Training Population Optimization for Prediction of Cassava Brown Streak Disease Resistance in West African Clones

G3: Genes, Genomes, Genetics

article

Alfred Ozimati¹  Robert Kawuki¹  Williams Esuma¹  Ismail Siraj Kayondo¹  Marnin Wolfe²  Roberto Lozano²  Ismail Rabbi³  Peter Kulakow³  Jean-Luc Jannink² 

[1] National Crops Resources Research Institute (NaCRRI), P.O. Box, 7084 Kampala, Uganda;School of Integrative Plant Science, Plant breeding and Genetics Section, Cornell University, Ithaca, New York;International Institute for Tropical Agriculture (IITA), Ibadan, Oyo, Nigeria;United States Department of Agriculture, Agricultural Research Service (USDA-ARS) R.W. Holley Center for Agriculture and Health, Ithaca 14853, NY

关键词: Key words: Cassava;    genomic selection;    training population;    and cassava brown streak disease;    Genomic Prediction;    GenPred;    Shared Data Resources;   

DOI  :  10.1534/g3.118.200710

学科分类：社会科学、人文和艺术（综合）

来源: Genetics Society of America

【 摘 要 】

Cassava production in the central, southern and eastern parts of Africa is under threat by cassava brown streak virus (CBSV). Yield losses of up to 100% occur in cases of severe infections of edible roots. Easy illegal movement of planting materials across African countries, and long-range movement of the virus vector ( Bemisia tabaci ) may facilitate spread of CBSV to West Africa. Thus, effort to pre-emptively breed for CBSD resistance in W. Africa is critical. Genomic selection (GS) has become the main approach for cassava breeding, as costs of genotyping per sample have declined. Using phenotypic and genotypic data (genotyping-by-sequencing), followed by imputation to whole genome sequence (WGS) for 922 clones from National Crops Resources Research Institute, Namulonge, Uganda as a training population (TP), we predicted CBSD symptoms for 35 genotyped W. African clones, evaluated in Uganda. The highest prediction accuracy (r = 0.44) was observed for cassava brown streak disease severity scored at three months (CBSD3s) in the W. African clones using WGS-imputed markers. Optimized TPs gave higher prediction accuracies for CBSD3s and CBSD6s than random TPs of the same size. Inclusion of CBSD QTL chromosome markers as kernels, increased prediction accuracies for CBSD3s and CBSD6s. Similarly, WGS imputation of markers increased prediction accuracies for CBSD3s and for cassava brown streak disease root severity (CBSDRs), but not for CBSD6s. Based on these results we recommend TP optimization, inclusion of CBSD QTL markers in genomic prediction models, and the use of high-density (WGS-imputed) markers for CBSD predictions across population.

【 授权许可】

CC BY|CC BY-NC