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Method for identifying marker of candidate gene related to milk production traits of buffaloes and application

A candidate gene, buffalo technology, applied in the directions of genomics, biochemical equipment and methods, microbial determination/inspection, etc., to achieve the effect of improving reliability

Active Publication Date: 2021-02-09
GUANGXI ZHUANG AUTONOMOUS REGION BUFFALO INST
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  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

The current selection signal detection method is mainly based on the estimated gene frequency of the research population and its related statistics to infer the genome selection signal, and the complex population background may affect the selection signal inference (Ma Yunlong, 2015), resulting in relatively large many false positives

Method used

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  • Method for identifying marker of candidate gene related to milk production traits of buffaloes and application
  • Method for identifying marker of candidate gene related to milk production traits of buffaloes and application
  • Method for identifying marker of candidate gene related to milk production traits of buffaloes and application

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Experimental program
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Effect test

Embodiment

[0044]1. Research steps:

[0045]1. Data download and SNP typing

[0046]Download the simplified buffalo genome sequencing (dd-RAD) data from the NCBI public database, a total of 116.00Gb, and the data download accession number is PRJNA554744. This batch of data includes two groups, one group is swamp-type buffalo with 25 individuals, and the other group is river-type Egyptian buffalo with 20 individuals.

[0047]SNP typing: Based on the dd-RAD data of these 45 individuals, this study used GATK v4.1.8.1 software for SNP typing.

[0048]The basic steps are: use Trimmomatic v0.39 software to perform quality control on the original data, then use BWA-0.7.17 (r1188) software to compare the quality-controlled data to the buffalo reference genome (UOA_WB_1), and finally use the GATK process SNP typing, where the quality control parameter is: the quality value after depth correction50.0, Phred quality value5. Evaluate the credibility value of the variation at the read position-12.5.

[0049]Use Beagle v5...

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Abstract

The invention relates to the technical field of molecular markers, and discloses a method for identifying a molecular marker of a candidate gene related to milk production traits of buffaloes. The method comprises the following specific steps: (1) obtaining SNP genotypes of 45 buffalo individuals by a dd-RAD method; (2) performing grouping based on population genetic diversity and population structures, further performing selection signal analysis by using Fst and XP-CLR strategies, and identifying the candidate gene related to the milk production traits; (3) using a comparative transcriptomestrategy to assist in verifying the relevance between the candidate gene and the milk production traits of the buffaloes; and (4) identifying the related molecular marker influencing the milk production traits of the buffaloes by using a marker-trait correlation analysis strategy. The candidate gene SCLO3A1 related to the milk production traits of the buffaloes and the molecular marker g.54621870G>T influencing the milk protein rate are identified by the method for the first time. The molecular marker can be used for breeding a buffalo population with high milk protein content.

Description

【Technical Field】[0001]The invention relates to the field of biotechnology, in particular to a method and application for identifying candidate gene markers for buffalo milk production traits.【Background technique】[0002]Water buffalo is an important special dairy species in southern my country. It has excellent milk quality and rich nutrition. It has the reputation of "king of milk" and is deeply loved by consumers. Water buffalo can be divided into two subspecies, river-type and marsh-type buffalo. Among them, river-type buffalo is mainly used for both milk and meat, which is the representative of high-yielding buffalo group, and swamp-type buffalo is mainly used for labor, which is the representative of low-yield buffalo group. However, low milk production performance has become a major scientific issue affecting the development of the buffalo industry. Exploring the causal genes related to the milk production traits of buffaloes has become a hotspot of scientific research on buff...

Claims

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Application Information

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IPC IPC(8): C12Q1/6888C12N15/11G16B20/20G16B10/00G16B30/10G16B25/00
CPCC12Q1/6888G16B20/20G16B10/00G16B30/10G16B25/00C12Q2600/156C12Q2600/124
Inventor 邓廷贤陆杏蓉段安琴马小娅梁莎莎
Owner GUANGXI ZHUANG AUTONOMOUS REGION BUFFALO INST
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