Software

GRainSX: Software for classical, ancestral, and sex-linked inbreeding analysis

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Abstract

Inbreeding coefficients remain fundamental for quantifying autozygosity, monitoring genetic drift, and evaluating biological consequences such as inbreeding depression, purging of deleterious load, and the expression of recessive harmful alleles. Although several extensions of the classical inbreeding coefficient have been developed for autosomes, including Kalinowski's new formulation and the ancestral measures of Ballou and Kalinowski, equivalent approaches for sex-linked inheritance have been largely absent. Because the X chromosome follows a distinct mode of transmission - with males being hemizygous and passing their single X chromosome unchanged to all daughters but never to sons - sex-linked inbreeding coefficients differ in expectation, variance, and interpretation from their autosomal counterparts. The objective of this study was to introduce GRainSX, an expanded implementation of GRain v2.2 that enables the calculation of classical, new, ancestral, and partial inbreeding coefficients for both autosomal and sex-linked loci using pedigree information. GRainSX was developed in FORTRAN 90 using a modular structure optimized for computational efficiency, clarity, and scalability, with updated routines for pedigree verification, allele initialization, gene-dropping simulations, and memory handling through the iso_c_binding interface. In addition to all autosomal coefficients available in GRain v2.2, GRainSX computes the sex-linked inbreeding coefficient (FSEX), Kalinowski's new sex-linked coefficient (FNEWSEX), Ballou's ancestral sex-linked coefficient (FABSEX), Kalinowski's ancestral sex-linked coefficient (FAKSEX), the sex-linked ancestral history coefficient (FAHCSEX), and their corresponding partial components tracing identity-by-descent from specific founders. To illustrate the behavior of these measures, we compared sex-linked and autosomal coefficients in two structurally identical pedigrees that differed only in the sex composition of their ancestors, thereby highlighting how changes in male-female patterns influence sex-linked inbreeding coefficients. In conclusion, GRainSX is the first publicly available software capable of computing classical, new, ancestral, and partial inbreeding coefficients for both autosomal and sex-linked loci. By enabling detailed quantification of X-linked autozygosity, it provides a valuable tool for evaluating sex-linked genetic load, recessive deleterious alleles, and potential inbreeding depression in livestock populations.

Keywords: 2026

How to Cite:

Kövér, G., Nagy, I., Nguyen, A., Farkas, J., Sölkner, J., Vostrý, L., Curik, I. & Hršak, D., (2026) “GRainSX: Software for classical, ancestral, and sex-linked inbreeding analysis”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2286950. doi: https://doi.org/10.31274/wcgalp.24178

Rights: 1