Developing expressed sequence tag libraries and the discovery of simple sequence repeat markers for two species of raspberry (Rubus L.)

Study on Supergenus Rubus L.: Edible, Medicinal, and Phylogenetic Characterization

Rubus L. is one of the most diverse genera belonging to Rosaceae; it consists of more than 700 species with a worldwide distribution. It thus provides an ideal natural "supergenus" for studying the importance of its edible, medicinal, and phylogenetic characteristics for application in our daily lives and fundamental scientific studies. The Rubus genus includes many economically important species, such as blackberry (R. fruticosus L.), red raspberry (R. ideaus L.), black raspberry (R. occidentalis L.), and raspberry (R. chingii Hu), which are widely utilized in the fresh fruit market and the medicinal industry. Although Rubus species have existed in human civilization for hundreds of years, their utilization as fruit and in medicine is still largely inadequate, and many questions on their complex phylogenetic relationships need to be answered. In this review, we briefly summarize the history and progress of studies on Rubus, including its domestication as a source of fresh fruit, its medicinal uses in pharmacology, and its systematic position in the phylogenetic tree. Recent available evidence indicates that (1) thousands of Rubus cultivars were bred via time- and labor-consuming methods from only a few wild species, and new breeding strategies and germplasms were thus limited; (2) many kinds of species in Rubus have been used as medicinal herbs, though only a few species (R. ideaus L., R. chingii Hu, and R. occidentalis L.) have been well studied; (3) the phylogeny of Rubus is very complex, with the main reason for this possibly being the existence of multiple reproductive strategies (apomixis, hybridization, and polyploidization). Our review addresses the utilization of Rubus, summarizing major relevant achievements and proposing core prospects for future application, and thus could serve as a useful roadmap for future elite cultivar breeding and scientific studies.

Basic concepts and methodologies of DNA marker systems in plant molecular breeding

The concepts, methodologies and applications of some of the major molecular or DNA markers commonly used in plant science have been presented. The general principles of molecular marker techniques have been elucidated with detailed explanation of some notable basic concepts associated with marker applications: marker polymorphism, dominant or co-dominant mode of inheritance, agronomic trait-marker linkage, genetic mutations and variation. The molecular marker methods that have been extensively reviewed are RFLP, RAPD, SCAR, AFLP, SSR, CpSSR, ISSR, RAMP, SAMPL, SRAP, SSCP, CAPS, SNP, DArT, EST, and STS. In addition, the practicality of the retrotransposon-based marker methods, IRAP, REMAP, RBIP, and IPBS, have been discussed. Moreover, some salient characteristics of DNA markers have been compared and the various marker systems classified as PCR- or non-PCR-based, dominantly or co-dominantly inherited, locus specific or non-specific as well as at the levels of marker polymorphism and efficiency of marker reproducibility. Furthermore, the principles and methods of the following DNA markers have been highlighted: Penta-primer amplification refractory mutation system (PARMS), Conserved DNA-Derived Polymorphism (CDDP), P450-based analogue (PBA) markers, Tubulin-Based Polymorphism (TBP), Inter-SINE amplified polymorphism (ISAP), Sequence specific amplified polymorphism (S-SAP), Intron length polymorphisms (ILPs), Inter small RNA polymorphism (iSNAP), Direct amplification of length polymorphisms (DALP), Promoter anchored amplified polymorphism (PAAP), Target region amplification polymorphism (TRAP), Conserved region amplification polymorphism (CoRAP), Start Codon Targeted (SCoT) Polymorphism, and Directed Amplification of Minisatellite DNA (DAMD). Some molecular marker applications that have been recently employed to achieve various objectives in plant research have also been outlined. This review will serve as a useful reference resource for plant breeders and other scientists, as well as technicians and students who require basic know-how in the use of molecular or DNA marker technologies.

[Molecular markers in the genetic diversity studies of representatives of the genus Rubus L. and prospects of their application in breeding]

Род Rubus L. (семейство Rosaceae Juss.), по оценкам разных систематиков, состоит из 12–16 подродов, объединяющих ~750 видов. Самые крупные по числу видов подроды – Idaeobatus (Focke) Focke, к которому относятся малины, и типовой подрод Rubus (=Eubatus Focke), включающий виды ежевик. Представители рода Rubus обладают высокой пищевой и хозяйственной ценностью, а также лекарственными свойствами. Селекционные исследования направлены на расширение генетического разнообразия и создание новых сортов малин и ежевик, устойчивых к биотическим и абиотическим стрессорам и отличающихся высоким качеством плодов. Современные селекционно-генетические программы все шире включают достижения молекулярной генетики и геномики. В данной статье представлен обзор фундаментальных и прикладных исследований генетического разнообразия культивируемых и дикорастущих видов рода Rubus, выполненных на основе методов молекулярного маркирования. Рассмотрены основные типы молекулярных маркеров (RFLP, RAPD, SSR, ISSR, AFLP, SCAR, SSCP, ретротранспозонные маркеры и т. д.) и области их применения в изучении представителей рода Rubus. Приведены результаты работ по использованию методов ДНК-маркирования для решения самых разных задач, включая: исследование межвидового и внутривидового генетического разнообразия, филогенетических связей видов и надвидовых таксонов, выяснение спорных вопросов систематики, генотипирование и уточнение родословных сортов малин и ежевик, изучение сомаклональной изменчивости и др. Наиболее важным результатом в практическом плане является создание насыщенных молекулярно-генетических карт для разных видов малин и ежевик, на которых локализованы многочисленные гены и QTL, детерминирующие различные хозяйственно ценные признаки. В то же время необходимо отметить, что число маркеров, перспективных для проведения эффективного молекулярного скрининга, пока еще недостаточно.

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

Strawberry (Fragaria) and raspberry (Rubus) are very popular crops, and improving their nutritional quality and disease resistance are important tasks in their breeding programs that are becoming increasingly based on use of functional DNA markers. We identified 118 microsatellite (simple sequence repeat-SSR) loci in the nucleotide sequences of flavonoid biosynthesis and pathogenesis-related genes and developed 24 SSR markers representing some of these structural and regulatory genes. These markers were used to assess the genetic diversity of 48 Fragaria and Rubus specimens, including wild species and rare cultivars, which differ in berry color, ploidy, and origin. We have demonstrated that a high proportion of the developed markers are transferable within and between Fragaria and Rubus genera and are polymorphic. Transferability and polymorphism of the SSR markers depended on location of their polymerase chain reaction (PCR) primer annealing sites and microsatellite loci in genes, respectively. High polymorphism of the SSR markers in regulatory flavonoid biosynthesis genes suggests their allelic variability that can be potentially associated with differences in flavonoid accumulation and composition. This set of SSR markers may be a useful molecular tool in strawberry and raspberry breeding programs for improvement anthocyanin related traits.

Genetic and genomic resources for Rubus breeding: a roadmap for the future

Rubus fruits are high-value crops that are sought after by consumers for their flavor, visual appeal, and health benefits. To meet this demand, production of red and black raspberries (R. idaeus L. and R. occidentalis L.), blackberries (R. subgenus Rubus), and hybrids, such as Boysenberry and marionberry, is growing worldwide. Rubus breeding programmes are continually striving to improve flavor, texture, machine harvestability, and yield, provide pest and disease resistance, improve storage and processing properties, and optimize fruits and plants for different production and harvest systems. Breeders face numerous challenges, such as polyploidy, the lack of genetic diversity in many of the elite cultivars, and until recently, the relative shortage of genetic and genomic resources available for Rubus. This review will highlight the development of continually improving genetic maps, the identification of Quantitative Trait Loci (QTL)s controlling key traits, draft genomes for red and black raspberry, and efforts to improve gene models. The development of genetic maps and markers, the molecular characterization of wild species and germplasm, and high-throughput genotyping platforms will expedite breeding of improved cultivars. Fully sequenced genomes and accurate gene models facilitate identification of genes underlying traits of interest and enable gene editing technologies such as CRISPR/Cas9.

In silico search, characterization and validation of new EST-SSR markers in the genus Prunus

BACKGROUND

Simple sequence repeats (SSRs) are defined as sequence repeat units between 1 and 6 bp that occur in both coding and non-coding regions abundant in eukaryotic genomes, which may affect the expression of genes. In this study, expressed sequence tags (ESTs) of eight Prunus species were analyzed for in silico mining of EST-SSRs, protein annotation, and open reading frames (ORFs), and the identification of codon repetitions.

RESULTS

A total of 316 SSRs were identified using MISA software. Dinucleotide SSR motifs (26.31 %) were found to be the most abundant type of repeats, followed by tri- (14.58 %), tetra- (0.53 %), and penta- (0.27 %) nucleotide motifs. An attempt was made to design primer pairs for 316 identified SSRs but these were successful for only 175 SSR sequences. The positions of SSRs with respect to ORFs were detected, and annotation of sequences containing SSRs was performed to assign function to each sequence. SSRs were also characterized (in terms of position in the reference genome and associated gene) using the two available Prunus reference genomes (mei and peach). Finally, 38 SSR markers were validated across peach, almond, plum, and apricot genotypes. This validation showed a higher transferability level of EST-SSR developed in P. mume (mei) in comparison with the rest of species analyzed.

CONCLUSIONS

Findings will aid analysis of functionally important molecular markers and facilitate the analysis of genetic diversity.