Analysis of SSR loci information in transcriptome of Sinopodophyllum hexandrum (Royle) Ying by RNA-Seq

Zheng Zhang; Zhenzhen Sui; Mingge Chen; Huanxing Chang; Luyao Yu; Tong Zhang; Dongxue Yin; Wei Liu

doi:10.30848/pjb2022-4(23)

In Silico Analyses of Autophagy-Related Genes in Rapeseed (Brassica napus L.) under Different Abiotic Stresses and in Various Tissues

Plants ◽

10.3390/plants9101393 ◽

2020 ◽

Vol 9 (10) ◽

pp. 1393

Author(s):

Elham Mehri Eshkiki ◽

Zahra Hajiahmadi ◽

Amin Abedi ◽

Mojtaba Kordrostami ◽

Cédric Jacquard

Keyword(s):

Brassica Napus ◽

Abiotic Stresses ◽

Genetic Manipulation ◽

Expression Patterns ◽

Rna Seq ◽

Brassica Napus L ◽

Genome Wide ◽

A Genome ◽

Ssr Loci ◽

Post Transcriptional Regulation

The autophagy-related genes (ATGs) play important roles in plant growth and response to environmental stresses. Brassica napus (B. napus) is among the most important oilseed crops, but ATGs are largely unknown in this species. Therefore, a genome-wide analysis of the B. napus ATG gene family (BnATGs) was performed. One hundred and twenty-seven ATGs were determined due to the B. napus genome, which belongs to 20 main groups. Segmental duplication occurred more than the tandem duplication in BnATGs. Ka/Ks for the most duplicated pair genes were less than one, which indicated that the negative selection occurred to maintain their function during the evolution of B. napus plants. Based on the results, BnATGs are involved in various developmental processes and respond to biotic and abiotic stresses. One hundred and seven miRNA molecules are involved in the post-transcriptional regulation of 41 BnATGs. In general, 127 simple sequence repeat marker (SSR) loci were also detected in BnATGs. Based on the RNA-seq data, the highest expression in root and silique was related to BnVTI12e, while in shoot and seed, it was BnATG8p. The expression patterns of the most BnATGs were significantly up-regulated or down-regulated responding to dehydration, salinity, abscisic acid, and cold. This research provides information that can detect candidate genes for genetic manipulation in B. napus.

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

10.21203/rs.3.rs-65083/v1 ◽

2020 ◽

Author(s):

Maiara Cornacini ◽

Ricardo Oliveira Manoel ◽

Marcelo Alcantara ◽

Mário Moraes ◽

Edvaldo Silva ◽

...

Keyword(s):

Ssr Markers ◽

Tree Species ◽

Natural Populations ◽

Transcriptome Data ◽

Rna Seq ◽

Endangered Tree ◽

Genetic Studies ◽

Endangered Tree Species ◽

Ssr Loci ◽

First Time

Abstract 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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Development of RNA-Seq SSR Markers and Application to Genetic Relationship Analysis among Sea Buckthorn Germplasm

Journal of the American Society for Horticultural Science ◽

10.21273/jashs04021-16 ◽

2017 ◽

Vol 142 (3) ◽

pp. 200-208 ◽

Cited By ~ 3

Author(s):

He Li ◽

Cheng-Jiang Ruan ◽

Li Wang ◽

Jian Ding ◽

Xing-Jun Tian

Keyword(s):

Ssr Markers ◽

Genetic Relationships ◽

Sea Buckthorn ◽

The Other ◽

Group Method ◽

Rna Seq ◽

Arithmetic Average ◽

Relationship Analysis ◽

Pair Group ◽

Ssr Loci

Sea buckthorn (Hippophae rhamnoides) is an ecologically and economically valuable species that has been widely cultivated as a new berry crop rich in nutritional and medicinal compounds. RNA Sequencing (RNA-Seq) simple sequence repeat (SSR) markers were developed to evaluate the genetic relationships among 91 plants of 31 cultivars from two subspecies, mongolica and sinensis, as well as intraspecific hybrids between them. A total of 7540 RNA-Seq SSRs were identified as potential molecular markers, in which AG/CT (27.57%) was the most abundant unit type. AT/AT (9.93%), and AAG/CTT (11.95%) are the other main repeat motifs. A total of 110 primer pairs were randomly selected for validation of amplification. Seventeen SSR loci, located in genes encoding metabolic processes and cellulose synthases, were identified to be polymorphic among different sea buckthorn cultivars. These SSR loci generated 48 alleles, ranging from 2 to 5 per locus. Cluster analysis based on the proportion of shared alleles and unweighted pair group method with arithmetic average (UPGMA) algorithm divided all the genotypes into two main groups, with all of the ssp. sinensis cultivars (native to China) and hybrids in one group and ssp. mongolica cultivars (introduced from Russia) in the other group, which was in good agreement with their taxonomic classification. The RNA-Seq SSRs developed in this study have a potential use in the conservation of sea buckthorn germplasm and marker-assisted breeding (MAB).

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A Novel Software and Method for the Efficient Development of Polymorphic SSR Loci Based on Transcriptome Data

Genes ◽

10.3390/genes10110917 ◽

2019 ◽

Vol 10 (11) ◽

pp. 917

Author(s):

Ruizheng Tian ◽

Cunhuan Zhang ◽

Yixiao Huang ◽

Xin Guo ◽

Maohua Chen

Keyword(s):

Expressed Sequence Tag ◽

The Body ◽

Pea Aphid ◽

New Method ◽

Transcriptome Data ◽

Rna Seq ◽

Ssr Loci ◽

Polymorphic Microsatellite ◽

Expressed Sequence ◽

Simple Sequence

Traditional methods for developing polymorphic microsatellite loci without reference sequences are time-consuming and labor-intensive, and the polymorphisms of simple sequence repeat (SSR) loci developed from expressed sequence tag (EST) databases are generally poor. To address this issue, in this study, we developed a new software (PSSRdt) and established an effective method for directly obtaining polymorphism details of SSR loci by analyzing diverse transcriptome data. The new method includes three steps, raw data processing, PSSRdt application, and loci extraction and verification. To test the practicality of the method, we successfully obtained 1940 potential polymorphic SSRs from the transcript dataset combined with 44 pea aphid transcriptomes. Fifty-two SSR loci obtained by the new method were selected for validating the polymorphic characteristics by genotyping in pea aphid individuals. The results showed that over 92% of SSR loci were polymorphic and 73.1% of loci were highly polymorphic. Our new software and method provide an innovative approach to microsatellite development based on RNA-seq data, and open a new path for the rapid mining of numerous loci with polymorphism to add to the body of research on microsatellites.

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