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Bases genéticas y moleculares de la fenología y la calidad del fruto en ciruelo japonés (Prunus salicina Lindl.) y estudio de la transmisión de la autocompatibilidad y resistencia al virus de la Sharka (Plum pox virus) en híbridos interespecíficos ciruelo japonés x albaricoquero (P. salicina x P. armeniaca L.)


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Título :
Bases genéticas y moleculares de la fenología y la calidad del fruto en ciruelo japonés (Prunus salicina Lindl.) y estudio de la transmisión de la autocompatibilidad y resistencia al virus de la Sharka (Plum pox virus) en híbridos interespecíficos ciruelo japonés x albaricoquero (P. salicina x P. armeniaca L.)
Autor :
Nicolás Almansa, María  
Tutor:
Martinez-Gomez, Pedro  
Ruiz González, David
Editor :
Universidad Miguel Hernández
Departamento:
Departamentos de la UMH::Producción Vegetal y Microbiología
Fecha de publicación:
2024-11-07
URI :
https://hdl.handle.net/11000/35692
Resumen :
El ciruelo japonés (Prunus salicina Lindl.) es uno de los frutales de hueso más cultivados en el mundo, ocupando el segundo lugar en producción después del melocotonero, con una producción global de más de 12 millones de toneladas. Sin embargo, el cultivo del ciruelo japonés presenta una serie de d...  Ver más
Japanese plum (Prunus salicina Lindl.) is one of the most widely cultivated stone fruit trees in the world, ranking second in production after peach, with a global production exceeding 12 million tons. However, in Spain, the cultivation of Japanese plum faces a series of deficiencies and challenges that must be addressed to ensure its viability and profitability. One of the main difficulties lies in the limited varietal assortment available for cultivation, with global production still heavily reliant on a limited number of traditional cultivars. A highly relevant and complex aspect of cultivating this species is its floral self-incompatibility, with only a few commercially self-compatible varieties, necessitating the design of plantations with pollinator varieties that are inter-compatible and have synchronized blooming periods. Another significant issue, particularly affecting the Region of Murcia and the Valencian Community, is the incidence of Sharka disease, caused by the plum pox virus (PPV), which causes considerable damage to this species, impacting both quality and yield. This problem presents a challenging solution, as there are no sources of resistance to the virus in Japanese plum, and all cultivated varieties are susceptible. Fruit quality is another aspect requiring improvement in this species, as some of the cultivated varieties do not meet the quality parameters demanded by the commercial industry and consumers. Attractive skin and flesh color, firmness, flavor, and good postharvest performance are the main characteristics to be considered in new varieties. The necessity to address these challenges arising from cultivation issues, the evolution of consumer demand and expectations, the growing market competition, as well as new technological, agronomic, and environmental challenges —including the impact of climate change and ecological sustainability, —requires genetic improvement programs that respond to these needs by developing new high-value and excellent varieties that increase the genetic and phenotypic diversity of the species. However, the improvement of this species, like other woody crops, entails very long improvement cycles due to the extended juvenility periods, complex reproductive biology, and high degree of heterozygosity. Currently, there are Japanese plum breeding programs around the world, and although the most advanced breeding programs are primarily in California, significant efforts are being made in other countries such as China, Japan, Chile, South Africa, Australia, and Spain. These breeding programs are based on classical procedures, including directed crosses, progeny generation, offspring evaluation, and genotype selection based on phenotypic characteristics, which require long periods of time, extensive field and laboratory work, and high economic costs. The use of biotechnological approaches, such as marker-assisted selection (MAS) and genomics, can help optimize Japanese plum breeding programs, significantly improving their efficiency and reducing the time required to develop new varieties. In this regard, the availability of molecular markers in Japanese plum is currently very limited, mainly focusing on the identification of incompatibility alleles, which facilitates the assessment of compatibility between genotypes and the strategic planning of crosses. More recently, molecular markers have been developed for skin color and flesh color, allowing the determination of the presence or absence of red pigmentation in both tissues. In this context, the Doctoral Thesis has been carried out within the framework of the Japanese plum breeding program developed jointly by CEBAS-CSIC and IMIDA, initiated in 2011 in the Region of Murcia. The main objectives are to obtain varieties with low chilling requirements, adapted to current and future climatic conditions, self-compatible, early maturing (May, June), highly productive, with high fruit quality, and, if possible, resistant to the Sharka disease virus through the generation of interspecific hybrids by crossing with resistant and self-compatible apricot varieties (plumcots). The overall objective of this doctoral thesis has been to study the genetic and molecular bases of the main traits involved in the phenology and fruit quality of Japanese plum, as well as the phenotypic and molecular characterization of Japanese plum × apricot (plumcot) interspecific hybrids. This includes the validation of their interspecific nature, the evaluation of resistance to the sharka virus (PPV), and the determination of floral compatibility alleles. To achieve this, within the intraspecific work line, a three-year phenotypic characterization has been conducted, and the inheritance patterns of the main phenological and fruit quality traits have been studied in three segregating F1 populations of Japanese plum ('Black Splendor' × 'Pioneer' ('BS×PIO'), 'Red Beaut' × 'Black Splendor' ('RB×BS'), and 'Red Beaut' × 'Santa Rosa Precoz' ('RB×SRP')). Additionally, molecular characterization of the three populations has been carried out by implementing a novel genotyping strategy in fruit trees, not previously used in Japanese plum or other species of the genus Prunus. This approach reduces costs by combining high coverage (Whole Genome Sequencing, WGS) of the parents and low coverage (Low Coverage Whole Genome Sequencing, LcWGS) of the progeny to develop genetic linkage maps and identify genome regions associated with traits of interest (QTLs) related to phenology and fruit quality. Furthermore, within the interspecific work line, phenotypic and molecular characterization of the interspecific hybrids resulting from crosses between Japanese plum varieties of interest and PPV-resistant, self-compatible apricot varieties has been performed. This has enabled the study of the transmission of PPV resistance and floral self- compatibility from apricot to plum in the interspecific hybrids. Regarding the results obtained, it is worth highlighting that the findings from the phenotypic characterization and inheritance study of the main phenological and fruit quality traits in the three Japanese plum populations under study (Chapter 3), show a great diversity and phenotypic segregation in all evaluated traits, corroborating the segregating nature of the populations—an essential condition for addressing the objectives of this doctoral thesis. Additionally, high variability was observed in the progeny of the three populations, presenting transgressive phenotypes compared to the parents in all phenological and fruit quality traits, which can be attributed to the genetic background influence of the parents. A very representative example is the presence of genotypes with yellow skin coloration in the progeny of the ‘RB×BS’ and ‘RB×SRP’ populations, despite neither parent exhibiting this characteristic, demonstrating the significant influence of the genetic heritage of the ‘RB’ and ‘SRP’ varieties, which have complex pedigrees resulting from crosses between different Prunus species. Moreover, statistical analyses and frequency histograms reveal a non-parametric distribution in all evaluated phenological traits and in most physical traits determining fruit quality, except for weight and diameter, which exhibit a normal distribution. Similarly, all analyzed organoleptic traits show a normal distribution in the three populations. Notably, flesh color in the ‘BS×PIO’ and ‘RB×BS’ populations exhibits a bimodal distribution, distinguishing between genotypes with red and yellow flesh. However, the ‘RB×SRP’ population shows a negatively skewed distribution, ranging from orange and bicolor flesh coloration to yellow. Most evaluated traits exhibit quantitative inheritance, supporting their polygenic nature, except for flesh color, which shows qualitative inheritance likely due to its oligogenic or monogenic nature. Finally, highly significant correlations were found between various evaluated traits, particularly those observed between different flowering dates (beginning, full, and end), and between the ripening date and fruit development period. Significant correlations were also observed between the fruit development period, weight and diameter, ripening date, fruit development period and firmness, fruit development period, firmness, and soluble solids content, among others. The implementation of the novel genotyping strategy, combining high coverage sequencing of the parents (Whole Genome Sequencing, WGS) and low coverage sequencing of the progeny (Low Coverage Whole Genome Sequencing, LcWGS) (Chapter 4), has successfully allowed the development of genetic linkage maps for all parents of the three evaluated populations. Subsequently, a large number of QTLs linked to the main phenological and fruit quality traits were identified in a more economically efficient manner compared to previously used techniques in this species. The generated linkage maps exhibit similar characteristics in terms of size and number of mapped SNPs to those developed by other authors using more expensive genotyping strategies. However, this technique has encountered some difficulties due to the use of low coverage in the progeny, resulting in some linkage groups being represented by unconnected segments. A significant number of QTLs have been identified with SNPs associated with the expression of many evaluated traits, showing a significant and stable allelic effect over the three years of study. Validation of these QTLs in future work can facilitate the development of specific molecular markers for use in marker-assisted breeding, thereby reducing the time and resources required in a traditional breeding program. It is noteworthy that most of the SNPs from the QTLs linked to flowering date in the three evaluated populations show a significant allelic effect associated with a late flowering date, except for those identified in the parent 'PIO' of the 'BS×PIO' population and in the parent 'BS' of the 'RB×BS' population, which are associated with an early flowering date. Additionally, QTLs linked to flowering intensity and productivity have been identified for the first time in the Japanese plum species, with SNPs showing different allelic effects depending on the parent and linkage group. Similarly, most QTLs linked to the ripening date and fruit development period are located in similar regions of the linkage groups depending on the population in which they were identified. The first QTL linked to split-pit disorder in fruit trees of the genus Prunus has been identified, with the one identified in linkage group 5 of the 'BS' parent in the 'BS×PIO' population being the only one stable over the three years of phenotyping. Genotypes presenting the SNP of this QTL show a lower incidence of this disorder. Regarding skin and flesh color traits, linkage groups 3 and 5 stand out for having the most significant QTLs. Additionally, SNPs have been associated with the expression of yellow, red, purple, and black skin color, as well as yellow, red, and bicolor flesh color, depending on the linkage group in which they were identified. Finally, concerning the results obtained for organoleptic traits, stable QTLs over three years of phenotyping have been identified for the first time, associated with soluble solids content, acidity, and fruit pH. Linkage group 5 is particularly noteworthy for having the highest number of stable QTLs identified. Regarding the results obtained in the interspecific line (Chapter 5), this study demonstrates the challenge of generating Prunus salicina Lindl. × Prunus armeniaca L. (plumcots) interspecific hybrids, having very low hybridization success rates, influenced by the direction of the cross, with only those involving P. salicina as the maternal parent being viable. The interspecific nature of the hybrids has been successfully verified using SSR molecular markers, as all confirmed hybrids presented one allele derived from the Japanese plum and another from the apricot, highlighting the high transferability of the markers used between Prunus species. These hybrids show genetic relationships more similar to apricots, also presenting phenotypic characteristics typical of that species, such as leaf morphology, gynoecium pubescence, and fruit pubescence, among others. Moreover, the S alleles of incompatibility were successfully genotyped in all hybrids, with most segregating for the Sc allele that confers self-compatibility to apricot, suggesting that they should be self-compatible and self-fertile. However, pollen viability studies have shown male sterility in all plumcots that flowered, suggesting that this interspecific hybridization causes male sterility in the progeny. Regarding the evaluation of PPV resistance, both phenotyping and genotyping results did not match the expected resistance, as most plumcots genetically classified as resistant, having the alleles that confer PPV resistance in apricot, did not show resistance in phenotypic evaluation. However, tolerant plumcots were identified, showing no symptoms of the disease despite positive ELISA and RT-PCR results in the laboratory. Most tolerant plumcots carried the alleles associated with resistance, suggesting that the presence of the resistance allele could result in reduced susceptibility, with a significant group of susceptible plumcots becoming tolerant/resistant after the first phenotyping cycle. The results highlight significant challenges to be resolved in interspecific crossings, such as male sterility or total PPV resistance, as well as the correct phenotypic and genotypic validation of plumcots, to avoid the incorrect designation of "plumcots" for plum genotypes that do not actually result from plum × apricot crosses
Notas:
Programa de Doctorado en Recursos y Tecnologías Agrarias, Agroambientales y Alimentarias
Palabras clave/Materias:
Ciruelos
Genética vegetal
Genética molecular
Fenología
Virus vegetales
Tipo de documento :
info:eu-repo/semantics/doctoralThesis
Derechos de acceso:
info:eu-repo/semantics/openAccess
Attribution-NonCommercial-NoDerivatives 4.0 Internacional
Aparece en las colecciones:
Tesis doctorales - Ciencias e Ingenierías



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