We relate the observed changes in transcript abundance with changes in ethylene production, sugar levels, carotenoid content, and fruit firmness to identify candidate genes involved in determining these and other traits associated with fruit ripening.
QTLs controlling fruit firmness at harvest were identified in the LG1 region colocating with EXP7 (EXP-RG); however, the QTL detected for fruit firmness on LG15 (Lg15a-BB and Lg15a-RG) did not colocate with ACS1, as ACS1 maps to the bottom of LG15, whereas the peak of the QTL maps consistently at the top of the LG.
Furthermore, candidate genes controlling fruit firmness in pear might be identified by utilising the stable QTL on LG3, to identify candidate genes in the aligned genome sequences of both Chinese and European pear, as well apple.
We identified selective sweeps underlying fruit size, flesh firmness, sweetness, and acidity, as well as highly divergent SNPs between rootstock and scion cultivars that are associated with dwarfing and disease resistance.
Clusters of QTLs that were identified on LG3 and associated with fruit firmness and epicatechin concentration were stable between 2011 and 2012, and between parents of each of the two populations as well as across these populations.
In future, candidate genes for QTLs controlling firmness, PPO activity, and polyphenolic compound concentration will be identified utilising the reference genome sequences of pears 'Bartlett', 'Dangshansuli' and syntenic apple 'Golden Delicious'.
In apple, several reports have already identified major genomic loci putatively involved in fruit firmness and softening control [ 22- 26], with the largest texture QTL mapping survey described by Longhi et al. [ 27].
QTLs in common were identified between control of fruit maturation date and loss of firmness during storage, especially on LGs 10 (QTL clusters PG1-BB, ACO1-BB and PG1-RG) and 16 (Lg16-BB).
For example, the LG6 and LG9 QTLs that contribute to higher fruit firmness at harvest and postharvest, with no influence on softening rate, were identified only in the population grown in Motueka (Supplementary Table S3).
Four proteins (NADP-dependent malic enzyme, beta-galactosidase, beta-galactosidase 3 and probable 6-phosphogluconolactonase 2) were identified potentially playing a role in changes in fruit respiration, firmness and soluble solids.
