Development and validation of new SSR markers from expressed regions in the garlic genome

Ipek, Meryem; Sahin, Nihan; Ipek, Ahmet; Cansev, Asuman; Simon, Philipp W.

doi:10.1590/0103-9016-2014-0138

Cited by 25 publications

(18 citation statements)

References 30 publications

(31 reference statements)

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“…In addition, dendrogram topologies for all tree marker technologies were found to be very similar (Belaj et al, 2003). Similarly, high concordance between the dendrograms of AFLP and expressed sequence tag-SSR markers (Ipek et al, 2015) and between AFLP and RAPD markers (r = 0.96) (Ipek et al, 2003) was determined.…”

Section: Introductionmentioning

confidence: 81%

Identification of molecular markers associated with fruit traits in olive and assessment of olive core collection with AFLP markers and fruit traits

et al. 2015

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ABSTRACT. The purpose of this study was to characterize olive core collection with amplified fragment length polymorphism (AFLP) markers and fruit traits and to determine AFLP markers significantly associated with these fruit characters in olive. A total of 168 polymorphic AFLP markers generated by five primer combinations and nine fruit traits were used to characterize relationships between 18 olive cultivars. Although all olive cultivars were discriminated from each other by either AFLP markers (<0.75 similarity level) or fruit traits, clustering based on the AFLP markers and fruit traits was not significantly correlated (r = 0.13). Partial clustering of olive cultivars by AFLP markers according to their geographical origin was observed. Associations of AFLP markers with fruits were determined using a multiple-regression analysis with stepwise addition of AFLP markers. Significant associations between eight AFLP markers and fruit traits were identified. While five AFLP markers demonstrated significant negative correlation with fruit and stone weight, width and length and total polyphenols (P < 0.05), three AFLP markers displayed significant positive correlation with α-tocopherol and γ-tocopherol (P < 0.01). This is the first report on the association of molecular markers with fruit traits in olive. Molecular markers associated with morphological and agronomic traits could be utilized for the breeding of olive cultivars. However, the association power of these markers needs to be confirmed in larger populations, and highly correlated markers should then be converted to PCR-based DNA markers such as sequence-characterized amplified region markers for better utilization.

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Section: Introductionmentioning

confidence: 81%

Identification of molecular markers associated with fruit traits in olive and assessment of olive core collection with AFLP markers and fruit traits

et al. 2015

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“…In the present study, 12,765 potential EST-SSR molecular markers were identified from 93,305 unigenes, including 3049 unigenes that contained more than one EST-SSR locus, using RNA sequencing. The di-nucleotide repeats in EST-SSRs were the most abundant type in Michelia coriacea (Magnoliaceae) [ 57 ], Brassica oleracea [ 58 ], garlic [ 59 ] and Z. jujube [ 60 ]. In the identified 12,765 SSR markers of A. miaotaiense , the major repeat type was di-nucleotide (2763, 24.72%) after the removal of the mono-nucleotide repeats, which was consistent with previous findings, followed by tri-nucleotide repeats (2362, 21.13%).…”

Section: Discussionmentioning

confidence: 99%

“…In our study, A. miaotaiense is only naturally distributed in the Qinling Mountains, but its genetic diversity is higher than those of Oryza sativa (N a = 4.8, H o = 0.07 and H e = 0.55) [ 72 ] and Phaseolus vulgaris (N a = 2.7, H o = 0.626 and H e = 0.308) [ 73 ]. For other endangered species, such as M. coriacea (Magnoliaceae) [ 59 ], a restricted and fragmented distribution were determined in southeastern Yunnan Province, China, but a high level of genetic diversity and a low level of genetic differentiation were determined (N a = 4.091, H e = 0.505 and H o = 0.412 for the SSR markers). Low levels of genetic diversity would not be beneficial in an expanded distribution region and could increase the possible susceptibility to diseases or insect pests.…”

Section: Discussionmentioning

confidence: 99%

De Novo Transcriptome Assembly and Population Genetic Analyses for an Endangered Chinese Endemic Acer miaotaiense (Aceraceae)

Liu

Hou

et al. 2018

Genes

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Acer miaotaiense (P. C. Tsoong) is a rare and highly endangered plant in China. Because of the lack of genomic information and the limited number of available molecular markers, there are insufficient tools to determine the genetic diversity of this species. Here, 93,305 unigenes were obtained by multiple assembled contigs with a transcriptome sequencing program. Furthermore, 12,819 expressed sequence tag-derived simple sequence repeat (EST-SSR) markers were generated, 300 were randomly selected and synthesized, 19 primer pairs were identified as highly polymorphic (average number of alleles (Na) = 8, expected heterozygosity (He) = 0.635, polymorphism information content (PIC) = 0.604) and were further used for population genetic analysis. All 261 samples were grouped into two genetic clusters by UPGMA, a principal component analyses and a STRUCTURE analyses. A moderate level of genetic differentiation (genetic differentiation index (Fst) = 0.059–0.116, gene flow = 1.904–3.993) among the populations and the major genetic variance (81.01%) within populations were revealed by the AMOVA. Based on the results, scientific conservation strategies should be established using in situ and ex situ conservation strategies. The study provides useful genetic information for the protection of precious wild resources and for further research on the origin and evolution of this endangered plant and its related species.

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“…SSRs have great advantages over other markers as they are simple, highly abundant, polymorphic, polyallelic, co-dominant and occur in both coding and non-coding regions of the genome [ 8 ]. Although several SSR markers have been identified in garlic [ 9 , 10 ], additional SSRs with polymorphism are needed, particularly for the development of linkage maps for use in trait specific mapping studies. In the recent years, high throughput next generation sequencing technologies has led to the generation of large databases of expressed sequence tags (ESTs) and genomic sequences.…”

Section: Introductionmentioning

confidence: 99%

Mining, characterization and validation of EST derived microsatellites from the transcriptome database of Allium sativum L

et al. 2015

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Expressed Sequence Tags (ESTs) with comprehensive transcript information are valuable resources for development of molecular markers as they are derived from conserved genic regions. The present study highlights the mining of EST database to deduce the class I hyper variable SSRs in A. sativum. From 21694 garlic EST sequences, 642 non-redundant SSRs were identified with an average frequency of 1 per 14.9 kb of garlic transcriptome. The most abundant SSR motifs were the mononucleotides (32.86%) followed by trinucleotides (28.50%) and dinucleotides (13.39%). Among the individual SSRs, (A/T)n accounted for the highest number (137; 21.33%) followed by (G/C)n (74; 11.52%) and (AAG)n (63;9.81%). Primers designed from a robust set of 7 AsESTSSRs resulted in the amplification of 63 polymorphic alleles in 14 accessions of garlic. The resolving power of the markers varied from 4.286 (AsSSR7) to 18.143 (AsSSR13) while the average marker index (MI) was 5.087. These EST-SSRs markers for garlic could be useful for the improvement of garlic linkage map and could be used for evaluating genetic variation and comparative genomics studies in Allium species.

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Development and validation of new SSR markers from expressed regions in the garlic genome

Cited by 25 publications

References 30 publications

Identification of molecular markers associated with fruit traits in olive and assessment of olive core collection with AFLP markers and fruit traits

Identification of molecular markers associated with fruit traits in olive and assessment of olive core collection with AFLP markers and fruit traits

De Novo Transcriptome Assembly and Population Genetic Analyses for an Endangered Chinese Endemic Acer miaotaiense (Aceraceae)

Mining, characterization and validation of EST derived microsatellites from the transcriptome database of Allium sativum L

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