Research Article
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Evaluation of genetic structure of pistachio through whole genome resequencing

Year 2022, Volume 6, Issue 1, 135 - 140, 15.03.2022
https://doi.org/10.31015/jaefs.2022.1.18

Abstract

Pistachio (Pistacia vera L.) is the only edible and cultivated species. Pistachio is the only economically importance and dioecious species in the genus Pistacia. There are basic problems in pistachio breeding such as dioecious flower structure, long juvenile period and alternate bearing. These problems can be overcome not with classical breeding methods, but with modern molecular breeding methods. In this study, very high numbers of single nucleotide polymorphism (SNP), insertion/deletion (InDel), structural variants (SV) and copy number variation (CNV) were determined by using the next generation sequencing data of the pistachio genotype obtained with 15x sequencing coverage. A total of 1,785,235 SNP, 260,683 InDel, 5,227 SV and 1,914 CNV variants identified in PvF217 pistachio genotype. The variant density was calculated as one variant per 292 base. The distribution of the obtained variants to the Siirt reference genome was obtained. In addition, all variants were annotated to the reference genome and exonic and genomic variants were described using Annovar. These data will be used to consist of a molecular database in pistachio breeding for DNA fingerprinting, discovering unique cultivar specific alleles and to identify quantitative trait loci related to important nut traits.

References

  • Bolger, A. M., Lohse, M., & Usadel, B. (2014). Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics, 30(15), 2114-2120. https://doi.org/10.1093/bioinformatics/btu170
  • Doyle, J. J., & Doyle, J. L. (1987). A rapid DNA isolation procedure for small quantities of fresh leaf tissue (No. RESEARCH).
  • Fan, L., Zhang, M. Y., Liu, Q. Z., Li, L. T., Song, Y., Wang, L. F., ... & Wu, J. (2013). Transferability of newly developed pear SSR markers to other Rosaceae species. Plant Molecular Biology Reporter, 31(6), 1271-1282. https://doi.org/10.1007/s11105-013-0586-z
  • Gündeşli, M. A., Kafkas, S., Zarifikhosroshahi, M., & Kafkas, N. E. (2019). Role of endogenous polyamines in the alternate bearing phenomenon in pistachio. Turkish Journal of Agriculture and Forestry, 43(3), 265-274. https://dx.doi.org/10.3906/tar-1807-74
  • Gündeşli, M.A. (2020a). Endogenous Gibberellins and Abscisic acid-metabolites: their role for flower bud abscission and embryo development in pistachio. Turkish Journal of Agriculture and Forestry. 44(3), 290-300. doi:10.3906/tar-1910-46
  • Gündeşli, M.A. (2020b). Determination of Sugar contents, Total Phenol and Antioxidant Activity of various parts ‘Uzun’ pistachio cultivar (Pistacia vera L.). International Journal of Agriculture Environment and Food Sciences, 4(1), 52-58. https://doi.org/10.31015/jaefs.2020.1.8
  • Güney, M., Kafkas, S., Keles, H., Aras, S., & Ercişli, S. (2018). Characterization of hawthorn (Crataegus spp.) genotypes by SSR markers. Physiology and Molecular Biology of Plants, 24(6), 1221-1230. https://doi.org/10.1007/s12298-018-0604-6
  • Hormaza, J. I. (2002). Molecular characterization and similarity relationships among apricot (Prunus armeniaca L.) genotypes using simple sequence repeats. Theoretical and Applied Genetics, 104(2), 321-328. https://doi.org/10.1007/s001220100684
  • Kafkas, S. (2019) Advances in breeding of pistachio. Chapter. Burleigh Dodds Science Publishing Limited. Doi.10.19103/AS.2018.0042.17
  • Kafkas, S. (2006). Phylogenetic analysis of the genus Pistacia by AFLP markers. Plant Systematics and Evolution, 262(1), 113-124. https://doi.org/10.1007/s00606-006-0460-7
  • Kafkas, S., Ozkan, H., Ak, B. E., Acar, I., Atli, H. S., & Koyuncu, S. (2006). Detecting DNA polymorphism and genetic diversity in a wide pistachio germplasm: Comparison of AFLP, ISSR, and RAPD markers. Journal of the American Society for Horticultural Science, 131(4), 522-529. https://doi.org/10.21273/JASHS.131.4.522
  • Kafkas, S., (2022) The pistachio genomes provide ınsights into nut tree domestication and zw sex chromosome evolution. (Unpublished).
  • Kafkas, S., Gozel, H., Karcı, H., Bozkurt, H., Paizila, A., Topçu, H., ... & Uzun, M. (2017, November). Marker-assisted cultivar breeding in pistachio. In VII International Symposium on Almonds and Pistachios 1219 (pp. 63-66). 10.17660/ActaHortic.2018.1219.11
  • Kafkas, S., Khodaeiaminjan, M., Güney, M., & Kafkas, E. (2015). Identification of sex-linked SNP markers using RAD sequencing suggests ZW/ZZ sex determination in Pistacia vera L. BMC genomics, 16(1), 1-11. https://doi.org/10.1186/s12864-015-1326-6
  • Kafkas, S., Perl-Treves, R., & Kaska, N. (2000). Unusual Pistacia atlantica Desf.(Anacardiaceae) monoecious sex type in the Yunt Mountains of the Manisa Province of Turkey. Israel Journal of Plant Sciences, 48(4), 277-280. doi: 10.1560/UFCU-7LF6-T0A3-UXWY
  • Karcı, H., Paizila, A., Güney, M., Zhaanbaev, M., & Kafkas, S. (2022). Revealing Genetic Diversity, Population Structure and Cultivar-Specific SSR Alleles in Pistachio Using SSR Markers. (Unpublished).
  • Karcι, H., Paizila, A., Topçu, H., Ilikçioğlu, E., & Kafkas, S. (2020). Transcriptome Sequencing and Development of Novel Genic SSR Markers From Pistacia vera L. Frontiers in Genetics, 1021. https://doi.org/10.3389/fgene.2020.01021
  • Khodaeiaminjan, M., Kafkas, E., Güney, M., & Kafkas, S. (2017). Development and linkage mapping of novel sex-linked markers for marker-assisted cultivar breeding in pistachio (Pistacia vera L.). Molecular Breeding, 37(8), 1-9. https://doi.org/10.1007/s11032-017-0705-x
  • Khodaeiaminjan, M., Kafkas, S., Motalebipour, E. Z., & Coban, N. (2018). In silico polymorphic novel SSR marker development and the first SSR-based genetic linkage map in pistachio. Tree Genetics & Genomes, 14(4), 1-14. https://doi.org/10.1007/s11295-018-1259-8
  • Langmead, B., & Salzberg, S. L. (2012). Fast gapped-read alignment with Bowtie 2. Nature methods, 9(4), 357-359. https://doi.org/10.1038/nmeth.1923
  • Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., ... & Durbin, R. (2009). The sequence alignment/map format and SAMtools. Bioinformatics, 25(16), 2078-2079. https://doi.org/10.1093/bioinformatics/btp352
  • Li, H., Hu, X., Lovell, J. T., Grabowski, P. P., Mamidi, S., Chen, C., ... & Lu, C. (2021). Genetic dissection of natural variation in oilseed traits of camelina by whole‐genome resequencing and QTL mapping. The plant genome, 14(2), e20110. https://doi.org/10.1002/tpg2.20110
  • Liu, X., Gu, X., Lu, H., Liu, P., Miao, H., Bai, Y., & Zhang, S. (2021). Identification of novel loci and candidate genes for resistance to powdery mildew in a resequenced cucumber germplasm. Genes, 12(4), 584. https://doi.org/10.3390/genes12040584
  • McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., ... & DePristo, M. A. (2010). The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome research, 20(9), 1297-1303. http://www.genome.org/cgi/doi/10.1101/gr.107524.110.
  • Potts, S. M., Han, Y., Khan, M. A., Kushad, M. M., Rayburn, A. L., & Korban, S. S. (2012). Genetic diversity and characterization of a core collection of Malus germplasm using simple sequence repeats (SSRs). Plant Molecular Biology Reporter, 30(4), 827-837. https://doi.org/10.1007/s11105-011-0399-x
  • Rausch, T., Zichner, T., Schlattl, A., Stütz, A. M., Benes, V., & Korbel, J. O. (2012). DELLY: structural variant discovery by integrated paired-end and split-read analysis. Bioinformatics, 28(18), i333-i339. https://doi.org/10.1093/bioinformatics/bts378
  • Ren, G., Zhang, X., Li, Y., Ridout, K., Serrano-Serrano, M. L., Yang, Y., ... & Fumagalli, L. (2021). Large-scale whole-genome resequencing unravels the domestication history of Cannabis sativa. Science advances, 7(29), eabg2286. DOI: 10.1126/sciadv.abg2286
  • Tamiru, M., Natsume, S., Takagi, H., White, B., Yaegashi, H., Shimizu, M., ... & Terauchi, R. (2017). Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination. BMC biology, 15(1), 1-20. https://doi.org/10.1186/s12915-017-0419-x
  • Wang, K., Li, M., & Hakonarson, H. (2010). ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic acids research, 38(16), e164-e164. https://doi.org/10.1093/nar/gkq603
  • Zaloğlu, S., Kafkas, S., Doğan, Y., & Güney, M. (2015). Development and characterization of SSR markers from pistachio (Pistacia vera L.) and their transferability to eight Pistacia species. Scientia Horticulturae, 189, 94-103. http://dx.doi.org/10.1016/j.scienta.2015.04.006
  • Ziya Motalebipour, E., Kafkas, S., Khodaeiaminjan, M., Çoban, N., & Gözel, H. (2016). Genome survey of pistachio (Pistacia vera L.) by next generation sequencing: development of novel SSR markers and genetic diversity in Pistacia species. BMC genomics, 17(1), 1-14. https://doi.org/10.1186/s12864-016-3359-x

Year 2022, Volume 6, Issue 1, 135 - 140, 15.03.2022
https://doi.org/10.31015/jaefs.2022.1.18

Abstract

References

  • Bolger, A. M., Lohse, M., & Usadel, B. (2014). Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics, 30(15), 2114-2120. https://doi.org/10.1093/bioinformatics/btu170
  • Doyle, J. J., & Doyle, J. L. (1987). A rapid DNA isolation procedure for small quantities of fresh leaf tissue (No. RESEARCH).
  • Fan, L., Zhang, M. Y., Liu, Q. Z., Li, L. T., Song, Y., Wang, L. F., ... & Wu, J. (2013). Transferability of newly developed pear SSR markers to other Rosaceae species. Plant Molecular Biology Reporter, 31(6), 1271-1282. https://doi.org/10.1007/s11105-013-0586-z
  • Gündeşli, M. A., Kafkas, S., Zarifikhosroshahi, M., & Kafkas, N. E. (2019). Role of endogenous polyamines in the alternate bearing phenomenon in pistachio. Turkish Journal of Agriculture and Forestry, 43(3), 265-274. https://dx.doi.org/10.3906/tar-1807-74
  • Gündeşli, M.A. (2020a). Endogenous Gibberellins and Abscisic acid-metabolites: their role for flower bud abscission and embryo development in pistachio. Turkish Journal of Agriculture and Forestry. 44(3), 290-300. doi:10.3906/tar-1910-46
  • Gündeşli, M.A. (2020b). Determination of Sugar contents, Total Phenol and Antioxidant Activity of various parts ‘Uzun’ pistachio cultivar (Pistacia vera L.). International Journal of Agriculture Environment and Food Sciences, 4(1), 52-58. https://doi.org/10.31015/jaefs.2020.1.8
  • Güney, M., Kafkas, S., Keles, H., Aras, S., & Ercişli, S. (2018). Characterization of hawthorn (Crataegus spp.) genotypes by SSR markers. Physiology and Molecular Biology of Plants, 24(6), 1221-1230. https://doi.org/10.1007/s12298-018-0604-6
  • Hormaza, J. I. (2002). Molecular characterization and similarity relationships among apricot (Prunus armeniaca L.) genotypes using simple sequence repeats. Theoretical and Applied Genetics, 104(2), 321-328. https://doi.org/10.1007/s001220100684
  • Kafkas, S. (2019) Advances in breeding of pistachio. Chapter. Burleigh Dodds Science Publishing Limited. Doi.10.19103/AS.2018.0042.17
  • Kafkas, S. (2006). Phylogenetic analysis of the genus Pistacia by AFLP markers. Plant Systematics and Evolution, 262(1), 113-124. https://doi.org/10.1007/s00606-006-0460-7
  • Kafkas, S., Ozkan, H., Ak, B. E., Acar, I., Atli, H. S., & Koyuncu, S. (2006). Detecting DNA polymorphism and genetic diversity in a wide pistachio germplasm: Comparison of AFLP, ISSR, and RAPD markers. Journal of the American Society for Horticultural Science, 131(4), 522-529. https://doi.org/10.21273/JASHS.131.4.522
  • Kafkas, S., (2022) The pistachio genomes provide ınsights into nut tree domestication and zw sex chromosome evolution. (Unpublished).
  • Kafkas, S., Gozel, H., Karcı, H., Bozkurt, H., Paizila, A., Topçu, H., ... & Uzun, M. (2017, November). Marker-assisted cultivar breeding in pistachio. In VII International Symposium on Almonds and Pistachios 1219 (pp. 63-66). 10.17660/ActaHortic.2018.1219.11
  • Kafkas, S., Khodaeiaminjan, M., Güney, M., & Kafkas, E. (2015). Identification of sex-linked SNP markers using RAD sequencing suggests ZW/ZZ sex determination in Pistacia vera L. BMC genomics, 16(1), 1-11. https://doi.org/10.1186/s12864-015-1326-6
  • Kafkas, S., Perl-Treves, R., & Kaska, N. (2000). Unusual Pistacia atlantica Desf.(Anacardiaceae) monoecious sex type in the Yunt Mountains of the Manisa Province of Turkey. Israel Journal of Plant Sciences, 48(4), 277-280. doi: 10.1560/UFCU-7LF6-T0A3-UXWY
  • Karcı, H., Paizila, A., Güney, M., Zhaanbaev, M., & Kafkas, S. (2022). Revealing Genetic Diversity, Population Structure and Cultivar-Specific SSR Alleles in Pistachio Using SSR Markers. (Unpublished).
  • Karcι, H., Paizila, A., Topçu, H., Ilikçioğlu, E., & Kafkas, S. (2020). Transcriptome Sequencing and Development of Novel Genic SSR Markers From Pistacia vera L. Frontiers in Genetics, 1021. https://doi.org/10.3389/fgene.2020.01021
  • Khodaeiaminjan, M., Kafkas, E., Güney, M., & Kafkas, S. (2017). Development and linkage mapping of novel sex-linked markers for marker-assisted cultivar breeding in pistachio (Pistacia vera L.). Molecular Breeding, 37(8), 1-9. https://doi.org/10.1007/s11032-017-0705-x
  • Khodaeiaminjan, M., Kafkas, S., Motalebipour, E. Z., & Coban, N. (2018). In silico polymorphic novel SSR marker development and the first SSR-based genetic linkage map in pistachio. Tree Genetics & Genomes, 14(4), 1-14. https://doi.org/10.1007/s11295-018-1259-8
  • Langmead, B., & Salzberg, S. L. (2012). Fast gapped-read alignment with Bowtie 2. Nature methods, 9(4), 357-359. https://doi.org/10.1038/nmeth.1923
  • Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., ... & Durbin, R. (2009). The sequence alignment/map format and SAMtools. Bioinformatics, 25(16), 2078-2079. https://doi.org/10.1093/bioinformatics/btp352
  • Li, H., Hu, X., Lovell, J. T., Grabowski, P. P., Mamidi, S., Chen, C., ... & Lu, C. (2021). Genetic dissection of natural variation in oilseed traits of camelina by whole‐genome resequencing and QTL mapping. The plant genome, 14(2), e20110. https://doi.org/10.1002/tpg2.20110
  • Liu, X., Gu, X., Lu, H., Liu, P., Miao, H., Bai, Y., & Zhang, S. (2021). Identification of novel loci and candidate genes for resistance to powdery mildew in a resequenced cucumber germplasm. Genes, 12(4), 584. https://doi.org/10.3390/genes12040584
  • McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., ... & DePristo, M. A. (2010). The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome research, 20(9), 1297-1303. http://www.genome.org/cgi/doi/10.1101/gr.107524.110.
  • Potts, S. M., Han, Y., Khan, M. A., Kushad, M. M., Rayburn, A. L., & Korban, S. S. (2012). Genetic diversity and characterization of a core collection of Malus germplasm using simple sequence repeats (SSRs). Plant Molecular Biology Reporter, 30(4), 827-837. https://doi.org/10.1007/s11105-011-0399-x
  • Rausch, T., Zichner, T., Schlattl, A., Stütz, A. M., Benes, V., & Korbel, J. O. (2012). DELLY: structural variant discovery by integrated paired-end and split-read analysis. Bioinformatics, 28(18), i333-i339. https://doi.org/10.1093/bioinformatics/bts378
  • Ren, G., Zhang, X., Li, Y., Ridout, K., Serrano-Serrano, M. L., Yang, Y., ... & Fumagalli, L. (2021). Large-scale whole-genome resequencing unravels the domestication history of Cannabis sativa. Science advances, 7(29), eabg2286. DOI: 10.1126/sciadv.abg2286
  • Tamiru, M., Natsume, S., Takagi, H., White, B., Yaegashi, H., Shimizu, M., ... & Terauchi, R. (2017). Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination. BMC biology, 15(1), 1-20. https://doi.org/10.1186/s12915-017-0419-x
  • Wang, K., Li, M., & Hakonarson, H. (2010). ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic acids research, 38(16), e164-e164. https://doi.org/10.1093/nar/gkq603
  • Zaloğlu, S., Kafkas, S., Doğan, Y., & Güney, M. (2015). Development and characterization of SSR markers from pistachio (Pistacia vera L.) and their transferability to eight Pistacia species. Scientia Horticulturae, 189, 94-103. http://dx.doi.org/10.1016/j.scienta.2015.04.006
  • Ziya Motalebipour, E., Kafkas, S., Khodaeiaminjan, M., Çoban, N., & Gözel, H. (2016). Genome survey of pistachio (Pistacia vera L.) by next generation sequencing: development of novel SSR markers and genetic diversity in Pistacia species. BMC genomics, 17(1), 1-14. https://doi.org/10.1186/s12864-016-3359-x

Details

Primary Language English
Subjects Horticulture
Published Date March 2022
Journal Section Research Articles
Authors

Harun KARCI (Primary Author)
ÇUKUROVA ÜNİVERSİTESİ, ZİRAAT FAKÜLTESİ
0000-0002-9037-4764
Türkiye


Salih KAFKAS This is me
ÇUKUROVA ÜNİVERSİTESİ
0000-0002-9037-4764
Türkiye

Supporting Institution Tübitak
Project Number 118O938
Publication Date March 15, 2022
Application Date January 4, 2022
Acceptance Date March 14, 2022
Published in Issue Year 2022, Volume 6, Issue 1

Cite

APA Karcı, H. & Kafkas, S. (2022). Evaluation of genetic structure of pistachio through whole genome resequencing . International Journal of Agriculture Environment and Food Sciences , 6 (1) , 135-140 . DOI: 10.31015/jaefs.2022.1.18


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