Department of Animal and Avian Sciences, University of Maryland, College Park, MD, 20742, USA.
Henry A. Wallace Beltsville Agricultural Research Center, Animal Genomics and Improvement Laboratory, ARS, USDA, Beltsville, MD, 20705-2350, USA.
BMC Bioinformatics. 2020 Mar 6;21(1):100. doi: 10.1186/s12859-020-3417-x.
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.
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 (i) 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).
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.
传统的家畜和作物选择侧重于个体的加性遗传值或育种值。虽然传统选择利用了个体之间的差异，但个体内部配子之间的差异在选择计划中较少被利用。随着基因组选择在家畜和作物中的成功实施，对配子变异的估计和选择变得成为可能。
gamevar.f90 软件旨在估计大群体中复杂性状个体配子遗传值的个体水平方差。该软件估计配子多样性的（协）方差以及其他对选择计划和交配设计有用的多样性参数。计算按染色体进行，可以轻松并行化。gamevar.f90 程序是用 Fortran 编写的，具有高效的计算算法，用户友好的软件包，易于处理的输入和输出文件。最后，我们应用该程序估计了数百头公牛的终生净效益、生产寿命和生存能力的配子方差。假设未来选择强度（i）为 1.5，RPTA（相对预测传递能力）显示出比 GEBV/2 更大的方差，这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来估计 95%置信区间内所需的样本量，以观察到终生净效益的后代变异的 90%（或允许从后代数据预测的 EBV 最多变化 10%）。
总之，我们开发了一个高效的计算机程序包 gamevar.f90，用于估计大量个体的配子方差。配子变异的新信息将在未来的动物和作物育种计划中有用。
