Development and Evaluation of SSR Markers Based on Large Scale Full-Length Transcriptome Sequencing in Sugarcane

Naiyan, Xiao; Wang, Hengbo; Yao, Wei; Ming, Ray; Zhang, Jisen

doi:10.1007/s12042-020-09260-5

Cited by 8 publications

(26 citation statements)

References 40 publications

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“…The ampli cation e ciency of SSR primers (51.72%) and the development e ciency of polymorphic primers (26.72%) in the full-length transcriptome of C. chekiangoleosa were higher than those in the C. oleifera transcriptome (48.95%, 13.99%) 14 and the P. americana transcriptome (31%, 16%) 33 but lower than those in a previous study on the C. chekiangoleosa genome (65.56%, 31.9%) 19 . Compared with other studies aimed at SSR marker development based on a full-length transcriptome, the SSR primer ampli cation e ciency and polymorphic primer development e ciency achieved in C. chekiangoleosa were lower than those reported in sugarcane (79.1%, 32.6%) 27 , but the polymorphic primer development e ciency was much higher than that in P. wulianensis (18%) 26 .…”

Section: Discussioncontrasting

confidence: 66%

“…For example, Wu et al 26 identi ed 23239 SSRs in 42323 Populus wulianensis transcript sequences, designed 100 EST-SSR markers for veri cation, and nally obtained 88 quali ed markers, 18 of which were polymorphic. Xiao et al obtained 847 (79.16%) ampli able markers from 1070 sugarcane EST-SSR markers, including 349 (32.60%) that were polymorphic 27 . These studies show that it is feasible to develop SSR markers using full-length transcriptome sequences.…”

Section: Introductionmentioning

confidence: 99%

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Microsatellite analysis and polymorphic marker development based on the full-length transcriptome of Camellia chekiangoleosa

Tian

Huang

et al. 2022

Preprint

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Camellia chekiangoleosa is a popular variety of oil-tea camellia and has high oil production and ornamental value. Microsatellite (SSR) markers are the preferred tool for the molecular marker-assisted breeding of C. chekiangoleosa. By focusing on the problems of the low development efficiency of polymorphic SSR markers and lack of available functional markers in oil-tea camellia, we identified 97510 SSR loci based on the full-length transcriptome sequence of C. chekiangoleosa. An analysis of microsatellite characteristics showed that mononucleotide (51.29%) and dinucleotide (34.36%) SSRs were the main repeat types. The main SSR distribution areas based on proportion covered were ordered as follows: 5'UTR > 3'UTR > CDS. By comparing our data with that in databases such as GO and KEGG, we obtained functional annotations of unigene sequences containing SSR sites. The data showed that the amplification efficiency of the SSR primers was 51.72%, and the development efficiency of polymorphic SSR primers was 26.72%. Experiments verified that dinucleotide and pentanucleotide SSRs located in UTR regions could produce more polymorphic markers. An investigation into the genetic diversity of several C. chekiangoleosa populations also suggested that the developed SSR markers had higher levels of polymorphism. This study will provide a reference and high-quality markers for the large-scale development of functional SSR markers and genetic research in oil-tea camellia.

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Section: Discussioncontrasting

confidence: 66%

Section: Introductionmentioning

confidence: 99%

Microsatellite analysis and polymorphic marker development based on the full-length transcriptome of Camellia chekiangoleosa

Tian

Huang

et al. 2022

Preprint

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“…ESTs have aided in the design of DNA microarrays and associated probes in gene function research. Besides, many highly valuable EST-based molecular markers, such as Restriction Fragment Length Polymorphism, Single Nucleotide Polymorphism, Inter Simple Sequence Repeats and Cleaved Amplified Polymorphic Sequences have been achieved ( Xiao et al., 2020 ). EST derived single or low-copy RFLPs applications have proven very useful in the creation of high-density genetic and physical maps ( Xia et al., 2007 ).…”

Section: The Concept Of Molecular or Dna Markersmentioning

confidence: 99%

Basic concepts and methodologies of DNA marker systems in plant molecular breeding

Amiteye

2021

Heliyon

104

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The concepts, methodologies and applications of some of the major molecular or DNA markers commonly used in plant science have been presented. The general principles of molecular marker techniques have been elucidated with detailed explanation of some notable basic concepts associated with marker applications: marker polymorphism, dominant or co-dominant mode of inheritance, agronomic trait-marker linkage, genetic mutations and variation. The molecular marker methods that have been extensively reviewed are RFLP, RAPD, SCAR, AFLP, SSR, CpSSR, ISSR, RAMP, SAMPL, SRAP, SSCP, CAPS, SNP, DArT, EST, and STS. In addition, the practicality of the retrotransposon-based marker methods, IRAP, REMAP, RBIP, and IPBS, have been discussed. Moreover, some salient characteristics of DNA markers have been compared and the various marker systems classified as PCR-or non-PCR-based, dominantly or co-dominantly inherited, locus specific or non-specific as well as at the levels of marker polymorphism and efficiency of marker reproducibility. Furthermore, the principles and methods of the following DNA markers have been highlighted: Penta-primer amplification refractory mutation system (PARMS), Conserved DNA-Derived Polymorphism (CDDP), P450-based analogue (PBA) markers, Tubulin-Based Polymorphism (TBP), Inter-SINE amplified polymorphism (ISAP), Sequence specific amplified polymorphism (S-SAP), Intron length polymorphisms (ILPs), Inter small RNA polymorphism (iSNAP), Direct amplification of length polymorphisms (DALP), Promoter anchored amplified polymorphism (PAAP), Target region amplification polymorphism (TRAP), Conserved region amplification polymorphism (CoRAP), Start Codon Targeted (SCoT) Polymorphism, and Directed Amplification of Minisatellite DNA (DAMD). Some molecular marker applications that have been recently employed to achieve various objectives in plant research have also been outlined. This review will serve as a useful reference resource for plant breeders and other scientists, as well as technicians and students who require basic know-how in the use of molecular or DNA marker technologies.

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“…The most highly represented EST-SSR type was dinucleotide (64.54%); TC/GA was the most common motif (48.46%) followed by CT/AG (39.52%), with other motif types comprising merely 12.02% of all EST-SSR dincleotides. TC/GA was revealed as the most common dinucleotide repeat unit in S. chinensis, which is identical to pigeonpea (Cajanus cajan) and tree rhododendron (Rhododendron arboreum) [26,35] but distinct from barley (Hordeum vulgare), wheat (Triticum aestivum), corn (Zea mays), sorghum (Sorghum bicolor), rice (Oryza sativa) [20], eggplant (Solanum melongena) [19], peanut (Arachis hypogaea) [24], sugarcane (Saccharum officinarum) [36], grass (Miscanthus) [18], daylily (Hemerocallis citrina) [37], Chinese gansui (Euphorbia kansui) [38], thorn pear (Rosa roxburghii) [27], and Chinese yew (Taxus chinensis) [22]. There were 30 types of trinucleotide repeat motifs among S. chinensis ESTs.…”

Section: Characteristics Of Est-ssrsmentioning

confidence: 99%

EST-SSR markers development and application in an important medicinal plant, Schisandra chinensis (Schisandraceae)

Shi

Wang

et al. 2020

Biotechnology & Biotechnological Equipment

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Schisandra chinensis, classed as a climbing woody vine, is representative of the Schisandraceae family regarded as a significant plant in Chinese herbal medicine. However, the application of molecular breeding is constrained by the fact that the number of genetic markers is small for this species. In this study, transcriptome sequencing of S. chinensis was performed using the Illumina HiSeq platform to construct a library of expressed sequence tag-simple sequence repeat (EST-SSR) markers. A total of 59,786 unigenes were obtained on the basis of 8.57 Gbp clean data. A total of 3460 putative SSR sites were detected with a frequency of 5.79%. The predominant type of repeat markers was dinucleotide (64.54%), followed by trinucleotide (23.87%), hexanucleotide (0.90%), tetranucleotide (0.12%) and pentanucleotide (0.40%). Besides, 50 pairs of EST-SSR primers were randomly selected for verification, among which 14 pairs (28%) showed polymorphism in 42 different types of S. chinensis accessions. The mean values of Na, Ne, PIC, Ho, He and SI were 2.71, 1.7642, 0.4295, 0.6016, 0.3934 and 0.6078, respectively. All of the 42 accessions were successfully identified and formed four major clusters, indicating that the EST-SSR markers are applicable for genetic diversity analysis and identification in S. chinensis. According to the result, the transcriptome data are an effective resource for developing SSR markers. These markers can provide a basis for the identification of S. chinensis accessions, genetic diversity analysis, the conservation and construction of genetic linkage maps as part of selective breeding and the conservation efforts for this valuable plant.

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Development and Evaluation of SSR Markers Based on Large Scale Full-Length Transcriptome Sequencing in Sugarcane

Cited by 8 publications

References 40 publications

Microsatellite analysis and polymorphic marker development based on the full-length transcriptome of Camellia chekiangoleosa

Microsatellite analysis and polymorphic marker development based on the full-length transcriptome of Camellia chekiangoleosa

Basic concepts and methodologies of DNA marker systems in plant molecular breeding

EST-SSR markers development and application in an important medicinal plant, Schisandra chinensis (Schisandraceae)

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