Chapter 11. RIndSel: selection Indices with R

Abstract

RIndSel is a graphical unit interface that uses selection index theory to select individual candidates as parents for the next selection cycle. The index can be a linear combination of phenotypic values, genomic estimated breeding values, or a linear combination of phenotypic values and marker scores. Based on the restriction imposed on the expected genetic gain per trait, the index can be unrestricted, null restricted, or predetermined proportional gain indices. RIndSel is compatible with any of the following versions of Windows: XP, 7, 8, and 10. Furthermore, it can be installed on 32-bit and 64-bit computers. In the context of fixed and mixed models, RIndSel estimates the phenotypic and genetic covariance using two main experimental designs: randomized complete block design and lattice or alpha lattice design. In the following, we explain how RIndSel can be used to determine individual candidates as parents for the next cycle of improvement.