14 research outputs found
Some bounds on the Laplacian eigenvalues of token graphs
The -token graph of a graph on vertices is the graph
whose vertices are the -subsets of vertices from , two of
which being adjacent whenever their symmetric difference is a pair of adjacent
vertices in .
It is known that the algebraic connectivity (or second Laplacian eigenvalue)
of equals the algebraic connectivity of .
In this paper, we give some bounds on the (Laplacian) eigenvalues of a
-token graph (including the algebraic connectivity) in terms of the
-token graph, with . For instance, we prove that if is an
eigenvalue of , but not of , then
As a consequence, we conclude that if , then
for every .Comment: arXiv admin note: text overlap with arXiv:2309.0708
On the spectra of token graphs of cycles and other graphs
The -token graph of a graph is the graph whose vertices are
the -subsets of vertices from , two of which being adjacent whenever
their symmetric difference is a pair of adjacent vertices in . It is a known
result that the algebraic connectivity (or second Laplacian eigenvalue) of
equals the algebraic connectivity of .
In this paper, we first give results that relate the algebraic connectivities
of a token graph and the same graph after removing a vertex. Then, we prove the
result on the algebraic connectivity of 2-token graphs for two infinite
families: the odd graphs for all , and the multipartite complete
graphs for all In the case of
cycles, we present a new method that allows us to compute the whole spectrum of
. This method also allows us to obtain closed formulas that give
asymptotically exact approximations for most of the eigenvalues of
An LTR retrotransposon in the promoter of a PsMYB10.2 gene associated with the regulation of fruit f lesh color in Japanese plum
Japanese plums exhibit wide diversity of fruit coloration. The red to black hues are caused by the accumulation of anthocyanins, while their absence results in yellow, orange or green fruits. In Prunus, MYB10 genes are determinants for anthocyanin accumulation. In peach, QTLs for red plant organ traits map in an LG3 region with three MYB10 copies (PpMYB10.1, PpMYB10.2 and PpMYB10.3). In Japanese plum the gene copy number in this region differs with respect to peach: there are at least three copies of PsMYB10.1, with the expression of one of them (PsMYB10.1a) correlating with fruit skin color. The objective of this study was to determine a possible role of LG3-PsMYB10 genes in the natural variability of the f lesh color trait and to develop a molecular marker for marker-assisted selection (MAS). We
explored the variability within the LG3-PsMYB10 region using long-range sequences obtained in previous studies through CRISPR-Cas9 enrichment sequencing. We found that the PsMYB10.2 gene was only expressed in red f lesh fruits. Its role in promoting anthocyanin biosynthesis was validated by transient overexpression in Japanese plum fruits. The analysis of long-range sequences identified an LTR retrotransposon in the promoter of the expressed PsMYB10.2 gene that explained the trait in 93.1% of the 145 individuals analyzed. We hypothesize that the LTR retrotransposon may promote the PsMYB10.2 expression and activate the anthocyanin biosynthesis pathway. We propose for the first time the PsMYB10.2 gene as candidate for the f lesh color natural variation in Japanese plum and provide a
molecular marker for MAS.info:eu-repo/semantics/publishedVersio
On the spectra of token graphs of cycles and other graphs
© 2023 Elsevier. This manuscript version is made available under the CC-BY-NC-ND 4.0 license http://creativecommons.org/licenses/by-nc-nd/4.0/The k-token graph of a graph G is the graph whose vertices are the k-subsets of vertices from G, two of which being adjacent whenever their symmetric difference is a pair of adjacent vertices in G. It is a known result that the algebraic connectivity (or second Laplacian eigenvalue) of equals the algebraic connectivity of G. In this paper, we first give results that relate the algebraic connectivities of a token graph and the same graph after removing a vertex. Then, we prove the result on the algebraic connectivity of 2-token graphs for two infinite families: the odd graphs for all r, and the multipartite complete graphs for all In the case of cycles, we present a new method that allows us to compute the whole spectrum of . This method also allows us to obtain closed formulas that give asymptotically exact approximations for most of the eigenvalues of .Peer ReviewedPostprint (author's final draft
Characterization of Japanese Plum (Prunus salicina) PsMYB10 Alleles Reveals Structural Variation and Polymorphisms Correlating With Fruit Skin Color
The red to blue hue of plant organs is caused due to anthocyanins, which are water-soluble flavonoid pigments. The accumulation of these pigments is regulated by a complex of R2R3-MYB transcription factors (TFs), basic-helix-loop-helix (bHLH), and WD-repeat (WDR) proteins (MBW complex). In Rosaceae species, R2R3-MYBs, particularly MYB10 genes, are responsible for part of the natural variation in anthocyanin colors. Japanese plum cultivars, which are hybrids of Prunus salicina, have high variability in the color hue and pattern, going from yellow-green to red and purple-blue, probably as a result of the interspecific hybridization origin of the crop. Because of such variability, Japanese plum can be considered as an excellent model to study the color determination in Rosaceae fruit tree species. Here, we cloned and characterized the alleles of the PsMYB10 genes in the linkage group LG3 region where quantitative trait loci (QTLs) for the organ color have been mapped to other Prunus species. Allele segregation in biparental populations as well as in a panel of varieties, combined with the whole-genome sequence of two varieties with contrasting fruit color, allowed the organization of the MYB10 alleles into haplotypes. With the help of this strategy, alleles were assigned to genes and at least three copies of PsMYB10.1 were identified in some varieties. In total, we observed six haplotypes, which were able to characterize 91.36% of the cultivars. In addition, two alleles of PsMYB10.1 were found to be highly associated with anthocyanin and anthocyanin-less skin. Their expression during the fruit development confirms their role in the fruit skin coloration. Here, we provide a highly efficient molecular marker for the early selection of colored or non-colored fruits in Japanese plum breeding programs.info:eu-repo/semantics/publishedVersio
Genetic characterization of the Japanese plum LG3-MYB10 region and development of molecular markers for fruit color
Tesis presentada el dÃa 5 de mayo de 2022 para la obtención del tÃtulo de doctor en BiologÃa y Biotecnologia Vegetal por la Universidad Autónoma de Barcelona.[EN] Japanese plum (P. salicina and its hybrids) is a highly heterozygous fruit tree originated by the interspecific hybridization of more than eleven diploid plum species. This event might explain that, within the Rosaceae family, it is one of the crops with the widest fruit color variability. Despite the economic importance of Japanese plum fruits in the fresh market, its marker-assisted breeding is still in its infancy. This applies for the fruit color trait, which influences the consumer acceptance and, consequently, is included within the key breeding objectives. The red to black hues are caused by the accumulation of anthocyanins, pigments synthesized from the flavonoid pathway that have nutraceutical properties. The MYB10 genes are candidates for anthocyanin accumulation in plant organs, and QTLs for red fruit color in Prunus have been mapped in linkage group 3 (LG3) in a region containing three gene copies in peach: PpMYB10. 1, PpMYB10. 2 and PpMYB10. 3. The objective of this thesis is to study the role of the LG3-MYB10 genes in the regulation of fruit color in Japanese plum and provide efficient molecular markers for marker-assisted breeding. To study the allelic variability of the Japanese plum LG3-MYB10 genes (PsMYB10), we used a set of primers designed in conserved sites of the peach PpMYB10 genes by using its genome assembly (Chapter 1). We found one allele (a356) highly associated with the fruit skin color, but none for the flesh. By means of progeny segregation and allele cloning we assigned the alleles into haplotypes and identified a PsMYB10. 1 triplication (Chapter 2). Allele a356 was a PpMYB10. 1 homolog, with allele a470 segregating as an alternative allele, recessive for the locus (PsMYB10. 1a). To sequence the LG3-PsMYB10 region, we used a novel long-read targeted sequencing technology, the CRISPR-Cas9 enrichment followed by Oxford Nanopore Technology sequencing (Chapter 3). Despite the target region was large, highly variable and with several duplicated genes, with our strategy we could extract polymorphisms from the genome alignments against reference genomes and from de novo aligned sequences. All these previous results served to find association of the LG3-MYB10 region with the red flesh color (Chapter 4), identifying a retrotransposon in the PsMYB10. 2 gene correlating with its expression. The gene function was validated by setting up a protocol for its transient overexpression in Japanese plum fruits. The main outputs of this thesis are 1) the development of efficient molecular markers for the fruit skin and flesh colors, 2) the validation of a strategy for the CRISPR-Cas9 enrichment of large and highly variable regions with gene duplications in a pool of samples, applicable in other plant and animal studies, and 3) a protocol for the transient gene overexpression in Japanese plum fruits, applicable for the validation of other candidate genes in the crop.[ES] El ciruelo japonés (P. salicina e hÃbridos) es un árbol frutal altamente heterocigoto, originado a partir de la hibridación interespecÃfica de más de once especies diploides de ciruelo. Este evento explicarÃa que, dentro de la familia de las Rosáceas, es uno de los cultivos con más variabilidad en el color de los frutos. A pesar de la importancia de sus frutos en el mercado, la mejora asistida por marcadores en ciruelo japonés está todavÃa en fase inicial. Esto se aplica al color de fruto, que influye en la aceptación del consumidor y, en consecuencia, es uno de los objetivos clave de mejora. Las tonalidades del rojo al negro son debidas a la acumulación de antocianos, pigmentos sintetizados desde la ruta de los flavonoides que tienen propiedades nutracéuticas. Los genes MYB10 son candidatos para su acumulación en los órganos de las plantas, y QTLs para el color de fruto en Prunus se han mapeado en el grupo de ligamiento 3 (LG3) en una región que contiene tres copias génicas en melocotonero: PpMYB10. 1, PpMYB10. 2 y PpMYB10. 3. El objetivo de esta tesis es estudiar el rol de los genes LG3-MYB10 en la regulación del color de fruto del ciruelo japonés y proporcionar marcadores moleculares eficientes para su mejora asistida por marcadores. Para estudiar la variabilidad alélica de los genes LG3-MYB10 (PsMYB10) en ciruelo japonés, usamos un conjunto de cebadores diseñados en sitios conservados de los genes PpMYB10 de melocotonero usando su genoma (CapÃtulo 1). Encontramos un alelo (a356) altamente asociado con el color de la piel, pero ninguno para la carne. A partir de la segregación y clonaje de los alelos, pudimos asignarlos en haplotipos e identificar una triplicación del gen PsMYB10. 1 (CapÃtulo 2). El alelo a356 era homólogo del PpMYB10. 1 y el a470 segregaba como alternativo, recesivo para el locus (PsMYB10. 1a). Para secuenciar la región LG3-PsMYB10 usamos una reciente tecnologÃa para la secuenciación de regiones concretas de genoma con lecturas largas: el enriquecimiento de secuencias por CRISPR-Cas9 seguido de la secuenciación con tecnologÃa Oxford Nanopore (CapÃtulo 3). A pesar que la región objetivo era larga, altamente variable y con duplicaciones de varios genes, la estrategia permitió extraer polimorfismos a partir de los alineamientos con las secuencias genómicas de referencia y el alineamiento de las secuencias de novo. Estos resultados sirvieron para encontrar asociación de la región LG3-MYB10 con el color rojo de la carne (CapÃtulo 4), identificando un retrotransposón en el gen PsMYB10. 2 correlacionado con su expresión. Su función se validó poniendo a punto un protocolo para su sobreexpresión en ciruelas japonesas. Esta tesis proporciona: 1) marcadores moleculares eficientes para el color de fruto en la piel y carne, 2) la validación de una estrategia para el enriquecimiento de secuencias por CRISPR-Cas9 en regiones altamente variables con duplicaciones génicas en un conjunto de muestras, aplicable a otros estudios en plantas y animales, y 3) un protocolo para la sobreexpresión transitoria de genes en frutos de ciruelo japonés, aplicable para la validación de otros genes candidatos en el cultivo.[FR] La prunera japonesa (P. salicina i hÃbrids) és un arbre fruiter altament heterozigot originat a partir de la hibridació interespecÃfica de més d'onze espècies diploides de pruna. Aquest esdeveniment explicaria que, dintre de la famÃlia de les Rosà cies, és un dels cultius amb més variabilitat en el color dels seus fruits. Malgrat la importà ncia dels seus fruits en el mercat, la millora assistida per marcadors en prunera japonesa està encara en fase inicial. Això s'aplica al color del fruit, que té influència en l'acceptació del consumidor i, en conseqüència, és un dels objectius clau de millora. Les tonalitats del vermell al negre es deuen a l'acumulació d'antocians, pigments sintetitzats des de la ruta dels flavonoides que tenen propietats nutracèutiques. Els gens MYB10 són candidats per la seva acumulació en els òrgans de les plantes, i QTLs pel color de fruit en Prunus s'han mapat en el grup de lligament 3 (LG3) en una regió que conté tres còpies gèniques en presseguer: PpMYB10. 1, PpMYB10. 2 i PpMYB10. 3. L'objectiu d'aquesta tesis és estudiar el rol dels gens LG3-MYB10 en la regulació del color en fruits de prunera japonesa i proporcionar marcadors molecular eficients per la seva millora assistida per marcadors. Per estudiar la variabilitat al·lèlica dels gens LG3-MYB10 (PsMYB10) en prunera japonesa, và rem fer servir un conjunt d'encebadors dissenyats en llocs conservats dels gens PpMYB10 de presseguer fent servir el seu genoma (CapÃtol 1). Và rem trobar un al·lel (a356) altament associat al color de pell, però cap per la carn. A partir de la segregació i clonatge dels al·lels, vam poder assignar-los a haplotips i identificar una triplicació del gen PsMYB10. 1 (CapÃtol 2). L'al·lel a356 era homòleg del PpMYB10. 1 i el a470 segregava com alternatiu, recessiu pel locus (PsMYB10. 1a). Per seqüenciar la regió LG3-MYB10 và rem fer servir una tecnologia recent per la seqüenciació de regions concretes del genoma amb lectures llargues: L'enriquiment de seqüències per CRISPR-Cas9 seguit de la seqüenciació per tecnologia Oxford Nanopore (CapÃtol 3). Malgrat que la regió objectiu era llarga, altament variable i amb duplicacions de varis gens, amb aquesta estratègia vam podem extraure polimorfismes a partir dels alineaments amb les seqüències genòmiques de referència i l'alineament de les seqüències de novo. Tots aquests resultats van servir per trobar associació de la regió LG3-MYB10 amb el color vermell de la carn (CapÃtol 4), identificant un retrotransposó en el gen PsMYB10. 2 correlacionat amb la seva expressió. La seva funció es va validar posant a punt un protocol per la seva sobreexpressió en fruits de prunera japonesa. Aquesta tesis proporciona: 1) marcadors moleculars eficients pel color de fruit de la pell i la carn, 2) la validació d'una estratègia per l'enriquiment de seqüències per CRISPR-Cas9 a regions altament variables amb duplicacions gèniques en un conjunt de mostres, aplicable a altres estudis a plantes i animals, i 3) un protocol per la sobreexpressió transitòria de gens en fruits de prunera japonesa, aplicable per la validació d'altres gen candidats al cultiu
Genetic characterization of the Japanese plum LG3-MYB10 region and development of molecular markers for fruit color
La prunera japonesa (P. salicina i hÃbrids) és un arbre fruiter altament heterozigot originat a partir de la hibridació interespecÃfica de més d'onze espècies diploides de pruna. Aquest esdeveniment explicaria que, dintre de la famÃlia de les Rosà cies, és un dels cultius amb més variabilitat en el color dels seus fruits. Malgrat la importà ncia dels seus fruits en el mercat, la millora assistida per marcadors en prunera japonesa està encara en fase inicial. Això s'aplica al color del fruit, que té influència en l'acceptació del consumidor i, en conseqüència, és un dels objectius clau de millora. Les tonalitats del vermell al negre es deuen a l'acumulació d'antocians, pigments sintetitzats des de la ruta dels flavonoides que tenen propietats nutracèutiques. Els gens MYB10 són candidats per la seva acumulació en els òrgans de les plantes, i QTLs pel color de fruit en Prunus s'han mapat en el grup de lligament 3 (LG3) en una regió que conté tres còpies gèniques en presseguer: PpMYB10.1, PpMYB10.2 i PpMYB10.3. L'objectiu d'aquesta tesis és estudiar el rol dels gens LG3-MYB10 en la regulació del color en fruits de prunera japonesa i proporcionar marcadors molecular eficients per la seva millora assistida per marcadors. Per estudiar la variabilitat al·lèlica dels gens LG3-MYB10 (PsMYB10) en prunera japonesa, và rem fer servir un conjunt d'encebadors dissenyats en llocs conservats dels gens PpMYB10 de presseguer fent servir el seu genoma (CapÃtol 1). Và rem trobar un al·lel (a356) altament associat al color de pell, però cap per la carn. A partir de la segregació i clonatge dels al·lels, vam poder assignar-los a haplotips i identificar una triplicació del gen PsMYB10.1 (CapÃtol 2). L'al·lel a356 era homòleg del PpMYB10.1 i el a470 segregava com alternatiu, recessiu pel locus (PsMYB10.1a). Per seqüenciar la regió LG3-MYB10 và rem fer servir una tecnologia recent per la seqüenciació de regions concretes del genoma amb lectures llargues: L'enriquiment de seqüències per CRISPR-Cas9 seguit de la seqüenciació per tecnologia Oxford Nanopore (CapÃtol 3). Malgrat que la regió objectiu era llarga, altament variable i amb duplicacions de varis gens, amb aquesta estratègia vam podem extraure polimorfismes a partir dels alineaments amb les seqüències genòmiques de referència i l'alineament de les seqüències de novo. Tots aquests resultats van servir per trobar associació de la regió LG3-MYB10 amb el color vermell de la carn (CapÃtol 4), identificant un retrotransposó en el gen PsMYB10.2 correlacionat amb la seva expressió. La seva funció es va validar posant a punt un protocol per la seva sobreexpressió en fruits de prunera japonesa. Aquesta tesis proporciona: 1) marcadors moleculars eficients pel color de fruit de la pell i la carn, 2) la validació d'una estratègia per l'enriquiment de seqüències per CRISPR-Cas9 a regions altament variables amb duplicacions gèniques en un conjunt de mostres, aplicable a altres estudis a plantes i animals, i 3) un protocol per la sobreexpressió transitòria de gens en fruits de prunera japonesa, aplicable per la validació d'altres gen candidats al cultiu.El ciruelo japonés (P. salicina e hÃbridos) es un árbol frutal altamente heterocigoto, originado a partir de la hibridación interespecÃfica de más de once especies diploides de ciruelo. Este evento explicarÃa que, dentro de la familia de las Rosáceas, es uno de los cultivos con más variabilidad en el color de los frutos. A pesar de la importancia de sus frutos en el mercado, la mejora asistida por marcadores en ciruelo japonés está todavÃa en fase inicial. Esto se aplica al color de fruto, que influye en la aceptación del consumidor y, en consecuencia, es uno de los objetivos clave de mejora. Las tonalidades del rojo al negro son debidas a la acumulación de antocianos, pigmentos sintetizados desde la ruta de los flavonoides que tienen propiedades nutracéuticas. Los genes MYB10 son candidatos para su acumulación en los órganos de las plantas, y QTLs para el color de fruto en Prunus se han mapeado en el grupo de ligamiento 3 (LG3) en una región que contiene tres copias génicas en melocotonero: PpMYB10.1, PpMYB10.2 y PpMYB10.3. El objetivo de esta tesis es estudiar el rol de los genes LG3-MYB10 en la regulación del color de fruto del ciruelo japonés y proporcionar marcadores moleculares eficientes para su mejora asistida por marcadores. Para estudiar la variabilidad alélica de los genes LG3-MYB10 (PsMYB10) en ciruelo japonés, usamos un conjunto de cebadores diseñados en sitios conservados de los genes PpMYB10 de melocotonero usando su genoma (CapÃtulo 1). Encontramos un alelo (a356) altamente asociado con el color de la piel, pero ninguno para la carne. A partir de la segregación y clonaje de los alelos, pudimos asignarlos en haplotipos e identificar una triplicación del gen PsMYB10.1 (CapÃtulo 2). El alelo a356 era homólogo del PpMYB10.1 y el a470 segregaba como alternativo, recesivo para el locus (PsMYB10.1a). Para secuenciar la región LG3-PsMYB10 usamos una reciente tecnologÃa para la secuenciación de regiones concretas de genoma con lecturas largas: el enriquecimiento de secuencias por CRISPR-Cas9 seguido de la secuenciación con tecnologÃa Oxford Nanopore (CapÃtulo 3). A pesar que la región objetivo era larga, altamente variable y con duplicaciones de varios genes, la estrategia permitió extraer polimorfismos a partir de los alineamientos con las secuencias genómicas de referencia y el alineamiento de las secuencias de novo. Estos resultados sirvieron para encontrar asociación de la región LG3-MYB10 con el color rojo de la carne (CapÃtulo 4), identificando un retrotransposón en el gen PsMYB10.2 correlacionado con su expresión. Su función se validó poniendo a punto un protocolo para su sobreexpresión en ciruelas japonesas. Esta tesis proporciona: 1) marcadores moleculares eficientes para el color de fruto en la piel y carne, 2) la validación de una estrategia para el enriquecimiento de secuencias por CRISPR-Cas9 en regiones altamente variables con duplicaciones génicas en un conjunto de muestras, aplicable a otros estudios en plantas y animales, y 3) un protocolo para la sobreexpresión transitoria de genes en frutos de ciruelo japonés, aplicable para la validación de otros genes candidatos en el cultivo.Japanese plum (P. salicina and its hybrids) is a highly heterozygous fruit tree originated by the interspecific hybridization of more than eleven diploid plum species. This event might explain that, within the Rosaceae family, it is one of the crops with the widest fruit color variability. Despite the economic importance of Japanese plum fruits in the fresh market, its marker-assisted breeding is still in its infancy. This applies for the fruit color trait, which influences the consumer acceptance and, consequently, is included within the key breeding objectives. The red to black hues are caused by the accumulation of anthocyanins, pigments synthesized from the flavonoid pathway that have nutraceutical properties. The MYB10 genes are candidates for anthocyanin accumulation in plant organs, and QTLs for red fruit color in Prunus have been mapped in linkage group 3 (LG3) in a region containing three gene copies in peach: PpMYB10.1, PpMYB10.2 and PpMYB10.3. The objective of this thesis is to study the role of the LG3-MYB10 genes in the regulation of fruit color in Japanese plum and provide efficient molecular markers for marker-assisted breeding. To study the allelic variability of the Japanese plum LG3-MYB10 genes (PsMYB10), we used a set of primers designed in conserved sites of the peach PpMYB10 genes by using its genome assembly (Chapter 1). We found one allele (a356) highly associated with the fruit skin color, but none for the flesh. By means of progeny segregation and allele cloning we assigned the alleles into haplotypes and identified a PsMYB10.1 triplication (Chapter 2). Allele a356 was a PpMYB10.1 homolog, with allele a470 segregating as an alternative allele, recessive for the locus (PsMYB10.1a). To sequence the LG3-PsMYB10 region, we used a novel long-read targeted sequencing technology, the CRISPR-Cas9 enrichment followed by Oxford Nanopore Technology sequencing (Chapter 3). Despite the target region was large, highly variable and with several duplicated genes, with our strategy we could extract polymorphisms from the genome alignments against reference genomes and from de novo aligned sequences. All these previous results served to find association of the LG3-MYB10 region with the red flesh color (Chapter 4), identifying a retrotransposon in the PsMYB10.2 gene correlating with its expression. The gene function was validated by setting up a protocol for its transient overexpression in Japanese plum fruits. The main outputs of this thesis are 1) the development of efficient molecular markers for the fruit skin and flesh colors, 2) the validation of a strategy for the CRISPR-Cas9 enrichment of large and highly variable regions with gene duplications in a pool of samples, applicable in other plant and animal studies, and 3) a protocol for the transient gene overexpression in Japanese plum fruits, applicable for the validation of other candidate genes in the crop
Development of molecular markers for fruit skin color in Japanese plum (Prunus salicina Lindl.)
Resumen del póster presentado al Congreso 'At the Forefront of Plant Research', celebrado en Barcelona (España) del 6 al 8 de mayo de 2019.Japanese plum is a diploid fruit tree species, member of the Rosaceae family, generated by hybridization of Prunus salicina with diverse Prunus species. Cultivars show great variability for fruit skin and flesh color, which are both major objectives in plum breeding. Subsequently, molecular markers for early selection of these traits in breeding programs are highly desirable. Despite candidate genes for fruit color have been identified in several Rosaceae species, no markers have been described for Japanese plum yet. In Rosaceae family, MYB10 transcription factor has been described as the main gene determining anthocyanin pigment accumulation, which is responsible for red, purple and black coloration. In order to design a useful marker for marker-assisted selection (MAS), we have explored the variability of the MYB10 gene group in Japanese plum
and its association with fruit color. Primers designed in peach (Prunus persica) conserved MYB10 domains were used to genotype a collection of P. salicina cultivars and several progenies. Allele cloning identified 12 MYB10 amplicons. Homology and segregation analysis in progenies allowed assigning some of them to five loci, homologous to the three MYB10 genes located in peach LG3, suggesting the duplication of the MYB10.1 peach gene. Whole genome-resequencing with Illumina technology of two varieties with contrasting phenotypes allowed full gene cloning and detection of polymorphisms. Our data identified one dominant allele associated with anthocyanin accumulation in the skin and two other recessive alleles associate with yellow/green skin phenotypes. Current work is focusing in the design of a marker specifically targeting the associated alleles. This marker will be validated in a wider germplasm collection of commercial varieties and segregating progenies. Future assembly of long-range reads of a red variety will give more insight into the complexity of the region, and will serve for other P.salicina genomic studies.Peer reviewe
Development of molecular markers for fruit color in Japanese plum
Trabajo presentado al Seminario del CRAG (Internal Webinar), celebrado Online el 4 de diciembre de 2020.Peer reviewe
Development of molecular markers for fruit skin color in Japanese plum (Prunus salicina Lindl.)
XV EUCARPIA Symposium on Fruit Breeding and Genetics.Japanese plum is a diploid fruit tree species, member of the Rosaceae family, generated by hybridization of Prunus salicina with diverse Prunus species. Japanese plum cultivars show great variability for fruit skin and flesh color, which are both major objectives in plum breeding. Subsequently, molecular markers for early selection of these traits in breeding programs are highly desirable. Despite candidate genes for fruit color have been identified in several Rosaceae species, no validated markers have been described for Japanese plum yet. In Rosaceae family, MYB10 transcription factor has been described as the main gene determining anthocyanin pigment accumulation in fruits, which is responsible for red, purple and black coloration. In order to design a useful marker for marker-assisted selection (MAS), we have explored the variability of the MYB10 gene group in Japanese plum and its association with fruit color. A set of primers were designed targeting conserved MYB10 domains using sequences from peach genome. Primer combinations were tested using a reduced set of P. salicina accessions. The primer pair amplifying more polymorphic alleles was selected and used to genotype a collection of 78 Japanese plum cultivars. One allele, present in all 51 skin-colored accessions and absent in the rest, was found associated with anthocyanin accumulation. This dominant marker can effectively predict the presence or absence of fruit skin coloration caused by anthocyanin pigments.Peer reviewe