KEY MESSAGE: The major quantitative trait loci associated with bunch weight and its component traits in the East African highland banana-breeding population are located on chromosome 3. Bunch weight increase is one of the major objectives of banana improvement programs, but little is known about the loci controlling bunch weight and its component traits. Here we report for the first time some genomic loci associated with bunch weight and its component traits in banana as revealed through a genome-wide association study. A banana-breeding population of 307 genotypes varying in ploidy was phenotyped in three locations under different environmental conditions, and data were collected on bunch weight, number of hands and fruits; fruit length and circumference; and diameter of both fruit and pulp for three crop cycles. The population was genotyped with genotyping by sequencing and 27,178 single nucleotide polymorphisms (SNPs) were generated. The association between SNPs and the best linear unbiased predictors of traits was performed with TASSEL v5 using a mixed linear model accounting for population structure and kinship. Using Bonferroni correction, false discovery rate, and long-range linkage disequilibrium (LD), 25 genomic loci were identified with significant SNPs and most were localized on chromosome 3. Most SNPs were located in genes encoding uncharacterized and hypothetical proteins, but some mapped to transcription factors and genes involved in cell cycle regulation. Inter-chromosomal LD of SNPs was present in the population, but none of the SNPs were significantly associated with the traits. The clustering of significant SNPs on chromosome 3 supported our hypothesis that fruit filling in this population was under control of a few quantitative trait loci with major effects.

Department of Plant Breeding Swedish University of Agricultural Sciences P O Box 101 23053 Alnarp Sweden

Institute of Experimental Botany Centre of the Region Haná for Biotechnological and Agricultural Research 78371 Olomouc Czech Republic

International Institute of Tropical Agriculture c o Nelson Mandela African Institution of Science and Technology P O Box 447 Arusha Tanzania

International Institute of Tropical Agriculture c o Nelson Mandela African Institution of Science and Technology P O Box 447 Arusha Tanzania Laboratory of Tropical Crop Improvement Division of Crop Biotechnics Katholieke Universiteit 3001 Leuven Belgium Bioversity International 3001 Leuven Belgium

International Institute of Tropical Agriculture P O Box 7878 Kampala Uganda

International Institute of Tropical Agriculture P O Box 7878 Kampala Uganda Bill and Melinda Gates Foundation Seattle 23350 USA

International Institute of Tropical Agriculture P O Box 7878 Kampala Uganda Department of Plant Pathology Kansas State University Manhattan KS 66506 USA

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