The use of genomic coancestry matrices in the optimisation of contributions to maintain genetic diversity at specific regions of the genome

Genetics, Selection, Evolution : GSE
Fernando Gómez-RomanoRicardo Pong-Wong

Abstract

Optimal contribution methods have proved to be very efficient for controlling the rates at which coancestry and inbreeding increase and therefore, for maintaining genetic diversity. These methods have usually relied on pedigree information for estimating genetic relationships between animals. However, with the large amount of genomic information now available such as high-density single nucleotide polymorphism (SNP) chips that contain thousands of SNPs, it becomes possible to calculate more accurate estimates of relationships and to target specific regions in the genome where there is a particular interest in maximising genetic diversity. The objective of this study was to investigate the effectiveness of using genomic coancestry matrices for: (1) minimising the loss of genetic variability at specific genomic regions while restricting the overall loss in the rest of the genome; or (2) maximising the overall genetic diversity while restricting the loss of diversity at specific genomic regions. Our study shows that the use of genomic coancestry was very successful at minimising the loss of diversity and outperformed the use of pedigree-based coancestry (genetic diversity even increased in some scenarios). The results also show th...Continue Reading

References

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Mar 10, 2001·Nature·R SachidanandamUNKNOWN International SNP Map Working Group
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Mar 19, 2013·BMC Genomics·Anna Esteve-CodinaMiguel Pérez-Enciso
Oct 4, 2013·Genetics, Selection, Evolution : GSE·Fernando Gómez-RomanoJesús Fernández
Nov 20, 2014·Genetics, Selection, Evolution : GSE·Jennie E PryceBen J Hayes
Jan 18, 2015·Genetics, Selection, Evolution : GSE·María SauraBeatriz Villanueva

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Citations

Dec 3, 2016·Animal Genetics·E PeripolliF Baldi
May 4, 2017·Journal of Animal Breeding and Genetics = Zeitschrift Für Tierzüchtung Und Züchtungsbiologie·J T HowardC Maltecca
Sep 10, 2020·Frontiers in Genetics·Theo H E MeuwissenJohn A Woolliams
Apr 7, 2017·Genetics·Herman De BeukelaerGeert De Meyer
Sep 25, 2019·Genetics, Selection, Evolution : GSE·Anna-Charlotte DoubletGwendal Restoux
Sep 3, 2019·Frontiers in Genetics·Robin Wellmann, Jörn Bennewitz
Nov 26, 2016·Genetics, Selection, Evolution : GSE·Jeremy T HowardChristian Maltecca
Nov 13, 2019·Journal of Animal Breeding and Genetics = Zeitschrift Für Tierzüchtung Und Züchtungsbiologie·Miguel A ToroJesús Fernández
May 3, 2021·Genetics, Selection, Evolution : GSE·Beatriz VillanuevaRicardo Pong-Wong

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Methods Mentioned

BETA
chips
genotyping

Software Mentioned

SDPA
OVE
CHR
REG

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