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Genomic prediction and quantitative trait locus discovery in a cassava training population constructed from multiple breeding stages

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Title Genomic prediction and quantitative trait locus discovery in a cassava training population constructed from multiple breeding stages
 
Creator Somo, M.
Kulembeka, H.
Mtunda, K.
Mrema, E.
Salum, K.
Wolfe, M.D.
Rabbi, Ismail Y.
Egesi, Chiedozie N.
Kawuki, R.S.
Ozimati, A.
Lozano, R.
Jannink, Jean-Luc
 
Subject cassava
plant breeding
genotypes
african cassava mosaic virus
quantitative trait loci
tanzania
uganda
east africa
 
Description Assembly of a training population (TP) is an important component of effective genomic selection‐based breeding programs. In this study, we examined the power of diverse germplasm assembled from two cassava (Manihot esculenta Crantz) breeding programs in Tanzania at different breeding stages to predict traits and discover quantitative trait loci (QTL). This is the first genomic selection and genome‐wide association study (GWAS) on Tanzanian cassava data. We detected QTL associated with cassava mosaic disease (CMD) resistance on chromosomes 12 and 16; QTL conferring resistance to cassava brown streak disease (CBSD) on chromosomes 9 and 11; and QTL on chromosomes 2, 3, 8, and 10 associated with resistance to CBSD for root necrosis. We detected a QTL on chromosome 4 and two QTL on chromosome 12 conferring dual resistance to CMD and CBSD. The use of clones in the same stage to construct TPs provided higher trait prediction accuracy than TPs with a mixture of clones from multiple breeding stages. Moreover, clones in the early breeding stage provided more reliable trait prediction accuracy and are better candidates for constructing a TP. Although larger TP sizes have been associated with improved accuracy, in this study, adding clones from Kibaha to those from Ukiriguru and vice versa did not improve the prediction accuracy of either population. Including the Ugandan TP in either population did not improve trait prediction accuracy. This study applied genomic prediction to understand the implications of constructing TP from clones at different breeding stages pooled from different locations on trait accuracy.
 
Date 2020-03
2020-03-13T10:10:12Z
2020-03-13T10:10:12Z
 
Type Journal Article
 
Identifier Somo, M., Kulembeka, H., Mtunda, K., Mrema, E., Salum, K., Wolfe, M.D., ... & Jannink, J. (2020). Genomic prediction and quantitative trait locus discovery in a cassava training population constructed from multiple breeding stages. Crop Science, 60, 896–913.
0011-183X
https://hdl.handle.net/10568/107742
https://doi.org/10.1002/csc2.20003
BIOTECH & PLANT BREEDING
 
Language en
 
Rights CC-BY-4.0
Open Access
 
Format 896–913
application/pdf
 
Publisher Wiley
 
Source Crop Science