Development and validation of simple sequence repeat markers from Arachis hypogaea transcript sequences

Wang, Houmiao; Lei, Yong; Yan, Liying; Wan, Ling‐Shu; Cai, Yan; Yang, Zefeng; Lv, Jianwei; Zhang, Xiaojie; Xu, Chenwu; Liao, Boshou

doi:10.1016/j.cj.2017.09.007

Cited by 17 publications

(22 citation statements)

References 51 publications

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“…For our work, among 33,974 assembled unigene sequences, 2644 potential EST-SSRs were identified, which represented ∼7.78% of the transcriptomic sequences ( Supplementary Table S2), and the distribution density was one SSR per 10.30 kb. The SSRs frequency and distribution density were higher than some species, such as Argyranthemum broussonetii (2.3%, 27 kb) (White et al, 2016) and Zingiber officinale (2.7%, 25.2 kb) (Awasthi et al, 2017), and lower than Arachis hypogaea (17.7%, 3.3 kb) (Wang et al, 2018), Curcuma longa (14.6%, 5.3 kb; 14.9%, 5.2 kb; 20.5%, 4.8 kb) (Annadurai et al, 2013), and Curcuma alismatifolia (12.5%, 6.6 kb) (Taheri et al, 2019). Differences in the frequency of SSRs in ESTs could be partially attributed to the different genetic basis of various plant species, the size of the unigene assembly dataset, SSR search criteria, sequence redundancy, as well as the mining tools utilized (Kumpatla and Mukhopadhyay, 2005;Chen et al, 2015;Wei et al, 2016;Liu et al, 2018;Taheri et al, 2019).…”

Section: Discussion the Development Of Est-ssrs Markers Based On Opismentioning

confidence: 86%

“…Meanwhile, the EST-SSR markers developed from Opisthopappus transcriptome data exhibited good transferability across different Opisthopappus species, indicating that these EST-SSR markers were useful tools for further genetic diversity analysis for this genus. The transferable nature of the EST-SSR markers between related species extended their usefulness in plant genetic studies (Varshney et al, 2005;Mathithumilan et al, 2013;Jia et al, 2016;Wang et al, 2018;Park et al, 2019).…”

Section: Figure 4 | Results Of the Bayesian Clustering Analysis Condumentioning

confidence: 99%

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Genetic Divergence and Relationship Among Opisthopappus Species Identified by Development of EST-SSR Markers

Chai

Wang

et al. 2020

Front. Genet.

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Opisthopappus Shih is an endemic and endangered genus restricted to the Taihang Mountains that has important ornamental and economic value. According to the Flora Reipublicae Popularis Sinicae (FRPS, Chinese version), this genus contains two species (Opisthopappus longilobus and Opisthopappus taihangensis), whereas in the Flora of China (English version) only one species O. taihangensis is present. The interspecific phylogenetic relationship remains unclear and undefined, which might primarily be due to the lack of specific molecular markers for phylogenetic analysis. For this study, 2644 expressed sequence tag-simple sequence repeats (EST-SSRs) from 33,974 unigenes using a de novo transcript assembly of Opisthopappus were identified with a distribution frequency of 7.78% total unigenes. Thereinto, mononucleotides (1200, 45.39%) were the dominant repeat motif, followed by trinucleotides (992, 37.52%), and dinucleotides (410, 15.51%). The most dominant trinucleotide repeat motif was ACC/GGT (207, 20.87%). Based on the identified EST-SSRs, 245 among 1444 designed EST-SSR primers were selected for the development of potential molecular markers. Among these markers, 63 pairs of primers (25.71%) generated clear and reproducible bands with expected sizes. Eventually, 11 primer pairs successfully amplified all individuals from the studied populations. Through the EST-SSR markers, a high level of genetic diversity was detected between Opisthopappus populations. A significant genetic differentiation between the O. longilobus and O. taihangensis populations was found. All studied populations were divided into two clusters by UPGMA, NJ, STRUCTURE, and PCoA. These results fully supported the view of the FRPS, namely, that O. longilobus and O. taihangensis should be regarded as two distinct species. Our study demonstrated that transcriptome sequences, as a valuable tool for the quick and cost-effective development of molecular markers, was helpful toward obtaining comprehensive EST-SSR markers that could contribute to an in-depth assessment of the genetic and phylogenetic relationships between Opisthopappus species.

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Section: Discussion the Development Of Est-ssrs Markers Based On Opismentioning

confidence: 86%

Section: Figure 4 | Results Of the Bayesian Clustering Analysis Condumentioning

confidence: 99%

Genetic Divergence and Relationship Among Opisthopappus Species Identified by Development of EST-SSR Markers

Chai

Wang

et al. 2020

Front. Genet.

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“…The cultivated groundnut has been analysed by several marker systems such as Restriction Fragment Length Polymorphism (RFLP), Random Amplified Polymorphic DNA (RAPD), Amplified Fragment Length Polymorphism (AFLP), Single Nucleotide Polymorphism (SNPs) and Simple Sequence Repeat markers (SSR) (Stalker and Mozingo 2001;Zhao et al 2016). Currently, SSR markers are commonly used in groundnut genetic analysis and breeding due to their co-dominance, simplicity, high polymorphism, repeatability, multi-allelic nature and transferability within the genus Arachis (He et al 2003;Pandey et al 2012;Wang et al 2018). Mondal et al (2012) identified three and four SSR alleles which were found associated with rust and late leaf spot resistance in groundnut, respectively.…”

Section: Genomic Toolsmentioning

confidence: 99%

“…About 376 highly informative SSR markers linked to resistance to early leaf spot, groundnut rosette disease, and rust and aflatoxin contamination across African cultivated groundnut varieties were identified useful to identify suitable parents for mapping populations or breeding (Kanyika et al 2015). There is approximately 14 392 publicly available SSR markers in the A. hypogeae database (Wang et al 2018). Recently, about 210 new SSRs were developed for A. hypogaea useful for genetic diversity analysis and cultivar development (Wang et al 2018).…”

Section: Genomic Toolsmentioning

confidence: 99%

“…There is approximately 14 392 publicly available SSR markers in the A. hypogeae database (Wang et al 2018). Recently, about 210 new SSRs were developed for A. hypogaea useful for genetic diversity analysis and cultivar development (Wang et al 2018). In addition, SSR markers have been developed specifically for different Arachis species such as A. duranensis A. paensis and A. stenosperma (Zhao et al 2012).…”

Section: Genomic Toolsmentioning

confidence: 99%

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Groundnut (Arachis hypogaeaL.) improvement in sub-Saharan Africa: a review

Abady

Shimelis

Janila

et al. 2019

Acta Agriculturae Scandinavica, Section B — Soil & Plant Sc

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Groundnut (Arachis hypogaea L.) is a multipurpose legume crop widely cultivated in sub-Saharan Africa (SSA). However, yield levels of the crop has remained relatively low in SSA owing to a range of biotic, abiotic and socioeconomic constraints. A dedicated groundnut improvement programme integrating new tools and methodologies to breed varieties suitable for current and emerging agro-ecologies and market needs is essential for enhanced and sustainable groundnut production in SSA. The objective of this review is to highlight breeding progress, opportunities and challenges on groundnut improvement with regard to cultivar development and deployment in SSA in order to guide future improvement of the crop. The review analysed the role of new tools in breeding such as, high-throughput and automated phenotyping techniques, rapid generation advancement, single seed descent approach, marker-assisted selection, genomic selection, next-generation sequencing, genetic engineering and genome editing for accelerated breeding and cultivar development of groundnut.

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De novo transcriptome assembly and development of EST-SSR markers for Pterocarpus santalinus L. f. (Red sanders), a threatened and endemic tree of India

Agasthikumar

Patturaj

Samji

et al. 2022

Genet Resour Crop Evol

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The endemic and precious timber Pterocarpus santalinus L. f. (Red sanders) is a drought hardy tree species for conservation in peninsular India due to its high risk of illegal timber harvest. It is only found in Eastern Ghats of India, and has become threatened owing to overexploitation of its valuable timber. The development of genomic resources, particularly simple sequence repeat (SSR) markers, is essential for strict implementation of in situ conservation measures and application of DNA information based red sanders genetic resource management. However, a lack of genomic data and e cient molecular markers limit the study of its spatial and temporal population genetic structure, identi cation of diversity hotspots and tree improvement. The current study aims at comprehensive molecular characterization of red sanders and the somatic chromosome counts, ow cytometry and EST-SSR analyses. The results revealed that red sanders is diploid with 2n=20 and the 2C genome size was 0.7872 ± 0.0561pg for the rst time in this species. A total of 3128 EST-SSRs were detected based on 25,854 de novo assembled unigenes from transcriptome data and primer sets designed for 1953 SSRs. Fifty-nine EST-SSR markers were evaluated for polymorphism in the natural populations of red sanders and 13 were found to be suitable for genetic analysis. Two major transcription factor families bHLH and ERF, responsible for abiotic stress and secondary metabolite synthesis were analysed which would provide the foundation for further research on production of medicinally important biocompounds.

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Development and validation of simple sequence repeat markers from Arachis hypogaea transcript sequences

Cited by 17 publications

References 51 publications

Genetic Divergence and Relationship Among Opisthopappus Species Identified by Development of EST-SSR Markers

Genetic Divergence and Relationship Among Opisthopappus Species Identified by Development of EST-SSR Markers

Groundnut (Arachis hypogaeaL.) improvement in sub-Saharan Africa: a review

De novo transcriptome assembly and development of EST-SSR markers for Pterocarpus santalinus L. f. (Red sanders), a threatened and endemic tree of India

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