Validación de la variante genómica estructural SNP para discriminar variedades de cerezo con distintos niveles de precocidad en la producción de frutos.
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Date
2025
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Publisher
Universidad de Concepción
Abstract
La diferenciación entre variedades frutales según características fenológicas, como la precocidad en la producción de frutos, es clave para el mejoramiento genético y la eficiencia productiva. En especies como el cerezo dulce (Prunus avium), permite optimizar la planificación de cosechas y acceder a mercados con ventanas comerciales diferenciadas. Tradicionalmente, la identificación varietal se ha basado en rasgos morfológicos, con limitaciones en etapas tempranas del desarrollo vegetal. Esta investigación tuvo como objetivo validar polimorfismos de nucleótido único (SNPs) como herramienta genómica para discriminar variedades de cerezo con distintos niveles de precocidad. A partir de datos de secuenciación de tercera generación, se identificaron regiones genómicas diferenciales entre variedades tempranas y tardías cultivadas en Chile (Royal Dawn y Royal Lee versus Regina y Kordia, respectivamente). Se seleccionó una región que contenía un gen ortólogo a la isopenteniltransferasa (IPT), enzima clave en la biosíntesis de citoquininas, hormonas relacionadas con el desarrollo y maduración de frutos. Se diseñaron partidores específicos para estos SNPs, optimizados mediante Temperature Switch PCR (TSP) y aplicados con PCR convencional y qPCR con High Resolution Melting (qPCR-HRM). Los análisis diferenciaron variedades mediante patrones de bandas en geles de agarosa y curvas de fusión en qPCR. La aplicación a un grupo ampliado de variedades mostró resultados consistentes con su clasificación por precocidad. No obstante, se observaron discrepancias en variedades autocompatibles (Sweetheart, Staccato, Cristobalina), lo que sugiere relación entre precocidad y autocompatibilidad. Estos resultados respaldan el uso de SNPs como herramientas de identificación varietal, con aplicaciones relevantes para la industria frutícola y los programas de mejoramiento genético del cerezo.
La fertilización mostró un efecto positivo principalmente en sitios más productivos, mientras que en IS 25 su impacto fue limitado. Los resultados confirman que es posible orientar el manejo silvícola hacia la producción de madera estructural, incluso en sitios tradicionalmente marginales, mejorando su valor y competitividad forestal.
The differentiation of fruit tree varieties based on phenological traits, such as earliness in fruit production, is key for genetic improvement and productive efficiency. In species such as sweet cherry (Prunus avium), it enables optimization of harvest planning and access to markets with differentiated commercial windows. Traditionally, varietal identification has relied on morphological traits, which show limitations at early stages of plant development. This study aimed to validate single nucleotide polymorphisms (SNPs) as a genomic tool to discriminate cherry varieties with different levels of earliness. Using third generation sequencing data, differential genomic regions were identified between early and late varieties cultivated in Chile (Royal Dawn and Royal Lee versus Regina and Kordia, respectively). A region containing a gene orthologous to isopentenyltransferase (IPT), a key enzyme in cytokinin biosynthesis, hormones related to fruit development and ripening, was selected. Specific primers for these SNPs were designed, optimized through Temperature Switch PCR (TSP), and applied using conventional PCR and qPCR with High Resolution Melting (qPCR HRM). Analyses differentiated varieties through specific band patterns in agarose gels and distinct melting curves in qPCR. Application to an expanded group of varieties showed results consistent with their classification by earliness. However, discrepancies were observed in self-compatible varieties (Sweetheart, Staccato, Cristobalina), suggesting a possible relationship between earliness and self compatibility. These results support the use of specific SNPs as varietal identification tools based on earliness, with relevant applications for the fruit industry and cherry breeding programs.
The differentiation of fruit tree varieties based on phenological traits, such as earliness in fruit production, is key for genetic improvement and productive efficiency. In species such as sweet cherry (Prunus avium), it enables optimization of harvest planning and access to markets with differentiated commercial windows. Traditionally, varietal identification has relied on morphological traits, which show limitations at early stages of plant development. This study aimed to validate single nucleotide polymorphisms (SNPs) as a genomic tool to discriminate cherry varieties with different levels of earliness. Using third generation sequencing data, differential genomic regions were identified between early and late varieties cultivated in Chile (Royal Dawn and Royal Lee versus Regina and Kordia, respectively). A region containing a gene orthologous to isopentenyltransferase (IPT), a key enzyme in cytokinin biosynthesis, hormones related to fruit development and ripening, was selected. Specific primers for these SNPs were designed, optimized through Temperature Switch PCR (TSP), and applied using conventional PCR and qPCR with High Resolution Melting (qPCR HRM). Analyses differentiated varieties through specific band patterns in agarose gels and distinct melting curves in qPCR. Application to an expanded group of varieties showed results consistent with their classification by earliness. However, discrepancies were observed in self-compatible varieties (Sweetheart, Staccato, Cristobalina), suggesting a possible relationship between earliness and self compatibility. These results support the use of specific SNPs as varietal identification tools based on earliness, with relevant applications for the fruit industry and cherry breeding programs.
Description
Tesis presentada para optar al título de Ingeniero/a en Biotecnología Vegetal.
Keywords
Cerezo, Arboles frutales Identificación, Cerezas dulces Maduración