Temporal and genomic analysis of additive genetic variance in breeding programmes

De Castro Lara, Leticia (author), Pocrnić, Ivan (author), De Paula Oliveira, Thiago (author), Gaynor, Robert Chris (author), Gorjanc, Gregor (author)

Genetic variance is a central parameter in quantitative genetics and breeding. Assessing changes in genetic variance over time as well as the genome is therefore of high interest. Here, we extend a previously proposed framework for temporal analysis of genetic variance using the pedigree-based model, to a new framework for temporal and genomic analysis of genetic variance using marker-based models. To this end, we describe the theory of partitioning genetic variance into genic variance and within-chromosome and between-chromosome linkage-disequilibrium, and how to estimate these variance components from a marker-based model fitted to observed phenotype and marker data. The new framework involves three steps: (i) fitting a marker-based model to data, (ii) sampling realisations of marker effects from the fitted model and for each sample calculating realisations of genetic values and (iii) calculating the variance of sampled genetic values by time and genome partitions. Analysing time partitions indicates breeding programme sustainability, while analysing genome partitions indicates contributions from chromosomes and chromosome pairs and linkage-disequilibrium. We demonstrate the framework with a simulated breeding programme involving a complex trait. Results show good concordance between simulated and estimated variances, provided that the fitted model is capturing genetic complexity of a trait. We observe a reduction of genetic variance due to selection and drift changing allele frequencies, and due to selection inducing negative linkage-disequilibrium.

• Language: English
• Keywords: agricultural genetics, agriculture, genetic variation, plant breeding, quantitative trait
• Work type: Article
• Typology: 1.01 - Original Scientific Article
• Organization: BF - Biotechnical Faculty
• Publication status: Published
• Publication version: Version of Record
• Year: 2022
• Number of pages: Str.21-32
• Numbering: Vol. 128, no. 1
• PID: 20.500.12556/RUL-134674
• UDC: 633
• ISSN on article: 1365-2540
• DOI: 10.1038/s41437-021-00485-y
• COBISS.SI-ID: 92142851
• Publication date in RUL: 25.01.2022

Record is a part of a journal

• Title: Heredity
• Shortened title: Heredity
• Publisher: Genetical Society of Great Britain
• ISSN: 1365-2540
• COBISS.SI-ID: 519011353

Licences

• License: CC BY 4.0, Creative Commons Attribution 4.0 International
• Link: http://creativecommons.org/licenses/by/4.0/
• Description: This is the standard Creative Commons license that gives others maximum freedom to do what they want with the work as long as they credit the author.
• Licensing start date: 15.12.2021

Secondary language

• Language: Slovenian
• Keywords: poljščine, pšenica, selekcija, selekcijski program, genetika, genomika, aditivna genetska varianca