Full-length transcriptome sequences of Agropyron cristatum facilitate the prediction of putative genes for thousand-grain weight in a wheat-A. cristatum translocation line

Abstract Background Agropyron cristatum (L.) Gaertn. (2n = 4x = 28; genomes PPPP) is a wild relative of common wheat (Triticum aestivum L.) and provides many desirable genetic resources of wheat improvement. However, there is still a lack of reference genome and transcriptome information for A. cristatum, which severely impedes functional and molecular breeding studies. Results Single-molecule long-read sequencing technology from Pacific Biosciences (PacBio) was used to sequence full-length cDNA from a mixture of leaves, roots, stems and caryopses and constructed the first full-length transcriptome dataset of A. cristatum, which comprised 44,372 transcripts. As expected, the PacBio transcripts were generally longer than the transcripts assembled via the Illumina sequencing platform in a previous study. By mapping the full-length transcripts in this study, we identified tissue-enriched expressed transcripts and enriched GO terms, indicating that tissue-enriched transcripts were enriched for particular molecular functions that varies with tissue. We identified 3,398 novel and 1,352 A. cristatum-specific transcripts compared with the wheat gene model set. In order to better apply this transcriptome of A. cristatum, the A. cristatum transcripts was integrated with wheat genome as a reference sequences to try to identify candidate A. cristatum transcripts associated with thousand-grain weight in a wheat-A. cristatum translocation line Pubing 3035. Conclusions Full-length transcriptome sequences were used in our study. The present study not only provides comprehensive transcriptomic insights and information for A. cristatum but also proposes a new method for exploring the functional genes of wheat relatives under a wheat genetic background. The sequence data have been deposited in the NCBI under BioProject accession number PRJNA534411.

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Full-length transcriptome sequences of Agropyron cristatum facilitate the prediction of putative genes for thousand-grain weight in a wheat-A. cristatum translocation line

BMC Genomics ◽

10.1186/s12864-019-6416-4 ◽

2019 ◽

Vol 20 (1) ◽

Cited By ~ 1

Author(s):

Shenghui Zhou ◽

Jinpeng Zhang ◽

Haiming Han ◽

Jing Zhang ◽

Huihui Ma ◽

...

Keyword(s):

Single Molecule ◽

Sequence Data ◽

Full Length ◽

Grain Weight ◽

Agropyron Cristatum ◽

Reference Sequence ◽

Translocation Line ◽

Thousand Grain Weight ◽

Sequencing Platform ◽

Transcriptome Sequences

Abstract Background Agropyron cristatum (L.) Gaertn. (2n = 4x = 28; genomes PPPP) is a wild relative of common wheat (Triticum aestivum L.) and provides many desirable genetic resources for wheat improvement. However, there is still a lack of reference genome and transcriptome information for A. cristatum, which severely impedes functional and molecular breeding studies. Results Single-molecule long-read sequencing technology from Pacific Biosciences (PacBio) was used to sequence full-length cDNA from a mixture of leaves, roots, stems and caryopses and constructed the first full-length transcriptome dataset of A. cristatum, which comprised 44,372 transcripts. As expected, the PacBio transcripts were generally longer and more complete than the transcripts assembled via the Illumina sequencing platform in previous studies. By analyzing RNA-Seq data, we identified tissue-enriched transcripts and assessed their GO term enrichment; the results indicated that tissue-enriched transcripts were enriched for particular molecular functions that varied by tissue. We identified 3398 novel and 1352 A. cristatum-specific transcripts compared with the wheat gene model set. To better apply this A. cristatum transcriptome, the A. cristatum transcripts were integrated with the wheat genome as a reference sequence to try to identify candidate A. cristatum transcripts associated with thousand-grain weight in a wheat-A. cristatum translocation line, Pubing 3035. Conclusions Full-length transcriptome sequences were used in our study. The present study not only provides comprehensive transcriptomic insights and information for A. cristatum but also proposes a new method for exploring the functional genes of wheat relatives under a wheat genetic background. The sequence data have been deposited in the NCBI under BioProject accession number PRJNA534411.

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Full-length transcriptome sequences of Agropyron cristatum facilitate the prediction of putative genes for thousand-grain weight in a wheat-A. cristatum translocation line

10.21203/rs.2.9773/v2 ◽

2019 ◽

Author(s):

Shenghui Zhou(Former Corresponding Author) ◽

Jinpeng Zhang ◽

Haiming Han ◽

Jing Zhang ◽

Ma Huihui ◽

...

Keyword(s):

Single Molecule ◽

Sequence Data ◽

Full Length ◽

Grain Weight ◽

Agropyron Cristatum ◽

Reference Sequence ◽

Translocation Line ◽

Thousand Grain Weight ◽

Sequencing Platform ◽

Transcriptome Sequences

Abstract Agropyron cristatum (L.) Gaertn. (2n = 4x = 28; genomes PPPP) is a wild relative of common wheat (Triticum aestivum L.) and provides many desirable genetic resources for wheat improvement. However, there is still a lack of reference genome and transcriptome information for A. cristatum, which severely impedes functional and molecular breeding studies.Results Single-molecule long-read sequencing technology from Pacific Biosciences (PacBio) was used to sequence full-length cDNA from a mixture of leaves, roots, stems and caryopses and constructed the first full-length transcriptome dataset of A. cristatum, which comprised 44,372 transcripts. As expected, the PacBio transcripts were generally longer and more complete than the transcripts assembled via the Illumina sequencing platform in previous studies. By analyzing RNA-Seq data, we identified tissue-enriched transcripts and assessed their GO term enrichment; the results indicated that tissue-enriched transcripts were enriched for particular molecular functions that varied by tissue. We identified 3,398 novel and 1,352 A. cristatum-specific transcripts compared with the wheat gene model set. To better apply this A. cristatum transcriptome, the A. cristatum transcripts were integrated with the wheat genome as a reference sequence to try to identify candidate A. cristatum transcripts associated with thousand-grain weight in a wheat-A. cristatum translocation line, Pubing 3035.Conclusions Full-length transcriptome sequences were used in our study. The present study not only provides comprehensive transcriptomic insights and information for A. cristatum but also proposes a new method for exploring the functional genes of wheat relatives under a wheat genetic background. The sequence data have been deposited in the NCBI under BioProject accession number PRJNA534411.

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Characterization of Full-Length Transcriptome Sequences and Splice Variants of Lateolabrax maculatus by Single-Molecule Long-Read Sequencing and Their Involvement in Salinity Regulation

Frontiers in Genetics ◽

10.3389/fgene.2019.01126 ◽

2019 ◽

Vol 10 ◽

Cited By ~ 4

Author(s):

Yuan Tian ◽

Haishen Wen ◽

Xin Qi ◽

Xiaoyan Zhang ◽

Shikai Liu ◽

...

Keyword(s):

Single Molecule ◽

Splice Variants ◽

Full Length ◽

Long Read ◽

Lateolabrax Maculatus ◽

Transcriptome Sequences

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Single molecule, near full-length genome sequencing of dengue virus

Scientific Reports ◽

10.1038/s41598-020-75374-1 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Thiruni N. Adikari ◽

Nasir Riaz ◽

Chathurani Sigera ◽

Preston Leung ◽

Braulio M. Valencia ◽

...

Keyword(s):

Dengue Virus ◽

Single Molecule ◽

Phylogenetic Trees ◽

Sequence Data ◽

Sequence Similarity ◽

Genetic Distances ◽

Full Length ◽

Denv Serotypes ◽

Consensus Sequences ◽

Pairwise Sequence Similarity

Abstract Current methods for dengue virus (DENV) genome amplification, amplify parts of the genome in at least 5 overlapping segments and then combine the output to characterize a full genome. This process is laborious, costly and requires at least 10 primers per serotype, thus increasing the likelihood of PCR bias. We introduce an assay to amplify near full-length dengue virus genomes as intact molecules, sequence these amplicons with third generation “nanopore” technology without fragmenting and use the sequence data to differentiate within-host viral variants with a bioinformatics tool (Nano-Q). The new assay successfully generated near full-length amplicons from DENV serotypes 1, 2 and 3 samples which were sequenced with nanopore technology. Consensus DENV sequences generated by nanopore sequencing had over 99.5% pairwise sequence similarity to Illumina generated counterparts provided the coverage was > 100 with both platforms. Maximum likelihood phylogenetic trees generated from nanopore consensus sequences were able to reproduce the exact trees made from Illumina sequencing with a conservative 99% bootstrapping threshold (after 1000 replicates and 10% burn-in). Pairwise genetic distances of within host variants identified from the Nano-Q tool were less than that of between host variants, thus enabling the phylogenetic segregation of variants from the same host.

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Introgression of Agropyron cristatum 6P chromosome segment into common wheat for enhanced thousand-grain weight and spike length

Theoretical and Applied Genetics ◽

10.1007/s00122-015-2550-9 ◽

2015 ◽

Vol 128 (9) ◽

pp. 1827-1837 ◽

Cited By ~ 31

Author(s):

Jing Zhang ◽

Jinpeng Zhang ◽

Weihua Liu ◽

Haiming Han ◽

Yuqing Lu ◽

...

Keyword(s):

Common Wheat ◽

Grain Weight ◽

Spike Length ◽

Agropyron Cristatum ◽

Chromosome Segment ◽

Thousand Grain Weight

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A comparison of cytoplasmic and chemically-induced male sterility systems for hybrid performance in wheat ( Triticum aestivum L.)

Acta Agronomica Hungarica ◽

10.1556/aagr.54.2006.1.11 ◽

2006 ◽

Vol 54 (1) ◽

pp. 109-120 ◽

Cited By ~ 3

Author(s):

A. Adugna ◽

G. S. Nanda ◽

N. S. Bains ◽

...

Keyword(s):

Grain Yield ◽

Male Sterility ◽

Triticum Aestivum L ◽

Grain Weight ◽

Hybrid Performance ◽

Thousand Grain Weight ◽

Yield Performance ◽

Chemically Induced ◽

B Lines ◽

Better Than

Cytoplasmic ( Triticum timopheevii -based) and chemically induced (CH9832- based) male sterility systems were compared for hybrid performance in wheat. A total of 40 genotypes including 10 CMS-based hybrids, 10 CHA-based hybrids, 10 B lines and 10 R lines were included in the experiment. analysis of variance revealed significant differences between the genotypes for all the characters studied. Differences between the hybrids and their parents were significant for all the characters. There were also significant differences between the hybrids resulting from the two systems of sterility. This study of 10 comparable hybrids showed, on average, midparent heterosis of 30.2 and 7.3% for CMS- and CHA-derived hybrids, respectively. Generally, the CMS-based hybrids were superior to their CHA-based equivalents for grain yield performance. In spite of the incomplete fertility the higher grain yield in CMS-based hybrids was attributed to the profuse tillering and high thousand-grain weight. On the other hand, the CHA-based hybrids had lower yield performance due to the lower thousand-grain weight and tillering. The lower grain weight and tillering in these hybrids compared with their CMS-based equivalents might be due to the toxic effect of the CHA, which was carried over to the hybrid and affected vigour. As a whole the CMS system was found to be better than the CHA system (based on the particular CHA used in this study) for hybrid performance in wheat.

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The development and validation of new DNA markers linked to the thousand-grain weight QTL in bread wheat (Triticum aestivum L.)

Czech Journal of Genetics and Plant Breeding ◽

10.17221/35/2019-cjgpb ◽

2020 ◽

Vol 56 (No. 2) ◽

pp. 52-61

Author(s):

Cong Cong Yang ◽

Jian Ma ◽

Cong Li ◽

Min Sun ◽

Ya Ya Zou ◽

...

Keyword(s):

Dna Markers ◽

High Resolution Melting ◽

Triticum Aestivum L ◽

Grain Weight ◽

Scar Markers ◽

Thousand Grain Weight ◽

Marker Assisted Breeding ◽

Positive Allele ◽

Important Trait ◽

Development And Validation

Thousand-grain weight (TGW) is an important trait affecting wheat production. We previously identified a major quantitative trait loci (QTL) controlling the TGW on the 2D chromosome of wheat using a recombinant inbred line (RIL) population constructed by the cross between Tibetan semi-wild wheat Q1028 (Q1028) and Zhengmai 9023 (ZM9023). The positive allele at this QTL is from ZM9023. To further characterise this QTL, here, we try to develop and validate the high-resolution melting (HRM) and sequence-characterised amplified region (SCAR) markers. One HRM marker (0C98-411) and two SCAR markers (E301-700 and B0BB-10470) were developed and integrated into the genetic map. All of these three markers were validated in three populations with different genetic backgrounds. 0C98-411 is the most closely linked marker that could trace QTgw.sau-2D in molecular marker assisted breeding.

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