Association genetics of bunch weight and its component traits in East African highland banana (Musa spp. AAA group)

Moses Nyine,Brigitte Uwimana,Violet Akech,Rodomiro Ortiz,Rony Swennen,Jaroslav Doležel,Jim Lorenzen,Allan Brown

doi:10.1007/s00122-019-03425-x

Abstract

Key messageThe 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.

Highlights

The ability of banana to produce seedless fruits was the key to banana domestication along with other attributes such as plant vigour, which was a consequence of polyploidization (Simmonds 1962; Heslop-Harrison and Schwarzacher 2007; Cenci et al 2019)
They showed a wide distribution on the two principal components (PCs), which was indicative of the high genetic variability despite some shared pedigree
Association genetics should rely on high-density genetic markers evenly distributed across the genome to identify quantitative trait loci (QTL) associated with traits of interest

Summary

Introduction

The ability of banana to produce seedless fruits was the key to banana domestication along with other attributes such as plant vigour, which was a consequence of polyploidization (Simmonds 1962; Heslop-Harrison and Schwarzacher 2007; Cenci et al 2019). The components of bunch weight include a number of traits such as number of hands and fruits; fruit length and circumference; and the diameter of both fruit and pulp (Nyine et al 2017). Fruit filling is one of the main traits that banana breeders use in the preliminary selection of hybrids because it contributes significantly to the bunch weight. Simmonds (1962) reported that parthenocarpy in banana was controlled by three genes designated as P1, P2 and P3, while Turner and Gibbs (2018) described the process of bunch formation and asserted that photosynthate availability plays an important role in regulating the number of fruits and hands on the developing banana inflorescence. There is still, a knowledge gap concerning the genetic factors regulating bunch component traits in this crop with important consequences to both food security and economic development in emerging markets

Methods

Results

Conclusion