Development and validation of genomic simple sequence repeat markers in Erianthus arundinaceus

Tsuruta, Shin-ichi; Ebina, Masumi; Kobayashi, Makoto; Takahashi, Wataru; Terajima, Yoshifumi

doi:10.1007/s11032-017-0675-z

Cited by 7 publications

(8 citation statements)

References 54 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Next-generation sequencing A total of 1682 candidate loci were used to developed 174 primer pairs and validate on eight Erianthus arundinaceus accessions. [34] Next-generation sequencing Illumina RNA-Seq platform were used on the de novo assembly of the sugarcane transcriptome, and a large number of molecular markers were found, including 5106 SSRs and 708,125 SNPs. [35] Next-generation sequencing Recent developments in plant science, particularly emerging genomic technologies, have the potential to increase the understanding of sugarcane genetics and breeding.…”

Section: Ests Librariesmentioning

confidence: 99%

See 1 more Smart Citation

Development and Use of Simple Sequence Repeats (SSRs) Markers for Sugarcane Breeding and Genetic Studies

et al. 2018

View full text Add to dashboard Cite

Recently-developed molecular markers are becoming powerful tools, with applications in crop genetics and improvement. Microsatellites, or simple sequence repeats (SSRs), are widely used in genetic fingerprinting, kinship analysis, and population genetics, because of the advantages of high variability from co-dominant and multi-allelic polymorphisms, and accurate and rapid detection. However, more recent evidence suggests they may play an important role in genome evolution and provide hotspots of recombination. This review describes the development of SSR markers through different techniques, and the detection of SSR markers and applications for sugarcane genetic research and breeding, such as cultivar identification, genetic diversity, genome mapping, quantitative trait loci (QTL) analysis, paternity analysis, cross-species transferability, segregation analysis, phylogenetic relationships, and identification of wild cross hybrids. We also discuss the advantages and disadvantages of SSR markers and highlight some future perspectives.

show abstract

Section: Ests Librariesmentioning

confidence: 99%

“…Genome mapping Genetic variability of 42 E. arundinaceus accessions native to Japan based on nuclear DNA content and 31 simple sequence repeat (SSR) markers [34] Genome mapping Low cost single strand conformation polymorphism of 16 genomic and 12 EST-SSRs marker and its utility in genetic evaluation of 22 sugarcane genotypes.…”

Section: Genetic Variabilitymentioning

confidence: 99%

Development and Use of Simple Sequence Repeats (SSRs) Markers for Sugarcane Breeding and Genetic Studies

et al. 2018

View full text Add to dashboard Cite

show abstract

“…Among 41 SSR primer pairs developed from Japanese E. arundinaceus [28], 28 primer pairs resulted in scorable amplicons of the expected sizes in all accessions tested (E. arundinaceus and E. procerus included), with a total of 316 alleles (Tables S1 and S2). Allele number per locus ranged from 1 (ETR098) to 32 (ETR129), with an average of 11.3 (Table 1).…”

Section: Ssr Analysismentioning

confidence: 99%

“…In the past decade, next generation sequencing (NGS) methodologies, which allow the genome-wide development of molecular markers and genotyping, have been applied to the polyploid species of warm-season grasses such as Paspalum [25], Panicum [26], and Pennisetum [27]. Using NGS data, we have developed simple sequence repeat (SSR or microsatellite) markers from the genomic DNA of hexaploid E. arundinaceus [28]. These SSR markers have been used successfully to estimate genetic diversity in E. arundinaceus collected in Japan and Indonesia [21].…”

Section: Introductionmentioning

confidence: 99%

Erianthus germplasm collection in Thailand: genetic structure and phylogenetic aspects of tetraploid and hexaploid accessions

et al. 2022

Self Cite

View full text Add to dashboard Cite

Background The genus Erianthus, which belongs to the “Saccharum complex”, includes C4 warm-season grasses. Erianthus species are widely distributed throughout Southeast Asia, East Asia and South Asia. Erianthus arundinaceus (Retz.) Jeswiet is highly adaptable to the environment, has a high percentage of dry matter, and is highly productive. Recently, this species has attracted attention as a novel bioenergy crop and as a breeding material for sugarcane improvement. Such interest in E. arundinaceus has accelerated the collection and conservation of its genetic resources, mainly in Asian countries, and also evaluation of morphological, agricultural, and cytogenetic features in germplasm collections. In Thailand, genetic resources of E. arundinaceus have been collected over the past 20 years and their phenotypic traits have been evaluated. However, the genetic differences and relatedness of the germplasms are not fully understood. Results A set of 41 primer pairs for nuclear simple sequence repeats (SSRs) developed from E. arundinaceus were used to assess the genetic diversity of 121 Erianthus germplasms collected in Thailand; of these primer pairs, 28 detected a total of 316 alleles. A Bayesian clustering approach with these alleles classified the accessions into four main groups, generally corresponding to the previous classification based on phenotypic analysis. The results of principal coordinate analysis and phylogenetic analysis of the 121 accessions on the basis of the SSR markers showed the same trend as Bayesian clustering, whereas sequence variations of three non-coding regions of chloroplast DNA revealed eight haplotypes among the accessions. The analysis of genetic structure and phylogenetic relationships, however, found some accessions whose classification contradicted the results of previous phenotypic classification. Conclusions The molecular approach used in this study characterized the genetic diversity and relatedness of Erianthus germplasms collected across Thailand. This knowledge would allow efficient maintenance and conservation of the genetic resources of this grass and would help to use Erianthus species as breeding materials for development of novel bioenergy crops and sugarcane improvement.

show abstract

“…In Japan, we have been collaborating with NARO to characterize our Erianthus genetic resources and develop varieties, with the aim of reducing greenhouse gas emissions by expanding the use of biofuels produced from biomass crops. In this project, we studied the phylogeny of Erianthus arundinaceus in Japan (Tsuruta et al 2017a(Tsuruta et al , 2017b(Tsuruta et al , 2017c. A review of Erianthus in a temperate zone in Japan has also been published (Matsunami et al 2018).…”

Section: Research and Variety Registration Of Erianthus In Japanmentioning

confidence: 99%

Technology Development for Stable Agricultural Production under Adverse Environments and Changing Climate Conditions

Nakashima

Urao

et al. 2021

JARQ

View full text Add to dashboard Cite

Development and validation of genomic simple sequence repeat markers in Erianthus arundinaceus

Cited by 7 publications

References 54 publications

Development and Use of Simple Sequence Repeats (SSRs) Markers for Sugarcane Breeding and Genetic Studies

Development and Use of Simple Sequence Repeats (SSRs) Markers for Sugarcane Breeding and Genetic Studies

Erianthus germplasm collection in Thailand: genetic structure and phylogenetic aspects of tetraploid and hexaploid accessions

Technology Development for Stable Agricultural Production under Adverse Environments and Changing Climate Conditions

Contact Info

Product

Resources

About