Deciphering the genetic control of fruit texture in apple by multiple family-based analysis and genome-wide association.

Mario Di Guardo,Alice Tadiello,Eric Van De Weg,Richard G.F Visser,Fabrizio Costa,Thomas Letschka,Nicola Busatto,Lidia Lozano,Luca Bianco,Marco C.A.M Bink,Lara Poles,Walter Guerra

doi:10.1093/jxb/erx017

Abstract

Fruit texture is a complex feature composed of mechanical and acoustic properties relying on the modifications occurring in the cell wall throughout fruit development and ripening. Apple is characterized by a large variation in fruit texture behavior that directly impacts both the consumer's appreciation and post-harvest performance. To decipher the genetic control of fruit texture comprehensively, two complementing quantitative trait locus (QTL) mapping approaches were employed. The first was represented by a pedigree-based analysis (PBA) carried out on six full-sib pedigreed families, while the second was a genome-wide association study (GWAS) performed on a collection of 233 apple accessions. Both plant materials were genotyped with a 20K single nucleotide polymorphism (SNP) array and phenotyped with a sophisticated high-resolution texture analyzer. The overall QTL results indicated the fundamental role of chromosome 10 in controlling the mechanical properties, while chromosomes 2 and 14 were more associated with the acoustic response. The latter QTL, moreover, showed a consistent relationship between the QTL-estimated genotypes and the acoustic performance assessed among seedlings. The in silico annotation of these intervals revealed interesting candidate genes potentially involved in fruit texture regulation, as suggested by the gene expression profile. The joint integration of these approaches sheds light on the specific control of fruit texture, enabling important genetic information to assist in the selection of valuable fruit quality apple varieties.

Highlights

Fruit ripening is an orchestra of physiological changes on the dismantling of the primary cell wall polysaccharide occurring to render fruits more attractive and palatable complex by a series of cell wall-modifying proteins (Brummell (Giovannoni, 2001)
The overall phenotypic fruit texture variability was initially represented by a principal component analysis (PCA) plot (Fig. 1)
PC1 explained 71.6% of the total phenotypic variance in the pedigreed full-sib families (Fig. 1A, B) and 79.6% in the germplasm collection (Fig. 1C, D), while PC2 accounted for 19.9% and 12.7%, respectively

Summary

Introduction

Fruit ripening is an orchestra of physiological changes on the dismantling of the primary cell wall polysaccharide occurring to render fruits more attractive and palatable complex by a series of cell wall-modifying proteins (Brummell (Giovannoni, 2001). This approach was initially employed in annual crops (Thornsberry et al, 2001; Weber et al, 2008; Stracke et al, 2009) and forest trees (Neale and Savolainen, 2004; González-Martínez et al, 2007, 2008; Eckert et al, 2009; Neale and Kremer, 2011), it has recently been exploited in fruit tree crops, such as grapevine (Cardoso et al, 2012), peach (Micheletti et al, 2015), and apple (Kumar et al, 2013, 2015) In the latter species, a major QTL for fruit firmness was observed on chromosome 10, which coincided with MdPG1, a gene known to encode polygalacturonase playing a pivotal role in the depolymerization of pectins (Sitrit and Bennett, 1998; Brummell and Harpster, 2001). These investigations, are characterized by a low phenotyping resolution, to date recognized as the major operational bottleneck limiting the power of genetic analysis (Cobb et al, 2013)

Methods

Results

Conclusion