Differential transferability of EST-SSR primers developed from the diploid species Pseudoroegneria spicata, Thinopyrum bessarabicum, and Thinopyrum elongatum

Genome ◽  
2017 ◽  
Vol 60 (6) ◽  
pp. 530-536 ◽  
Author(s):  
Richard R.-C. Wang ◽  
Steve R. Larson ◽  
Kevin B. Jensen
Keyword(s):  
Expressed Sequence Tag ◽  
Genome Mapping ◽  
Diploid Species ◽  
Genetic Maps ◽  
Pseudoroegneria Spicata ◽  
Ssr Primers ◽  
Polymorphic Species ◽  
Thinopyrum Bessarabicum ◽  
Species Specific ◽  
Thinopyrum Elongatum

Simple sequence repeat technology based on expressed sequence tag (EST-SSR) is a useful genomic tool for genome mapping, characterizing plant species relationships, elucidating genome evolution, and tracing genes on alien chromosome segments. EST-SSR primers developed from three perennial diploid species of Triticeae, Pseudoroegneria spicata (Pursh) Á. Löve (having St genome), Thinopyrum bessarabicum (Savul. & Rayss) Á. Löve (Jb = Eb = J), and Thinopyrum elongatum (Host) D.R. Dewey (Je = Ee = E), were used to produce amplicons in these three species to (i) assess relative transferability, (ii) identify polymorphic species-specific markers, and (iii) determine genome relationships among the three species. Because of the close relationship between Jb and Je genomes, EST-SSR primers derived from Th. bessarabicum and Th. elongatum had greater transferability to each other than those derived from the St-genome P. spicata. A large number of polymorphic species- and genome-specific EST-SSR amplicons were identified that will be used for construction of genetic maps of these diploid species, and tracing economically useful genes in breeding or gene transfer programs in various species of Triticeae.

Genome evolution of intermediate wheatgrass as revealed by EST-SSR markers developed from its three progenitor diploid species

Genome ◽  
2015 ◽  
Vol 58 (2) ◽  
pp. 63-70 ◽  
Author(s):  
Richard R.-C. Wang ◽  
Steve R. Larson ◽  
Kevin B. Jensen ◽  
B. Shaun Bushman ◽  
Lee R. DeHaan ◽  
...  
Keyword(s):  
Scientific Literature ◽  
Diploid Species ◽  
Triticum Aestivum L ◽  
Thinopyrum Intermedium ◽  
Forage Crop ◽  
Intermediate Wheatgrass ◽  
Ssr Primers ◽  
Thinopyrum Bessarabicum ◽  
Thinopyrum Elongatum ◽  
Available Information

Intermediate wheatgrass (Thinopyrum intermedium (Host) Barkworth & D.R. Dewey), a segmental autoallohexaploid (2n = 6x = 42), is not only an important forage crop but also a valuable gene reservoir for wheat (Triticum aestivum L.) improvement. Throughout the scientific literature, there continues to be disagreement as to the origin of the different genomes in intermediate wheatgrass. Genotypic data obtained from newly developed EST-SSR primers derived from the putative progenitor diploid species Pseudoroegneria spicata (Pursh) Á. Löve (St genome), Thinopyrum bessarabicum (Savul. & Rayss) Á. Löve (J = Jb = Eb), and Thinopyrum elongatum (Host) D. Dewey (E = Je = Ee) indicate that the V genome of Dasypyrum (Coss. & Durieu) T. Durand is not one of the three genomes in intermediate wheatgrass. Based on all available information in the literature and findings in this study, the genomic designation of intermediate wheatgrass should be changed to JvsJrSt, where Jvs and Jr represent ancestral genomes of present-day Jb of Th. bessarabicum and Je of Th. elongatum, with Jvs being more ancient. Furthermore, the information suggests that the St genome in intermediate wheatgrass is most similar to the present-day St found in diploid species of Pseudoroegneria from Eurasia.

Dilemma of genome relationship in the diploid species Thinopyrum bessarabicum and Thinopyrum elongatum (Triticeae: Poaceae)

Genome ◽  
1990 ◽  
Vol 33 (6) ◽  
pp. 944-946 ◽  
Author(s):  
Prem P. Jauhar
Keyword(s):  
Chromosome Pairing ◽  
Constitutive Heterochromatin ◽  
Diploid Species ◽  
Total Content ◽  
Ploidy Levels ◽  
5S Dna ◽  
Thinopyrum Bessarabicum ◽  
Thinopyrum Elongatum ◽  
Relationship Of ◽  
The Relationship

Evidence on the relationship of the J genome of diploid Thinopyrum bessarabicum and the E genome of diploid Thinopyrum elongatum (= Lophopyrum elongatum) is discussed. Low chromosome pairing between J and E at different ploidy levels, suppression of J–E pairing by the Ph1 pairing regulator that inhibits homoeologous pairing, complete sterility of the diploid hybrids (JE), karyotypic differentiation of the two genomes and differences in their biochemical organization as reflected in total content and distribution of constitutive heterochromatin, and marked differences in isozymes, 5S DNA, and rDNA indicate that J and E are distinct genomes. These genomes are homoeologous and not homologous. There is no justification for the merger of J and E genomes.Key words: chromosome pairing, Ph1 pairing regulator, C-banding, isozymes, 5S DNA, rDNA.

The heterochromatin distribution and genome evolution in diploid species of Elymus and Agropyron

1984 ◽  
Vol 26 (6) ◽  
pp. 669-678 ◽  
Author(s):  
T. Ryu Endo ◽  
Bikram S. Gill
Keyword(s):  
Diploid Species ◽  
Banding Technique ◽  
Agropyron Elongatum ◽  
Pseudoroegneria Spicata ◽  
Banding Patterns ◽  
C Banding ◽  
Psathyrostachys Juncea ◽  
High Level ◽  
Thinopyrum Elongatum ◽  
Genome Designation

The acetocarmine–Giemsa C-banding technique was used to study heterochromatin distribution in somatic chromosomes of diploid Elymus junceus (= Psathyrostachys juncea) (2n = 14) (genome designation Ju = N) and nine diploid Agropyron species (2n = 14): A. cristatum (C = P), A. imbricatum (C = P), A. elongatum (= Elytrigia elongata = Thinopyrum elongatum) (E = J), A. junceum (= E. bessarabicum = T. bessarabicum) (J = E), A. spicatum (= Pseudoroegneria spicata) (S), A. libanoticum (= P. libanotica) (S), A. ferganense (S), A. stipifolium (= P. stipifolia) (S), and A. velutinum (V). With the exception of A. elongatum and A. velutinum, which were self-fertile, all species were cross-pollinating and self-sterile. The cross-pollinating species showed large terminal C-bands and a high level of C-band polymorphism. Agropyron elongatum, moderately self-fertile, showed small terminal and interstitial bands and a minimal C-band polymorphism. Agropyron velutinum, fully self-fertile, almost totally lacked C-bands. The Ju, C, E, and J genomes appeared to be distinctive and the equivalence of the E and J genomes was not supported from their C-banding patterns. Four species sharing the S genome, A. spicatum, A. libanoticum, A. ferganense, and A. stipifolium had C-band patterns similar to one another, although C-bands were less prominent in A. stipifolium than others.Key words: C-banding, karyotype, wheatgrass, cytology.

scholarly journals Genomic insights from the first chromosome-scale assemblies of oat (Avena spp.) diploid species

BMC Biology ◽  
2019 ◽  
Vol 17 (1) ◽  
Author(s):  
Peter J. Maughan ◽  
Rebekah Lee ◽  
Rachel Walstead ◽  
Robert J. Vickerstaff ◽  
Melissa C. Fogarty ◽  
...  
Keyword(s):  
Diploid Species ◽  
Genetic Maps ◽  
Human Consumption ◽  
Past Century ◽  
Genome Wide ◽  
Species Analysis ◽  
Homoeologous Relationships ◽  
Species Specific ◽  
Nutritional Benefits ◽  
Genome Assemblies

Abstract Background Cultivated hexaploid oat (Common oat; Avena sativa) has held a significant place within the global crop community for centuries; although its cultivation has decreased over the past century, its nutritional benefits have garnered increased interest for human consumption. We report the development of fully annotated, chromosome-scale assemblies for the extant progenitor species of the As- and Cp-subgenomes, Avena atlantica and Avena eriantha respectively. The diploid Avena species serve as important genetic resources for improving common oat’s adaptive and food quality characteristics. Results The A. atlantica and A. eriantha genome assemblies span 3.69 and 3.78 Gb with an N50 of 513 and 535 Mb, respectively. Annotation of the genomes, using sequenced transcriptomes, identified ~ 50,000 gene models in each species—including 2965 resistance gene analogs across both species. Analysis of these assemblies classified much of each genome as repetitive sequence (~ 83%), including species-specific, centromeric-specific, and telomeric-specific repeats. LTR retrotransposons make up most of the classified elements. Genome-wide syntenic comparisons with other members of the Pooideae revealed orthologous relationships, while comparisons with genetic maps from common oat clarified subgenome origins for each of the 21 hexaploid linkage groups. The utility of the diploid genomes was demonstrated by identifying putative candidate genes for flowering time (HD3A) and crown rust resistance (Pc91). We also investigate the phylogenetic relationships among other A- and C-genome Avena species. Conclusions The genomes we report here are the first chromosome-scale assemblies for the tribe Poeae, subtribe Aveninae. Our analyses provide important insight into the evolution and complexity of common hexaploid oat, including subgenome origin, homoeologous relationships, and major intra- and intergenomic rearrangements. They also provide the annotation framework needed to accelerate gene discovery and plant breeding.

DNA sequence-based mapping and comparative genomics of the St genome of Pseudoroegneria spicata (Pursh) Á. Löve versus wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.)

Genome ◽  
2020 ◽  
Vol 63 (9) ◽  
pp. 445-457
Author(s):  
Richard R.-C. Wang ◽  
Xingfeng Li ◽  
Matthew D. Robbins ◽  
Steve R. Larson ◽  
Shaun B. Bushman ◽  
...  
Keyword(s):  
Triticum Aestivum ◽  
Hordeum Vulgare ◽  
Expressed Sequence Tag ◽  
Diploid Species ◽  
Genotyping By Sequencing ◽  
Triticum Aestivum L ◽  
Hordeum Vulgare L ◽  
Forage Crops ◽  
Pseudoroegneria Spicata ◽  
Mapping Populations

Bluebunch wheatgrass (referred to as BBWG) [Pseudoroegneria spicata (Pursh) Á. Löve] is an important rangeland Triticeae grass used for forage, conservation, and restoration. This diploid has the basic St genome that occurs also in many polyploid Triticeae species, which serve as a gene reservoir for wheat improvement. Until now, the St genome in diploid species of Pseudoroegneria has not been mapped. Using a double-cross mapping populations, we mapped 230 expressed sequence tag derived simple sequence repeat (EST-SSR) and 3468 genotyping-by-sequencing (GBS) markers to 14 linkage groups (LGs), two each for the seven homologous groups of the St genome. The 227 GBS markers of BBWG that matched those in a previous study helped identify the unclassified seven LGs of the St sub-genome among 21 LGs of Thinopyrum intermedium (Host) Barkworth & D.R. Dewey. Comparisons of GBS sequences in BBWG to whole-genome sequences in bread wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.) revealed that the St genome shared a homology of 35% and 24%, a synteny of 86% and 84%, and a collinearity of 0.85 and 0.86, with ABD and H, respectively. This first-draft molecular map of the St genome will be useful in breeding cereal and forage crops.

SNP discovery by amplicon sequencing and multiplex SNP genotyping in the allopolyploid species Brassica napusThis article is one of a selection of papers from the conference “Exploiting Genome-wide Association in Oilseed Brassicas: a model for genetic improvement of major OECD crops for sustainable farming”.

Genome ◽  
2010 ◽  
Vol 53 (11) ◽  
pp. 948-956 ◽  
Author(s):  
G. Durstewitz ◽  
A. Polley ◽  
J. Plieske ◽  
H. Luerssen ◽  
E. M. Graner ◽  
...  
Keyword(s):  
Genetic Analysis ◽  
Oilseed Rape ◽  
Expressed Sequence Tag ◽  
Diploid Species ◽  
Amplicon Sequencing ◽  
Snp Markers ◽  
Snp Analysis ◽  
Genome Wide ◽  
A Genome ◽  
Illumina Goldengate

Oilseed rape ( Brassica napus ) is an allotetraploid species consisting of two genomes, derived from B. rapa (A genome) and B. oleracea (C genome). The presence of these two genomes makes single nucleotide polymorphism (SNP) marker identification and SNP analysis more challenging than in diploid species, as for a given locus usually two versions of a DNA sequence (based on the two ancestral genomes) have to be analyzed simultaneously during SNP identification and analysis. One hundred amplicons derived from expressed sequence tag (ESTs) were analyzed to identify SNPs in a panel of oilseed rape varieties and within two sister species representing the ancestral genomes. A total of 604 SNPs were identified, averaging one SNP in every 42 bp. It was possible to clearly discriminate SNPs that are polymorphic between different plant varieties from SNPs differentiating the two ancestral genomes. To validate the identified SNPs for their use in genetic analysis, we have developed Illumina GoldenGate assays for some of the identified SNPs. Through the analysis of a number of oilseed rape varieties and mapping populations with GoldenGate assays, we were able to identify a number of different segregation patterns in allotetraploid oilseed rape. The majority of the identified SNP markers can be readily used for genetic mapping, showing that amplicon sequencing and Illumina GoldenGate assays can be used to reliably identify SNP markers in tetraploid oilseed rape and to convert them into successful SNP assays that can be used for genetic analysis.

Anchored Reference Loci in Loblolly Pine (Pinus taeda L.) for Integrating Pine Genomics

Genetics ◽  
2001 ◽  
Vol 159 (2) ◽  
pp. 799-809 ◽  
Author(s):  
Garth R Brown ◽  
Edward E Kadel ◽  
Daniel L Bassoni ◽  
Kristine L Kiehne ◽  
Berhanu Temesgen ◽  
...  
Keyword(s):  
Pinus Taeda ◽  
Loblolly Pine ◽  
Comparative Mapping ◽  
Expressed Sequence Tag ◽  
Single Species ◽  
Douglas Fir ◽  
Genetic Maps ◽  
Multiple Sources ◽  
Primer Sets ◽  
Pinus Taeda L

Abstract Anchored reference loci provide a framework for comparative mapping. They are landmarks to denote conserved chromosomal segments, allowing the synthesis of genetic maps from multiple sources. We evaluated 90 expressed sequence tag polymorphisms (ESTPs) from loblolly pine (Pinus taeda L.) for this function. Primer sets were assayed for amplification and polymorphism in six pedigrees, representing two subgenera of Pinus and a distant member of the Pinaceae, Douglas-fir (Pseudotsuga menziesii [Mirb.] Franco). On average, 89% of primer sets amplified in four species of subgenus Pinus, 49% in one species of subgenus Strobus, and 22% in Douglas-fir. Polymorphisms were detected for 37–61% of the ESTPs within each pedigree. Comparative mapping in loblolly and slash pine (P. elliottii Englm.) revealed that ESTPs mapped to the same location. Disrupted synteny or significant disruptions in colinearity were not detected. Thirty-five ESTPs met criteria established for anchor loci. The majority of those that did not meet these criteria were excluded when map location was known in only a single species. Anchor loci provide a unifying tool for the community, facilitating the creation of a “generic” pine map and serving as a foundation for studies on genome organization and evolution.

scholarly journals Development of EST-SSR markers based on transcriptome and its validation in ginger (Zingiber officinale Rosc.)

PLoS ONE ◽  
2021 ◽  
Vol 16 (10) ◽  
pp. e0259146
Author(s):  
Venugopal Vidya ◽  
Duraisamy Prasath ◽  
Mohandas Snigdha ◽  
Ramasamy Gobu ◽  
Charles Sona ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Expressed Sequence Tag ◽  
Zingiber Officinale ◽  
Eastern India ◽  
Coding Sequences ◽  
North Eastern ◽  
Ssr Primers ◽  
Ssr Loci ◽  
North Eastern India

Ginger (Zingiber officinale Rosc.) is an economically important and valuable spice crop around the world. It is used as food, spice, condiment, and medicine. A considerable extent of genetic diversity in ginger occurs in the Western Ghats and North-Eastern India. However, genetic diversity studies at the molecular level in ginger is limited due to limited availability of genetic and genomic information. In the present study, for the first time, we have identified and validated expressed sequence tag (EST)-simple sequence repeat (SSR) markers from ginger. We obtained 16,790 EST-SSR loci from 78987 unigenes, and 4597 SSR loci in the predicted 76929 coding sequences from RNA-Seq assembled contigs of ginger through Illumina paired-end sequencing. Gene ontology results indicate that the unigenes with SSR loci participate in various biological processes such as metabolism, growth, and development in ginger. One hundred and twenty-five primer pairs were designed from unigenes and coding sequences. These primers were tested for PCR optimization, characterization, and amplification and identified 12 novel EST-SSR markers. Twelve flanking polymorphic EST-SSR primers were validated using 48 ginger genotypes representing North-Eastern India and different eco-geographical adaptations by PCR amplification and allele sizing through capillary electrophoresis. Twelve EST-SSR primers generated a total of 111 alleles with an average of 9.25 alleles per locus and allele sizes ranging between 115-189bp. This study implies that the SSR markers designed from transcriptome sequences provides ample EST-SSR resources, which are helpful for genetic diversity analysis of Zingiberaceae species and molecular verification of ginger genotypes.

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