecular marker L10 closely linked with rice high stalk QTL as well as application thereof. In the SSR molecular marker L10 closely linked with the rice high stalk QTL, the nucleotide sequence of the upstream marker is as shown in SEQ ID NO.5, and the nucleotide sequence of the downstream marker is as shown in SEQ ID NO.6. The SSR marker can perform genetic analysis and fine positioning on the first chromosome high stalk gene of the rice and can be used for establishing a rice high-density genetic map and a variety fingerprint spectrum.

Description

technical field [0001] The present invention relates to the SSR molecular marker L10 closely linked with the rice tall stem QTL and its application, in particular to the rice simple repeat sequence (SSR, Simple sequence repeats) analysis marker and its application in the genetic analysis and fine positioning of the rice tall stem gene, belonging to DNA molecular marker technology and molecular biology technology field. Background technique [0002] SSR (simple sequence repeat, simple repeat sequence), also known as microsatellites (Microsatellites), is a sequence formed by repeating units of 1-6 nucleotides in series (Sharma et al., 2007), and is also a A DNA molecular genetic marker based on PCR (polymerase chain reaction), which is widely distributed throughout the plant genome. Different materials in the same species have different repetition times of the SSR motif. Use relatively conserved single-copy sequences on both sides of the repeat region to design primers to amp...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): C12Q1/6895C12N15/11
CPCC12Q1/6895C12Q2600/13C12Q2600/156C12Q2600/158
Inventor 姚方印陈高张华柳絮宣宁杨永义
Owner BIOTECH RES CENT SHANDONG ACADEMY OF AGRI SCI
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