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Mapping QTLs associated with fruit quality traits in peach [Prunus persica (L.) Batsch] using SNP maps

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Abstract

Fruit quality is an essential criterion used to select new cultivars in peach breeding programs and is determined based on a combination of organoleptic and nutritional traits. The aim of this study was to identify quantitative trait loci (QTLs) for fruit quality traits in an F1 nectarine population derived from ‘Venus’ and ‘Big Top’ cultivars. The progeny were evaluated over 4 years for agronomical and biochemical characteristics and genotyped using simple sequence repeat (SSR) markers and ‘IPSC 9K peach SNP array v1’. Two genetic maps were constructed using 411 markers. The ‘Venus’ map spanned 259 cM on nine linkage groups (LGs) with 104 markers. The ‘Big Top’ map spanned 464 cM on 10 LGs with 122 markers. Single or Multiple QTL models mapping was applied separately for each year and all years combined. A total of 54 QTLs mapped over 12 LGs belonged to seven peach chromosomes. Most of the QTLs were consistent over the 4 years of study and were validated with the multi-year analysis. QTLs for total phenolic, flavonoid, and anthocyanin contents were reported for the first time in peach. LG 4 in ‘Venus’ and LG 5 in ‘Big Top’ showed the highest numbers of QTLs. This work represents the first study in an F1 nectarine family to identify peach genomic regions that control fruit quality traits using ‘IPSC 9K SNP array v1’ and provides useful information for marker-assisted breeding to produce peaches with better antioxidant content and healthy attributes.

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Acknowledgments

We are grateful to C.H. Crisosto (University of California, Davis) for providing SSR markers (UCDCH15 and BINEPPCU6377). We thank E. Sierra and S. Segura for the technical assistance and plant management in the field and N. Ksouri for the bioinformatic assistance. We are grateful to A. Casas and E. Igartua for the assistance and support with the statistical analysis using JoinMap® 4 software. This study was funded by the Spanish Ministry of Economy and Competitiveness (MINECO) grants AGL-2008-00283, AGL2011-24576, and AGL2014-52063-R and was co-funded by the FEDER and the Regional Government of Aragón (A44) with European Social Fund. W. Abidi was supported by a JAE-Pre fellowship from the Consejo Superior de Investigaciones Científicas (CSIC), which enabled him to visit the University of California, Davis, and the IBMCP, Valencia, Spain. J.L. Zeballos received a master fellow funded by the Spanish Agency for International Cooperation and Development (AECID).

Data Archiving Statement

V x BT linkage maps and QTL positions are available on Genome Database for Rosaceae at tfGDR1025 accesion number.

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    1. Department of Pomology, Estación Experimental de Aula Dei-CSIC, P.O. Box 13034, 50080, Zaragoza, Spain

      José Luis Zeballos, Walid Abidi, Rosa Giménez, María Ángeles Moreno & Yolanda Gogorcena

    2. Instituto de Biología Molecular y Celular de Plantas-(CSIC-UPV), 46022, Valencia, Spain

      Antonio J. Monforte

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    1. José Luis Zeballos
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    José Luis Zeballos and Walid Abidi contributed equally to this work.

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    Zeballos, J.L., Abidi, W., Giménez, R. et al. Mapping QTLs associated with fruit quality traits in peach [Prunus persica (L.) Batsch] using SNP maps. Tree Genetics & Genomes 12, 37 (2016). https://doi.org/10.1007/s11295-016-0996-9

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