Conversion of barley SNPs into PCR-based markers using dCAPS method

Shahinnia, Fahimeh; Sayed-Tabatabaei, Badraldin Ebrahim

doi:10.1590/s1415-47572009005000047

Cited by 16 publications

(7 citation statements)

References 15 publications

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“…This is consistent with the EST-SSRs distributions reported in other plant species (Ahn et al, 2013;Wang et al, 2014). In plants, SNPs are predominantly beneficial in the construction of high-resolution genetic maps, positional cloning, marker assisted selection (MAS) of important genes, genome wide linkage disequilibrium associate analysis, and species origin, relationship and evolutionary studies (Shahinnia and Sayed-Tabatabaei, 2009).…”

Section: Analysis Of Simple Sequence Repeats (Ssrs)supporting

confidence: 85%

Cambium-specific Transcriptome Analysis of Paulownia to Study the Molecular Impacts of Winter and Spring Seasons on Tree Growth

Perry

Saminathan

Arun

et al. 2020

Preprint

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Paulownia (Paulownia elongata) is a fast growing, multipurpose deciduous hardwood species that grows in a wide range of temperatures from minus 30 degrees celsius to 45 degrees celsius. Seasonal cues influence the secondary growth of tree stems, including cambial activity, wood chemistry, and transition to latewood formation. In this study, a de novo transcriptome approach was conducted to identify the transcripts expressed in vascular cambial tissue from senescent winter and actively growing spring seasons. Illumina paired-end sequenced cambial transcriptome generated 297,049,842 clean reads which finally yielded 61,639 annotated unigenes. Based on non-redundant protein database analyses, Paulownia cambial unigenes shared highest homology (64.8%) with Erythranthe guttata. A total of 35,471 unigenes resulted from KEGG annotation that were mapped to 128 pathways with metabolic pathways dominated among all. Additionally, DEG analysis showed that 2,688 and 7,411 genes were significantly upregulated and downregulated, respectively in spring compared to winter. Interestingly, quite a number of transcripts belonging to heat shock proteins were upregulated in spring season. qPCR expression results of fifteen wood-forming candidate genes involved in hemicellulose, cellulose, lignin, auxin and cytokinin pathways showed that the hemicellulose genes (CSLC4, FUT1, AXY4, GATL1, and IRX19) were significantly upregulated in spring season tissues when compared to winter tissues. In contrast, lignin pathway genes CCR1 and CAD1 were upregulated in winter cambium. Finally, a transcriptome-wide marker analysis identified 11,338 Simple Sequence Repeat (SSRs). The AG/CT dinucleotide repeat predominately represented all SSRs. Altogether, the cambial transcriptomic analysis reported here highlights the molecular events of wood formation during winter and spring. The identification of candidate genes involved in the cambial growth provides a roadmap of wood formation in Paulownia and other trees for the seasonal growth variation.

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Section: Analysis Of Simple Sequence Repeats (Ssrs)supporting

confidence: 85%

Cambium-specific Transcriptome Analysis of Paulownia to Study the Molecular Impacts of Winter and Spring Seasons on Tree Growth

Perry

Saminathan

Arun

et al. 2020

Preprint

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“…They can contribute directly to a phenotype or can be associated with a phenotype as a result of linkage disequilibrium (Neff et al, 1998 ). In plants, SNPs are particularly useful in the construction of high resolution genetic maps, the positional cloning of target loci, marker assisted breeding of important genes, genome wide large-scale linkage disequilibrium associate analysis, DNA fingerprinting, and species origin, relationship and evolutionary studies (Shahinnia and Sayed-Tabatabaei, 2009 ). Most conventional molecular markers, such as restriction fragment length polymorphism (RFLP) and cleaved amplified polymorphic sequence (CAPS), are based on SNPs, i.e., nucleotide substitutions or insertions/deletions (Nasu et al, 2002 ).…”

Section: Discussionmentioning

confidence: 99%

RNA-Seq of Guar (Cyamopsis tetragonoloba, L. Taub.) Leaves: De novo Transcriptome Assembly, Functional Annotation and Development of Genomic Resources

2017

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Genetic improvement in industrially important guar (Cyamopsis tetragonoloba, L. Taub.) crop has been hindered due to the lack of sufficient genomic or transcriptomic resources. In this study, RNA-Seq technology was employed to characterize the transcriptome of leaf tissues from two guar varieties, namely, M-83 and RGC-1066. Approximately 30 million high-quality pair-end reads of each variety generated by Illumina HiSeq platform were used for de novo assembly by Trinity program. A total of 62,146 non-redundant unigenes with an average length of 679 bp were obtained. The quality assessment of assembled unigenes revealed 87.50% of complete and 97.18% partial core eukaryotic genes (CEGs). Sequence similarity analyses and annotation of the unigenes against non-redundant protein (Nr) and Gene Ontology (GO) databases identified 175,882 GO annotations. A total of 11,308 guar unigenes were annotated with various enzyme codes (EC) and categorized in six categories with 55 subclasses. The annotation of biochemical pathways resulted in a total of 11,971 unigenes assigned with 145 KEGG maps and 1759 enzyme codes. The species distribution analysis of the unigenes showed highest similarity with Glycine max genes. A total of 5773 potential simple sequence repeats (SSRs) and 3594 high-quality single nucleotide polymorphisms (SNPs) were identified. Out of 20 randomly selected SSRs for wet laboratory validation, 13 showed consistent PCR amplification in both guar varieties. In silico studies identified 145 polymorphic SSR markers in two varieties. To the best of our knowledge, this is the first report on transcriptome analysis and SNPs identification in guar till date.

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“…To detect GR genes more accurately, we developed allele‐specific markers using CAPS technology, a tool to identify single nucleotide polymorphisms (SNPs) effectively and accurately (Shahinnia and Tabatabaei, 2009). Cleaved amplified polymorphic sequence technology combines PCR with RE digestion, with PCR used to obtain subgenome‐specific target fragments and RE digestion to differentiate the target alleles with polymorphic SNP.…”

Section: Methodsmentioning

confidence: 99%

Preliminary Exploration of the Source, Spread, and Distribution of Rht24 Reducing Height in Bread Wheat

et al. 2019

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Rht24 is a major dwarfing allele that not only reduces plant height but also increases grain weight. The objective of this study was to trace the source, spread, and distribution of Rht24 and determine its frequency in conjunction with other important dwarfing alleles for Rht1 (Rht‐B1b), Rht2 (Rht‐D1b), and Rht8. Allele‐specific cleaved amplified polymorphic sequence (CAPS) markers were developed for accurate and effective genotyping of Rht1 and Rht2, and closely linked flanking markers were used for genotyping of Rht8 and Rht24. Marker analysis showed that Rht24 occurs at a higher frequency (84.2%) than other important dwarfing alleles in elite wheat (Triticum aestivum L.) varieties and usually couples with Rht2 or Rht8. Genotyping of old varieties and landraces showed that Rht24 was widely used in wheat breeding before the Green Revolution (GR). ‘Akakomugi’ and ‘Norin 10’, the donors of Rht8 and GR genes Rht1 and Rht2, respectively, harbored Rht24, so Rht24 likely followed the transfer routes of GR genes and Rht8 to spread worldwide. Pedigree analysis showed that many Chinese elite lines and backbone parents were derived from Akakomugi, contributing to the high frequency of Rht24 in Chinese varieties. Additionally, Norin 10‐derived semidwarf varieties from the CIMMYT were widely used in Chinese wheat breeding. Finally, Rht24 was also detected in 30 old Chinese varieties and landraces. Overall, these findings show that the presence of Rht24 in modern Chinese elite varieties originated from Akakomugi, Norin 10, or Chinese landraces. Thus, Rht24 was introgressed early, spread widely, and became genetically fixed in a wide range of modern Chinese wheat germplasm.

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Conversion of barley SNPs into PCR-based markers using dCAPS method

Cited by 16 publications

References 15 publications

Cambium-specific Transcriptome Analysis of Paulownia to Study the Molecular Impacts of Winter and Spring Seasons on Tree Growth

Cambium-specific Transcriptome Analysis of Paulownia to Study the Molecular Impacts of Winter and Spring Seasons on Tree Growth

RNA-Seq of Guar (Cyamopsis tetragonoloba, L. Taub.) Leaves: De novo Transcriptome Assembly, Functional Annotation and Development of Genomic Resources

Preliminary Exploration of the Source, Spread, and Distribution of Rht24 Reducing Height in Bread Wheat

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