Deciphering the genetic control of fruit texture in apple by multiple family-based analysis and genome-wide association.
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.
Fondazione Edmund Mach, via Mach 1, 38010 San Michele all'Adige, Trento, Italy.|Graduate School Experimental Plant Sciences, Wageningen University, PO Box 386, 6700 AJ Wageningen, The Netherlands.
Mario
M
Di Guardo
Biometris, Wageningen University and Research Centre, Wageningen, The Netherlands.
Marco C A M
MCAM
Bink
Laimburg Research Centre for Agriculture and Forestry, via Laimburg 6, 39040 Ora (BZ),Italy.
Walter
W
Guerra
Laimburg Research Centre for Agriculture and Forestry, via Laimburg 6, 39040 Ora (BZ),Italy.
Thomas
T
Letschka
Laimburg Research Centre for Agriculture and Forestry, via Laimburg 6, 39040 Ora (BZ),Italy.
Lidia
L
Lozano
Fondazione Edmund Mach, via Mach 1, 38010 San Michele all'Adige, Trento,Italy.
Nicola
N
Busatto
Innovation Fruit Consortium (CIF), via Mach 1, 38010 San Michele all'Adige, Trento, Italy.
Lara
L
Poles
Fondazione Edmund Mach, via Mach 1, 38010 San Michele all'Adige, Trento,Italy.
Alice
A
Tadiello
Fondazione Edmund Mach, via Mach 1, 38010 San Michele all'Adige, Trento,Italy.
Luca
L
Bianco
Wageningen UR Plant Breeding, Wageningen University and Research Centre, Droevendaalsesteeg 1, PO Box 386, 6700 AJ Wageningen, The Netherlands.
Richard G F
RGF
Visser
Wageningen UR Plant Breeding, Wageningen University and Research Centre, Droevendaalsesteeg 1, PO Box 386, 6700 AJ Wageningen, The Netherlands.
Eric
E
van de Weg
Fondazione Edmund Mach, via Mach 1, 38010 San Michele all'Adige, Trento,Italy.
Fabrizio
F
Costa
D005638:Fruit / Q000235:genetics* / Q000502:physiology; D055106:Genome-Wide Association Study; D005838:Genotype; D027845:Malus / Q000235:genetics* / Q000502:physiology; D005810:Multigene Family; D010641:Phenotype; D040641:Quantitative Trait Loci
Apple; Bayesian statistics; RT–qPCR; SNP.; fruit texture; genome-wide association study (GWAS); high-resolution phenotyping; pedigree-based analysis (PBA)