基于GBS技术对梅花鹿、马鹿及其杂交后代基因组SNP特征的分析

doi:10.11843/j.issn.0366-6964.2019.12.006

摘要/Abstract

摘要： 旨在利用基因分型测序（genotyping by sequencing，GBS）技术对梅花鹿、马鹿及其杂交后代（F1、F2）基因组的SNP特征进行分析。本试验采用GBS技术对梅花鹿（63个）、马鹿（12个）及其杂交后代（F1代112个，F2代38个，未知类型个体1个）共226个个体的血液基因组DNA进行测序，并利用本实验室前期110只梅花鹿、197只马鹿和1只F1代杂交鹿的测序数据，以梅花鹿全基因组为参考序列进行比对分析。结果，226个个体共产生Clean data 322.683 Gb，平均每个样品1 427.802 Mb；将所有样本作为一个群体检测SNP变异，共检测出SNP位点23 943 582个，质控过滤后得到SNP位点31 630个。对31 630个SNPs使用最大似然（maximum likelihood，ML）法构建的分子进化树显示，梅花鹿、马鹿、F1及F2代区分明显。对梅花鹿和马鹿的SNPs进行比对分析，筛选出可用于鉴别马鹿、梅花鹿、F1、F2的物种特异SNP位点1 032个（马鹿特异SNP位点474个，梅花鹿特异SNP位点558个），计算结果显示，F1代个体包含马鹿特异SNPs的比例主要在40%~60%之间，F2代个体含马鹿特异SNPs的比例主要在10%~30%之间，马鹿个体中不含梅花鹿的特异SNPs，梅花鹿中55.49%的个体不含马鹿特异SNPs，17.34%的个体含马鹿特异SNPs的比例低于1%，13.29%的个体含马鹿特异SNPs的比例在1%~10%之间，其余个体含马鹿特异SNPs的比例为10%~20%（其中有一个个体含马鹿特异SNPs的比例为33.3%）。该研究为花马杂交鹿后代的鉴定提供了可靠标记，并定量估计了F1和F2代个体含马鹿特异SNPs的比例，马鹿个体中不含梅花鹿的特异SNPs，这对梅花鹿、马鹿及其杂交后代（F1、F2）的鉴别具有重要意义。

关键词: GBS, 梅花鹿, 马鹿, 杂交鹿, SNP, 鉴别

Abstract: The purpose of this study was to analyze the genomic SNP characteristics of sika deer, red deer and their hybrid progenies (F1, F2) based on GBS(genotyping by sequencing) technology. In this experiment, the genomic DNA from 226 blood samples was sequenced by GBS. All samples were consisted of 63 sika deer, 12 red deer, 112 F1 generation individuals, 38 F2 generation individuals and 1 unknown individual. Furthermore, the previous sequencing data contained 110 sika deer, 197 red deer and 1 F1 generation individual. All the sequencing data was mapped to the reference genome of the sika deer which assembled at the chromosomal level. The sequence results produced 322.683 Gb Clean data for 226 individuals, averaging of 1 427.802 Mb for per sample. All samples were used as a population to detect SNP variation, and a total of 23 943 582 SNP loci were identified, while 31 630 SNP loci were remained after screening and filtering. A phylogenetic tree was constructed with 31 630 SNP loci by the maximum likelihood(ML) method, sika deer, red deer, F1, and F2 individuals were significantly distinguished in the phylogenetic. The SNPs of sika deer and red deer were compared and analyzed, and 1 032 specific SNPs were screened out for identifying red deer, sika deer, F1 and F2 generation (474 specific SNP loci for red deer, 558 specific SNP loci for sika deer). The calculation results showed that the proportion of F1 generation individuals containing red deer specific SNPs was mainly between 40% to 60%, and the proportion of F2 generation individuals containing red deer specific SNPs was mainly between 10% to 30%. The red deer did not contain the specific SNPs for sika deer; 55.49% of the individuals in the sika deer did not contain the specific SNPs for red deer,17.34% of the individuals contained less than 1% specific SNPs for red deer, and 13.29% of the individuals contained the 1%-10% specific SNPs for red deer, the rest individuals contained the 10%-20% specific SNPs for red deer except one individual who contained 33.3% specific SNPs for red deer. This study had established reliable markers for identifying hybrid progenies of sika deer and red deer, and the proportion of red deer's specific SNPs in F1 and F2 generation individuals was estimated. The red deer doesn't contain any specific SNPs for sika deer. The result of this study is of great significance to the identification of sika deer, red deer and their hybrid progenies (F1, F2).

Key words: GBS, sika deer, red deer, hybrid deer, SNP, identification

中图分类号:

S825.2

董世武, 王天骄, 刘华淼, 王磊, 唐丽昕, 邢秀梅. 基于GBS技术对梅花鹿、马鹿及其杂交后代基因组SNP特征的分析[J]. 畜牧兽医学报, 2019, 50(12): 2422-2430.

DONG Shiwu, WANG Tianjiao, LIU Huamiao, WANG Lei, TANG Lixin, XING Xiumei. Analysis of Genomic SNP Characteristics of Sika Deer, Red Deer and Their Hybrid Progenies Based on GBS Technology[J]. Acta Veterinaria et Zootechnica Sinica, 2019, 50(12): 2422-2430.

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