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Gamevar.f90: a software package for calculating individual gametic diversity.
BMC Bioinformatics ( IF 3 ) Pub Date : 2020-03-06 , DOI: 10.1186/s12859-020-3417-x
Daniel Jordan de Abreu Santos 1 , John B Cole 2 , George E Liu 2 , Paul M VanRaden 2 , Li Ma 1
Affiliation  

BACKGROUND Traditional selection in livestock and crops focuses on additive genetic values or breeding values of the individuals. While traditional selection utilizes variation between individuals, differences between gametes within individuals have been less frequently exploited in selection programs. With the successful implementation of genomic selection in livestock and crops, estimation and selection for gametic variation is becoming possible. RESULTS The gamevar.f90 software is designed to estimate individual-level variance of genetic values of gametes for complex traits in large populations. The software estimates the (co)variances of gametic diversity as well as other diversity parameters that are useful for selection programs and mating designs. The calculation is carried out chromosome by chromosome and can be easily parallelized. The gamevar.f90 program is written in Fortran with efficient computing algorithms in a user-friendly software package with easily-handled input and output files. Finally, we applied the program to estimate gametic variance for hundreds of bulls for lifetime net merit, productive life, and livability. The RPTA (relative predicted transmitting ability), assuming a future selection intensity (if) of 1.5, showed larger variance than GEBV/2, indicating that greater future genetic gains can be obtained using an index that includes gametic variances. We also used the relative coefficient of variation to estimate with 95% confidence the sample sizes required to observe 90% variability of the progeny for lifetime net merit (or to allow at maximum 10% of change in the EBV predicted from progeny data). CONCLUSIONS Collectively, we develop an efficient computer program package, gamevar.f90, for estimating gametic variance for large numbers of individuals. The novel information on gametic variation will be useful in future animal and crop breeding programs.

中文翻译:

Gamevar.f90:用于计算个体配子多样性的软件包。

背景技术牲畜和农作物中的传统选择集中于个体的附加遗传价值或育种价值。尽管传统选择利用个体之间的变异,但是在选择程序中很少利用个体内配子之间的差异。随着牲畜和农作物中基因组选择的成功实施,估计和选择配子变异成为可能。结果gamevar.f90软件旨在评估大种群中复杂性状配子遗传值的个体水平变异。该软件估计配子多样性的(共)方差以及对选择程序和配对设计有用的其他多样性参数。计算是逐个染色体进行的,可以很容易地并行化。gamevar.f90程序使用高效的计算算法用Fortran编写,并包含在易于使用的输入和输出文件的用户友好软件包中。最后,我们使用该程序来估算数百头公牛的配子方差,以了解其终生净功绩,生产寿命和宜居性。假设未来选择强度(if)为1.5,则RPTA(相对预测的传播能力)显示出比GEBV / 2大的方差,表明使用包含配子方差的指数可以获得更大的未来遗传增益。我们还使用相对变异系数以95%的置信度估算了观察样本的大小,以观察子代90%的终生净值(或允许从子代数据预测的EBV的最大变化10%)。结论集体而言,我们开发了一种有效的计算机程序包gamevar.f90,用于估计大量个体的游戏差异。有关配子变异的新信息将在未来的动物和农作物育种计划中有用。
更新日期:2020-03-06
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