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Method for positioning rice complex trait gene

A technology of gene positioning and rice, applied in the direction of genomics, biochemical equipment and methods, microbial measurement/inspection, etc., to achieve the effect of low cost, high efficiency and short time

Active Publication Date: 2019-05-07
GUANGXI ZHUANG AUTONOMOUS REGION ACAD OF AGRI SCI
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Problems solved by technology

However, this method only constructs two phenotypic extreme pools, and only associates 1-2 major genes related to the target trait

Method used

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  • Method for positioning rice complex trait gene
  • Method for positioning rice complex trait gene
  • Method for positioning rice complex trait gene

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Embodiment 1

[0036]A method for gene mapping of rice complex traits, comprising the following steps:

[0037] (1) Population construction: Donglanmo with black seed coat and anthocyanin content as high as 1642.99 μg / g and Huang Huazhan with white seed coat and as low as 3.84 μg / g anthocyanin were selected as parents. F 2 group;

[0038] (2) Phenotype identification and grouping: the parents Huang Huazhan, Donglan Momi and F of the detection step (1) 2 The seed coat color of each individual plant in the population was determined by high performance liquid chromatography, and the anthocyanin content of brown rice was determined. According to the seed coat color and anthocyanin content of each individual plant, the F 2 The population is divided into 4 subgroups: completely black, partially black, brown, white;

[0039] The above-mentioned brown rice anthocyanins include 6 kinds of anthocyanins: geranium pigment, morning glory pigment, delphinium pigment, paeoniflorin pigment, cyanidin pigm...

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Abstract

The invention relates to the field of plant gene positioning technology, and particularly to a method for positioning a rice complex trait gene. The method comprises the steps of constructing an F2 group by means of two rice parents with remarkable target trait difference, dividing the F2 group into more than 3 or 3 subgroups according to a phenotype, selecting more than 30 or 30 single strains with the same phenotype in each subgroup, extracting DNA for constructing a plurality of mixing pools and performing re-sequencing, through comparing the sequencing reads of each mixing pool with a reference genome sequence, detecting SNP by means of software GATK, calculating the SNP-index and deltaSNP-index value of the corresponding site by means of an SNP-index method, drawing the distribution map of the deltaSNP-index, using the area which corresponds with a substantial associated deltaSNP-index as a candidate area, using the area which corresponds with the interaction of different deltaSNP-indexes at the same physical positions as a final candidate area, and predicting the candidate gene according to a gene annotation website, a sequencing depth and the deltaSNP-index value. The methodhas advantages of low cost, short time consumption and high efficiency. A plurality of candidate genes can be positioned. A candidate area with the target gene can be quickly shortened. The number oftarget genes which are closely linked can be accurately predicted.

Description

【Technical field】 [0001] The invention relates to the technical field of plant gene positioning, in particular to a method for gene positioning of rice complex traits. 【Background technique】 [0002] Complex traits generally refer to a class of traits that are jointly affected by polygenic and non-genetic factors. Complex traits cover a wide range, including classical quantitative traits, traits with discontinuous distribution of phenotypes, and other complex traits. The study of complex traits controlled by multiple genes is of great significance for crop adaptation to the environment and genetic improvement. However, due to the complexity of genetic control methods for complex traits, individual genes have relatively small phenotypic effects and are easily affected by the environment. Therefore, it has been difficult to resolve the control genes of complex traits. [0003] Traditional QTL mapping can be used to locate complex trait genes, but this method requires the co...

Claims

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Application Information

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IPC IPC(8): G16B20/30G16B20/20C12Q1/6869C12Q1/6806
Inventor 杨行海张宗琼夏秀忠农保选李丹婷邓国富曾宇熊发前戴高兴梁海福荘洁
Owner GUANGXI ZHUANG AUTONOMOUS REGION ACAD OF AGRI SCI
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