Development and Characterization of EST-SSR Markers From RNA-Seq Data in Phyllostachys violascens

Cai, Kaiyong; Zhu, Longfei; Zhang, Keke; Li, Ling; Zhao, Zhongyu; Zeng, Wei; Lin, Xinchun

doi:10.3389/fpls.2019.00050

Cited by 52 publications

(31 citation statements)

References 44 publications

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“…3). These frequencies of AG/CT repeats are higher than found for other species such bamboo (17.11%) [12], but less than for Magnolia (37.8%) [11]. High frequencies of AG repeats are also reported for other plant species being suggested that could be related to mutation mechanism of generation of SSRs or selective pressure to particular sequences [9,10,11,13,14].…”

Section: Discussionmentioning

confidence: 60%

Discovery of novel SSR markers from transcriptome data of Astronium fraxinifolium Schott, a threatened tree species in Brazil

Cornacini¹,

Manoel²,

Alcântara³

et al. 2020

Preprint

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Background Astronium fraxinifolium is an endangered tree species from Brazil. Due to its high importance for environmental reforestation, as well as for the use of its wood, it is necessary to implement management programs for conservation of this species. Simple sequence repeats (SSR) or microsatellite markers have been widely used in population genetic studies across diverse organisms. In this study, we reported for the first time SSR markers for A. fraxinifolium as well as its frequency and distribution from transcriptome data. Results More than 125 thousand RNA-seq sequences derived microsatellites, with predominant distribution of trinucleotides repeats. From the initial screening, we selected 20 microsatellite loci, validated and evaluated genetic indexes in two natural populations. All loci were polymorphic, ranging from four to eleven alleles per locus. The observed and expected heterozygosities ranged from 0 to 1.0 and from 0.533 to 1.0, respectively. Genetic differentiation between populations (= 0.363) showed higher diversity within than among populations. Conclusions The developed SSR loci from RNA-seq consists in a base for future studies of genetic diversity and population structure, mating system and gene flow in A. fraxinifolium populations as well as related species, aiming the conservation and management of the species.

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Section: Discussionmentioning

confidence: 60%

Discovery of novel SSR markers from transcriptome data of Astronium fraxinifolium Schott, a threatened tree species in Brazil

Cornacini¹,

Manoel²,

Alcântara³

et al. 2020

Preprint

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“…Similar in silico approaches in EST-SSR marker development were performed by other studies focusing on other plants, such as bamboo (Cai et al, 2019), mint (Kumar et al, 2015), castor (Thatikunta et al, 2016), Ethiopian potato (Gadissa et al, 2018) and Elymus species (Zhang et al, 2019). The EST-derived SSR markers generated in this study can be used for functional analysis of R genes, once verified by wet lab experiments.…”

Section: Resultsmentioning

confidence: 91%

Transcriptome-wide analysis of expressed resistance gene analogs (RGAs) in mango

Lantican

Cortaga

Manohar

et al. 2020

Preprint

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10Plants have developed mechanisms to recognize pathogen and insect attacks and to 11 activate defense response against them through the action of resistance genes (R genes). 12Hence, R gene analogs (RGAs) have been widely studied and efficiently used for breeding of 13 resistant crops. Mango is an economic fruit crop largely cultivated in the (sub)tropics and thus, 14 is constantly challenged by a myriad of insect pests and diseases. RGAs of mango from 15 different varieties were identified and characterized via de novo assembly of raw transcriptome 16 sequences currently available in biological repositories. Using bioinformatics pipelines, a core 17 RGA database of mango with 747 protein models was established and were classified based 18 on their conserved domains and motifs: 53 nucleotide binding site protein (NBS); 27 nucleotide 19 binding site-leucine rich repeat proteins (NBS-LRR); 17 coiled-coil NBS-LRR (CNL); 2 20 toll/interleukin-1 receptor NBS-LRR (TNL); 29 coiled-coil NBS (CN); 4 toll/interleukin-1 21 receptor NBS (TN); 17 toll/interleukin-1 receptor with unknown domain (TX); 158 receptor-like 22 proteins (RLP); 362 receptor-like kinases (RLK); 72 transmembrane coiled-coil domain protein 23 (TM-CC), and 6 NBS-encoding proteins with other domains. Phylogenetic analysis broadly 24 clustered the core RGAs into 6 major clades based on their domain classification, while TM- 25CC formed subclades all across the tree. The phylogenetic results suggest highly divergent 26 functions of the RGAs which also provide insights into the mango-pest co-evolutionary arms 27 race. The various molecular functions, biological processes, and cellular localizations of these RGAs were functionally well-annotated through gene ontology (GO) analysis, and their 29 expression profiles across different mango varieties were also determined. From the mango 30 RGA transcripts, 134 unique EST-SSRs loci were identified, and primers were designed 31 targeting these potential markers. To date, this is the most comprehensive analysis of mango 32 RGAs which offer a trove of markers for direct utilization in resistance breeding of mango. 33 34 35 36 Introduction 37 Mango (Mangifera indica L.) is a globally popular fruit crop with economical and 38 agricultural significance, especially in the (sub)tropics where it is largely cultivated. One of the 39 constraints in mango production worldwide include a myriad of insect pests (e.g., oriental fruit 40 fly, mango hopper, cecid fly, etc.) and diseases, (e.g., anthracnose, stem-end rot, scab, etc.) 41 which can affect mango at different life stages thus significantly reducing fruit quality and yield 42 (Bally, 2006). These are major barriers to the export market and can impede international 43 trade as many pests and diseases in mango are important quarantine considerations. 44 Along the course of evolution, plants have generally developed mechanisms to 45 recognize pathogen and insect attacks and to activate defense response against them (Dangl 46 and Jones., 2001; Acevedo et al., 2015). The mole...

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“…Deep transcriptome sequencing, which generates quantities of data exponentially, provides comprehensive information and good resources for developing new SSR markers and identifying novel genes [38][39][40]. Currently, a plenty of SSR markers, based on transcriptome sequences, have been successfully developed and used for functional variation detection and gene-related genetic analysis in many organisms, accelerating progress in MAS breedings [41][42][43]. In this study, we rst reported the SSR markers of S. oblata basing transcriptome sequences generated via NGS technologies.…”

Section: Discussionmentioning

confidence: 99%

Development of EST-SSR Markers and Association Mapping with Floral Traits in Syringa oblata

Yang

Zheng

et al. 2020

Preprint

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Background Syringa oblata is an important woody plant with high ornamental value. However, very limited genetic marker resources are currently available, and little is known about the genetic architecture of important ornamental traits for S. oblata , which is hindering its genetic studies. Therefore, it is of great significance to develop effective molecular markers and understand the genetic architecture of complex floral traits for the genetic research of S. oblata . Results In this study, a total of 10,988 SSRs were obtained from 9,864 unigene sequences with an average of one SSR per 8.13 kb, of which di-nucleotide repeats were the dominant type (32.86%, 3,611). A set of 2,042 primer pairs were validated, out of which 932 (45.7%) exhibited successful amplifications, and 248 (12.1%) were polymorphic in eight S. oblata individuals. In addition, 30 polymorphic EST-SSR markers were further used to assess the genetic diversity and the population structure of 192 cultivated S. oblata individuals. 234 alleles were detected, and the PIC values ranged from 0.23 to 0.88 with an average of 0.51, indicating a high level of genetic diversity within this cultivated population. The analysis of population structure showed two major subgroups in the association population. Finally, 20 significant associations were identified involving 17 markers with 9 floral traits using the mixed linear model. Moreover, marker SO104, SO695 and SO790 had significant relationship with more than one trait. Conclusion The results showed newly developed markers were valuable resource and provided powerful tools for genetic breeding of lilac. Beyond that, our study could serve an efficient foundation for further facilitate genetic improvement of ﬂoral traits for lilac.

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Development and Characterization of EST-SSR Markers From RNA-Seq Data in Phyllostachys violascens

Cited by 52 publications

References 44 publications

Discovery of novel SSR markers from transcriptome data of Astronium fraxinifolium Schott, a threatened tree species in Brazil

Discovery of novel SSR markers from transcriptome data of Astronium fraxinifolium Schott, a threatened tree species in Brazil

Transcriptome-wide analysis of expressed resistance gene analogs (RGAs) in mango

Development of EST-SSR Markers and Association Mapping with Floral Traits in Syringa oblata

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