De novo assembly, annotation, marker discovery, and genetic diversity of the Stipa breviflora Griseb. (Poaceae) response to grazing

Grassland is one of the most widely-distributed ecosystems on Earth and provides a variety of ecosystem services. Grasslands, however, currently suffer from severe degradation induced by human activities, overgrazing pressure and climate change. In the present study, we explored the transcriptome response of Stipa breviflora, a dominant species in the desert steppe, to grazing through transcriptome sequencing, the development of simple sequence repeat (SSR) markers, and analysis of genetic diversity. De novo assembly produced 111,018 unigenes, of which 88,164 (79.41%) unigenes were annotated. A total of 686 unigenes showed significantly different expression under grazing, including 304 and 382 that were upregulated and downregulated, respectively. These differentially expressed genes (DEGs) were significantly enriched in the “alpha-linolenic acid metabolism” and “plant-pathogen interaction” pathways. Based on transcriptome sequencing data, we developed eight SSR molecular markers and investigated the genetic diversity of S. breviflora in grazed and ungrazed sites. We found that a relatively high level of S. breviflora genetic diversity occurred under grazing. The findings of genes that improve resistance to grazing are helpful for the restoration, conservation, and management of desert steppe.

Download Full-text

Microsatellites characteristics analysis and SSR marker development for Paphiopedilum hirsutissimum based on transcriptome sequencing

Plant Genetic Resources ◽

10.1017/s1479262117000375 ◽

2018 ◽

Vol 16 (4) ◽

pp. 394-396 ◽

Cited By ~ 1

Author(s):

Lin Chen ◽

Hui Dong ◽

Jianwen Wang ◽

Longna Li ◽

Meng Xu

Keyword(s):

Ssr Markers ◽

Transcriptome Sequencing ◽

De Novo ◽

Average Density ◽

Conservation Strategy ◽

Distribution Centre ◽

Characteristics Analysis ◽

Primer Sets ◽

High Level ◽

Simple Sequence

AbstractPaphiopedilum hirsutissimum (Lindl. ex Hook. f.) Stein (Orchidaceae) is a valuable but endangered ornamental plant. In the present study, the microsatellites characteristics were analysed and 14 polymorphic simple sequence repeat (SSR) markers were developed based on the de novo transcriptome sequencing for P. hirsutissimum using Illumina pair-end sequencing technology. A total of 7406 SSRs were detected in 56,688 unigenes, with the occurrence frequency of 13.06% and an average density of one SSR per 5.42 kb; and 150 primer pairs randomly selected from 2090 pairs except mononucleotide repeats were synthesized for verification. These loci were validated in 32 individuals from the concentrated distribution centre, and were successfully amplified using 14 primer sets showing a high level of polymorphism. These SSR markers will be useful in future studies of genetic diversity, the population structure of P. hirsutissimum and make effective conservation strategy.

Download Full-text

Simple Sequence Repeat Marker Analysis of Genetic Diversity among Progeny of a Biparental Mapping Population of Sweetpotato

HortScience ◽

10.21273/hortsci.50.8.1143 ◽

2015 ◽

Vol 50 (8) ◽

pp. 1143-1147 ◽

Cited By ~ 8

Author(s):

Benard Yada ◽

Gina Brown-Guedira ◽

Agnes Alajo ◽

Gorrettie N. Ssemakula ◽

Robert O.M. Mwanga ◽

...

Keyword(s):

Genetic Diversity ◽

Linkage Analysis ◽

Ssr Markers ◽

Simple Sequence Repeat ◽

Polymorphic Information Content ◽

Genetic Distances ◽

Sequence Repeat ◽

Population Improvement ◽

High Level ◽

Simple Sequence

Genetic diversity is critical in sweetpotato improvement as it is the source of genes for desired genetic gains. Knowledge of the level of genetic diversity in a segregating family contributes to our understanding of the genetic diversity present in crosses and helps breeders to make selections for population improvement and cultivar release. Simple sequence repeat (SSR) markers have become widely used markers for diversity and linkage analysis in plants. In this study, we screened 405 sweetpotato SSR markers for polymorphism on the parents and progeny of a biparental cross of New Kawogo × Beauregard cultivars. Thereafter, we used the informative markers to analyze the diversity in this population. A total of 250 markers were polymorphic on the parents and selected progeny; of these, 133 were informative and used for diversity analysis. The polymorphic information content (PIC) values of the 133 markers ranged from 0.1 to 0.9 with an average of 0.7, an indication of high level of informativeness. The pairwise genetic distances among the progeny and parents ranged from 0.2 to 0.9, and they were grouped into five main clusters. The 133 SSR primers were informative and are recommended for use in sweetpotato diversity and linkage analysis.

Download Full-text

Genome-wide identification of SSR markers in the Brassica A genome and their utility in breeding

Canadian Journal of Plant Science ◽

10.1139/cjps-2015-0250 ◽

2016 ◽

Vol 96 (5) ◽

pp. 808-818 ◽

Cited By ~ 4

Author(s):

Neil Hobson ◽

Habibur Rahman

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Low Cost ◽

Pak Choi ◽

Genome Wide ◽

A Genome ◽

Wide Range ◽

Genetic Pools ◽

High Level ◽

Simple Sequence

Simple sequence repeat (SSR) markers can be applied to genotyping projects at low cost with inexpensive equipment. The objective of this study was to develop SSR markers from the publically-available genome sequence of Brassica rapa and provide the physical position of these markers on the chromosomes for use in breeding and research. To assess the utility of these new markers, a subset of 60 markers were used to genotype 43 accessions of B. rapa. Fifty-five markers from the 10 chromosome scaffolds produced a total of 730 amplicons, which were then used to perform a phylogenetic analysis of the accessions, illustrating their utility in distinguishing between a wide range of germplasm. In agreement with similar studies of genetic diversity, our markers separated accessions into distinct genetic pools including Chinese cabbage, Chinese winter oilseed, European winter oilseed, Canadian spring oilseed, pak-choi, turnip, and yellow sarson. The results further illustrate the presence of a high level of genetic diversity in B. rapa, and demonstrate the potential of these SSR markers for use in breeding and research.

Download Full-text

Analysis of genetic diversity of Ficus carica L. (Moraceae) collection using simple sequence repeat (SSR) markers

Acta Scientiarum Polonorum Hortorum Cultus ◽

10.24326/asphc.2019.4.9 ◽

2019 ◽

Vol 18 (4) ◽

pp. 93-109

Author(s):

Ilaria Marcotuli ◽

Andrea Mazzeo ◽

Domenica Nigro ◽

Stefania Lucia Giove ◽

Angelica Giancaspro ◽

...

Keyword(s):

Genetic Diversity ◽

Ficus Carica ◽

Accurate Information ◽

Main Crop ◽

Polymorphic Pattern ◽

Genetic Diversity And Structure ◽

The Mean ◽

High Level ◽

Simple Sequence ◽

Modern Technologies

Modern technologies and accurate information on genetic diversity and structure are contributing to improve the plant breeding, in particular for all the minor species with a lack of data. Genetic diversity of 139 different Ficus carica L. genotypes collected from Italy and Croatia, and divided into two subgroups: uniferous (only main crop) and biferous (breba and main crop), was investigated using 49 microsatellite markers. A total of 70 alleles were generated, of which 64 (91.4%) showed a polymorphic pattern indicating high level of genetic diversity within the studied collection. The mean heterozygosity over the 64 single locus microsatellites was 0.33 and the expected and observed averaged variance were 16.50 and 184.08, respectively. The 139 fig genotypes formed two clusters in the PCoA analysis, suggesting a division between Italian and Croatian genotypes. Moreover, the fig accessions could be divided into two main clusters based on the STRUCTURE analysis according to the biological type, uniferous or biferous, with partly overlapping varieties. In conclusion, our results demonstrated that molecular markers were able to discriminate among genotypes and useful for the authentication of fig tree varieties (homonymies and synonymies).

Download Full-text

De novo assembly and transcriptome characterization of an endemic species of Vietnam, Panax vietnamensis Ha et Grushv., including the development of EST-SSR markers for population genetics

10.21203/rs.2.18797/v4 ◽

2020 ◽

Author(s):

Duy Dinh Vu ◽

Syed Noor Muhammad Shah ◽

Mai Phuong Pham ◽

Van Thang Bui ◽

Minh Tam Nguyen ◽

...

Keyword(s):

Genetic Diversity ◽

Endangered Species ◽

De Novo ◽

Average Length ◽

Species Conservation ◽

Illumina Hiseq ◽

Bottleneck Analysis ◽

Genetic Diversity And Structure ◽

Geographical Distances ◽

High Level

Abstract Background: Understanding the genetic diversity in endangered species that occur in forest remnants is necessary to establish efficient strategies for the species conservation, restoration and management. Panax vietnamensis Ha et Grushv. is medicinally important, endemic and endangered species of Vietnam. However, genetic diversity and structure of population are unknown due to lack of efficient molecular markers. Results: In this study, we employed Illumina HiSeqTM 4000 sequencing to analyze the transcriptomes of P. vietnamensis (roots, leaves and stems). Raw reads total of 23,741,783 was obtained and then assembled, from which the generated unigenes were 89,271 (average length = 598.3191 nt). The 31,686 unigenes were annotated in different databases i.e. Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, Nucleotide Collection (NR/NT) and Swiss-Prot for functional annotation. Further, 11,343 EST-SSRs were detected. From 7,774 primer pairs, 101 were selected for polymorphism validation, in which; 20 primer pairs were successfully amplified to DNA fragments and significant amounts of polymorphism was observed within population. The nine polymorphic microsatellite loci were used for population structure and diversity analyses. The obtained results revealed high levels of genetic diversity in populations, the average observed and expected heterozygosity were HO = 0.422 and HE = 0.479, respectively. During the Bottleneck analysis using TPM and SMM models (p < 0.01) shows that targeted population is significantly heterozygote deficient. This suggests sign of the bottleneck in all populations. Genetic differentiation between populations was moderate (FST = 0.133) and indicating slightly high level of gene flow (Nm = 1.63). Analysis of molecular variance (AMOVA) showed 63.17% of variation within individuals and 12.45% among populations. Our results shows two genetic clusters related to geographical distances. Conclusion: Our study will assist conservators in future conservation management, breeding, production and habitats restoration of the species.

Download Full-text

Simple Sequence Repeat (SSR) Polymorphisms and Population Genetics in Sichuan Wild Rhesus Macaques

Advanced Materials Research ◽

10.4028/www.scientific.net/amr.343-344.690 ◽

2011 ◽

Vol 343-344 ◽

pp. 690-697

Author(s):

Di Yan Li ◽

Yong Fang Yao ◽

Xiao Feng Huang ◽

An Chun Cheng ◽

Huai Liang Xu ◽

...

Keyword(s):

Genetic Diversity ◽

Polymorphic Information Content ◽

Rhesus Macaques ◽

Genetic Management ◽

Future Studies ◽

Ssr Loci ◽

Different Populations ◽

Polymerase Chain ◽

High Level ◽

Simple Sequence

Cross-species amplification of twenty-five SSR loci from the DNA of five rhesus macaques of diverse regional origins was conducted using human primers for the polymerase chain reaction (PCR). Seven of these primer pairs, which consistently and unambiguously amplified polymorphic fragments from these five samples, were also used to amplify SSR loci for 111 Sichuan wild rhesus macaques of five different populations. The analysed microsatellite markers produced 109 alleles, varied from 4 to 16 alleles each locus. The number of alleles per population ranged from 6.79 to 11.38. Polymorphic information content showed that all seven loci were highly informative (mean = 0.9017±0.0166, >0.5). The average observed heterozygosity was less than the expected (mean = 0.6795 and mean = 0.8559, respectively). Genetic differentiation among the populations was considerably low with the overall and pairwise FST values (mean = 0.0375), and showed fairly low level of inbreeding (indicated by a mean FIS value of 0. 0.1991). Maintaining genetic diversity is a major issue in conservation biology. In comparison to other captive Macaca mulatta studies, these wild rhesus macaque populations showed a relatively high level of genetic diversity, and there was low gene flow among these populations. Careful genetic management is important for maintaining genetic variability levels. None of the seven informative loci are linked which screened in this study can be applied in future studies on population and conservation genetics of natural primate populations.

Download Full-text

A de novo Transcriptome Assembly of the European Flounder (Platichthys flesus): The Preselection of Transcripts Encoding Active Forms of Enzymes

Frontiers in Marine Science ◽

10.3389/fmars.2021.618779 ◽

2021 ◽

Vol 8 ◽

Author(s):

Konrad Pomianowski ◽

Artur Burzyński ◽

Ewa Kulczykowska

Keyword(s):

De Novo ◽

Transcriptome Assembly ◽

Head Kidney ◽

Sequencing Data ◽

Mrna Isoforms ◽

Protein Database ◽

Next Generation Sequencing Technology ◽

Platichthys Flesus ◽

European Flounder ◽

High Level

The RNA sequencing data sets available for different fish species show a potentially high variety of forms of enzymes just in teleosts. This is primarily considered an effect of the first round of whole-genome duplication with mutations in duplicated genes (isozymes) and alternative splicing of mRNA (isoforms). However, the abundance of the mRNA transcript variants is not necessarily reflected in the abundance of active forms of proteins. We have investigated the transcriptional profiles of two enzymes, aralkylamine N-acetyltransferase (AANAT: EC 2.3.1.87) and N-acetylserotonin O-methyltransferase (ASMT: EC 2.1.1.4), in the eyeball, brain, intestines, spleen, heart, liver, head kidney, gonads, and skin of the European flounder (Platichthys flesus). High-throughput next-generation sequencing technology NovaSeq6000 was used to generate 500M sequencing reads. These were then assembled and filtered producing 75k reliable contigs. Gene ontology (GO) terms were assigned to the majority of annotated contigs/unigenes based on the results of PFAM, PANTHER, UniProt, and InterPro protein database searches. BUSCOs statistics for metazoa, vertebrata, and actinopterygii databases showed that the reported transcriptome represents a high level of completeness. In this article, we show how to preselect transcripts encoding the active enzymes (isozymes or isoforms), using AANAT and ASMT in the European flounder as the examples. The data can be used as a tool to design the experiments as well as a basis for discussion of diversity of enzyme forms and their physiological relevance in teleosts.

Download Full-text

Transcriptome Sequencing of the Endangered Species Elongate Loach (Leptobotia elongata) From the Yangtze River: De novo Transcriptome Assembly, Annotation, Identification and Validation of EST-SSR Markers

Frontiers in Marine Science ◽

10.3389/fmars.2021.616727 ◽

2021 ◽

Vol 8 ◽

Author(s):

Yunbang Zhang ◽

Jian Gao ◽

Yunhai Zhang ◽

Yuanchao Zou ◽

Xiaojuan Cao

Keyword(s):

Endangered Species ◽

Genetic Information ◽

Transcriptome Sequencing ◽

Yangtze River ◽

Expressed Sequence Tag ◽

De Novo ◽

Transcriptome Assembly ◽

Habitat Destruction ◽

The Yangtze River ◽

Simple Sequence

Elongate loach (Leptobotia elongata) is endemic to middle and upper reaches of the Yangtze River in China. Due to overfishing and habitat destruction, this loach has become an endangered species. So far, lack of reliable genetic information and molecular markers has hindered the conservation and utilization of elongate loach resources. Therefore, we here performed an Illumina sequencing and de novo transcriptome assembly in elongate loach, and then developed polymorphic simple sequence repeat markers (SSRs). After assembly, 51,185 unigenes were obtained, with an average length of 1,496 bp. A total of 23,901 expressed sequence tag-simple sequence repeats (EST-SSRs) were identified, distributing in 14,422 unigenes, with a distribution frequency of 28.18%. Out of 16,885 designed EST-SSR primers, 150 primers (3 or 4 base repetition-dominated) were synthesized for polymorphic EST-SSR development. Then, 52 polymorphic EST-SSRs were identified, with polymorphism information contents (PIC) ranging from 0.03 to 0.88 (average 0.54). In conclusion, this was the first report of transcriptome sequencing of elongate loach. Meanwhile, we developed a set of polymorphic EST-SSRs for the loach. This study will provide an important basis, namely genetic information and polymorphic SSRs, for further population genetics and breeding studies of this endangered and economic loach in China.

Download Full-text

De Novo Transcriptome Assembly, Functional Annotation and SSR Marker Discovery of Qinling Takin (Budorcas taxicolor bedfordi)

Animals ◽

10.3390/ani11082366 ◽

2021 ◽

Vol 11 (8) ◽

pp. 2366

Author(s):

Ju Qiu ◽

Rui Guo ◽

Yidan Li ◽

Yuyao Zhang ◽

Kangsheng Jia ◽

...

Keyword(s):

Ssr Marker ◽

Reference Genome ◽

De Novo ◽

Transcriptome Assembly ◽

The Public ◽

Ruminant Species ◽

Budorcas Taxicolor ◽

Marker Discovery ◽

Simple Sequence ◽

Identification Tool

The takin (Budorcas taxicolor) is an endemic ruminant species belonging to the bovine family. The International Union for Conservation of Nature (IUCN) has listed it as an endangered and vulnerable species. However, little is known about its molecular characterization since it lacks a reference genome. This study used RNA sequencing followed by de novo assembly, annotation and simple sequence repeats (SSRs) prediction to assess the transcriptome of Qinling takin (Budorcas taxicolor bedfordi) muscles. In total, 21,648 unigenes with an N50 and mean length of 1388 bp and 817 bp, respectively, were successfully detected and annotated against the public databases (NR, GO, KEGG, and EggNOG). Furthermore, 6222 SSRs were identified using the MIcroSAtellite (MISA) identification tool software. Taken together, these findings will provide valuable information for genetic, genomic, and evolutionary studies on takin.

Download Full-text

Genetic diversity in three groups of barley germplasm assessed by simple sequence repeats

Genome ◽

10.1139/g02-071 ◽

2002 ◽

Vol 45 (6) ◽

pp. 1095-1106 ◽

Cited By ~ 111

Author(s):

I A Matus ◽

P M Hayes

Keyword(s):

Genetic Diversity ◽

Hordeum Vulgare ◽

Molecular Marker ◽

Mapping Population ◽

Allelic Diversity ◽

Breeding Lines ◽

Barley Germplasm ◽

High Level ◽

Elite Breeding Lines ◽

Simple Sequence

Genetic diversity can be measured by several criteria, including phenotype, pedigree, allelic diversity at marker loci, and allelic diversity at loci controlling phenotypes of interest. Abundance, high level of polymorphism, and ease of genotyping make simple sequence repeats (SSRs) an excellent molecular marker system for genetics diversity analyses. In this study, we used a set of mapped SSRs to survey three representative groups of barley germplasm: a sample of crop progenitor (Hordeum vulgare subsp. spontaneum) accessions, a group of mapping population parents, and a group of varieties and elite breeding lines. The objectives were to determine (i) how informative SSRs are in these three sets of barley germplasm resources and (ii) the utility of SSRs in classifying barley germplasm. A total of 687 alleles were identified at 42 SSR loci in 147 genotypes. The number of alleles per locus ranged from 4 to 31, with an average of 16.3. Crop progenitors averaged 10.3 alleles per SSR locus, mapping population parents 8.3 alleles per SSR locus, and elite breeding lines 5.8 alleles per SSR locus. There were many exclusive (unique) alleles. The polymorphism information content values for the SSRs ranged from 0.08 to 0.94. The cluster analysis indicates a high level of diversity within the crop progenitors accessions and within the mapping population parents. It also shows a lower level of diversity within the elite breeding germplasm. Our results demonstrate that this set of SSRs was highly informative and was useful in generating a meaningful classification of the germplasm that we sampled. Our long-term goal is to determine the utility of molecular marker diversity as a tool for gene discovery and efficient use of germplasm.Key words: Hordeum vulgare subsp. vulgare, Hordeum vulgare subsp. spontaneum, SSR, genetic diversity, germplasm.

Download Full-text