Comparative analysis of SSR markers developed in Exon, Intron, and Intergenic regions and distributed in regions controlling fruit quality traits in Prunus species: genetic diversity and association studies
Author
dc.contributor.author
García Gómez, Beatriz
Author
dc.contributor.author
Razi, Mitra
Author
dc.contributor.author
Salazar, Juan A.
Author
dc.contributor.author
Prudencio, Angela S.
Author
dc.contributor.author
Ruiz, David
Author
dc.contributor.author
Dondini, Luca
Author
dc.contributor.author
Martínez Gómez, Pedro
Admission date
dc.date.accessioned
2018-07-31T15:03:22Z
Available date
dc.date.available
2018-07-31T15:03:22Z
Publication date
dc.date.issued
2018
Cita de ítem
dc.identifier.citation
Plant Molecular Biology Reporter (2018) 36:23–35
es_ES
Identifier
dc.identifier.other
10.1007/s11105-017-1058-7
Identifier
dc.identifier.uri
https://repositorio.uchile.cl/handle/2250/150478
Abstract
dc.description.abstract
Simple sequence repeats (SSRs) are genome domains located in both coding and non-coding regions in eukaryotic genomes. Although SSRs are often characterized by low polymorphism, their DNA-flanking sequences could be a useful source of DNA markers, which could help in genetic studies and breeding because they are associated with genes that control traits of interest. In this study, 56 genotypes from different Prunus species were used, including peach, apricot, plum, and almond (already phenotyped for several agronomical traits, including self-compatibility, flowering and ripening time, fruit type, skin and flesh color, and shell hardness). These Prunus genotypes were molecularly characterized using 28 SSR markers developed in exons, introns, and intergenic regions. All these genes were located in specific regions where quantitative trait loci (QTLs) for certain fruit quality traits were also located, including flowering and ripening times and fruit flesh and skin color. A sum of 309 SSR alleles were identified in the whole panel of analyzed cultivars, with expected heterozygosity values of 0.61 (upstream SSRs), 0.17 (exonic SSRs), 0.65 (intronic SSRs), and 0.58 (downstream SSRs). These values prove the low level of polymorphism of the exonic (gene-coding regions) markers. Cluster and structural analysis based on SSR data clearly differentiated the genotypes according to either specie (for the four species) and pedigree (apricot) or geographic origin (Japanese plum). In addition, some SSR markers mainly developed in intergenic regions could be associated with genes that control traits of interest in breeding and could therefore help in marker-assisted breeding. These findings highlight the importance of using molecular markers able to discriminate between the functional roles of the gene allelic variants.
es_ES
Patrocinador
dc.description.sponsorship
University of Zajan
Chilean government (FONDECYT)
3160080
"Apricot breeding" project of the Spanish Ministry of Economy and Competiveness
AGL2013-41452-R
Seneca Foundation of the Region of Murcia
19879/GERM/15
Comparative analysis of SSR markers developed in Exon, Intron, and Intergenic regions and distributed in regions controlling fruit quality traits in Prunus species: genetic diversity and association studies