A candidate gene based approach validates Md-PG1 as the main responsible for a QTL impacting fruit texture in apple (Malus x domesticaBorkh)

Abstract

BackgroundApple is a widely cultivated fruit crop for its quality properties and extended storability. Among the several quality factors, texture is the most important and appreciated, and within the apple variety panorama the cortex texture shows a broad range of variability. Anatomically these variations depend on degradation events occurring in both fruit primary cell wall and middle lamella. This physiological process is regulated by an enzymatic network generally encoded by large gene families, among which polygalacturonase is devoted to the depolymerization of pectin. In apple, Md-PG1, a key gene belonging to the polygalacturonase gene family, was mapped on chromosome 10 and co-localized within the statistical interval of a major hot spot QTL associated to several fruit texture sub-phenotypes.ResultsIn this work, a QTL corresponding to the position of Md-PG1 was validated and new functional alleles associated to the fruit texture properties in 77 apple cultivars were discovered. 38 SNPs genotyped by gene full length resequencing and 2 SSR markers ad hoc targeted in the gene metacontig were employed. Out of this SNP set, eleven were used to define three significant haplotypes statistically associated to several texture components. The impact of Md-PG1 in the fruit cell wall disassembly was further confirmed by the cortex structure electron microscope scanning in two apple varieties characterized by opposite texture performance, such as ‘Golden Delicious’ and ‘Granny Smith’.ConclusionsThe results here presented step forward into the genetic dissection of fruit texture in apple. This new set of haplotypes, and microsatellite alleles, can represent a valuable toolbox for a more efficient parental selection as well as the identification of new apple accessions distinguished by superior fruit quality features.

Using genomics to improve fruit quality

“…In spite of this, QTLs for fl owering and ripening time, fruit quality, tree architecture and resistance to pathogens have been reported (Dirlewanger et al, 1996;Abbott et al, 1998;Dirlewanger et al, 1999;Etienne et al, 2002;Quilot et al 2004;Dirlewanger et al, 2006;Lambert et al, 2007;Ogundiwin et al, 2008;Dirlewanger et al, 2009 (Zini et al, 2005;Dunemann et al, 2009;Dunemann et al, 2012;Khan et al, 2012;Chagne et al, 2012b;Vogt et al, 2013;, texture (King et al, 2000;King et al, 2001;Kenis et al, 2008;Costa et al, 2008;Costa et al, 2010;Longhi et al, 2012;Longhi et al, 2013), ethylene production (Costa et al, 2014), Vitamin C content (Davey et al, 2006;Mellidou et al, 2012;) and fl esh browning (Kenis et al, 2008;Di Guardo et al, 2013). Also, as the cost of map construction was higher, the eff orts were concentrated in a few mapping populations and often they were considered as reference progenies, but these populations only segregated for a few traits.…”

“…In model plant species such as Arabidopsis (Aranzana et al, 2005;Tracy et al, 2006;Belo et al, 2008;) and economically important crops such as maize (Andersen et al, 2005;Salvi, 2007), sorghum (Casa et al, 2008) and barley (Kraakman et al, 2006) association mapping studies have been reported. In Rosaceae, Longhi et al (2013) determined the LD among markers identifi ed within the apple cultivar collection, and haplotypes for these markers were associated with fl esh textures. A genome-wide association study (GWAS) in 1,200 apple (Malus × domestica Borkh.)…”

Identification of QTLs for Flesh Mealiness in Apple (<i>Malus</i> × <i>domestica</i> Borkh.)

“…Among the many genes studied, MdPG1 is recognized as a main genetic determinant of flesh texture properties after harvest (Longhi et al, 2013b). Simultaneous recordings of mechanical and acoustic parameters allow a comprehensive characterization of flesh texture (Costa et al, 2010).…”

“…They have shown that the QTLs for texture parameters two months after harvest colocalize in the middle of the linkage group (LG) 10, where MdPG1 is located. An unfavorable allele of MdPG1, expected to cause high enzymatic activity, is associated with the allele "3" of a tri-allelic simple sequence repeat (SSR) marker Md-PG1 SSR 10kd, 10 kb downstream of the MdPG1 coding region (Longhi et al, 2013b). There are no significant phenotypic differences between the favorable alleles "1" and "2" of Md-PG1 SSR 10kd (Longhi et al, 2013b).…”

“…An unfavorable allele of MdPG1, expected to cause high enzymatic activity, is associated with the allele "3" of a tri-allelic simple sequence repeat (SSR) marker Md-PG1 SSR 10kd, 10 kb downstream of the MdPG1 coding region (Longhi et al, 2013b). There are no significant phenotypic differences between the favorable alleles "1" and "2" of Md-PG1 SSR 10kd (Longhi et al, 2013b). The significance of Md-PG1 SSR 10kd was confirmed using populations with different genetic backgrounds (Longhi et al, 2013a).…”