Development of trinucleotide (GGC)n SSR markers in peanut (Arachis hypogaea L.)

Yüan, Ming; Gong, Limin; Meng, Ronghua; Li, Shuangling; Dang, Phat; Guo, Bao‐Zhu; Guo, He

doi:10.2225/vol13-issue6-fulltext-6

Cited by 16 publications

(7 citation statements)

References 34 publications

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“…The PIC values of polymorphic primers ranged from 0.028 to 0.375 with an average of 0.325 ( Table 7 ). In general, the PIC values of less than 0.5 is also reported for the EST-SSR markers developed by other research groups in cultivated peanut [ 14 , 87 ], which is evident of low level of polymorphism in those genotypes. It has also been well documented that EST-SSRs are less polymorphic than genomic SSRs because of greater DNA sequence conservation in transcribed regions [ 14 , 88 ].…”

Section: Resultsmentioning

confidence: 55%

Novel and Stress Relevant EST Derived SSR Markers Developed and Validated in Peanut

et al. 2015

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With the aim to increase the number of functional markers in resource poor crop like cultivated peanut (Arachis hypogaea), large numbers of available expressed sequence tags (ESTs) in the public databases, were employed for the development of novel EST derived simple sequence repeat (SSR) markers. From 16424 unigenes, 2784 (16.95%) SSRs containing unigenes having 3373 SSR motifs were identified. Of these, 2027 (72.81%) sequences were annotated and 4124 gene ontology terms were assigned. Among different SSR motif-classes, tri-nucleotide repeats (33.86%) were the most abundant followed by di-nucleotide repeats (27.51%) while AG/CT (20.7%) and AAG/CTT (13.25%) were the most abundant repeat-motifs. A total of 2456 EST-SSR novel primer pairs were designed, of which 366 unigenes having relevance to various stresses and other functions, were PCR validated using a set of 11 diverse peanut genotypes. Of these, 340 (92.62%) primer pairs yielded clear and scorable PCR products and 39 (10.66%) primer pairs exhibited polymorphisms. Overall, the number of alleles per marker ranged from 1-12 with an average of 3.77 and the PIC ranged from 0.028 to 0.375 with an average of 0.325. The identified EST-SSRs not only enriched the existing molecular markers kitty, but would also facilitate the targeted research in marker-trait association for various stresses, inter-specific studies and genetic diversity analysis in peanut.

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Section: Resultsmentioning

confidence: 55%

Novel and Stress Relevant EST Derived SSR Markers Developed and Validated in Peanut

et al. 2015

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“…Those most recently reported include: 14 by Gimenes et al [27]; 51 by Mace et al [28]; 188 by Proite et al [29]; 104 by Cuc et al [30]; 138 by Yuan et al [31]; 33 by Song et al [32]; 123 by Wang et al [33]; 290 by Liang et al [34]; and 1,571 by Koilkonda et al [35]. Five hundred and ninety-eight of these markers are included in the A. duranensis map (Figure 2).…”

Section: Resultsmentioning

confidence: 99%

A high-density genetic map of Arachis duranensis, a diploid ancestor of cultivated peanut

et al. 2012

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BackgroundCultivated peanut (Arachis hypogaea) is an allotetraploid species whose ancestral genomes are most likely derived from the A-genome species, A. duranensis, and the B-genome species, A. ipaensis. The very recent (several millennia) evolutionary origin of A. hypogaea has imposed a bottleneck for allelic and phenotypic diversity within the cultigen. However, wild diploid relatives are a rich source of alleles that could be used for crop improvement and their simpler genomes can be more easily analyzed while providing insight into the structure of the allotetraploid peanut genome. The objective of this research was to establish a high-density genetic map of the diploid species A. duranensis based on de novo generated EST databases. Arachis duranensis was chosen for mapping because it is the A-genome progenitor of cultivated peanut and also in order to circumvent the confounding effects of gene duplication associated with allopolyploidy in A. hypogaea.ResultsMore than one million expressed sequence tag (EST) sequences generated from normalized cDNA libraries of A. duranensis were assembled into 81,116 unique transcripts. Mining this dataset, 1236 EST-SNP markers were developed between two A. duranensis accessions, PI 475887 and Grif 15036. An additional 300 SNP markers also were developed from genomic sequences representing conserved legume orthologs. Of the 1536 SNP markers, 1054 were placed on a genetic map. In addition, 598 EST-SSR markers identified in A. hypogaea assemblies were included in the map along with 37 disease resistance gene candidate (RGC) and 35 other previously published markers. In total, 1724 markers spanning 1081.3 cM over 10 linkage groups were mapped. Gene sequences that provided mapped markers were annotated using similarity searches in three different databases, and gene ontology descriptions were determined using the Medicago Gene Atlas and TAIR databases. Synteny analysis between A. duranensis, Medicago and Glycine revealed significant stretches of conserved gene clusters spread across the peanut genome. A higher level of colinearity was detected between A. duranensis and Glycine than with Medicago.ConclusionsThe first high-density, gene-based linkage map for A. duranensis was generated that can serve as a reference map for both wild and cultivated Arachis species. The markers developed here are valuable resources for the peanut, and more broadly, to the legume research community. The A-genome map will have utility for fine mapping in other peanut species and has already had application for mapping a nematode resistance gene that was introgressed into A. hypogaea from A. cardenasii.

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“…In another study, 138 SSR markers were developed and evaluated on four wild genotypes and 20 cultivated genotypes. The majority of the SSR markers revealed allelic polymorphisms in the wilds while relatively few detected genetic variation among the cultivated types (Yuan et al, 2010). Conversely, high intraspecific variability was observed in a separate study evaluating wild Arachis species using intron sequences and microsatellite markers (Moretzsohn et al, 2012;Stalker and Mozingo, 2001).…”

Section: Molecular and Genomic Variationmentioning

confidence: 90%

“…Molecular markers have been fairly extensively utilized to assess inter-and intraspecific genetic variation in cultivated and wild peanut germplasm (Pandey et al, 2012). Many researchers have found the diversity levels to be low within the cultivated types (Liang et al, 2009;Moretzsohn et al, 2004;Pandey et al, 2012;Stalker and Mozingo, 2001;Yuan et al, 2010) especially when using expressed sequence tag-derived SSRs or diversity arrays technology (DArT) markers. Out of 67 newly developed SSR markers only three were polymorphic in cultivated peanuts (Moretzsohn et al, 2004).…”

Section: Molecular and Genomic Variationmentioning

confidence: 99%

Global Resources of Genetic Diversity in Peanut

Barkley

Upadhyaya

Liao

et al. 2016

Peanuts

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This chapter was originally published in the book Peanuts. The copy attached is provided by Elsevier for the author's benefit and for the benefit of the author's institution, for non-commercial research, and educational use. This includes without limitation use in instruction at your institution, distribution to specific colleagues, and providing a copy to your institution's administrator. All other uses, reproduction and distribution, including without limitation commercial reprints, selling or licensing copies or access, or posting on open internet sites, your personal or institution's website or repository, are prohibited. For exceptions, permission may be sought for such use through Elsevier's

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Development of trinucleotide (GGC)n SSR markers in peanut (Arachis hypogaea L.)

Cited by 16 publications

References 34 publications

Novel and Stress Relevant EST Derived SSR Markers Developed and Validated in Peanut

Novel and Stress Relevant EST Derived SSR Markers Developed and Validated in Peanut

A high-density genetic map of Arachis duranensis, a diploid ancestor of cultivated peanut

Global Resources of Genetic Diversity in Peanut

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