林木多地点半同胞子代测定遗传分析
R语言程序包及其应用

王德源; 童春发

doi:10.3969/j.issn.1000-2006.2015.05.008

林木多地点半同胞子代测定遗传分析 R语言程序包及其应用

王德源,童春发

南京林业大学学报（自然科学版） ›› 2015, Vol. 39 ›› Issue (05) : 45-51.

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南京林业大学学报（自然科学版） ›› 2015, Vol. 39 ›› Issue (05) : 45-51. DOI: 10.3969/j.issn.1000-2006.2015.05.008

研究论文

林木多地点半同胞子代测定遗传分析 R语言程序包及其应用

王德源,童春发^*

作者信息 +

HalfsibMS: An R package for genetic analysis of half-sib progeny test at multiple sites in forest trees

WANG Deyuan, TONG Chunfa^*

Author information +

文章历史 +

摘要

子代测定是林木育种中的关键环节,有关子代测定的遗传参数和统计量计算还存在不少问题。用于计算多种遗传参数的R语言程序包HalfsibMS,可以对多地点或单地点的半同胞子代测定遗传统计模型进行分析计算,并且可以处理平衡数据或不平衡数据。该程序包首先采用固定效应模型计算亲本配合力及其他固定效应; 然后再用随机效应模型计算遗传方差和协方差进而估算遗传力,并计算每一个参数估计的标准误和显著性检验统计量; 最后,对于多个数量性状,给出了它们在家系效应、地点与家系互作效应及区组与家系互作效应水平上的遗传相关系数及其标准误。该程序包可在网站http://fgbio.njfu.edu.cn/tong/halfsibms/halfsibms.html上自由下载使用。

Abstract

A progeny test plays an important role in forest breeding programs, but there still exist some problems in half-sib progeny test in calculating the estimates of genetic parameters and some statistics, especially when the experimental data are unbalanced. HalfsibMS is a new R-based package developed for calculating genetic parameters with balanced or unbalanced data in half-sib progeny test at multiple sites in forest trees. For the fixed-effect model, the package used the methods of restricted linear model to estimate the general combining abilities of parents and other fixed effects. For the random effect model, the package applied variance analysis method of mixed linear model to compute the genetic variance components and further the heritabilities. Moreover, HalfsibMS can calculate standard error of each parameter estimate and statistics of significance tests. For multiple traits, the new tool can also provide the genetic correlation coefficient between any two traits at the levels of family, site×family and block×family effects. This package can be downloaded from the site of http://fgbio.njfu.edu.cn/tong/halfsibms/halfsibms.html free.

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王德源,童春发. 林木多地点半同胞子代测定遗传分析 R语言程序包及其应用[J]. 南京林业大学学报（自然科学版）. 2015, 39(05): 45-51 https://doi.org/10.3969/j.issn.1000-2006.2015.05.008

WANG Deyuan, TONG Chunfa. HalfsibMS: An R package for genetic analysis of half-sib progeny test at multiple sites in forest trees[J]. JOURNAL OF NANJING FORESTRY UNIVERSITY. 2015, 39(05): 45-51 https://doi.org/10.3969/j.issn.1000-2006.2015.05.008

中图分类号： S722.3 Q348

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基金

收稿日期:2014-09-22 修回日期:2015-05-06
基金项目:国家自然科学基金面上项目(31070601); 江苏高校优势学科建设工程资助项目(PAPD)
第一作者:王德源,硕士生。*通信作者:童春发,教授。E-mail: tongchf@njfu.edu.cn。
引文格式:王德源,童春发. 林木多地点半同胞子代测定遗传分析R语言程序包及其应用[J]. 南京林业大学学报:自然科学版,2015,39(5):45-51.