Novel method for estimating genome variety composition of aquatic animals based on ADMIXTURE-MCP model

A technology of aquatic animals and genome, applied in the fields of genomics, proteomics, bioinformatics, etc.

Active Publication Date: 2020-06-30
OCEAN UNIV OF CHINA
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  • Abstract
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Problems solved by technology

Aiming at the problem that the previous ADMIXTURE model produces small components for similar gene sequences of different species of scallops, this invention uses a sparse optimization method to generate a sparse solution to reduce the estimated GBC noise generated by the genetic similarity of the traditional model

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  • Novel method for estimating genome variety composition of aquatic animals based on ADMIXTURE-MCP model
  • Novel method for estimating genome variety composition of aquatic animals based on ADMIXTURE-MCP model
  • Novel method for estimating genome variety composition of aquatic animals based on ADMIXTURE-MCP model

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Embodiment

[0052] The specific implementation manners of the present invention will be further described in detail below in conjunction with the accompanying drawings and embodiments. The following bivalve scallop among aquatic animals is taken as an example to illustrate the present invention, but not to limit the scope of the present invention.

[0053] Gulf scallop is one of the most important cultured shellfish in my country, but the germplasm degradation problem in recent years has become a serious obstacle restricting the development of my country's bay scallop aquaculture industry. Both purple scallop and bay scallop belong to the excellent species of bay scallop, and they have complementary traits. Through interspecific hybridization, it is expected to breed scallops with fast growth speed, large individual size and wide temperature adaptation range, which can improve the germplasm of bay scallop and improve the quality of scallop. The economic output of aquaculture.

[0054] Th...

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Abstract

The invention provides a novel method for genome variety composition of aquatic animals based on an ADMIXTURE-MCP model, and belongs to the field of aquatic animal variety composition, and the methodcomprises the following steps: obtaining genome SNP marker data of an unknown variety of aquatic animals; screening the reference aquatic animals; and estimating the genome variety composition of theaquatic animals. For solving the problem that the traditional ADMIXTURE model generates small components for similar gene sequences of different scallops, the invention uses a sparse optimization method to generate a sparse solution to reduce estimated GBC noise generated by gene similarity of the traditional model. It is found that a sparse solution generated by a traditional L1 norm constraint model is unstable, and although the problem of ADMIXTURE small components can be reduced, estimation of the GBC composition and the real GBC composition often deviate greatly. In order to overcome thedefect of serious GBC estimation deviation caused by L1 norm constraint used in a traditional algorithm, the invention provides a method for replacing L1 norm constraint with non-convex function MCP constraint, which can generate a result closer to an unbiased estimation GBC result while reducing GBC noise.

Description

technical field [0001] The invention belongs to the field of species composition of aquatic animals, and in particular relates to a new method for estimating the species composition of aquatic animal genomes based on the ADMIXTURE-MCP model. Background technique [0002] Using basic scientific research to promote the high-quality development of animal husbandry and provide consumers with high-quality, low-priced and safe livestock and poultry products is the starting point and goal of animal genomics research. The genomic breed composition (GBC) of an individual animal refers to the genetic contribution ratio of the animal's ancestors to the individual genome of the animal. Accurate estimation of animal individual GBC is of great significance to animal genetics research and breeding work, such as identification of animal kinship from the genome level, evaluation of the breeding history and purity of a certain animal breed, protection of local characteristic breeds, and predi...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G16B20/20G16B35/20
CPCG16B20/20G16B35/20
Inventor 王扬帆任强倪萍胡晓丽黄晓婷邢强焦文倩张玲玲王师胡景杰包振民
Owner OCEAN UNIV OF CHINA
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