Gene Discovery
Understanding the genetic bases of agronomic traits.
IGA has several collaborative projects for QTL mapping and gene discovery to understand the genetic basis of agronomic traits and identify useful alleles.
We give priority to these topics:
- morphological and developmental traits in barley
- phenology and biomass in poplar
- disease resistance in grapevine
- self-incompatibility in olive
For several crops, we have generated molecular tools for gene mapping, such as SNP arrays, genetic maps.
Barley
Druka et al (2011) Genetic dissection of barley morphology and development. Plant Physiology 155:617-627
Shahinnia et al (2012) High resolution mapping of Dense spike-ar (dsp.ar) to the genetic centromere of barley chromosome 7H. Theoretical & Applied Genetics 124:373-384
Houston et al (2012) Analysis of the barley bract suppression gene Trd1. Theoretical & Applied Genetics 125:33-45
Poplar
Rohde et al (2011) Bud set in poplar-genetic dissection of a complex trait in natural and hybrid populations. New Phytologist 189:106-121
Fabbrini et al (2012) Phenotypic plasticity, QTL mapping and genomic characterization of bud set in black poplar. BMC Plant Biology 12:47
Allwright et al (2016) Biomass traits and candidate genes for bioenergy revealed through association genetics in coppiced European Populus nigra (L.). Biotechnol Biofuels 9:195
Taylor et al (2019) Sustainable bioenergy for climate mitigation: developing drought-tolerant trees and grasses. Annals of Botany 124:513-520
Scaglione et al (2019) Single primer enrichment technology as a tool for massive genotyping: a benchmark on black poplar and maize. Annals of Botany 124:543-552
Grapevine
IGA focuses on three loci controlling downy or powdery mildew resistance: Rpv3, Rpv12, Ren1. Ren1 is the first resistance gene that naturally evolved functional specificity against powdery mildew in the cultivated species Vitis vinifera. Rpv3 and Rpv12 were originally present in undomesticated grapes in North America and Asia and were historically used in introgression breeding.
Coleman et al (2009) The powdery mildew resistance gene REN1 co-segregates with an NBS-LRR gene cluster in two Central Asian grapevines. BMC Genomics 10:89
Di Gaspero et al (2012) Selective sweep at the Rpv3 locus during grapevine breeding for downy mildew resistance. Theoretical & Applied Genetics 12:277-286
Venuti et al (2013) Historical introgression of the downy mildew resistance gene Rpv12 from the Asian species Vitis amurensis into grapevine varieties. PLoS One 8(4):e61228. doi: 10.1371/journal.pone.0061228
Foria et al (2020) Gene duplication and transposition of mobile elements drive evolution of the Rpv3 resistance locus in grapevine. The Plant Journal 101(3):529-542
Chitarrini et al (2020) Two-omics data revealed commonalities and differences between Rpv12- and Rpv3-mediated resistance in grapevine. Scientific Reports 10(1):12193
Olive
IGA is collaborating with the Institute of Biosciences and Bioresources of the National Research Council (CNR-IBBR) in Perugia (Italy) for studying the locus responsible for self-incompatibility in olive cultivars. We mapped the locus on olive chromosome 18 and developed a DNA marker for a rapid screening of inter-compatibility in olive germplasm.
Thanks to information generated by our genome sequencing projects and resequencing of intraspecific diversity, we produced and released SNP databases.
We also have used SNP and InDel databases for developing and validating SNP arrays and InDel markers and for generating SNP-based genetic maps.
SNP chips
SNP arrays have been developed for black poplar, wheat, peach, and grape.
Faivre-Rampant et al (2016) New resources for genetic studies in Populus nigra: genome wide SNP discovery and development of a 12k Infinium array. Molecular Ecology Resources doi: 10.1111/1755-0998.12513
Wang et al (2014) Characterization of polyploid wheat genomic diversity using a high-density 90,000 single nucleotide polymorphism array. Plant Biotechnology Journal 12:787-796.
Le Paslier et al (2014) The GrapeReSeq 18k Vitis genotyping chip. IX International Symposium of Grapevine Physiology and Biotechnology. Chile 21-26 April 2013. https://urgi.versailles.inra.fr/Species/Vitis/GrapeReSeq_Illumina_20K
Verde et al (2012) Development and evaluation of a 9K SNP array for peach by internationally coordinated SNP detection and validation in breeding germplasm. PLoS One 7(4):e35668. doi: 10.1371/journal.pone.0035668
SNP datasets
We have released validated SNP datasets for durum wheat, black poplar and maize
Vendramin et al (2019) Genomic tools for durum wheat breeding: de novo assembly of Svevo transcriptome and SNP discovery in elite germplasm. BMC Genomics 20:278
Scaglione et al (2019) Single primer enrichment technology as a tool for massive genotyping: a benchmark on black poplar and maize. Annals of Botany 124:543-552
SNP and InDel markers
We have released validated InDel markers for grapevine.
Foria et al (2018) InDel markers for monitoring the introgression of downy mildew resistance from wild relatives into grape varieties. Molecular Breeding 38:124
Genetic maps
Genetic maps have been developed for wheat and Norway spruce.
Maccaferri et al (2015) A high-density, SNP-based consensus map of tetraploid wheat as a bridge to integrate durum and bread wheat genomics and breeding. Plant Biotechnology Journal 13:648-663
Lind et al (2014) A Picea abies linkage map based on SNP markers identifies QTLs for four aspects of resistance to Heterobasidion parviporum infection. PLoS One 9(7):e101049. doi: 10.1371/journal.pone.0101049