Novel stable QTLs identification for berry quality traits based on high-density genetic linkage map construction in table grape

Abstract

Background: Aroma, berry firmness and berry shape are three main quality traits in table grape production, and also the important target traits in grapevine breeding. However, the information about their genetic mechanisms is limited, which results in low accuracy and efficiency of quality breeding in grapevine. Mapping and isolation of quantitative trait locus (QTLs) based on the construction of genetic linkage map is a powerful approach to decipher the genetic determinants of complex quantitative traits. Results: In the present work, a final integrated map consisting of 3411 SLAF markers on 19 linkage groups (LGs) with an average distance of 0.98 cM between adjacent markers was generated using the specific length amplified fragment sequencing (SLAF-seq) technique. A total of 9 significant stable QTLs for Muscat flavor, berry firmness and berry shape were identified on two linkage groups among the hybrids analyzed over three consecutive years from 2016 to 2018. Notably, new stable QTLs for berry firmness and berry shape were found on LG 8 respectively for the first time. Based on biological function and expression profiles of candidate genes in the major QTL regions, 3 genes (VIT_08s0007g00440, VIT_08s0040g02740 and VIT_08s0040g02350) related to berry firmness and 3 genes (VIT_ 08s0032g01110, VIT_08s0032g01150 and VIT_08s0105g00200) linked to berry shape were highlighted. Overexpression of VIT_08s0032g01110 in transgenic Arabidopsis plants caused the change of pod shape. Conclusions: A new high-density genetic map with total 3411 markers was constructed with SLAF-seq technique, and thus enabled the detection of narrow interval QTLs for relevant traits in grapevine. VIT_08s0007g00440, VIT_ 08s0040g02740 and VIT_08s0040g02350 were found to be related to berry firmness, while VIT_08s0032g01110, VIT_ 08s0032g01150 and VIT_08s0105g00200 were linked to berry shape.

Towards Sensor-Based Phenotyping of Physical Barriers of Grapes to Improve Resilience to Botrytis Bunch Rot

“…To answer the question about the involvement of wax- and cuticle-related genes on the phenotypic expression of berry impedance and berry texture, further fine mapping of detected regions are necessary to detect candidate genes. However, QTL analysis for berry firmness (TA AREA ) is mostly performed on table grape populations where QTLs and candidate genes like expansin are identified on LG 8 ( Wang et al, 2020 ), LG 18 ( Carreño et al, 2015 ; Ni et al, 2020 ; Crespan et al, 2021 ), and further on LG1, 4, 5, 9, 10, and LG13 ( Carreño et al, 2015 ). Recently, Crespan et al (2021) identified VviAGL11 on LG18, one main gene that regulates seedlessness in table grape that seems to be involved in the phenotypic behavior of berry texture.…”

“…However, QTL analysis for berry firmness (TA AREA ) is mostly performed on table grape populations where QTLs and candidate genes like expansin are identified on LG 8 (Wang et al, 2020),…”

A Major QTL is associated with berry grape texture characteristics

“…In particular, the methods developed by Carreño et al (2014) and used also by Wang et al (2020), define berry "firmness" as values expressed in N required for a 20 % deformation of the berry grape. This mechanical variable can be associated with berry hardness evaluated in the present study calculated using deformation of the berry equal to 25 %.…”

“…MAS is particularly useful for traits linked to fruit quality in perennial plants because it is time, space, and cost-saving while allowing an early selection of seedlings with the required traits. Some efforts were already done focused on searching QTLs and candidate genes linked to berry "firmness" (Carreño et al, 2014;Ban et al, 2016;Correa et al, 2016;Guo et al, 2019;Wang et al, 2020). In these works, grape ripening status was established through sensory evaluation or measured according to berries soluble solid content or the ratio between sugar content and acidity.…”

Genome-wide association scan and transcriptome analysis reveal candidate genes for waterlogging tolerance in cultivated barley

“…Recently, numerous quantitative trait loci (QTL) that are involved in waterlogging tolerance in barley, including leaf chlorosis, plant survival, plant biomass reduction, chlorophyll fluorescence, root porosity, and aerenchyma development, have been identified by linkage analysis of doubled haploid (DH) ( Zhou, 2011 ; Zhou et al., 2012 ; Broughton et al., 2015 ; Zhang et al., 2016 ; Zhang et al., 2017 ). However, QTL mapping for targeted traits is dependent on the polymorphisms between the parents and the population size ( Wang et al., 2020 ).…”