BIANNUALREPORT2012-2013

Group Structure

Group Leader: Pere Arús (IRTA Researcher)
Researchers: María José Aranzana, Werner Howad, Amparo Monfort
Postdoctoral Researchers: Andrea Blas (until November 2012), Iban Eduardo, José Ramón Hernández, Diego Micheletti, Raúl Tonda (until Febuary 2013), Carmen Villatoro (until June 2012)
PhD Students: José Manuel Donoso, Xiongwei Li, Elena López, Octávio Serra (since June 2013), Maria Urrutia
Undergrad or Master Students: Carles Amat, Meltem Berber, Neus Busquets, Isabelle Follon, Marta Gòdia, Sebastián González, José Manuel Hidalgo, Miquel Llimós, Eduard Rojas, Octávio Serra, Sergi Tosal, Elisenda Vilaplana, Cristina Vives
General Research Support: Manoli Cencerrero, Esteve Collell, Alicia Norat, Josep Maria San Millan, Ana Sesé, Joana Ribes.

Summary

The main objective of the group is to understand the genetics of key characters in cultivated species of this family, particularly those related to disease resistance and fruit quality, and to develop tools for marker-assisted breeding. The main species of interest are peach, strawberry, almond, apricot, plum, raspberry and blackberry.

During this period the whole genome sequence of peach was published with participation of our group. Genome sequence data have boosted fine mapping and cloning of two fruit quality major genes: subacid fruit and flat peach. Other targets have been the slow ripening and slow melting traits, both basic to understand peach post harvest life, one of the key commercial traits. A 9k Illumina Infinium SNP chip was developed in an international collaboration and used to evaluate a large sample (>1,500) of peach cultivars and five Prunus mapping populations peach×peach (3) and interspecific (2). Results on germplasm were in agreement with the history of peach as cultivated species, allowed estimating a high level of linkage disequilibrium conservation and were used to perform genome-wide association analyses with major genes of fruit and flower characters. SNP data on mapping populations were used to construct linkage maps.

The peach gene pool is strongly eroded and introgression of genes from other species may be a way for its enrichment. We are progressing towards the construction of peach lines that contain single chromosomal fragments of almond. Several interesting characters, such as disease resistance, skin and flesh color, fruit size and maturity date determined by almond alleles at single genes or major QTLs have been identified. In other stone fruit species (apricot and plum) we are developing markers for the selection of self-compatibility alleles.

In strawberry we have completed a collection of 35 lines selected to have one chromosomal fragment of F. bucharica in the background of F. vesca and cover almost the complete F. bucharica genome. These lines have been phenotyed for characters including morphological, phenological and different fruit metabolites. Many major genes have been identified and mapped. A 90 k SNP chip (Affymetrix Axiom) has been developed to facilitate genome analysis of the octoploid genome of the cultivated strawberry (F. × ananassa) and is currently being used for mapping. Transcriptomic and metabolomic analyses have been performed in F. x ananassa mature fruits of an F2 population to detect nutritional QTL and expression QTL (eQTLs). A set of candidate genes has been identified.

Research Projects

• Whole genome analysis of variability and association genetics in peach
• Introgression of genes from wild or exotic sources into the cultivated genomes of peach and woodland strawberry
• Positional gene cloning of major genes for fruit quality in peach
• Comparative genomics of major rosaceous crops (strawberry-peach-apple)
• Development of diagnostic markers for marker assisted breeding in several rosaceous crops

Selected Publications

Aranzana M.J., Illa E., Howad W., Arús P.
A first insight into peach [Prunus persica (L.) Batsch] SNP variability
(2012) Tree Genetics and Genomes, vol. 8 (6), pp. 1359-1369

Arús P., Verde I., Sosinski B., Zhebentyayeva T., Abbott A.G.
The peach genome
(2012) Tree Genetics and Genomes, vol. 8 (3), pp. 531-547

Dirlewanger E., Quero-Garcia J., Le Dantec L., Lambert P., Ruiz D., Dondini L., Illa E., Quilot-Turion B., Audergon J.-M., Tartarini S., Letourmy P., Arús P.
Comparison of the genetic determinism of two key phenological traits, flowering and maturity dates, in three Prunus species: Peach, apricot and sweet cherry
(2012) Heredity, vol. 109 (5), pp. 280-292

Jung S., Cestaro A., Troggio M., Main D., Zheng P., Cho I., Folta K.M., Sosinski B., Abbott A., Celton J.-M., Arús P., Shulaev V., Verde I., Morgante M., Rokhsar D., Velasco R., Sargent D.J.
Whole genome comparisons of Fragaria, Prunus and Malus reveal different modes of evolution between Rosaceous subfamilies
(2012) BMC Genomics, vol. 13 (1), Art. number 129

Lahaye M., Falourd X., Quemener B., Ralet M.C., Howad W., Dirlewanger E., Arús P.
Cell wall polysaccharide chemistry of peach genotypes with contrasted textures and other fruit traits
(2012) Journal of Agricultural and Food Chemistry, vol. 60 (26), pp. 6594-6605

Laurens F., Aranzana M.J., Arús P., Bassi D., Bonany J., Corelli L., Durel C.E., Mes J., Pascal T., Patocchi A., Peil A., Quilot B., Salvi S., Tartarini S., Troggio M., Vecchietti A., Velasco R., Van De Weg E.
Review of fruit genetics and breeding programmes and a new European initiative to increase fruit breeding efficiency
(2012) Acta Horticulturae, vol. 929, pp. 95-102

Verde I., Bassil N., Scalabrin S., Gilmore B., Lawley C.T., Gasic K., Micheletti D., Rosyara U.R., Cattonaro F., Vendramin E., Main D., Aramini V., Blas A.L., Mockler T.C., Bryant D.W., Wilhelm L., Troggio M., Sosinski B., Aranzana M.J., Arús P., Iezzoni A., Morgante M., Peace C.
Development and evaluation of a 9k snp array for peach by internationally coordinated snp detection and validation in breeding germplasm
(2012) PLoS ONE, vol. 7 (4), Art. number e35668

Li X.-W., Meng X.-Q., Jia H.-J., Yu M.-L., Ma R.-J., Wang L.-R., Cao K., Shen Z.-J., Niu L., Tian J.-B., Chen M.-J., Xie M., Arús P., Gao Z.-S., Aranzana M.J.
Peach genetic resources: Diversity, population structure and linkage disequilibrium
(2013) BMC Genetics, vol. 14, Art. number 84

Molina-Hidalgo F.J., Franco A.R., Villatoro C., Medina-Puche L., Mercado J.A., Hidalgo M.A., Monfort A., Caballero J.L., Muñoz-Blanco J., Blanco-Portales R.
The strawberry (Fragaria×ananassa) fruit-specific rhamnogalacturonate lyase 1 (FaRGLyase1) gene encodes an enzyme involved in the degradation of cell-wall middle lamellae
(2013) Journal of Experimental Botany, vol. 64 (6), pp. 1471-1483

Picañol R., Eduardo I., Aranzana M.J., Howad W., Batlle I., Iglesias I., Alonso J.M., Arús P.
Combining linkage and association mapping to search for markers linked to the flat fruit character in peach
(2013) Euphytica, vol. 190 (2), pp. 279-288

Ring L., Yeh S.-Y., Hucherig S., Hoffmann T., Blanco-Portales R., Fouche M., Villatoro C., Denoyes B., Monfort A., Caballero J.L., Muñoz-Blanco J., Gershenson J., Schwab W.
Metabolic interaction between anthocyanin and lignin biosynthesis is associated with peroxidase FaPRX27 in strawberry fruit
(2013) Plant Physiology, vol. 163 (1), pp. 43-60

Verde I., Abbott A.G., Scalabrin S., Jung S., Shu S., Marroni F., Zhebentyayeva T., Dettori M.T., Grimwood J., Cattonaro F., Zuccolo A., Rossini L., Jenkins J., Vendramin E., Meisel L.A., Decroocq V., Sosinski B., Prochnik S., Mitros T., Policriti A., Cipriani G., Dondini L., Ficklin S., Goodstein D.M., Xuan P., Del Fabbro C., Aramini V., Copetti D., Gonzalez S., Horner D.S., Falchi R., Lucas S., Mica E., Maldonado J., Lazzari B., Bielenberg D., Pirona R., Miculan M., Barakat A., Testolin R., Stella A., Tartarini S., Tonutti P., Arús P., Orellana A., Wells C., Main D., Vizzotto G., Silva H., Salamini F., Schmutz J., Morgante M., Rokhsar D.S.
The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution
(2013) Nature Genetics, vol. 45 (5), pp. 487-494