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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Publications at this Location » Publication #332002
Title: Marker-based estimates reveal significant non-additive effects in clonally propagated cassava (Manihot esculenta): implications for the prediction of total genetic value and the selection of varieties

Author
item WOLFE, MARNIN - Cornell University
item KULAKOW, PETER - International Institute For Tropical Agriculture
item RABBI, ISMAIL - International Institute For Tropical Agriculture
item Jannink, Jean-Luc

Submitted to: G3, Genes/Genomes/Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/21/2016
Publication Date: 8/31/2016
Citation: Wolfe, M.D., Kulakow, P., Rabbi, I.Y., Jannink, J. 2016. Marker-based estimates reveal significant non-additive effects in clonally propagated cassava (Manihot esculenta): implications for the prediction of total genetic value and the selection of varieties. G3, Genes/Genomes/Genetics. https://doi.org/10.1534/g3.116.033332.

Interpretive Summary: Additive genetic effects are those reliably passed down from parent to offspring in breeding. In clonally propagated crops, however, clones retain the non-additive genetic effects of their progenitors. Thus, non-additive genetic effects can be exploited by the identification of superior genetic individuals as varieties. Cassava (Manihot esculenta Crantz) is a clonally propagated staple food crop that feeds hundreds of millions. We quantified the amount and nature of non-additive genetic variation for three key traits in a breeding population of cassava from sub-Saharan Africa using additive and non-additive genome-wide marker-based relationship matrices. We then assessed the accuracy of genomic prediction of additive compared to total (additive plus non-additive) genetic value. We confirmed previous findings based on diallel populations, that non-additive genetic variation is significant, especially for root yield. Further, we show that total genetic value predicts observed phenotypes more accurately than additive value for root yield but not for dry matter content or for cassava mosaic disease resistance. We address the implication of these results for cassava breeding and put our work in the context of previous results in cassava, and other plant and animal species.

Technical Abstract: In clonally propagated crops, non-additive genetic effects can be effectively exploited by the identification of superior genetic individuals as varieties. Cassava (Manihot esculenta Crantz) is a clonally propagated staple food crop that feeds hundreds of millions. We quantified the amount and nature of non-additive genetic variation for three key traits in a breeding population of cassava from sub-Saharan Africa using additive and non-additive genome-wide marker-based relationship matrices. We then assessed the accuracy of genomic prediction of additive compared to total (additive plus non-additive) genetic value. We confirmed previous findings based on diallel populations, that non-additive genetic variation is significant, especially for root yield. Further, we show that total genetic value predicts observed phenotypes more accurately than additive value for root yield but not for dry matter content, which is mostly additive or for CMD resistance, which has high narrow-sense heritability. We address the implication of these results for cassava breeding and put our work in the context of previous results in cassava, and other plant and animal species.