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Transcriptome-based SNP discovery by GBS and the construction of a genetic map for olive.
Funct Integr Genomics. 2017 Sep; 17(5):493-501.FI

Abstract

Molecular markers located in the genic regions of plants are valuable tools for the identification of candidate genes of economically important traits and consequent use in marker-assisted selection (MAS). In the past, simple sequence repeat markers (SSRs) and single-nucleotide polymorphisms (SNPs) located in expressed sequence tags (ESTs) were developed by sequencing RNA derived from different plant tissues, which involves laborious RNA extraction, mRNA isolation, and cDNA synthesis. In order to develop SNP markers located in olive transcriptomes, we used the recently developed genotyping-by-sequencing (GBS) technique. An analysis was done for 125 olive DNA samples (123 DNA samples from a cross-pollinated F1 mapping population, and two samples from parents). From 45 to 66% of Illumina reads from GBS analysis were aligned to the olive transcriptome. A total of 22,033 transcriptome-based SNP markers were identified, and 3384 of these were mapped in the olive genome. The genetic linkage map constructed in this study consists of 1 cleaved amplified polymorphic sequence (CAPS), 19 SSR, and 3384 transcriptome-based SNP markers. The map covers 3340.8 cM of the olive genome in 23 linkage groups, with the length of the linkage groups ranging from 55.6 to 248.7 cM. Average map distance between flanking markers was 0.98 cM. This genetic linkage map is a saturated genetic map and will be a useful tool for the localization of quantitative trait loci (QTLs) and gene(s) of interest and for the identification of candidate genes for economically important traits.

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Publisher Full Text (DOI)

Authors+Show Affiliations

İpek A
Faculty of Agriculture, Horticulture Department, Uludag University, Bursa, Turkey. maipek@uludag.edu.tr.
İpek M
Faculty of Agriculture, Horticulture Department, Uludag University, Bursa, Turkey.
Ercişli S
Faculty of Agriculture, Horticulture Department, Atatürk University, Erzurum, Turkey.
Tangu NA
Atatürk Horticultural Central Research Institute, Yalova, Turkey.

MeSH

Genetic LinkageGenome, PlantGenotyping TechniquesMicrosatellite RepeatsOleaPolymorphism, Single NucleotideQuantitative Trait LociTranscriptomeWhole Genome Sequencing

Pub Type(s)

Journal Article

Language

eng

PubMed ID

28213629

Citation

İpek, Ahmet, et al. "Transcriptome-based SNP Discovery By GBS and the Construction of a Genetic Map for Olive." Functional & Integrative Genomics, vol. 17, no. 5, 2017, pp. 493-501.
İpek A, İpek M, Ercişli S, et al. Transcriptome-based SNP discovery by GBS and the construction of a genetic map for olive. Funct Integr Genomics. 2017;17(5):493-501.
İpek, A., İpek, M., Ercişli, S., & Tangu, N. A. (2017). Transcriptome-based SNP discovery by GBS and the construction of a genetic map for olive. Functional & Integrative Genomics, 17(5), 493-501. https://doi.org/10.1007/s10142-017-0552-1
İpek A, et al. Transcriptome-based SNP Discovery By GBS and the Construction of a Genetic Map for Olive. Funct Integr Genomics. 2017;17(5):493-501. PubMed PMID: 28213629.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Transcriptome-based SNP discovery by GBS and the construction of a genetic map for olive. AU - İpek,Ahmet, AU - İpek,Meryem, AU - Ercişli,Sezai, AU - Tangu,Nesrin Aktepe, Y1 - 2017/02/18/ PY - 2016/02/17/received PY - 2017/02/07/accepted PY - 2017/02/04/revised PY - 2017/2/19/pubmed PY - 2018/2/23/medline PY - 2017/2/19/entrez KW - CAPS KW - Genetic mapping KW - Olive KW - SNP KW - SSR KW - Transcriptome SP - 493 EP - 501 JF - Functional & integrative genomics JO - Funct Integr Genomics VL - 17 IS - 5 N2 - Molecular markers located in the genic regions of plants are valuable tools for the identification of candidate genes of economically important traits and consequent use in marker-assisted selection (MAS). In the past, simple sequence repeat markers (SSRs) and single-nucleotide polymorphisms (SNPs) located in expressed sequence tags (ESTs) were developed by sequencing RNA derived from different plant tissues, which involves laborious RNA extraction, mRNA isolation, and cDNA synthesis. In order to develop SNP markers located in olive transcriptomes, we used the recently developed genotyping-by-sequencing (GBS) technique. An analysis was done for 125 olive DNA samples (123 DNA samples from a cross-pollinated F1 mapping population, and two samples from parents). From 45 to 66% of Illumina reads from GBS analysis were aligned to the olive transcriptome. A total of 22,033 transcriptome-based SNP markers were identified, and 3384 of these were mapped in the olive genome. The genetic linkage map constructed in this study consists of 1 cleaved amplified polymorphic sequence (CAPS), 19 SSR, and 3384 transcriptome-based SNP markers. The map covers 3340.8 cM of the olive genome in 23 linkage groups, with the length of the linkage groups ranging from 55.6 to 248.7 cM. Average map distance between flanking markers was 0.98 cM. This genetic linkage map is a saturated genetic map and will be a useful tool for the localization of quantitative trait loci (QTLs) and gene(s) of interest and for the identification of candidate genes for economically important traits. SN - 1438-7948 UR - https://www.unboundmedicine.com/medline/citation/28213629/Transcriptome_based_SNP_discovery_by_GBS_and_the_construction_of_a_genetic_map_for_olive_ L2 - https://dx.doi.org/10.1007/s10142-017-0552-1 DB - PRIME DP - Unbound Medicine ER -