Molecular, genetic and cellular study of grapevine seedless genotypes from different origins as new genetic sources for innovation in table grapevine breeding

Project Information

GRAPEINNOVATION

Grant agreement ID: 896290

DOI

10.3030/896290

Project closed

EC signature date 26 March 2020

Start date 1 September 2020

End date 31 October 2022

Funded under

• EXCELLENT SCIENCE - Marie Skłodowska-Curie Actions

Total cost

€ 172 932,48

EU contribution

€ 172 932,48

Coordinated by

AGENCIA ESTATAL CONSEJO SUPERIOR DE INVESTIGACIONES CIENTIFICAS
Spain

Periodic Reporting for period 1 - GRAPEINNOVATION (Molecular, genetic and cellular study of grapevine seedless genotypes from different origins as new genetic sources for innovation in table grapevine breeding)

Reporting period: 2020-09-01 to 2022-08-31

Summary of the context and overall objectives of the project

Genetic research worldwide has been moving towards the application of very rich and diverse cultivars with invaluable genetic potential and establishment of new hybrids and novel cultivars to become more attractive for both market demands and consumer’s tastes. A wide understanding of the genetic variation for seedlessness, therefore, is paramount to boost the success of table grape breeding and fulfill such demands. Most breeding programs and marker assisted selection (MAS) focused on the generation of new table grape cultivars combining seedlessness with berry quality traits, such as large size, muscat flavour, crispiness, high yield, tolerance to diseases and adaptability to global climate change. The expansion of the genetic diversity of table grape varieties and hybrids with demanded characteristics for table grapevines innovation would be a suitable strategy to fulfill these needs and can become a base for new trends and prospects in the international fresh and dry food trade, competitiveness of breeding programs promoting the economic growth and national agriculture autonomy.
The general goal of this project was to widen the genetic sources of seedlessness in grapevine, to increase the genetic diversity used in breeding programs and improve their innovation. In this proposal we planed to perform a multidisciplinary approach to understand the cellular, genetic and molecular basis of new seedless grape variants.
We were proposing the following Specific Aims:
1. Identification and initial characterization of seedless accessions from Armenian, Spanish and Italian collections, genetic confirmation of their variety genotype, morphological and histological characterization and sequence analyses of VviAGL11 gene related to seedlessness.
2. Genetic and molecular characterization of mutations responsible for seedlessness in seedless (parthenocarpic) cultivar Corinto Bianco.
3. Comparative genetic and phenotypic characterization of polyploid seedless samples derived from Corinto bianco polyploid seeds.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

In this action Marie Skłodowska Curie Action (MSCA) we focused on the analyses of natural genetic variants of grapevine to identify and characterize different sources of stenospermocarpic and parthenocarpic seedlessness in Spanish, Italian and Armenian genetic resources. These variants were characterized at the phenotypic, histological and molecular levels using target sequencing approaches to widen the genetic basis of table grape breeding programs. The main genetic variation for breeding programs is stenospermocarpic seedlessness originated in an ancestor of the cultivar 'Sultanine' through spontaneous somatic mutation. By using SSR and SNP molecular markers we characterized additional seedless accessions existing in Armenian grapevine collections and private vineyards. On the base of the available pedigree in VIVC database and database of SSR and SNP genotypes of the Host Institute we identified and compared their genetic profiles and established their genetic relationships with Sultanina and other seedless cultivars. We re-sequenced the VviAGL11 gene in the seedless varieties from Armenia to discard mutations in this gene and try to find new sources of seedlessness for grape breeding. On the base of detailed completed analysis of the seedless grapevine varieties in Armenia including genetic, genomic, phenotypic and histological study it was revealed that all investigated varieties are Sultanina-derived and carry the same known stenospermocarpy-associated Arg197Leu substitution. VviAGL11 genotyping of Armenian seedless genotypes did not revealed new seedless mutations in this gene.
In addition, we characterized the seedless phenotype of Corinto Bianco (CB) to identify the causing mutation. With this purposed we used a segregating population derived from selfing Pedro Ximenez (PX) the ancestor variety were parthenocarpy CB appeared as well as plants developed from CB spontaneous seeds.We performed a comparative genetic and phenotypic study of diploid and triploid and tetraploid plants derived from unfrequently developing seeds in parthenocarpic CB berries. Phenotypic analysis of the hermaphroditic part of PX self-cross progeny confirmed the hypothesis of segregation of parthenocarpy and CB-like phenotype in near ¼ plants. Our results indicated that PX is heterozygous for a recessive mutation that produces the parthenocarpy. It supports the hypothesis that CB could accumulate another mutation in the other allele of the gene mutated in PX causing the parthenocarpy CB phentotype. In our research the ploidy level in CB is more related to a rise of parthenocarpy or CB-like phenotype formation than to an increase of berry weight. Thus, polyploid plants cannot be used as new raisin varieties for the increasing of berry weight and improvement new cultivars in grape breeding programs.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

Thanks to practical work on cutting-edge methods, attendance to workshops and seminars, the researcher specialized in the grapevine molecular genetics, including the target sequencing and basic bioinformatics tools for analysis sequence data. The potential of these methods for any biological research are massive, which opens plenty of possibilities for the career of Anna Nebish either in academia or industry. In addition, with hands-on work and attendance to ongoing courses on bioinformatics analysis, the researcher will complete her toolkit with computational biology skills to boost her career on genomics research.
All the skills, experience and contacts acquired by the researcher as well as ongoing courses of bioinformatics in this project will put her at the forefront of the crop genetics, genomics and bioinformatics research field. She will acquire further competencies and experience in a multidisciplinary range of molecular and cellular approaches in grape genetics. This new knowledge will endow her, as a researcher, with a suite of highly relevant generic and specialized research skills and improved research standards appropriate for her scientific career. Communication abilities developed in the context of new collaborations impact very positively the current skill portfolio, thus accelerating the transition towards independence and maturity.
Our findings confirm that large diversity of natural genetic variants of stenospermocarpic grapevines in Armenia are Sultanina-derived and contain a mutation in AGL11 which confirmed previously published data. The Italian colleagues found the same mutation in the seedless mutant of the variety with different genetic backgrounds. New mutations related to stenospermocarpy in grapevine were not discovered in our research. Thus, it can motivate scientists to initiate experiments in the search for variation in the seed content of the grapes in other genetic sources which can be used as alternative sources of seedlessness in breeding programs for production of global fresh and dried fruit crops.
Our study of grapevine genetic variants associated with two different types of seedlessness is important for policymakers and table grape breeders in order to use genetic variations with different phenotypic characteristics which carry mutations in AGL11 or possibly in HAL2 for innovation towards future sustainable viticulture.

Pollen study using Scanning Electron Microscope

Screening of seedless phenotype in Pedro Ximenez self progeny and Corinto Bianco progeny

Histological analysis of the flowers of seeded and seedless Armenian and Italian grapevines

Targeted sequencing of VviAGL11 gene in Armenian seedless grapevine cultivars