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Improvement of genomic prediction in advanced wheat breeding lines by including additive-by-additive epistasis

Raffo, Miguel Angel and Sarup, Pernille and Guo, Xiangyu and Liu, Huiming and Andersen, Jeppe Reitan and Orabi, Jihad and Jahoor, Ahmed and Jensen, Just (2022). Improvement of genomic prediction in advanced wheat breeding lines by including additive-by-additive epistasis. TAG Theoretical and Applied Genetics. 135 :3 , 965-978
[Research article]

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Abstract

Key message Including additive and additive-by-additive epistasis in a NOIA parametrization did not yield orthogonal partitioning of genetic variances, nevertheless, it improved predictive ability in a leave-one-out cross-validation for wheat grain yield. Additive-by-additive epistasis is the principal non-additive genetic effect in inbred wheat lines and is potentially useful for developing cultivars based on total genetic merit; nevertheless, its practical benefits have been highly debated. In this article, we aimed to (i) evaluate the performance of models including additive and additive-by-additive epistatic effects for variance components (VC) estimation of grain yield in a wheat-breeding population, and (ii) to investigate whether including additive-by-additive epistasis in genomic prediction enhance wheat grain yield predictive ability (PA). In total, 2060 sixth-generation (F-6) lines from Nordic Seed A/S breeding company were phenotyped in 21 year-location combinations in Denmark, and genotyped using a 15 K-Illumina-BeadChip. Three models were used to estimate VC and heritability at plot level: (i) "I-model" (baseline), (ii) "I + G(A)-model", extending I-model with an additive genomic effect, and (iii) "I + G(A) + G(AA)-model", extending I + G(A)-model with an additive-by-additive genomic effects. The I + G(A)-model and I + G(A) + G(AA)-model were based on the Natural and Orthogonal Interactions Approach (NOIA) parametrization. The I + G(A) + G(AA)-model failed to achieve orthogonal partition of genetic variances, as revealed by a change in estimated additive variance of I + G(A)-model when epistasis was included in the I + G(A) + G(AA)-model. The PA was studied using leave-one-line-out and leave-one-breeding-cycle-out cross-validations. The I + G(A) + G(AA)-model increased PA significantly (16.5%) compared to the I + G(A)-model in leave-one-line-out cross-validation. However, the improvement due to including epistasis was not observed in leave-one-breeding-cycle-out cross-validation. We conclude that epistatic models can be useful to enhance predictions of total genetic merit. However, even though we used the NOIA parameterization, the variance partition into orthogonal genetic effects was not possible.

Authors/Creators:Raffo, Miguel Angel and Sarup, Pernille and Guo, Xiangyu and Liu, Huiming and Andersen, Jeppe Reitan and Orabi, Jihad and Jahoor, Ahmed and Jensen, Just
Title:Improvement of genomic prediction in advanced wheat breeding lines by including additive-by-additive epistasis
Series Name/Journal:TAG Theoretical and Applied Genetics
Year of publishing :2022
Volume:135
Number:3
Page range:965-978
Number of Pages:14
Publisher:SPRINGER
ISSN:0040-5752
Language:English
Publication Type:Research article
Article category:Scientific peer reviewed
Version:Published version
Copyright:Creative Commons: Attribution 4.0
Full Text Status:Public
Subjects:(A) Swedish standard research categories 2011 > 1 Natural sciences > 106 Biological Sciences (Medical to be 3 and Agricultural to be 4) > Genetics (medical genetics to be 30107 and agricultural genetics to be 40402)
URN:NBN:urn:nbn:se:slu:epsilon-p-115403
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-p-115403
Additional ID:
Type of IDID
DOI10.1007/s00122-021-04009-4
Web of Science (WoS)000736942600001
ID Code:27506
Faculty:LTV - Fakulteten för landskapsarkitektur, trädgårds- och växtproduktionsvetenskap
Department:(LTJ, LTV) > Department of Plant Breeding (from 130101)
Deposited By: SLUpub Connector
Deposited On:04 Apr 2022 12:25
Metadata Last Modified:04 Apr 2022 12:31

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