Computation of the inverse additive relationship matrix for autopolyploid and multiple-ploidy populations

Computation of the inverse additive relationship matrix for autopolyploid and multiple-ploidy... −1 Key message Rules to generate the inverse additive relationship matrix (A ) are defined to enable the adoption restricted maximum likelihood (REML) and best linear unbiased prediction (BLUP) in autopolyploid populations with multiple ploidy levels. Abstract Many important agronomic, horticultural, ornamental, forestry, and aquaculture species are autopolyploids. How- ever, the adoption of restricted maximum likelihood (REML), for estimating co/variance components, and best linear unbiased prediction (BLUP), for predicting breeding values, has been hampered in autopolyploid breeding by the absence −1 of an appropriate means of generating the inverse additive relationship matrix (A ). This paper defines rules to generate −1 the A of autopolyploid populations comprised of individuals of the same or different ploidy-levels, including populations exhibiting (1) odd-numbered ploidy levels (e.g. triploids), (2) sex-based differences in the probability that gametic genes are identical by descent and (3) somatic chromosome doubling. Inbreeding, due to double reduction, in autopolyploid founders in the absence of mating among relatives is also accounted for. A previously den fi ed approach is modie fi d, whereby rules are −1 −1 initially defined to build an inverse matrix of kinship coefficients ( K ), which is then used to generate A . An R package http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png TAG Theoretical and Applied Genetics Springer Journals

Computation of the inverse additive relationship matrix for autopolyploid and multiple-ploidy populations

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Publisher
Springer Berlin Heidelberg
Copyright
Copyright © 2017 by Springer-Verlag GmbH Germany, part of Springer Nature
Subject
Life Sciences; Plant Breeding/Biotechnology; Plant Genetics and Genomics; Agriculture; Plant Biochemistry; Biochemistry, general; Biotechnology
ISSN
0040-5752
eISSN
1432-2242
D.O.I.
10.1007/s00122-017-3041-y
Publisher site
See Article on Publisher Site

Abstract

−1 Key message Rules to generate the inverse additive relationship matrix (A ) are defined to enable the adoption restricted maximum likelihood (REML) and best linear unbiased prediction (BLUP) in autopolyploid populations with multiple ploidy levels. Abstract Many important agronomic, horticultural, ornamental, forestry, and aquaculture species are autopolyploids. How- ever, the adoption of restricted maximum likelihood (REML), for estimating co/variance components, and best linear unbiased prediction (BLUP), for predicting breeding values, has been hampered in autopolyploid breeding by the absence −1 of an appropriate means of generating the inverse additive relationship matrix (A ). This paper defines rules to generate −1 the A of autopolyploid populations comprised of individuals of the same or different ploidy-levels, including populations exhibiting (1) odd-numbered ploidy levels (e.g. triploids), (2) sex-based differences in the probability that gametic genes are identical by descent and (3) somatic chromosome doubling. Inbreeding, due to double reduction, in autopolyploid founders in the absence of mating among relatives is also accounted for. A previously den fi ed approach is modie fi d, whereby rules are −1 −1 initially defined to build an inverse matrix of kinship coefficients ( K ), which is then used to generate A . An R package

Journal

TAG Theoretical and Applied GeneticsSpringer Journals

Published: Dec 19, 2017

References

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