Genome survey sequencing of purple elephant grass (Pennisetum purpureum Schum ‘Zise’) and identification of its SSR markers

Wang, Chengran; Yan, Haidong; Ji, Li; Zhou, Sifan; Liu, Ting; Zhang, Xinquan; Huang, Linkai

doi:10.1007/s11032-018-0849-3

Cited by 32 publications

(30 citation statements)

References 49 publications

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“…The DArTseq sequence reads corresponding to the SNP and SilicoDArT markers were aligned to Napier grass genomic [30] and transcriptome [31] sequences using the bwa mem sequence alignment method [32], and the sequences were annotated using the GeneBank NCBI blastx tool (https://blast. ncbi.nlm.nih.gov/Blast.cgi).…”

Section: Marker-trait Association Analysismentioning

confidence: 99%

“…Nucleotide sequences of the associated markers were retrieved from the available Napier grass genomic [30] and transcriptomic [31] sequence data by aligning the DArTseq short sequence reads (approximately 55 nucleotides (nt)) corresponding to each SilicoDArT marker ( Supplementary Table S1). Seven of the SilicoDArT markers were aligned with the assembled genomic sequences [30]. The genomic sequences ranged from 278 to 6143 nt in length, which is suitable for the design of PCR primers, amplicon sequencing and in silico functional analysis of the associated markers.…”

Section: Analysis Of Nucleotide Sequences Corresponding To the Associmentioning

confidence: 99%

“…The DArTseq genotyping platform [52] produces short sequence reads, averaging about 55 nt in length, corresponding to each of the SilicoDArT and SNP markers [12]. In this study, the short sequence reads corresponding to the associated markers were compared with previously reported Napier grass genomic [30] and transcriptome [31] sequences. Very few of the DArTseq sequence reads aligned with the assembled genomic sequences, as only assembled sequences longer than 200 nt were used in the comparison.…”

Section: Markers Associated With Dry Weight Yields and Metabolizable mentioning

confidence: 99%

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Forage Performance and Detection of Marker Trait Associations with Potential for Napier Grass (Cenchrus purpureus) Improvement

Habte¹,

Muktar²,

Abdena³

et al. 2020

Agronomy

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The evaluation of forage crops for adaptability and performance across production systems and environments is one of the main strategies used to improve forage production. To enhance the genetic resource base and identify traits responsible for increased feed potential of Napier grass, forty-five genotypes from Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA), Brazil, were evaluated for forage biomass yield and feed nutritional quality in a replicated trial under wet and dry season conditions in Ethiopia. The results revealed significant variation in forage yield and feed nutritional qualities among the genotypes and between the wet and dry seasons. Feed fiber components were lower in the dry season, while crude protein, in vitro organic matter digestibility, and metabolizable energy were higher. Based on the cumulative biomass and metabolizable energy yield, top performing genotypes were identified that are candidates for future forage improvement studies. Furthermore, the marker-trait association study identified diagnostic single nucleotide polymorphisms (SNP) and SilicoDArT markers and potential candidate genes that could differentiate high biomass yielding and high metabolizable energy genotypes in the collection.

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Section: Marker-trait Association Analysismentioning

confidence: 99%

Section: Analysis Of Nucleotide Sequences Corresponding To the Associmentioning

confidence: 99%

Section: Markers Associated With Dry Weight Yields and Metabolizable mentioning

confidence: 99%

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Forage Performance and Detection of Marker Trait Associations with Potential for Napier Grass (Cenchrus purpureus) Improvement

Habte¹,

Muktar²,

Abdena³

et al. 2020

Agronomy

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“…Recently, genome survey sequencing by next generation sequencing (NGS) has emerged as an important and cost-effective strategy for generating a wide range of genetic and genomic information for different plant species [11][12][13][14][15][16][17][18]. It can also identify a large number of molecular markers for breeding [19].…”

Section: Introductionmentioning

confidence: 99%

“…The SSR marker is the most widely used molecular marker system. SSR molecular markers have been developed for many species through NGS [11,13,15,16,18]. An increased molecular marker density will enable better genome-wide association and molecular breeding studies [20,21].…”

Section: Introductionmentioning

confidence: 99%

Genome Survey Sequencing of Acer truncatum Bunge to Identify Genomic Information, Simple Sequence Repeat (SSR) Markers and Complete Chloroplast Genome

Wang

Fan

Pan

et al. 2019

Forests

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The Acer truncatum Bunge is a particular forest tree species found in the north of China. Due to the recent discovery that its seeds contain a considerable amount of nervonic acid, this species has received more and more attention. However, there have been no reports of the genome in this species. In this study, we report on the Acer truncatum genome sequence produced by genome survey sequencing. In total, we obtained 61.90 Gbp of high-quality data, representing approximately 116x coverage of the Acer truncatum genome. The genomic characteristics of Acer truncatum include a genome size of 529.88 Mbp, a heterozygosis rate of 1.06% and a repeat rate of 48.8%. A total of 392,961 high-quality genomic SSR markers were developed and a graphical map of the annotated circular chloroplast genome was generated. Thus far, this is the first report of de novo whole genome sequencing and assembly of Acer truncatum. We believe that this genome sequence dataset may provide a new resource for future genomic analysis and molecular breeding studies of Acer truncatum.

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The complete chloroplast genome sequences of three lilies: genome structure, comparative genomic and phylogenetic analyses

Zhang

Wang

et al. 2022

J Plant Res

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Genome survey sequencing of purple elephant grass (Pennisetum purpureum Schum ‘Zise’) and identification of its SSR markers

Cited by 32 publications

References 49 publications

Forage Performance and Detection of Marker Trait Associations with Potential for Napier Grass (Cenchrus purpureus) Improvement

Forage Performance and Detection of Marker Trait Associations with Potential for Napier Grass (Cenchrus purpureus) Improvement

Genome Survey Sequencing of Acer truncatum Bunge to Identify Genomic Information, Simple Sequence Repeat (SSR) Markers and Complete Chloroplast Genome

The complete chloroplast genome sequences of three lilies: genome structure, comparative genomic and phylogenetic analyses

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