High‐throughput development of <scp>SSR</scp> marker candidates and their chromosomal assignment in rye (<i>Secale cereale</i> L.)

Jianjian, Li; Zhou, Ruonan; Endo, Takashi R.; Stein, Nils

doi:10.1111/pbr.12619

Cited by 16 publications

(5 citation statements)

References 83 publications

(111 reference statements)

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“…Overall, the consensus map of rye contains 123 microsatellites. The list of mapped SSRs can be broaden in the future based on 856 SSRs recently found in rye genome shotgun survey sequences (Li et al, 2018).…”

Section: Resultsmentioning

confidence: 99%

The consensus rye microsatellite map with EST-SSRs transferred from wheat

Perović

Semilet

et al. 2020

Vestn. VOGiS

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Microsatellite (SSR) markers with known precise intrachromosomal locations are widely used for mapping genes in rye and for the investigation of wheat-rye translocation lines and triticale highly demanded for mapping economically important genes and QTL-analysis. One of the sources of novel SSR markers in rye are microsatellites transferable from the wheat genome. Broadening the list of available SSRs in rye mapped to chromosomes is still needed, since some rye chromosome maps still have just a few microsatellite loci mapped. The goal of the current study was to integrate wheat EST-SSRs into the existing rye genetic maps and to construct a consensus rye microsatellite map. Four rye mapping populations (P87/P105, N6/N2, N7/N2 and N7/N6) were tested with CFE (EST-SSRs) primers. A total of 23 Xcfe loci were mapped on rye chromosomes: Xcfe023, -136 and -266 on chromosome 1R, Xcfe006, -067, -175 and -187 on 2R, Xcfe029 and -282 on 3R, Xcfe004, -100, -152, -224 and -260 on 4R, Xcfe037, -208 and -270 on 5R, Xcfe124, -159 and -277 on 6R, Xcfe010, -143 and -228 on 7R. With the exception of Xcfe159 and Xcfe224, all the Xcfe loci mapped were found in orthologous positions considering multiple evolutionary translocations in the rye genome relative to those of common wheat. The consensus map was constructed using mapping data from the four bi-parental populations. It contains a total of 123 microsatellites, 12 SNPs, 118 RFLPs and 2 isozyme loci.

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Section: Resultsmentioning

confidence: 99%

The consensus rye microsatellite map with EST-SSRs transferred from wheat

Perović

Semilet

et al. 2020

Vestn. VOGiS

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“…Because of their high abundance and polymorphism, and ubiquitous distribution, SSRs have been extensively used as versatile DNA markers in plant genetic and genomic studies [36]. SSR length and abundance, as well as the motif type, are the key characteristics of microsatellites [37]. Besides complex SSRs, five types of perfect SSRs (mono-/di-/tri-/tetra-/penta-nucleotide repeats) were found in the E. ophiuroides cp genome sequences.…”

Section: Repeat Sequencementioning

confidence: 99%

Molecular Characterization and Phylogenetic Analysis of Centipedegrass [Eremochloa ophiuroides (Munro) Hack.] Based on the Complete Chloroplast Genome Sequence

Wang,

Zhang,

Zhang

et al. 2024

CIMB

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Centipedegrass (Eremochloa ophiuroides) is an important warm-season grass plant used as a turfgrass as well as pasture grass in tropical and subtropical regions, with wide application in land surface greening and soil conservation in South China and southern United States. In this study, the complete cp genome of E. ophiuroides was assembled using high-throughput Illumina sequencing technology. The circle pseudomolecule for E. ophiuroides cp genome is 139,107 bp in length, with a quadripartite structure consisting of a large single copyregion of 82,081 bp and a small single copy region of 12,566 bp separated by a pair of inverted repeat regions of 22,230 bp each. The overall A + T content of the whole genome is 61.60%, showing an asymmetric nucleotide composition. The genome encodes a total of 131 gene species, composed of 20 duplicated genes within the IR regions and 111 unique genes comprising 77 protein-coding genes, 30 transfer RNA genes, and 4 ribosome RNA genes. The complete cp genome sequence contains 51 long repeats and 197 simple sequence repeats, and a high degree of collinearity among E. ophiuroide and other Gramineae plants was disclosed. Phylogenetic analysis showed E. ophiuroides, together with the other two Eremochloa species, is closely related to Mnesithea helferi within the subtribe Rottboelliinae. These findings will be beneficial for the classification and identification of the Eremochloa taxa, phylogenetic resolution, novel gene discovery, and functional genomic studies for the genus Eremochloa.

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“…Because of their abundance, high rate of polymorphism, ubiquitous distribution throughout the genome, and high extent of allelic diversity, SSRs have been extensively used as versatile DNA-based markers in plant genetic and genomic research [39]. The motif type, length and abundance of SSRs are the main characteristics of microsatellites [40]. Besides complex SSRs, ve types of perfect SSRs (mono-/di-/tri-/tetra-/penta-nucleotide repeats) were detected in the E. ophiuroides cp genome sequences.…”

Section: Repeat Sequencementioning

confidence: 99%

Complete Chloroplast Genome Sequence of a Major Warm-Season Turfgrass Species, Centipedegrass [Eremochloa ophiuroides (Munro) Hack.]: Genome Characterization, Comparative and Phylogenetic Analysis

Jianjian¹,

Zong²,

Wang³

et al. 2021

Preprint

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Background: Chloroplast (cp) genome sequence data could provide valuable information for molecular taxonomy and phylogenetic reconstruction among plant species and individuals. However, as one of the most important warm-season turfgrasses widely used in USA and China, cp genome characteristics and phylogenetic position of centipedegrass (Eremochloa ophiuroides) were poorly understood.Results: In this study, we determined the complete chloroplast genome sequences of E. ophiuroides using high-throughput Illumina sequencing technology. The circle pseudomolecule for E. ophiuroides cp genome is 139,107 bp in length, and has a typical quadripartite structure consisting of a pair of inverted repeat (IR) regions of 22,230 bp each separated by a large single copy (LSC) region of 82,081 bp and a small single copy (SSC) region of 12,566 bp. The nucleotide composition of E. ophiuroides cp genome is asymmetric with an overall A + T content of 61.60%. It encodes a total of 131 gene species, composed of 20 duplicated genes within the IR regions and 111 unique genes including 77 protein-coding genes (PCGs), 30 transfer RNA (tRNA) genes and four ribosome RNA (rRNA) genes. Analysis of the repetitive sequences revealed that E. ophiuroides cp genome contains 51 tandem repeats including 29 forward, 20 palindromic and 2 reverse repeats, and 197 simple sequence repeats (SSRs) which were mainly composed of adenine (A) and thymine (T) bases. Comparison of the E. ophiuroides complete cp genome with the genomes of other seven Gramineae species showed a high degree of collinearity among Gramineae plants. Phylogenetic analysis showed that E. ophiuroides was closely related to E. ciliaris and E. eriopoda, and was placed in a clade with the two Eremochloa species and Mnesithea helferi within the subtribe Rottboelliinae, which clarified evolutionary status of E. ophiuroides in tribe Andropogoneae and also authenticated the current taxonomy of the tribe Andropogoneae.Conclusions: The present study provides the complete structure of the E. ophiuroides cp genome, and preliminarily ascertains the phylogenetic position of E. ophiuroides in tribe Andropogonodae. This will be of value to grass taxa identification, phylogenetic resolution, population structure and biodiversity, novel gene discovery and functional genomic studies for the genus Eremochloa.

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High‐throughput development of SSR marker candidates and their chromosomal assignment in rye (Secale cereale L.)

Cited by 16 publications

References 83 publications

The consensus rye microsatellite map with EST-SSRs transferred from wheat

The consensus rye microsatellite map with EST-SSRs transferred from wheat

Molecular Characterization and Phylogenetic Analysis of Centipedegrass [Eremochloa ophiuroides (Munro) Hack.] Based on the Complete Chloroplast Genome Sequence

Complete Chloroplast Genome Sequence of a Major Warm-Season Turfgrass Species, Centipedegrass [Eremochloa ophiuroides (Munro) Hack.]: Genome Characterization, Comparative and Phylogenetic Analysis

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