Transcriptomic resources for prairie grass (Bromus catharticus): expressed transcripts, tissue-specific genes, and identification and validation of EST-SSR markers

Abstract Background Prairie grass (Bromus catharticus) is a typical cool-season forage crop with high biomass production and fast growth rate during winter and spring. However, its genetic research and breeding has remained stagnant due to limited available genomic resources. The aim of this study was to generate large-scale genomic data using high-throughput transcriptome sequencing, and perform a preliminary validation of EST-SSR markers of B. catharticus. Results Eleven tissue samples including seeds, leaves, and stems were collected from a new high-yield strain of prairie grass BCS1103. A total of 257,773 unigenes were obtained, of which 193,082 (74.90%) were annotated. Comparison analysis between tissues identified 1803, 3030, and 1570 genes specifically and highly expressed in seed, leaf, and stem, respectively. A total of 37,288 EST-SSRs were identified from unigene sequences, and more than 80,000 primer pairs were designed. We synthesized 420 primer pairs and selected 52 ones with high polymorphisms to estimate genetic diversity and population structure in 24 B. catharticus accessions worldwide. Despite low diversity indicated by an average genetic distance of 0.364, the accessions from South America and Asia and wild accessions showed higher genetic diversity. Moreover, South American accessions showed a pure ancestry, while Asian accessions demonstrated mixed internal relationships, which indicated a different probability of gene flow. Phylogenetic analysis clustered the studied accessions into four clades, being consistent with phenotypic clustering results. Finally, Mantel analysis suggested the total phenotypic variation was mostly contributed by genetic component. Stem diameter, plant height, leaf width, and biomass yield were significantly correlated with genetic data (r > 0.6, P < 0.001), and might be used in the future selection and breeding. Conclusion A genomic resource was generated that could benefit genetic and taxonomic studies, as well as molecular breeding for B. catharticus and its relatives in the future.

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Transcriptomic resources for prairie grass (Bromus catharticus): expressed transcripts, tissue-specific genes, and identification and validation of EST-SSR markers

10.21203/rs.3.rs-306875/v1 ◽

2021 ◽

Author(s):

Ming Sun ◽

Zhixiao Dong ◽

Jian Yang ◽

Wendan Wu ◽

Chenglin Zhang ◽

...

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Large Scale ◽

Genetic Research ◽

High Yield ◽

Yield Strain ◽

Tissue Samples ◽

Prairie Grass ◽

The Future ◽

Genomic Resource

Abstract Background: Prairie grass (Bromus catharticus) is a typical cool-season forage crop with high biomass production and fast growth rate during winter and spring. However, its genetic research and breeding has remained stagnant due to limited available genomic resources. The aim of this study was to generate large-scale genomic data using high-throughput transcriptome sequencing, and perform a preliminary validation of EST-SSR markers of B. catharticus.Results: Eleven tissue samples including seeds, leaves, and stems were collected from a new high-yield strain of prairie grass BCS1103. A total of 257,773 unigenes were obtained, of which 193,082 (74.90%) were annotated. Comparison analysis between tissues identified 1803, 3030, and 1570 genes specifically expressed in the seed, leaf, and stem, respectively. A total of 37,288 EST-SSRs were identified from unigene sequences, and more than 80,000 primer pairs were designed. We synthesized 420 primer pairs and selected 52 ones with high polymorphisms to estimate genetic diversity and population structure in 24 B. catharticus accessions worldwide. Despite low diversity indicated by an average genetic distance of 0.358, the accessions from South America and Asia and wild accessions showed higher genetic diversity. Moreover, South American accessions showed a pure ancestry, but Asian accessions demonstrated mixed relationships, which indicated a different probability of gene flow among the two regions. Phylogenetic analysis clustered the studied accessions into four clades. Finally, phenotypic clustering and Mantel analysis suggested the total phenotypic variation was mostly contributed by the genetic component. Stem diameter, plant height, leaf width, and biomass yield significantly correlated with genetic data (r > 0.6, P < 0.001), and might be genetically stable in the future selection and breeding.Conclusion: A genomic resource was generated that could benefit genetic and taxonomic studies, as well as molecular breeding for B. catharticus and it relatives in the future.

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Genome-Wide Novel Genic Microsatellite Marker Resource Development and Validation for Genetic Diversity and Population Structure Analysis of Banana

Genes ◽

10.3390/genes11121479 ◽

2020 ◽

Vol 11 (12) ◽

pp. 1479

Author(s):

Manosh Kumar Biswas ◽

Mita Bagchi ◽

Dhiman Biswas ◽

Jennifer Ann Harikrishna ◽

Yuxuan Liu ◽

...

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Comparative Mapping ◽

In Silico ◽

Large Scale ◽

Crop Improvement ◽

Musa Spp ◽

Population Structure Analysis ◽

A Genome ◽

Development And Validation

Trait tagging through molecular markers is an important molecular breeding tool for crop improvement. SSR markers encoded by functionally relevant parts of a genome are well suited for this task because they may be directly related to traits. However, a limited number of these markers are known for Musa spp. Here, we report 35136 novel functionally relevant SSR markers (FRSMs). Among these, 17,561, 15,373 and 16,286 FRSMs were mapped in-silico to the genomes of Musa acuminata, M. balbisiana and M. schizocarpa, respectively. A set of 273 markers was validated using eight accessions of Musa spp., from which 259 markers (95%) produced a PCR product of the expected size and 203 (74%) were polymorphic. In-silico comparative mapping of FRSMs onto Musa and related species indicated sequence-based orthology and synteny relationships among the chromosomes of Musa and other plant species. Fifteen FRSMs were used to estimate the phylogenetic relationships among 50 banana accessions, and the results revealed that all banana accessions group into two major clusters according to their genomic background. Here, we report the first large-scale development and characterization of functionally relevant Musa SSR markers. We demonstrate their utility for germplasm characterization, genetic diversity studies, and comparative mapping in Musa spp. and other monocot species. The sequences for these novel markers are freely available via a searchable web interface called Musa Marker Database.

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Development of Microsatellite Markers Derived from Expressed Sequence Tags of Polyporales for Genetic Diversity Analysis of EndangeredPolyporus umbellatus

BioMed Research International ◽

10.1155/2015/941357 ◽

2015 ◽

Vol 2015 ◽

pp. 1-11 ◽

Cited By ~ 2

Author(s):

Yuejin Zhang ◽

Yuanyuan Chen ◽

Ruihong Wang ◽

Ailin Zeng ◽

Michael K. Deyholos ◽

...

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Expressed Sequence Tags ◽

Large Scale ◽

Gene Diversity ◽

High Genetic Diversity ◽

Information Index ◽

Polyporus Umbellatus ◽

Ssr Primers ◽

Expressed Sequence

A large scale of EST sequences of Polyporales was screened in this investigation in order to identify EST-SSR markers for various applications. The distribution of EST sequences and SSRs in five families of Polyporales was analyzed, respectively. Mononucleotide was the most abundant type, followed by trinucleotide. Among five families, Ganodermataceae occupied the most SSR markers, followed by Coriolaceae. Functional prediction of SSR marker-containing EST sequences inGanoderma lucidumobtained three main groups, namely, cellular component, biological process, and molecular function. Thirty EST-SSR primers were designed to evaluate the genetic diversity of 13 naturalPolyporus umbellatusaccessions. Twenty one EST-SSRs were polymorphic with average PIC value of 0.33 and transferability rate of 71%. These 13P.umbellatusaccessions showed relatively high genetic diversity. The expected heterozygosity, Nei’s gene diversity, and Shannon information index were 0.41, 0.39, and 0.57, respectively. Both UPGMA dendrogram and principal coordinate analysis (PCA) showed the same cluster result that divided the 13 accessions into three or four groups.

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Evaluation of rice and sugarcane SSR markers for phylogenetic and genetic diversity analyses in bambooIHBT Publication No. 0732.

Genome ◽

10.1139/g07-101 ◽

2008 ◽

Vol 51 (2) ◽

pp. 91-103 ◽

Cited By ~ 42

Author(s):

R. K. Sharma ◽

P. Gupta ◽

V. Sharma ◽

A. Sood ◽

T. Mohapatra ◽

...

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Large Scale ◽

Bamboo Species ◽

Ssr Primers ◽

Taxonomical Classification ◽

High Level ◽

The Tropics ◽

Diversity Studies

Simple sequence repeat (SSR) markers are valuable tools for many purposes such as phylogenetic, fingerprinting, and molecular breeding studies. However, only a few SSR markers are known and available in bamboo species of the tropics ( Bambusa spp.). Considering that grass genomes have co-evolved and share large-scale synteny, theoretically it should be possible to use the genome sequence based SSR markers of field crops such as rice ( Oryza sativa ) and sugarcane ( Saccharum spp.) for genome analysis in bamboo. To test this, 98 mapped SSR primers representing 12 linkage groups of rice and 20 EST-derived sugarcane SSR primers were evaluated for transferability to 23 bamboo species. Of the tested markers, 44 (44.9%) rice and 15 (75%) sugarcane SSR primers showed repeatable amplification in at least one species of bamboo and thus were successfully utilized for phylogenetic and genetic diversity analyses. Transferred SSR primers revealed complex amplification patterns in bamboo, with an average of 9.62 fragments per primer, indicating a high level of polyploidy and genetic variability in bamboo. Forty-two of these primers (34 rice and 8 sugarcane SSR primers) detected an average of 2.12 unique fragments per primer and thus could be exploited for species identification. Six bamboo SSR primers exhibited cross transferability, to varying degrees, to different bamboo species. The genetic similarity coefficient indicated a high level of divergence at the species level (73%). However, a relatively low level of diversity was observed within species (25% in 20 accessions of Dendrocalamus hamiltonii ). Further, cluster analysis revealed that the major grouping was in accordance with the taxonomical classification of bamboo. Thus, the rice and sugarcane SSRs can be utilized for phylogenetic and genetic diversity studies in bamboo.

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Conservation genetics of red pandas in the wild

10.1093/oso/9780198759805.003.0029 ◽

2018 ◽

Author(s):

Yibo Hu ◽

Dunwu Qi ◽

Fuwen Wei

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Conservation Genetics ◽

Human Activities ◽

Population Genetic ◽

Large Scale ◽

Demographic History ◽

Genetic Research ◽

Phylogeographic Structure ◽

Red Panda

The red panda is listed on the 2016 IUCN red list as Endangered. It is now distributed only in China, Myanmar, India, Bhutan and Nepal. Human activities such as poaching and large-scale deforestation have caused serious declines in this forest-dwelling species. Although its ecological research has made much progress in the past decades, only recently witnessed the population genetic research advances of this species. This chapter reviews the advances in wild red panda conservation genetics from non-invasive genetics, genetic diversity, phylogeographic structure, population genetic structure, demographic history, subspecies differentiation, to its conservation and management. It presents detailed estimates of genetic diversity, assesses the role of paleo-climate changes, human activities and landscape features in shaping the genetic structure and demographic history of red pandas, and discusses the implications of conservation genetics findings for effective genetic monitoring and conservation management.

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Development and use of EST-SSR markers for assessing genetic diversity in the brown planthopper (Nilaparvata lugensStål)

Bulletin of Entomological Research ◽

10.1017/s0007485311000435 ◽

2011 ◽

Vol 102 (1) ◽

pp. 113-122 ◽

Cited By ~ 27

Author(s):

S. Jing ◽

B. Liu ◽

L. Peng ◽

X. Peng ◽

L. Zhu ◽

...

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Expressed Sequence Tags ◽

Large Scale ◽

Brown Planthopper ◽

Nilaparvata Lugens ◽

Rice Varieties ◽

Genetics And Genomics ◽

Expressed Sequence ◽

Simple Sequence

AbstractTo assess genetic diversity in populations of the brown planthopper (Nilaparvata lugensStål) (Homoptera: Delphacidae), we have developed and applied microsatellite, or simple sequence repeat (SSR), markers from expressed sequence tags (ESTs). We found that the brown planthopper clusters of ESTs were rich in SSRs with unique frequencies and distributions of SSR motifs. Three hundred and fifty-one EST-SSR markers were developed and yielded clear bands from samples of four brown planthopper populations. High cross-species transferability of these markers was detected in the closely related planthopperN. muiri. The newly developed EST-SSR markers provided sufficient resolution to distinguish within and among biotypes. Analyses based on SSR data revealed host resistance-based genetic differentiation among different brown planthopper populations; the genetic diversity of populations feeding on susceptible rice varieties was lower than that of populations feeding on resistant rice varieties. This is the first large-scale development of brown planthopper SSR markers, which will be useful for future molecular genetics and genomics studies of this serious agricultural pest.

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ISOLATING THE MONOKARYON COLLECTION OF Pleurotus spp.

Vietnam Journal of Science and Technology ◽

10.15625/2525-2518/55/1a/12384 ◽

2018 ◽

Vol 55 (1A) ◽

pp. 73

Author(s):

Tran Thi Ngoc My

Keyword(s):

Genetic Diversity ◽

Genetic Distance ◽

Large Scale ◽

High Yield ◽

Biological Efficiency ◽

Mating Types ◽

Fruiting Bodies ◽

South Vietnam ◽

Pleurotus Species ◽

Similar Coefficient

Pleurotus spp. is one of the most important cultivated mushrooms in the world by their nutrition and medicinal property. In Vietnam, although many Pleurotus species are popularly cultivated, but most of them are imported. These strains are easily degenerated when they are cultivated in large scale, because they are difficult to adapt to the environment of Vietnam. This research aims to construct the monokaryon collection of Pleurotus spp. with details of taxonomy, genetic diversity, cultivating traits, monokaryotic mating types focused on Pleurotus strains with the high yield, genetic stable and adaptability to Vietnam environment. 09 Pleurotus strains were collected in South Vietnam and signed PL1 to PL9. Identification by morphology and phylogenetic analysis based on ITS sequences showed that PL1 is P. citrinopileatus; PL2, PL6 and PL9 are P. ostreatus; PL3 is P. cystidiosus; PL4 and PL8 are P. pulmonarius; PL5 is P. cornucopiae; PL7 is P. incarnatus. AFLP analyses indicated a wide genetic diversity of the collected strains with the similar coefficient 52 – 90 %. Pair of PL2 and PL9 is the most closed genetic distance and pair of PL6 and PL7 is the furthest genetic distance. PL4, PL8 and PL1 adapted well to Vietnam environment. PL2, PL5, PL6 and PL9 are cold strains and formed fruiting bodies slowly. PL3 had the highest biological efficiency, but the longest harvesting period (2.5 – 3 months). Except PL7, the biological efficiencies of other strains are over 50 %. 120 monokaryotic isolates of PL1, PL2 and PL8 are collected and determined the mating type.

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Revealing Genetic Diversity, Population Structure and Cultivar-Specific SSR Alleles in Pistachio Using SSR Markers

10.21203/rs.3.rs-1104578/v1 ◽

2021 ◽

Author(s):

Harun Karcı ◽

Aibibula Paizila ◽

Murat Güney ◽

Mederbek Zhaanbaev ◽

Salih Kafkas

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Large Scale ◽

Germplasm Collection ◽

Mean Value ◽

Group Method ◽

Arithmetic Average ◽

Genic Ssr ◽

Pair Group ◽

Average Analysis

Abstract Pistachio (Pistacia vera L.) is the only cultivated species in Pistacia genus and one of the most important nut crop in terms of production. Pistachio cultivars have significant level of variation in their phenotypic appearance and productivity. Understanding the genetic diversity between pistachio cultivars could facilitate breeding programs. Simple sequence repeat (SSR) markers are powerful tools in genetic diversity and germplasm collection studies. However, published information about the characterization of large scale pistachio cultivar germplasm with adequate number of SSR markers is limited. In this study, sixty-six pistachio cultivars and genotypes originated from six different countries were characterized and fingerprinted by 74 genomic and 18 genic SSR markers. SSR analysis identified 576 alleles for all 66 cultivars and genotypes. The number of alleles per locus ranged from 2 to 20 (CUPOhBa1592) alleles with a mean value of six alleles per locus. The polymorphism information content (PIC) values ranged from 0.07 (CUPVEST2939) to 0.87 (CUPSiOh2460) with a mean PIC value of 0.58. The pistachio cultivars and genotypes were divided into five clusters according to Structure and UPGMA (Unweighted Pair Group Method with Arithmetic Average) analysis. Total of 61 cultivar specific alleles were detected in 34 cultivars, among them three primers (CUPOhBa1592, CUPBaPa1606 and CUPOhBa2127) produced more than four cultivar-specific loci therefore very promising for cultivar identification, fingerprinting and breeding studies in pistachio.

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Development of EST-SSR markers and association mapping with floral traits in Syringa oblata

BMC Plant Biology ◽

10.1186/s12870-020-02652-5 ◽

2020 ◽

Vol 20 (1) ◽

Author(s):

Yunyao Yang ◽

Ruiqing He ◽

Jian Zheng ◽

Zenghui Hu ◽

Jing Wu ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Ssr Markers ◽

Genetic Architecture ◽

Genetic Research ◽

Mixed Linear Model ◽

Floral Traits ◽

Dominant Type ◽

High Level ◽

Nucleotide Repeats

Abstract Background Lilac (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 9864 unigene sequences with an average of one SSR per 8.13 kb, of which di-nucleotide repeats were the dominant type (32.86%, 3611). A set of 2042 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. Two hundred thirty-four 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 nine 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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Ethical Principles for Research Governance of Biobanks

Journal of International Biotechnology Law ◽

10.1515/jibl.2006.028 ◽

2006 ◽

Vol 3 (6) ◽

Cited By ~ 1

Author(s):

Don Chalmers

Keyword(s):

Health Care ◽

Clinical Trial ◽

Large Scale ◽

Genetic Research ◽

Pharmaceutical Research ◽

Epidemiological Studies ◽

Pharmaceutical Companies ◽

Tissue Samples ◽

Causes Of Disease ◽

Ethics Council

AbstractBiobanks of collected human tissue samples are rapidly expanding and becoming „essential tools in translating biomedical research into real improvements in health care”. Biobanks are rich sources for genetic research. The German National Ethics Council has noted, for example, the potential of biobanks for the identification of causes of disease and for breakthroughs in medical and pharmaceutical research. Unsurprisingly, many pharmaceutical companies operate biobank collections for research purposes and to enrol suitable clinical trial recruits so as to minimise side effects and achieve better results. Biobanks are also essential tools for conducting large-scale epidemiological studies, involving whole populations (with the neologism „epigenetic”). One commentator has noted that biobanks are invariably ”staggeringly expensive”

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