Differential expression of transcription factor- and further growth-related genes correlates with contrasting cluster architecture in Vitis vinifera ‘Pinot Noir’ and Vitis spp. genotypes

Abstract

Grapevine (Vitis vinifera L.) is an economically important crop that needs to comply with high quality standards for fruit, juice and wine production. Intense plant protection is required to avoid fungal damage. Grapevine cultivars with loose cluster architecture enable reducing protective treatments due to their enhanced resilience against fungal infections, such as Botrytis cinerea-induced gray mold. A recent study identified transcription factor gene VvGRF4 as determinant of pedicel length, an important component of cluster architecture, in samples of two loose and two compact quasi-isogenic ‘Pinot Noir’ clones. Here, we extended the analysis to 12 differently clustered ‘Pinot Noir’ clones from five diverse clonal selection programs. Differential gene expression of these clones was studied in three different locations over three seasons. Two phenotypically opposite clones were grown at all three locations and served for standardization. Data were correlated with the phenotypic variation of cluster architecture sub-traits. A set of 14 genes with consistent expression differences between loosely and compactly clustered clones—independent from season and location—was newly identified. These genes have annotations related to cellular growth, cell division and auxin metabolism and include two more transcription factor genes, PRE6 and SEP1-like. The differential expression of VvGRF4 in relation to loose clusters was exclusively found in ‘Pinot Noir’ clones. Gene expression studies were further broadened to phenotypically contrasting F1 individuals of an interspecific cross and OIV reference varieties of loose cluster architecture. This investigation confirmed PRE6 and six growth-related genes to show differential expression related to cluster architecture over genetically divergent backgrounds.

Relieving the Phenotyping Bottleneck for Grape Bunch Architecture in Grapevine Breeding Research: Implementation of a 3D-Based Phenotyping Approach for Quantitative Trait Locus Mapping

“…They identified an SNP on chromosome 17 related to berry weight. In recent years, several studies have identified meaningful QTL regions, SNP positions, and possible candidate genes that influence bunch-architecture-related traits [5,9,23,25,58,60,64,66]. The results in the present study and the findings of the mentioned studies indicate that genetic regions, affecting bunch-architecture-related traits, are conserved within a broader genetic background, and the proposed 3D phenotyping method is feasible for the rapid and precise screening of phenotypic material.…”

“…However, for Botrytis, no reports on mapping successful defense-related genes are available yet. Therefore, alternative strategies are applied in breeding programs [9,10]. Breeders hereby mainly focus on a loose bunch architecture to strengthen the resilience of grape berries against Botrytis bunch rot [2,3,11].…”

“…Besides these phytosanitary aspects, a loose grape bunch architecture is additionally associated with positive effects on the berry ripening rate and berry compositions (see the detailed overview of Tello and Ibanez, 2018 [7]). The compactness of a grape bunch depends strongly on the synergy of two structure-defining traits: (1) berry characteristics, i.e., berry number and size; and (2) stem-related traits, i.e., rachis length, pedicel length, and width of the grape bunch [9,12,13]. The degree of bunch compactness is, thus, determined by the interaction of individual bunch-architecture-related traits.…”

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

“…As a consequence, in loose bunches, the growing conditions for Botrytis are less favorable than in compact bunches (Gabler et al, 2003;Töpfer et al, 2011;Rist et al, 2018;Tello and Ibáñez, 2018). Therefore, recent studies started to determine genetic factors associated with loose bunch architecture (Richter et al, 2019(Richter et al, , 2020, which opens up the possibility of developing markers for a complex morphological trait in order to early select Botrytis-resilient genotypes. However, it can be observed that in 1 http://www.vivc.de/loci some varieties with compact bunches, other traits contribute to reduce Botrytis infection risk.…”

Genetic mapping and selection of table grape fruit quality characteristics in a segregating population and evaluation of marker transferability

“…Cluster traits, such as weight and length, in addition to shape, are also important in grapes. QTLs for cluster weight have been found on chr 4, 9, and 16 using a wine grape cross with a diverse genetic background (Underhill et al, 2020) and on chr 13 using a diverse panel of grape lines (Laucou et al, 2020), and 14, 15 and 16 (Richter et al, 2019b). Our study also located a QTL on chr 14 associated with cluster weight in all three years evaluated, controlling 15-24% of the variability, indicating that it is likely to be stable.…”