Genetic structure based on EST–SSR: a putative tool for fruit color selection in Japanese plum (Prunus salicina L.) breeding programs

Abstract

Prunus salicina is one of the most economically important stone fruits. However, there is scarce genetic information available, which makes it difficult to implement marker-assisted selection (MAS) in genetic improvement programs. Recently, next-generation sequencing has greatly enhanced breeding program strategies, generating information associated with the identification of expressed sequence tag-simple sequence repeats (EST-SSRs) and single-nucleotide polymorphisms (SNPs), two of the most used molecular markers in MAS. Few studies have focused on developing EST-SSR markers considering both gene expression levels of contrasting phenotypes and specific transcription factors of metabolic pathways. This study investigated the transcriptome profile of P. salicina in fruits with contrasting skin colors, obtaining 54,224 unique contigs. From this dataset, 44 EST-SSRs have been generated, considering gene expression levels of contrasting phenotypes and specific transcription factor from three metabolic pathways: citric acid, carbohydrate metabolism and flavonoid pathways. Three EST-SSR markers developed from the putative flavonoid pathway transcription factors PsMYB10, PsMYB1 and PsbHLH35 were selected to determine genetic structure in 29 cultivars. This structure was contrasted with the genetic structure generated using genomic SNPs obtained by genotyping-by-sequencing (GBS). The analysis using SNPs identified two groups, while the use of selected EST-SSRs identified three. In contrast to the structure given by the SNPs, the EST-SSRs grouped all the yellow cultivars in one cluster, which was composed mainly of cultivars of this color. The EST-SSRs developed in this study may be considered as candidate markers to be evaluated in MAS strategies in genetic improvement programs.Comision Nacional de Investigacion Cientifica y Tecnologica, CONICYT Doctorado en Chile 21090118 Apoyo a la Tesis Doctoral 24110179 Tesis en la Industria 781211008 FONDECYT 1120261 Consorcio Tecnologico de Industria Hortofruticula S.A. Fondo Instituto de Investigaciones Agropecuarias-Ministerio de Agricultura (INIA-MINAGRI) Project 501453-7

Transferability and Polymorphism of SSR Markers Located in Flavonoid Pathway Genes in Fragaria and Rubus Species

“…A relatively high proportion of hexanucleotide SSRs was also in exons (33%). The nucleotide distribution was approximately equal in the exons (21,24,26, and 28% for T, G, A, and C, respectively), while in NCDS T (46%) and A (34%) prevailed over C (12%) and G (8%). Table 2.…”

“…The SSR markers in the TF gene in plants were first developed by Kujur et al [73], which showed the influence of the SSR polymorphism on secondary structure of proteins and on such traits as seed weight and number of pods and seeds. Since then, there have been few similar studies in Rosaceae where similar markers have been developed for Japanese plum [24], but no such markers have been reported for Rubus and Fragaria before our first study, where we developed a SSR marker representing the RiMYB10 TF gene, an activator of transcription of flavonoid biosynthesis [23]. The association between the MYB10 gene and fruit color has been demonstrated for apple [45] and peach [74].…”

“…The association between the MYB10 gene and fruit color has been demonstrated for apple [45] and peach [74]. Gonzalez et al [24] found three allele variants in the EST-SSRs designed for the PsMYB10 TF gene. In our study of 21 varieties of red and black raspberries presented here, we showed that the RiMY01 marker representing the R. idaeus MYB10 gene had a significantly greater polymorphism compared to six markers representing structural genes of flavonoid biosynthesis-9 vs. 2-4 alleles per locus and PIC of 0.82 vs. 0.05-0.35 [23].…”

“…Many MAS studies are aimed at developing markers representing key genes, but only few studies have focused on the developing markers representing structural and regulatory genes of metabolic pathways in cultivars with contrasting phenotypic traits of interest [24]. We are especially interested in developing SSR markers representing flavonoid pathway genes because the main polyphenols in fruits are flavonoids ( Figure 1).…”

Genome-wide SNP identification in Prunus rootstocks germplasm collections using Genotyping-by-Sequencing: phylogenetic analysis, distribution of SNPs and prediction of their effect on gene function

“…In Prunus species, single-digest GBS has been used for identification of a high number of SNPs for linkage maps construction [32][33][34][35] and analysis of population genetic structure [36][37][38] . The use of double-digest GBS in Prunus has not been reported as far as the authors know.…”