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AFEchidna is an R package for genetic evaluation of plant and animal breeding datasets
bioRxiv - Plant Biology Pub Date : 2021-09-07 , DOI: 10.1101/2021.06.24.449740
Weihua Zhang , Ruiyan Wei , Yan Liu , Yuanzhen Lin

Progeny tests play important roles in plant and animal breeding programs, and mixed linear models are usually performed to estimate variance components of random effects, estimate the fixed effects (Best Linear Unbiased Estimates, BLUEs) and predict the random effects (Best Linear Unbiased Predictions, BLUPs) via restricted maximum likehood (REML) methods in progeny test datasets. The current pioneer software for genetic assessment is ASReml, but it is commercial and expensive. Although there is free software such as Echidna or the R package sommer, the Echidna syntax is complex and the R package functionality is limited. Therefore, this study aims to develop an R package named AFEchidna based on Echidna software. The mixed linear models are conveniently implemented for users through the AFEchidna package to solve variance components, genetic parameters and the BLUP values of random effects, and the batch analysis of multiple traits, multiple variance structures and multiple genetic parameters can be also performed, as well as comparison between different models and genomic BLUP analysis. The AFEchidna package is free, please email us (yzhlinscau{at}163.com) to get a copy if reader is interested for it. The AFEchidna package is developed to expand free genetic assessment software with the expectation that its efficiency could be close to the commercial software.

中文翻译:

AFEchidna 是一个用于植物和动物育种数据集遗传评估的 R 包

后代检验在动植物育种计划中发挥着重要作用,混合线性模型通常用于估计随机效应的方差分量、估计固定效应(Best Linear Unbiased Estimates,BLUEs)和预测随机效应(Best Linear Unbiased Predictions, BLUPs)通过后代测试数据集中的受限最大似然(REML)方法。目前用于遗传评估的先驱软件是 ASReml,但它是商业化的且价格昂贵。尽管有 Echidna 或 R 包 sommer 等免费软件,但 Echidna 语法复杂且 R 包功能有限。因此,本研究旨在基于 Echidna 软件开发一个名为 AFEchidna 的 R 包。通过 AFEchidna 包为用户方便地实现混合线性模型以解决方差分量,遗传参数和随机效应的BLUP值,也可以进行多性状、多方差结构和多遗传参数的批量分析,以及不同模型之间的比较和基因组BLUP分析。AFEchidna 包是免费的,请给我们发电子邮件 (yzhlinscau{at}163.com ) 以获取副本,如果读者对此感兴趣。开发 AFEchidna 软件包是为了扩展免费的遗传评估软件,期望其效率可以接近商业软件。
更新日期:2021-09-08
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