肉鸡腹脂率双向选择系群体表型数据库(NEAUHLFPD)的设计及其功能实现

摘要

表型性状的准确记录及其有效管理和分析是选育优良畜禽品种(系)工作的重要内容.东北农业大学肉鸡腹脂率双向选择系(Northeast Agricultural University High and Low Fat,NEAUHLF)经过20年的选育工作积累了大量与肉鸡脂肪沉积的分子遗传基础研究相关的表型数据.为了有效并系统地存储、管理和分析利用这些表型数据,本研究建立了东北农业大学肉鸡腹脂率双向选择系表型数据库(The NEAUHLF Phenome Database,NEAUHLFPD)管理系统.NEAUHLFPD主要涵盖以下表型记录和信息:1～19世代系谱记录和29项表型数据(分别为鸡体尺性状、体重性状、屠体性状及相应的率性状信息等).该表型数据库的架构和设计过程具体如下:(1)架构信息.WEB服务器—Apache;数据库—MySQL;数据库管理工具—Navicat;用于动态交互性站点创建的服务器端脚本语言—PHP;超文本标记语言—HTML. (2)结构信息.主界面上有数据库整体组成及功能的详细介绍,以及数据库各部分基本结构的索引按钮.功能模块主要包含两方面内容:第一模块,表型(phenotype)数据的物理存储空间,可实现数据指标的选定、筛选、范围设定和查找等功能;第二模块,表型数据的基本描述性统计计算(descriptive statistics),可对条件筛选后的数据进行基本统计量的计算,同时还可实现对筛选数据的按条件排序等功能.NEAUHLFPD不仅能有效储存和管理表型数据,还可以兼容高通量基因组学数据,有利于今后进一步开展鸡脂肪组织生长发育的分子遗传基础研究以及推进低脂肉鸡的选育工作.%Effective management and analysis of precisely recorded phenotypic traits are important components of the selection and breeding of superior livestocks.Over two decades,we divergently selected chicken lines for abdominal fat content at Northeast Agricultural University (Northeast Agricultural University High and Low Fat,NEAUHLF),and collected large volume of phenotypic data related to the investigation on molecular genetic basis of adipose tissue deposition in broilers.To effectively and systematically store,manage and analyze phenotypic data,we built the NEAUHLF Phenome Database (NEAUHLFPD).NEAUHLFPD included the following phenotypic records:pedigree (generations 1-19) and 29 phenotypes,such as body sizes and weights,carcass traits and their corresponding rates.The design and construction strategy of NEAUHLFPD were executed as follows:(1) Framework design.We used Apache as our web server,MySQL and Navicat as database management tools,and PHP as the HTML-embedded language to create dynamic interactive website.(2) Structural components.On the main interface,detailed introduction on the composition,function,and the index buttons of the basic structure of the database could be found.The functional modules of NEAUHLFPD had two main components:the first module referred to the physical storage space for phenotypic data,in which functional manipulation on data can be realized,such as data indexing,filtering,range-setting,searching,etc.;the second module related to the calculation of basic descriptive statistics,where data filtered from the database can be used for the computation of basic statistical parameters and the simultaneous conditional sorting.NEAUHLFPD could be used to effectively store and manage not only phenotypic,but also genotypic and genomics data,which can facilitate further investigation on the molecular genetic basis of chicken adipose tissue growth and development,and expedite the selection and breeding of broilers with low fat content.