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Population genetic evolution map and construction method thereof

A population genetic and map technology, applied in the field of population genetic evolution map and its construction, can solve the problem of inaccurate population genetic evolution map

Active Publication Date: 2020-03-24
CHINA NAT RICE RES INST
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  • Claims
  • Application Information

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Problems solved by technology

[0011] The main purpose of the present invention is to provide a population genetic evolution map and its construction method, to solve the problem that the population genetic evolution map (i.e. phylogenetic tree) constructed in the prior art is not accurate enough

Method used

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  • Population genetic evolution map and construction method thereof
  • Population genetic evolution map and construction method thereof
  • Population genetic evolution map and construction method thereof

Examples

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Embodiment 1

[0066] Example 1 Study on the evolution of rice using the region where recombination does not occur at the left and right ends of the rice centromere

[0067] (1) Determined the centromere position of the rice IRGSP 4.0 reference genome

[0068] The 1.155bp CentO satellite repeat sequence is the core element of rice centromere DNA. At the centromere of each chromosome in rice, CentO is variable in number, ranging in size from 65 kb to 2 Mb. Use the CentO sequence as the seed sequence to compare each chromosome of the IRGSP4.0 reference genome. According to the position information on the comparison, use the 10Kb window for quantitative statistics to determine the centromere boundary of each chromosome.

[0069] 2. The SNP distribution of the statistical data set, with a window of 10Kb.

[0070] 3. Select the SNP of the 200Kb sequence that does not recombine at both ends of the centromere.

[0071] The result is as figure 1 shown. figure 1 (See color picture reference pict...

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Abstract

The invention provides a population genetic evolution map and a construction method thereof. The construction method comprises the following steps: selecting a recombined cold spot region; constructing a phylogenetic tree by utilizing the SNP sites of the recombined cold spot region; performing clustering analysis on the phylogenetic tree, and determining an evolution relationship between speciesso as to obtain a population genetic evolution map. According to the method, the phylogenetic tree is constructed by selecting SNP sites of the recombined cold spot region (such as a centromere region); on one hand, due to low recombination occurrence rate and stable inheritance between parents and filial generations, the genetic evolution relationship is clear, the constructed phylogenetic tree is more accurate, and on the other hand, the number of SNP sites in the selected sequence is smaller than that of whole genome sequences and is more and more comprehensive than that of SNP sites in a haplotype analysis method. Therefore, the phylogenetic tree can be quickly and accurately constructed.

Description

technical field [0001] The invention relates to the field of population genetic evolution, in particular to a population genetic evolution map and a construction method thereof. Background technique [0002] Phylogenetics refers to the branched evolutionary history of biological lineages, or the entire genetic evolutionary history of life since its origin. [0003] Phylogenetic trees are graph-theoretic models that describe phylogenetic relationships between species or operational taxa. An operational taxonomic unit can be an extant species, a gene, a genome, or any other operational unit. The construction of a phylogenetic tree is a scientific exploration of recreating the evolutionary history of life from the evidence of extant species and paleontological records. The importance of phylogenetic trees is aptly emphasized by the great evolutionary biologist's famous quote "Without the theory of evolution, nothing in biology makes sense." [0004] Due to technical limitati...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G16B30/10G06F16/36
CPCG16B30/10G06F16/367Y02A90/10
Inventor 王克剑刘庆孙亭亭王春焦晓真
Owner CHINA NAT RICE RES INST
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