Domestication in Solanaceae

The consequences of domestication on the nucleotide and expression patterns have been examined using RNAseq data in a set of crop and wild accessions (http://www.arcad-project.org/, Sarah et al., 2016). We extended this approach to the Solanaceae family to conduct a comparative genomic approach in pepper, eggplant and wild green-fruited tomatoes to test for convergent domestication. RNAseq data have been produced for 24 accessions (12 crops/12 wild) in the three species. Thus, from site frequency spectrum, we aim at modelling the most probable demographic scenario that occurred during the domestication phase in these three species and compare these scenarios together.

Relevant Publications

Zhao JT, C Sauvage, J Zhao, F Bitton, G Bauchet, D Liu, S Huang, D Tieman, HJ Klee, and M Causse (2019) Meta-analysis of genome-wide association studies provide new insights into genetic control of tomato flavour. Nat Comm vol.10;  https://doi.org/10.1038/s41467-019-09462-w

Burgos E, De Luca B, Diouf I, de Haro LA, Albert E, Sauvage C, Zhao J, Bermudez L, Asís R, Nunes Nesi A, Guiraud T, Matringe M, Brehelin C, Ferrand C, Atienza I, Jorly J , Mauxion JP, Baldet P, Fernie AR, Quadrana L, Rothan C, Causse M, Carrari F (2021) Vitamin E contents in tomato fruits is associated to natural variation in chorismate metabolism. Plant J 105,907-923. https://doi.org/10.1111/tpj.15077

Sauvage C, Rau A, Aichholtz C, Chadoeuf J, Sarah G, Ruiz M, Santoni S, Causse M, David J, Glémin S (2017) Domestication rewired gene expression and nucleotide diversity patterns in tomato. The Plant J 91, 631-645 ; doi: 10.1111/tpj.13592

Bauchet  G, S Grenier, N Samson, V Segura, A Kende, J Beekwilder, K Cankar, JL Gallois, J Gricourt, J Bonnet, C Baxter, L Grivet, M Causse (2017) Identification of major loci and genomic regions controlling acid and volatile content in tomato fruit and implications for flavor improvement. New Phytologist (doi: 10.1111/nph.14615)

Bauchet G, Grenier S, Samson N, Bonnet J, Grivet L, Causse M (2017) Use of modern tomato breeding germplasm for deciphering the genetic control of agronomical traits by Genome Wide Association study. Theor Appl Genet 130(5), 875-889 ; DOI 10.1007/s00122-017-2857-9

Pascual L, E Albert, C Sauvage, J Duangjit, JP Bouchet, F Bitton, N Desplat, D Brunel, MC Le Paslier, N Ranc, L Bruguier, B Chauchard, P Verschave, M Causse (2016) Dissecting quantitative trait variation in the resequencing era: complementarity of bi-parental, multi-parental and association panels. Plant Science 242: 120-130

Blanca J, J Montero-Pau, C Sauvage, G Bauchet, E Illa, MJ Diez, D Francis, M Causse, E van der Knaap and J Cañizares (2015) Genomic variation in the tomato, from wild ancestors to contemporary breeding accessions. BMC Genomics 16 : 257, doi:10.1186/s12864-015-1444-1

Lin T, G Zhu, J Zhang, X Xu, Q Yu, Z Zheng, Z Zhang, Y Lun, S Li, X Wang, Z Huang, J Li, Ci Zhang, T Wang, Y Zhang, A Wang, Y Zhang, K Lin, C Li, G Xiong, Y Xue, A Mazzucato, M Causse, Z Fei, JJ Giovannoni, R T Chetelat, D Zamir, T Städler, J Li, Z Ye, Y Du & S Huang 2014. Genomic analyses provide insights into the history of tomato breeding. Nature Genetics 46: 1220-1226; doi:10.1038/ng.3117

Sauvage C, V Segura, G Bauchet, R Stevens, P T Do, Z Nikoloski, A R Fernie and M Causse 2014. Genome Wide Association in tomato reveals 44 candidate loci for fruit metabolic traits. Plant Physiology 165: 1120–1132

Prunus diversity

The collections conserved in the GRC and in the team is a valuable resource which can be exploited in order to: screen our genetic resources for different traits in order to broaden the genetic basis used in crosses, including wild-relative species; search for resilient genotypes to be used as genetic backgrounds in which to introgress targeted traits; study the structure and diversity of our collections, analyze the polymorphism of loci of interest; develop GWAS analyses.

Relevant Publications

Pérez de los Cobos, F., P. J. Martínez-García, et al. (2021). Pedigree analysis of 220 almond genotypes reveals two world mainstream breeding lines based on only three different cultivars. Horticulture Research 8(1): 11. doi.org/ 10.1038/s41438-020-00444-4 https://www.nature.com/articles/s41438-020-00444-4

Groppi, A., S. Liu, et al. (2021). Population genomics of apricots unravels domestication history and adaptive events. Nature Communications 12(1): 3956. Doi.org/10.1038/s41467-021-24283-6 https://www.nature.com/articles/s41467-021-24283-6

Cirilli, M., S. Gattolin, et al. (2021). The Di2/pet Variant in the PETALOSA Gene Underlies a Major Heat Requirement-Related QTL for Blooming Date in Peach [Prunus persica (L.) Batsch]. Plant and Cell Physiology 62(2): 356-365. doi.org/10.1093/pcp/pcaa166 https://academic.oup.com/pcp/article/62/2/356/6064162?login=true

Cirilli, M., S. Micali, et al. (2020). The multi-site PeachRefPop collection: a true cultural heritage and international scientific tool for fruit trees. Plant Physiology: pp.01412.02019. doi.org/10.1104/pp.19.01412 https://academic.oup.com/plphys/article/184/2/632/6117870

Jung, M., Roth, M., Aranzana, M.J. et al. The apple REFPOP—a reference population for genomics-assisted breeding in apple. Hortic Res 7, 189 (2020). doi.org/10.1038/s41438-020-00408-8 https://www.nature.com/articles/s41438-020-00408-8

Alioto, T., K. G. Alexiou, et al. (2020). Transposons played a major role in the diversification between the closely related almond and peach genomes: results from the almond genome sequence. The Plant Journal 101(2): 455-472. doi.org/10.1111/tpj.14538https://onlinelibrary.wiley.com/doi/10.1111/tpj.14538

Conrad, A. O., J. Yu, et al. (2019). Association of the phenylpropanoid pathway with dormancy and adaptive trait variation in apricot (Prunus armeniaca). Tree Physiology 39(7): 1136-1148. doi.org/10.1093/treephys/tpz053 https://academic.oup.com/treephys/article/39/7/1136/5486580?login=true

Gattolin, S., M. Cirilli, et al. (2018). Deletion of the miR172 target site in a TOE-type gene is a strong candidate variant for dominant double-flower trait in Rosaceae. The Plant Journal. doi.org/10.1111/tpj.14036 https://onlinelibrary.wiley.com/doi/full/10.1111/tpj.14036

Hollender, C. A., T. Pascal, et al. (2018). Loss of a highly conserved sterile alpha motif domain gene (WEEP) results in pendulous branch growth in peach trees. Proceedings of the National Academy of Sciences 115(20): 4690-4699. doi.org/10.1073/pnas.1704515115 https://www.pnas.org/content/115/20/E4690

Le Bourvellec, C., Gouble, B., Bureau, S., Reling, P., Bott, R., Ribas-Agusti, A., Audergon, J. M., Renard, C. (2018). Impact of canning and storage on apricot carotenoids and polyphenols. Food Chemistry, 1-50. , DOI : 10.1016/j.foodchem.2017.07.147 https://www.sciencedirect.com/science/article/pii/S0308814617313018?via%3Dihub

 Hernández Mora, J. R., Micheletti, D., Bink, M., Van de Weg, E., Cantín, C., Nazzicari, N., Caprera, A., Dettori, M. T., Micali, Banchi, Campoy, J. A., Dirlewanger, E., Lambert, P., Pascal, T., Troggio, Bassi, D., Rossini, L., Verde, Quilot-Turion, B., Laurens, F., Arus, P., Aranzana (2017). Integrated QTL detection for key breeding traits in multiple peach progenies. BMC Genomics, 18 (1). , DOI : 10.1186/s12864-017-3783-6 https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-3783-6

Bourguiba, H., Batnini, M.-A., Krichen, L., Trifi-Farah, N., Audergon, J. M. (2017). Population structure and core collection construction of apricot (Prunus armeniaca L.) in north Africa based on microsatellite markers. Plant Genetic Resources Characterization and Utilization, 15 (1), 21-28. https://www.cambridge.org/core/journals/plant-genetic-resources/article/population-structure-and-core-collection-construction-of-apricot-prunus-armeniaca-l-in-north-africa-based-on-microsatellite-markers/D8C1CD82712C4A9F485D1AB2B4C95211#

Ayour, J., Gouble, B., Reling, P., Ribas-Agustí, A., Audergon, J. M., Maingonnat , J. F., Benichou, M., Renard, C. (2017). Impact of cooking on apricot texture as a function of cultivar and maturity. LWT - Food Science and Technology, 85 (Part B), 385-389. , DOI : 10.1016/j.lwt.2016.10.040 https://www.sciencedirect.com/science/article/pii/S0023643816306351?via%3Dihub