Development of RNA-seq-based molecular markers for characterizing Thinopyrum bessarabicum and Secale introgressions in wheat

Sequence-based markers have added a new dimension in the efficiency of identifying alien introgressions in wheat. Expressed sequence tag-sequence tagged sites (EST-STS) markers have proved useful in tracing alien chromatin. In this study, we report the development of Thinopyrum bessarabicum- and Secale anatolicum-specific EST-STS markers and their application in tracing respective alien chromatin introgressions in wheat. The parental lines, Chinese Spring (CS), ISR991.1 (CS/Th. bessarabicum amphidiploid), and ISR1049.2 (CS/Secale anatolicum amphidiploid), were used as core experimental materials. Using comparative analysis of RNA-Seq data, 10 903 and 10 660 candidate sequences specific to Th. bessarabicum and S. anatolicum, respectively, were assembled and identified. To validate the genome specificity of these candidate sequences, 68 and 64 EST-STS markers were developed from randomly selected candidate sequences of Th. bessarabicum and S. anatolicum, respectively, and tested on sets of alien addition lines. Fifty-five and 53 markers for Th. bessarabicum and S. anatolicum chromatin, respectively, were assigned to chromosomal location(s), covering all seven chromosomes. Approximately 83% of S. anatolicum-specific markers were transferable to S. cereale. The genome-specific candidate sequences identified and the EST-STS markers developed will be valuable resources for exploitation of Th. bessarabicum and Secale species diversity in wheat and triticale breeding.

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A Novel Software and Method for the Efficient Development of Polymorphic SSR Loci Based on Transcriptome Data

Genes ◽

10.3390/genes10110917 ◽

2019 ◽

Vol 10 (11) ◽

pp. 917

Author(s):

Ruizheng Tian ◽

Cunhuan Zhang ◽

Yixiao Huang ◽

Xin Guo ◽

Maohua Chen

Keyword(s):

Expressed Sequence Tag ◽

The Body ◽

Pea Aphid ◽

New Method ◽

Transcriptome Data ◽

Rna Seq ◽

Ssr Loci ◽

Polymorphic Microsatellite ◽

Expressed Sequence ◽

Simple Sequence

Traditional methods for developing polymorphic microsatellite loci without reference sequences are time-consuming and labor-intensive, and the polymorphisms of simple sequence repeat (SSR) loci developed from expressed sequence tag (EST) databases are generally poor. To address this issue, in this study, we developed a new software (PSSRdt) and established an effective method for directly obtaining polymorphism details of SSR loci by analyzing diverse transcriptome data. The new method includes three steps, raw data processing, PSSRdt application, and loci extraction and verification. To test the practicality of the method, we successfully obtained 1940 potential polymorphic SSRs from the transcript dataset combined with 44 pea aphid transcriptomes. Fifty-two SSR loci obtained by the new method were selected for validating the polymorphic characteristics by genotyping in pea aphid individuals. The results showed that over 92% of SSR loci were polymorphic and 73.1% of loci were highly polymorphic. Our new software and method provide an innovative approach to microsatellite development based on RNA-seq data, and open a new path for the rapid mining of numerous loci with polymorphism to add to the body of research on microsatellites.

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A 1Ns Disomic Addition from Psathyrostachys Huashanica Keng Confers Resistance to Powdery Mildew in Wheat

Agronomy ◽

10.3390/agronomy10020312 ◽

2020 ◽

Vol 10 (2) ◽

pp. 312

Author(s):

Jing Han ◽

Yuxiu Liu ◽

Chenchen Hou ◽

Jiachuang Li ◽

Jinglin Wang ◽

...

Keyword(s):

Powdery Mildew ◽

Expressed Sequence Tag ◽

Growth Stages ◽

Addition Line ◽

Psathyrostachys Huashanica ◽

Chromosome Configuration ◽

Sts Markers ◽

Strong Hybridization ◽

Expressed Sequence

Powdery mildew is a fungal disease that threatens wheat production throughout the world. Breeding resistant cultivars is an effective way to reduce harm caused by powdery mildew. In this study, 35 wheat-Psathyrostachys huashanica-derived lines were developed by crossing common wheat and P. huashanica Keng (2n = 2x = 14, NsNs) using embryo culture. Resistance to powdery mildew in the derived lines was identified at the seedling and adult stages. Line H5-5-4-2 was selected with immunity to powdery mildew at both growth stages. The chromosome structure of this line was characterized by cytology, genomic in situ hybridization (GISH), and expressed sequence tag-sequence-tagged site (EST-STS) analysis. The chromosome configuration was 2n = 44 = 22II. Two P. huashanica chromosomes with strong hybridization signals were detected by GISH analysis. Among 83 EST-STS markers that covered all seven homologous groups in wheat, three pairs of STS markers, BE497584, BF202643, and BG262410, located in wheat homologous group 1 amplified clear specific bands related to P. huashanica. The results indicated that resistant line H5-5-4-2 was a wheat-P. huashanica 1Ns disomic addition line.

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Genome Update of Botrytis cinerea Strains B05.10 and T4

Eukaryotic Cell ◽

10.1128/ec.00164-12 ◽

2012 ◽

Vol 11 (11) ◽

pp. 1413-1414 ◽

Cited By ~ 89

Author(s):

Martijn Staats ◽

Jan A. L. van Kan

Keyword(s):

Botrytis Cinerea ◽

Expressed Sequence Tag ◽

De Novo ◽

Rna Seq ◽

High Coverage ◽

Protein Coding ◽

Content Type ◽

Gene Predictor ◽

Structure Annotation ◽

Expressed Sequence

ABSTRACT We report here an update of the Botrytis cinerea strains B05.10 and T4 genomes, as well as an automated preliminary gene structure annotation. High-coverage de novo assemblies and reference-based alignments led to a correction of wrong base calls, elimination of sequence gaps, and improved joining of contigs. The new assemblies have substantially lower numbers of scaffolds and a concomitant increase in the N 50 .The list of protein-coding genes was generated using the evidence-driven gene predictor Augustus, with expressed sequence tag evidence and RNA-Seq data as input.

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Fine Mapping of Leaf Rust Resistance Gene LrZH84 Using Expressed Sequence Tag and Sequence-Tagged Site Markers, and Allelism with Other Genes on Wheat Chromosome 1B

Phytopathology ◽

10.1094/phyto-08-12-0186-r ◽

2013 ◽

Vol 103 (2) ◽

pp. 169-174 ◽

Cited By ~ 7

Author(s):

Yue Zhou ◽

Xianchun Xia ◽

Zhonghu He ◽

Xing Li ◽

Zaifeng Li ◽

...

Keyword(s):

Leaf Rust ◽

Resistance Gene ◽

Fine Mapping ◽

Rust Resistance ◽

Expressed Sequence Tag ◽

Leaf Rust Resistance ◽

Rust Resistance Gene ◽

Leaf Rust Resistance Gene ◽

Sts Markers ◽

Expressed Sequence

Zhou 8425B, possessing the leaf rust resistance gene LrZH84, is an elite wheat (Triticum aestivum) parental line in the Yellow-Huai Valley region of China. In the present study, 2,086 F2 plants derived from Zhou 8425B/Chinese Spring were used for fine mapping of LrZH84 with expressed sequence tag (EST) and sequence-tagged site (STS) markers. Seventy inter-simple sequence repeat EST and STS markers on 1BL were used to screen the two parents and resistant and susceptible bulks; those polymorphic were used to analyze the entire F2 population. Three EST markers (BF474863, BE497107, and CD373538) were closely linked to LrZH84, with genetic distances of 0.7, 0.7, and 1.7 cM, respectively. STS marker Hbsf-1 was developed from the sequences of polymerase chain reaction fragments amplified from EST marker BF474863. LrZH84 was 8.19 cM proximal to Lr44, but may be allelic to LrXi and LrG98 although they showed different reactions with some Puccinia triticina pathotypes.

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Evolutionary Character of Alternative Splicing in Plants

Bioinformatics and Biology Insights ◽

10.4137/bbi.s33716 ◽

2015 ◽

Vol 9s1 ◽

pp. BBI.S33716 ◽

Cited By ~ 14

Author(s):

Chengjun Zhang ◽

Hong Yang ◽

Huizhao Yang

Keyword(s):

Alternative Splicing ◽

Functional Diversity ◽

Expressed Sequence Tag ◽

Standard Protocol ◽

Environmental Response ◽

Rna Seq ◽

Gene Set ◽

Expressed Sequence

Alternative splicing (AS) is one of the most important ways to enhance the functional diversity of genes. Huge amounts of data have been produced by microarray, expressed sequence tag, and RNA-seq, and plenty of methods have been developed specifically for this task. The most frequently asked questions in previous research were as follows. What is the content rate of AS genes among the whole gene set? How many AS types are presented in the genome, and which type is dominant? How about the conservation ability of AS among different species? Which kinds of isoforms from some genes have the environmental response to help individual adaptation? Based on this background, we collected analysis results from 17 species to try to map out the landscape of AS studies in plants. We have noted the shortages of previous results, and we appeal to all scientists working in the AS field to make a standard protocol so that analyses between different projects are comparable.

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Survey of a cDNA library from the turkey (Meleagris gallopavo)

Genome ◽

10.1139/g04-088 ◽

2005 ◽

Vol 48 (1) ◽

pp. 12-17 ◽

Cited By ~ 14

Author(s):

L D Chaves ◽

J A Rowe ◽

K M Reed

Keyword(s):

Single Nucleotide Polymorphism ◽

Expressed Sequence Tags ◽

Expressed Sequence Tag ◽

Meleagris Gallopavo ◽

Whole Genome Sequence ◽

Snp Discovery ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Important Species ◽

Expressed Sequence

Genome characterization and analysis is an imperative step in identifying and selectively breeding for improved traits of agriculturally important species. Expressed sequence tags (ESTs) represent a transcribed portion of the genome and are an effective way to identify genes within a species. Downstream applications of EST projects include DNA microarray construction and interspecies comparisons. In this study, 694 ESTs were sequenced and analyzed from a library derived from a 24-day-old turkey embryo. The 437 unique sequences identified were divided into 76 assembled contigs and 361 singletons. The majority of significant comparative matches occurred between the turkey sequences and sequences reported from the chicken. Whole genome sequence from the chicken was used to identify potential exon–intron boundaries for selected turkey clones and intron-amplifying primers were developed for sequence analysis and single nucleotide polymorphism (SNP) discovery. Identified SNPs were genotyped for linkage analysis on two turkey reference populations. This study significantly increases the number of EST sequences available for the turkey.Key words: turkey, cDNA, expressed sequence tag, single nucleotide polymorphism.

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Screening and analysis of differentially expressed genes from an alien addition line of wheat Thinopyrum intermedium induced by barley yellow dwarf virus infection

Genome ◽

10.1139/g04-070 ◽

2004 ◽

Vol 47 (6) ◽

pp. 1114-1121 ◽

Cited By ~ 8

Author(s):

Shu-Mei Jiang ◽

Long Zhang ◽

Jun Hu ◽

Rui Shi ◽

Guang-He Zhou ◽

...

Keyword(s):

Differentially Expressed Genes ◽

Expressed Sequence Tag ◽

Barley Yellow Dwarf Virus ◽

Differentially Expressed ◽

Addition Line ◽

Alien Chromosome ◽

Thinopyrum Intermedium ◽

Barley Yellow Dwarf ◽

Yellow Dwarf Virus ◽

Expressed Sequence

The alien addition line TAI-27 contains a pair of chromosomes of Thinopyrum intermedium that carry resistance against barley yellow dwarf virus (BYDV). A subtractive library was constructed using the leaves of TAI-27, which were infected by Schizaphis graminum carrying the GAV strain of BYDV, and the control at the three-leaf stage. Nine differentially expressed genes were identified from 100 randomly picked clones and sequenced. Two of the nine clones were highly homologous with known genes. Of the remaining seven cDNA clones, five clones matched with known expressed sequence tag (EST) sequences from wheat and (or) barley whereas the other two clones were unknown. Five of the nine differentially expressed sequences (WTJ9, WTJ11, WTJ15, WTJ19, and WTJ32) were highly homologous (identities >94%) with ESTs from wheat or barley challenged with pathogens. These five sequences and another one (WTJ18) were also highly homologous (identities >86%) with abiotic stress induced ESTs in wheat or barley. Reverse Northern hybridization showed that seven of the nine differentially expressed cDNA sequences hybridized with cDNA of T. intermedium infected by BYDV. Three of these also hybridized with cDNA of line 3B-2 (a parent of TAI-27) infected by BYDV. The alien chromosome in TAI-27 was microdissected. The second round linker adaptor mediated PCR products of the alien chromosomal DNA were labeled with digoxygenin and used as the probe to hybridize with the nine differentially expressed genes. The analysis showed that seven differentially expressed genes were homologous with the alien chromosome of TAI-27. These seven differentially expressed sequences could be used as ESTs of the alien chromosome of TAI-27. This research laid the foundation for screening and cloning of new specific functional genes conferring resistance to BYDV and probably other pathogens.Key words: suppression subtractive hybridization (SSH), expressed sequence tag (EST), linker adaptor mediated polymerase chain reaction (LA-PCR), chromosome microdissection.

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Characterization of expressed sequence tag-derived simple sequence repeat markers for 17 Linum species

Botany ◽

10.1139/b10-019 ◽

2010 ◽

Vol 88 (5) ◽

pp. 537-543 ◽

Cited By ~ 11

Author(s):

Yong-Bi Fu ◽

Gregory W. Peterson

Keyword(s):

Simple Sequence Repeat ◽

Expressed Sequence Tag ◽

Sequence Repeat ◽

Simple Sequence Repeat Markers ◽

Linum Usitatissimum L ◽

Evolutionary Studies ◽

Expressed Sequence ◽

Simple Sequence ◽

Cultivated Flax

One major challenge in genetic and evolutionary studies of wild flax species is the lack of informative molecular markers. A set of 100 informative expressed sequence tag-derived simple sequence repeat (EST-SSR) primer pairs developed in cultivated flax ( Linum usitatissimum L.) were characterized on 35 Linum accessions representing 17 Linum species for their transferability to other Linum species. Ninety-nine primer pairs displayed scorable polymorphisms across 35 Linum samples and generated 627 bands likely from 121 loci. About 50% of the detected bands occurred only in three or fewer samples. A total of 393 bands, likely from 116 loci, were detected by 97 primer pairs in Linum bienne Mill. samples, but only up to 60 bands, likely from up to 39 loci, were revealed by 6 to 37 primer pairs in the samples of the other 15 Linum species. The L. bienne samples displayed 23.7% more EST-SSR variation than the L. usitatissimum samples. These characterized EST-SSR markers should be useful for future genetic diversity and evolutionary studies of Linum species, particularly for the progenitor of cultivated flax.

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