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QTL) and Mendelian Trait Loci (MTL) Analysis in Prunus: a Breeding Perspective and Beyond

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QTL) and Mendelian Trait Loci (MTL) Analysis in Prunus: a Breeding Perspective and Beyond Plant Mol Biol Rep (2014) 32:1–18 DOI 10.1007/s11105-013-0643-7 REVIEW Quantitative Trait Loci (QTL) and Mendelian Trait Loci (MTL) Analysis in Prunus: a Breeding Perspective and Beyond Juan Alfonso Salazar & David Ruiz & José Antonio Campoy & Raquel Sánchez-Pérez & Carlos H. Crisosto & Pedro J. Martínez-García & Anna Blenda & Sook Jung & Dorrie Main & Pedro Martínez-Gómez & Manuel Rubio Published online: 7 September 2013 # Springer Science+Business Media New York 2013 Abstract Trait loci analysis, a classic procedure in quantitative Rosaceae family. Since 2011, the number of published Prunus (quantitative trait loci, QTL) and qualitative (Mendelian trait QTLs and MTLs has doubled. With increased genomic re- loci, MTL) genetics, continues to be the most important ap- sources, such as whole genome sequences and high-density proach in studies of gene labeling in Prunus species from the genotyping platforms, trait loci analysis can be more readily converted to markers that can be directly utilized in marker- Electronic supplementary material The online version of this article assisted breeding. To provide this important resource to the (doi:10.1007/s11105-013-0643-7) contains supplementary material, community and to integrate it with other genomic, genetic, which is available to authorized users. and breeding data, a global review of the QTLs and MTLs : : : J. A. Salazar D. Ruiz P. Martínez-Gómez (*) M. Rubio linked to agronomic traits in Prunus has been performed and Departamento de Mejora Vegetal, CEBAS-CSIC, PO Box 164, the data made available in the Genome Database for Rosaceae. 30100 Espinardo, Murcia, Spain e-mail: [email protected] We describe detailed information on 760 main QTLs and MTLs linked to a total of 110 agronomic traits related to tree develop- J. A. Campoy ment, pest and disease resistance, flowering, ripening, and fruit UMR 1332 de Biologie du Fruit et Pathologie, Université de and seed quality. Access to these trait loci enables the applica- Bordeaux, 33140 Villenave d’Ornon, France tion of this information in the post-genomic era, characterized J. A. Campoy by the availability of a high-quality peach reference genome and UMR 1332 de Biologie du Fruit et Pathologie, INRA, new high-throughput DNA and RNA analysis technologies. 33140 Villenave d’Ornon, France R. Sánchez-Pérez Keywords Prunus . Breeding . Phenotype . Quantitative trait Plant Biochemistry Lab, Faculty of Science, University of loci . QTL . Mendelian trait loci . MTL . eQTL . Copenhagen, 1871 Copenhagen C, Denmark Marker-assisted breeding C. H. Crisosto : P. J. Martínez-García Department of Plant Science, University of California-Davis, Davis, CA 95616, USA Introduction A. Blenda Department of Genetics and Biochemistry, Clemson University, The Prunus genus (family Rosaceae, order Rosales) com- Clemson, SC 29634, USA prises about 230 species, many of which produce edible drupes (with fruits and seeds of economic interest depending S. Jung : D. Main (*) Department of Horticulture, Washington State University, on species) and are widely grown around the world (Potter 45 Johnson Hall, Pullman, WA 99164-6414, USA 2012). The annual worldwide production of Prunus species e-mail: [email protected] cultivated for edible fruits and seeds were around 41 million metric tons in 2011, including 21.52 million tons of peach and A. Blenda Department of Biology, Erskine College, nectarine fruits [Prunus persica (L.) Batsch] (2n =2x =16); Due West, SC 29639, USA 11.35 million tons of prune (Prunus domestica L.) (2n =6x = 2 Plant Mol Biol Rep (2014) 32:1–18 48), plum (Prunus salicina Lindl) (2n =2x =16),sloe(Prunus era (Martínez-Gómez et al. 2012). However, even with a spinosa L.) (2n =4x =32), and cherry plum fruits (Prunus complete reference sequence available for Prunus species, cerasifera Ehrh.) (2n =2x =16); 3.84 million tons of apricot molecular genetic linkage maps will continue to be a major fruits (Prunus armeniaca L.) (2n =2x =16); 2.24 million tons tool in genetics, genomics, and breeding. of sweet (Prunus avium L.) (2n =2x =16), sour (Prunus As important as QTL and MTL identification has been in cerasus L.) (2n =4x =32), and ground (Prunus fruticosa Pall.) Prunus, their use in breeding has been limited due to several (2n =4x =32) cherry fruits; and 2.01 million tons of almond factors. These include dispersion of the information in many kernels [Prunus amygdalus (Batsch) syn. Prunus dulcis publications, the specifics of the assayed population, and the (Miller) Webb] (2n =2x =16) (http://faostat.fao.org). lack of standardization in nomenclature and methodology. Prunus breeding must address challenges arising from The development of a Prunus QTL and MTL database would the specifics of the species physiology, including growth be very useful for data comparison, data mining, and meta- duration resulting from an extended juvenile period analysis of the huge range of information disseminated in (between 3 and 10 years depending on the species) many publications (Hu et al. 2012). Trait loci data are usually and a complex physiology due to multi-annual mecha- stored in clade-oriented databases that integrate genomic and nisms of dormancy. The physiology is also significantly genetic data for closely related organisms. These databases influenced by environmental conditions. For this reason, offer more integrated and complete data for the organisms developing new Prunus cultivars is an expensive and than general nucleotide sequence databases, such as Genbank, time-consuming process involving generation of large DDJB, and EMBL (Arús et al. 2012; Wergzyn et al. 2012). populations of seedlings from which the best genotypes The Genome Database for Rosaceae (GDR, www.rosaceae. are selected (Gradziel and Martínez-Gómez 2013). In org;Jungetal.2008) is the community database for Rosaceae, this context, the development of efficient marker- which integrates genetic, genomic, and breeding data. ESTree assisted selection strategies is particularly useful in Pru- database (www.itb.cnr.it/estree/) specializes in functional nus (Arús et al. 2005). The first approach to gene genomics data for Prunus. At the inception of this work, labeling and development of molecular markers for GDR contained 885 QTLs and MTLs linked to agronomic marker-assisted selection (MAS) used segregating prog- traits in different species from the Rosaceae family and 228 in enies (mapping populations) for molecular characterization Prunus (peach and sour cherry). Associated data includes the and establishment of the relationship with agronomic traits by name of the studied population, the significance of the QTL or genetic linkage maps and trait loci analysis including quanti- MTL (log of odds (LOD) and R2), the effect, and the name tative (quantitative trait loci, QTL) and qualitative (Mendelian and symbol of the QTL or MTL. trait loci, MTL) traits. The purposes of this study were (1) to complete the A QTL can be described as a genomic region hypotheti- curation of the information available for the Prunus QTLs cally responsible for quantitative genetic variation of a trait and MTLs from literature and to integrate the data in GDR, where the allelic variation of a locus is associated with the and (2) to provide a comprehensive review of the QTLs and variation of the trait (polygenic traits) (Asins 2002; Collard MTLs including a discussion of the main implications of this et al. 2005). In addition, a MTL can be described as a genomic information for the development of MAS strategies. region linked for a unique gene responsible for a trait (mono- genic traits) (Lionneton et al. 2004). However, in the case of Prunus studies, in the original manuscripts, most of MTLs Methodology were named as QTLs. In the absence of information about specific genes, loci trait analysis can be performed using To compare information about the identification of QTLs and model parameters considered as quantitative or qualitative MTLs linked to polygenic and monogenic agronomic traits in traits, and then for each mapping population, the values of the different Prunus species, the following criteria were genotypic parameters can be predicted based on the allelic recorded: mapping population assayed, genetic linkage anal- composition of the molecular markers flanking the QTLs or ysis performed, and trait loci analysis applied. MTLs (Bertin et al. 2010). A well-established procedure in quantitative genetics, trait loci analysis, continues to be the most important approach in the preliminary studies of gene Mapping Populations identification of Prunus breeding traits. The recent sequenc- ing of the complete genome of peach (Verde et al. 2013), The following information about the studied populations was together with the availability of new technologies for high- recorded: “species” (including interspecific hybrids and relat- throughput genome and transcriptome analysis, offers new ed species), “population pedigree,”“population name” (using possibilities for QTL and MTL application and candidate gene the most recent publications as a main reference), “country,” identification in what has been described as the post-genomic “population type,” and “population size.” Plant Mol Biol Rep (2014) 32:1–18 3 Genetic Linkage best genetically characterized species in the Rosaceae and the model species for the genus Prunus (Baird et al. 1994;Arús In the genetic linkage analysis, the following information was et al. 2012). collected: “type of markers assayed,”“number of markers In plants, the construction of a linkage map and the subse- mapped,”“linkage map size” (in centimorgan), “total number quent analysis of QTLs require a segregating population de- of linkage groups,” and “mean distance” of mapped marker rived from sexual crosses between parents differing in as (in centimorgan/marker). many agronomic traits of interest as possible. In the case of Prunus, most QTL studies have been based on intraspecific QTL and MTL Identification crosses with the exception of peach, where some studies have been performed with interspecific crosses (Tables 1 and 2). We integrated various types of QTL and MTL information Cultivated peaches are characterized by a genetic origin with a from peer-reviewed publications.
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