Utility of EST-derived SSR in cultivated peanut (Arachis hypogaea L.) and Arachis wild species

Liang, Xuanqiang; Chen, Xiaoping; Hong, Yanbin; Liu, Haiyan; Guiyuan, Zhou; Li, Shaoxiong; Guo, Bao‐Zhu

doi:10.1186/1471-2229-9-35

Cited by 158 publications

(131 citation statements)

References 58 publications

(70 reference statements)

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“…But that is different from many crop plants including barley, wheat, maize, rice and peanut, in which tri-nucleotide repeats generally exhibit a higher abundance. Moreover, of all repeat motifs types, AG/CT, AC/GT and AAG/CCT were the most abundant types, similar to sweet potato (Wang et al, 2011), peanut (Liang et al, 2009), and Epimedium . AAG motifs have been observed to commonly present in dicots, such as Arabidopsis (Cardle et al, 2000), Soybean (Gao et al, 2003) and Medicago (Liang et al, 2009).…”

Section: Discussionmentioning

confidence: 90%

SSR Development and Utilization with Rehmannia glutinosa Transcriptome

Li¹,

Yang²,

Feng³

et al. 2016

IJAB

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Rehmannia glutinosa Libosch is a well-known medicinal plant in China. Despite its common use, very few molecular markers are available for this species, severely impeding any improvement of key agronomic traits. In this study, gene-based SSR (simple sequence repeat) markers were mined from the R. glutinosa transcriptome, assembled from leaf and root libraries, to obtain polymorphic information content (PIC). A total of 1,812 SSR (≥18 bp) loci were identified from 1,747 transcripts, in which 1,018 transcripts had significant homology to known proteins, and 35 transcripts were identified as non-coding RNA. Of all SSR loci, AG/GT was the most frequent SSRs repeat type, and bias of base composition presented SSRs loci from noncoding RNA. A set of 279 SSR primers (≥20 bp) were synthesized, of which 204 were successfully amplified in the Wen85-5 genome and 91 had a polymorphic information content between 0.33 and 0.90. Seven pairs of polymorphic SSR primers were selected to evaluate the genetic diversity of 36 R. glutinosa germplasms, and results demonstrated that cultivars are differ considerably from wild strains and that distinct genetic relationships exist among wild strains. The SSRs identified in this study provide critical information for future R. glutinosa breeding.

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Section: Discussionmentioning

confidence: 90%

SSR Development and Utilization with Rehmannia glutinosa Transcriptome

Li¹,

Yang²,

Feng³

et al. 2016

IJAB

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“…Amplification of more than one fragment by primer pairs/markers in peanut was reported in earlier studies (Hopkins et al, 1999;Krishna et al, 2004;Kottapalli et al, 2007;Varshney et al, 2009) and has been attributed to either amplification of duplicated loci or different loci, because of the tetraploid genome. Liang et al (2009) observed 3-18 alleles in wild species, which was attributed mainly to differences in repeat type and length in the microsatellite regions.…”

Section: Discussionmentioning

confidence: 99%

Identification of stable sources for surrogate traits in Arachis glabrata and marker-trait association for tolerance to water deficit stress

Bera¹,

Chandrashekar²,

Patel³

et al. 2014

Turk J Bot

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Diploid and tetraploid wild relatives of cultivated peanut are genetically diverse, providing rich sources of genetic resources for tapping resistance to various biotic and abiotic stresses. Arachis glabrata Benth. is a tetraploid (2n = 40) rhizomatous species that is reported to be tolerant to water deficit stress. Identification of A. glabrata accessions with high SPAD chlorophyll meter reading (SCMR) and low specific leaf area (SLA) values would be an option for improving water deficit stress tolerance in peanut. An investigation was undertaken to study the genetic diversity of A. glabrata accessions using molecular markers as well as surrogate traits (SLA and SCMR) for water deficit stress to identify stable sources for SCMR and to identify DNA markers linked to SCMR. SCMR showed high heritability and genetic advance as percent of mean (GAM) and a negative relation with SLA in A. glabrata. High heritability and high GAM indicates additive gene action. A high level of genetic diversity was observed in A. glabrata accessions, indicating that these populations had not experienced major genetic bottlenecks or genetic drift. Eight random amplified polymorphic DNA markers were identified with significant association to SCMR.

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“…Due to the vast amount of ESTs deposited in public databases, a large number of EST-SSRs have been developed, and the polymorphism and transferability of EST-SSRs were checked in many plant species (Aggarwal et al, 2007;Luro et al,2008;Poncet et al, 2006) including cereals (Kantety et al,2002), wheat (Yu et al, 2004), citrus (Chen et al,2006), coffee (Aggarwal et al, 2007), rubber (Feng et al, 2009), chickpea (Choudhary et al, 2009), peanut (Liang et al,2009) and grape (Huang et al, 2011).…”

Section: Est-ssr Primer Designmentioning

confidence: 99%

Development of EST-SSR Markers to Assess Genetic Diversity in Elettaria Cardamomum Maton

Anjali

Dharan²,

Nadiya

et al. 2015

Int J Appl Sci Biotechnol

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Elettaria cardamomum Maton is one of the most ancient and valuable spice crops. Cardamom is cultivated following intensive pesticide usage where alleles present in the wild cardamom genotypes could positively contribute towards genetic improvement of the cultivars. However, the genetic map or whole-genome sequence of E. cardamomum is not available and very limited information on simple sequence repeat (SSR) markers are publicly available. We have tested whether SSRs from Curcuma longa can be used to analyze genetic diversity E. cardamomum.Int J Appl Sci Biotechnol, Vol 3(2): 188-192 DOI: http://dx.doi.org/10.3126/ijasbt.v3i2.12380

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Utility of EST-derived SSR in cultivated peanut (Arachis hypogaea L.) and Arachis wild species

Cited by 158 publications

References 58 publications

SSR Development and Utilization with Rehmannia glutinosa Transcriptome

SSR Development and Utilization with Rehmannia glutinosa Transcriptome

Identification of stable sources for surrogate traits in Arachis glabrata and marker-trait association for tolerance to water deficit stress

Development of EST-SSR Markers to Assess Genetic Diversity in Elettaria Cardamomum Maton

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