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Research article
ZHIYONG Chen
Hunan Agricultural University
Corresponding Author
ORCiD: https://orcid.org/0000-0001-5604-9514
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Background: Miscanthus, which is a leading dedicated-energy grass in Europe and in parts of Asia, is expected to play a key role in the development of the future bioeconomy. However, due to its complex genetic background, it is difficult to investigate phylogenetic relationships and the evolution of gene function in this genus. Here, we investigated 50 Miscanthus germplasms: 1 female parent (M. lutarioriparius), 30 candidate male parents (M. lutarioriparius, M. sinensis, and M. sacchariflorus), and 19 offspring. We used high-throughput Specific-Locus Amplified Fragment sequencing (SLAF-seq) to identify informative single nucleotide polymorphisms (SNPs) in all germplasms.
Results: We identified 800,081 SLAF tags, of which 160,368 were polymorphic. Each tag was 264–364 bp long. The obtained SNPs were used to investigate genetic relationships within Miscanthus. We constructed a phylogenetic tree of the 50 germplasms using the obtained SNPs, and found that the germplasms fell into two clades: one clade of M. sinensis only and one clade that included the offspring, M. lutarioriparius, and M. sacchariflorus. Genetic cluster analysis indicated that M. lutarioriparius germplasm C3 was the most likely male parent of the offspring.
Conclusions: As a high-throughput sequencing method, SLAF-seq can be used to identify informative SNPs in Miscanthus germplasms and to rapidly characterize genetic relationships within this genus. Our results will support the development of breeding programs utilizing Miscanthus cultivars with elite biomass- or fiber-production potential.
Keywords
Miscanthus, SLAF-seq, SNP, SLAF tags, high-throughput sequencing, identification of genetic relationship.
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CURRENT STATUS: Under Review
Version 1
Posted 25 Jan, 2021
No community comments so far
Review #2 received
Received 29 Apr, 2021
Editorial decision: Major revision
On 29 Apr, 2021
Review #1 received
Received 21 Apr, 2021
Reviewer #2 agreed
On 12 Apr, 2021
Reviewer #1 agreed
On 06 Apr, 2021
Reviewers invited
Invitations sent on 01 Apr, 2021
Editor invited
On 19 Jan, 2021
Editor assigned
On 12 Jan, 2021
Submission checks complete
On 12 Jan, 2021
First submitted
On 11 Jan, 2021
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Subject Areas
Epigenetics & Genomics
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A new preprint design is coming!
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This preprint is under consideration at BMC Genomics. A preprint is a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Learn more about In Review
Research article
ZHIYONG Chen
Hunan Agricultural University
Corresponding Author
ORCiD: https://orcid.org/0000-0001-5604-9514
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
Peer Review Timeline
CURRENT STATUS: Under Review
Version 1
Posted 25 Jan, 2021
No community comments so far
Review #2 received
Received 29 Apr, 2021
Editorial decision: Major revision
On 29 Apr, 2021
Review #1 received
Received 21 Apr, 2021
Reviewer #2 agreed
On 12 Apr, 2021
Reviewer #1 agreed
On 06 Apr, 2021
Reviewers invited
Invitations sent on 01 Apr, 2021
Editor invited
On 19 Jan, 2021
Editor assigned
On 12 Jan, 2021
Submission checks complete
On 12 Jan, 2021
First submitted
On 11 Jan, 2021
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
Subject Areas
Epigenetics & Genomics
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Background: Miscanthus, which is a leading dedicated-energy grass in Europe and in parts of Asia, is expected to play a key role in the development of the future bioeconomy. However, due to its complex genetic background, it is difficult to investigate phylogenetic relationships and the evolution of gene function in this genus. Here, we investigated 50 Miscanthus germplasms: 1 female parent (M. lutarioriparius), 30 candidate male parents (M. lutarioriparius, M. sinensis, and M. sacchariflorus), and 19 offspring. We used high-throughput Specific-Locus Amplified Fragment sequencing (SLAF-seq) to identify informative single nucleotide polymorphisms (SNPs) in all germplasms.
Results: We identified 800,081 SLAF tags, of which 160,368 were polymorphic. Each tag was 264–364 bp long. The obtained SNPs were used to investigate genetic relationships within Miscanthus. We constructed a phylogenetic tree of the 50 germplasms using the obtained SNPs, and found that the germplasms fell into two clades: one clade of M. sinensis only and one clade that included the offspring, M. lutarioriparius, and M. sacchariflorus. Genetic cluster analysis indicated that M. lutarioriparius germplasm C3 was the most likely male parent of the offspring.
Conclusions: As a high-throughput sequencing method, SLAF-seq can be used to identify informative SNPs in Miscanthus germplasms and to rapidly characterize genetic relationships within this genus. Our results will support the development of breeding programs utilizing Miscanthus cultivars with elite biomass- or fiber-production potential.
Figure 1
Figure 2
Figure 3
This is a list of supplementary files associated with this preprint. Click to download.
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