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High-Throughput Genomic Simple Sequence Repeat (SSR) Marker Development and Construction of a High Resolution Physical Map in Button Mushroom (Agaricus bisporus) Genome

Yıl 2018, Cilt: 9 Sayı: 1, 28 - 35, 25.04.2018

Öz

Button mushroom [Agaricus bisporus (J.E. Lange) Imbach], is both a model organism and a worldwide cultivated edible mushroom species. Despite its scientific and economic relevance, efforts to develop molecular markers in A. bisporus genome are scarce and relatively recent. The present research reports the development of 3943 novel simple sequence repeat (SSR) markers specific to the A. bisporus genome. The marker set is well-distributed among the 13 A. bisporus chromosomes, saturating the entire genome with sequence-specific markers. The large number of novel, A. bisporus specific DNA markers introduced in the present work constitute a valuable resource for molecular genetic research in button mushroom, including strain identification and protection, and gene/QTL (Quantitative Trait Locus) mapping.

Kaynakça

  • Celik I, Gultekin V., Allmer J., Doganlar S., Frary A., Development of genomic simple sequence repeat markers in opium poppy by next-generation sequencing, Molecular Breeding, 34(2), 323-334 (2014).
  • Barroso G., Sonnenberg A. S. M., Van Griensven L. J. L. D., Labarѐre J., Molecular cloning of a widely distributed microsatellite core sequence from the cultivated mushroom Agaricus bisporus, Fungal Genetics and Biology, 31, 115-123 (2000).
  • Berendsen R. L., Baars J. J. P., Kalkhove S. I. C., Lugones L. G., Wösten H. A. B., Bakker P. A. H. M., Pathogen profile Lecanicillium fungicola: causal agent of dry bubble disease in white-button mushroom, Molecular Plant Pathology, 11(5), 585-595 (2010).
  • Foulongne-Oriol M., Spataro C., Savo,e J. M., Novel microsatellite markers suitable for genetic studies in the white button mushroom Agaricus bisporus, Applied Microbiology and Biotechnology, 84, 1125-1135 (2009).
  • Foulongne-Oriol M., Rodier A., Rousseau T., Savoie J. M., QTL mapping of yield-related components and oligogenic control of the cap colour in the button mushroom Agaricus bisporus, Applied and Environmental Microbiology, 78(7), 2422-2434 (2012).
  • Foulongne-Oriol M., Murat C., Castanera R., Ramírez L., Sonnenberg A. S. M., Genome-wide survey of repetitive DNA elements in the button mushroom Agaricus bisporus, Fungal Genetics and Biology, 55, 6-21 (2013).
  • Gao W., Baars J. J. P., Maliepaard C., Visser R. G. F., Zhang J., Sonnenberg A. S. M., Multi-trait QTL analysis for agronomic and quality characters of Agaricus bisporus (button mushrooms), AMB Express, 6(1), 67 (2016).
  • Gu T., Tan S., Gou X., Araki H., Tian D., Avoidance of long mononucleotide repeats in codon pair usage, Genetics, 186, 1077-1084 (2010).
  • Heneghan M. N., Burns C., Costa A. M. S. B., Burton K. S., Challen M. P., Bailey M., Foster G. D., Functional analysis of Agaricus bisporus serine proteinase 1 reveals roles in utilization of humic rich substrates and adaptation to the leaf-litter ecological niche, Environmental Microbiology, 18(12), 4687-4696 (2016).
  • Jeong S. C., Jeong Y. T., Yang B. K., Islam R., Koyyalamudi S. R., Pang G., Cho K. Y., Song C. H., White button mushroom (Agricus bisporus) lowers blood glucose and cholesterol levels in diabetic and hypercholesterolemic rats, Nutrition Research, 30, 49-56 (2010).
  • Jones, N., Ougham H., Thomas H., Pasakinskiene I., Markers and mapping revisited: Finding your gene, New Phytologist, 183, 935-966 (2009).
  • Liu J., Jia L., Kan J., Jin C. H., In vitro and in vivo antioxidant activity of ethanolic extract of white button mushroom (Agaricus bisporus), Food and Chemical Toxicology, 51, 310-316 (2013).
  • Loftus M.G., Moore D., Elliott T. J., DNA polymorphisms in commercial and wild strains of the cultivated mushroom, Agaricus bisporus, Theoretical and Applied Genetics, 76, 712-718 (1988).
  • Morin E., Kohler A., Baker A. R., Foulongne-Oriol M., Lombard V., Nagy L. G., et al. Genome sequence of the button mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche, Proceedings of the National Academy of Sciences, 109(43), 17501-17506 (2012).
  • Samuels G. J., Dodd S. L., Gams W., Castlebury L. A., Petrini O., Trichoderma species associated with the green mold epidemic of commercially grown Agaricus bisporus, Mycologia, 94(1), 146-170 (2002).
  • Schuler G. D., Sequence mapping by electronic PCR, Genome Research, 7, 541-550 (1997).
  • Sokovic M., Van Griensven L. J. L. D., Antimicrobial activity of essential oils and their components against the three major pathogens of the cultivated button mushroom, Agaricus bisporus, European Journal of Plant Pathology, 116, 211-224 (2006).
  • Sonnenberg A. S. M., Gao W., Lavrijssen B., Hendrickx P., Sedaghat-Tellgerd N., Foulongne-Oriol M., et al. A detailed analysis of the recombination landscape of the button mushroom Agaricus bisporus var. bisporus, Fungal Genetics and Biology, 93, 35-45 (2016).
  • Uncu A. O, Uncu A. T., Celık, İ, Doganlar S., Frary A., A primer to molecular phylogenetic analysis in plants, Critical Reviews in Plant Sciences, 34, 454-468 (2015a).
  • Uncu A. O., Gultekin V., Allmer J., Frary A., Doganlar S., Genomic simple sequence repeat markers reveal patterns of genetic relatedness and diversity in sesame, The Plant Genome, 8, doi: 10.3835/plantgenome2014.11.0087 (2015b).
  • Voorrips R. E., MapChart: software for the graphical presentation of linkage maps and QTLs, Journal of Heredity, 93, 77-78 (2002).
  • Wang X., Wang L., GMATA: An integrated software package for genome-scale SSR mining, marker development and viewing, Frontiers in Plant Science, 7, 1350 (2016).

Kültür Mantarı (Agaricus bisporus) Genomuna Özel Yüksek Miktarda Basit Dizi Tekrarı (SSR) Markörünün Geliştirilmesi ve Yüksek Çözünürlükte Fiziksel Genom Haritasının Oluşturulması

Yıl 2018, Cilt: 9 Sayı: 1, 28 - 35, 25.04.2018

Öz

Kültür mantarı [Agaricus bisporus (J.E. Lange) Imbach], bir model organizma olmasının yanı sıra dünya genelinde yetiştirilen bir yenilebilir mantar türüdür. Bilimsel ve ekonomik önemine rağmen A. bisporus genomuna özel moleküler markör geliştirme çalışmaları ancak yakın zamanda gerçekleştirilmeye başlanmış olup, oldukça kısıtlı sayıdadır. Bu çalışma kapsamında A. bisporus genomuna özel 3943 adet yeni basit dizi tekrarı (SSR) markörü geliştirilmiştir. Geliştirilen markörler A. bisporus kromozomlarına dengeli şekilde dağılmakta olup, genomun sekans-spesifik markörler ile doyurulmasını sağlamaktadır. Çalışma kapsamında tanıtılmakta olan yüksek sayıdaki A. bisporus’a özel yeni DNA markörü, bu türde gerçekleştirilecek moleküler genetik çalışmalar için kıymetli bir kaynak teşkil edecektir.

Kaynakça

  • Celik I, Gultekin V., Allmer J., Doganlar S., Frary A., Development of genomic simple sequence repeat markers in opium poppy by next-generation sequencing, Molecular Breeding, 34(2), 323-334 (2014).
  • Barroso G., Sonnenberg A. S. M., Van Griensven L. J. L. D., Labarѐre J., Molecular cloning of a widely distributed microsatellite core sequence from the cultivated mushroom Agaricus bisporus, Fungal Genetics and Biology, 31, 115-123 (2000).
  • Berendsen R. L., Baars J. J. P., Kalkhove S. I. C., Lugones L. G., Wösten H. A. B., Bakker P. A. H. M., Pathogen profile Lecanicillium fungicola: causal agent of dry bubble disease in white-button mushroom, Molecular Plant Pathology, 11(5), 585-595 (2010).
  • Foulongne-Oriol M., Spataro C., Savo,e J. M., Novel microsatellite markers suitable for genetic studies in the white button mushroom Agaricus bisporus, Applied Microbiology and Biotechnology, 84, 1125-1135 (2009).
  • Foulongne-Oriol M., Rodier A., Rousseau T., Savoie J. M., QTL mapping of yield-related components and oligogenic control of the cap colour in the button mushroom Agaricus bisporus, Applied and Environmental Microbiology, 78(7), 2422-2434 (2012).
  • Foulongne-Oriol M., Murat C., Castanera R., Ramírez L., Sonnenberg A. S. M., Genome-wide survey of repetitive DNA elements in the button mushroom Agaricus bisporus, Fungal Genetics and Biology, 55, 6-21 (2013).
  • Gao W., Baars J. J. P., Maliepaard C., Visser R. G. F., Zhang J., Sonnenberg A. S. M., Multi-trait QTL analysis for agronomic and quality characters of Agaricus bisporus (button mushrooms), AMB Express, 6(1), 67 (2016).
  • Gu T., Tan S., Gou X., Araki H., Tian D., Avoidance of long mononucleotide repeats in codon pair usage, Genetics, 186, 1077-1084 (2010).
  • Heneghan M. N., Burns C., Costa A. M. S. B., Burton K. S., Challen M. P., Bailey M., Foster G. D., Functional analysis of Agaricus bisporus serine proteinase 1 reveals roles in utilization of humic rich substrates and adaptation to the leaf-litter ecological niche, Environmental Microbiology, 18(12), 4687-4696 (2016).
  • Jeong S. C., Jeong Y. T., Yang B. K., Islam R., Koyyalamudi S. R., Pang G., Cho K. Y., Song C. H., White button mushroom (Agricus bisporus) lowers blood glucose and cholesterol levels in diabetic and hypercholesterolemic rats, Nutrition Research, 30, 49-56 (2010).
  • Jones, N., Ougham H., Thomas H., Pasakinskiene I., Markers and mapping revisited: Finding your gene, New Phytologist, 183, 935-966 (2009).
  • Liu J., Jia L., Kan J., Jin C. H., In vitro and in vivo antioxidant activity of ethanolic extract of white button mushroom (Agaricus bisporus), Food and Chemical Toxicology, 51, 310-316 (2013).
  • Loftus M.G., Moore D., Elliott T. J., DNA polymorphisms in commercial and wild strains of the cultivated mushroom, Agaricus bisporus, Theoretical and Applied Genetics, 76, 712-718 (1988).
  • Morin E., Kohler A., Baker A. R., Foulongne-Oriol M., Lombard V., Nagy L. G., et al. Genome sequence of the button mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche, Proceedings of the National Academy of Sciences, 109(43), 17501-17506 (2012).
  • Samuels G. J., Dodd S. L., Gams W., Castlebury L. A., Petrini O., Trichoderma species associated with the green mold epidemic of commercially grown Agaricus bisporus, Mycologia, 94(1), 146-170 (2002).
  • Schuler G. D., Sequence mapping by electronic PCR, Genome Research, 7, 541-550 (1997).
  • Sokovic M., Van Griensven L. J. L. D., Antimicrobial activity of essential oils and their components against the three major pathogens of the cultivated button mushroom, Agaricus bisporus, European Journal of Plant Pathology, 116, 211-224 (2006).
  • Sonnenberg A. S. M., Gao W., Lavrijssen B., Hendrickx P., Sedaghat-Tellgerd N., Foulongne-Oriol M., et al. A detailed analysis of the recombination landscape of the button mushroom Agaricus bisporus var. bisporus, Fungal Genetics and Biology, 93, 35-45 (2016).
  • Uncu A. O, Uncu A. T., Celık, İ, Doganlar S., Frary A., A primer to molecular phylogenetic analysis in plants, Critical Reviews in Plant Sciences, 34, 454-468 (2015a).
  • Uncu A. O., Gultekin V., Allmer J., Frary A., Doganlar S., Genomic simple sequence repeat markers reveal patterns of genetic relatedness and diversity in sesame, The Plant Genome, 8, doi: 10.3835/plantgenome2014.11.0087 (2015b).
  • Voorrips R. E., MapChart: software for the graphical presentation of linkage maps and QTLs, Journal of Heredity, 93, 77-78 (2002).
  • Wang X., Wang L., GMATA: An integrated software package for genome-scale SSR mining, marker development and viewing, Frontiers in Plant Science, 7, 1350 (2016).
Toplam 22 adet kaynakça vardır.

Ayrıntılar

Birincil Dil İngilizce
Bölüm MİKOLOJİ
Yazarlar

Ali Tevfik Uncu

Ayse Ozgur Uncu

Yayımlanma Tarihi 25 Nisan 2018
Yayımlandığı Sayı Yıl 2018 Cilt: 9 Sayı: 1

Kaynak Göster

APA Uncu, A. T., & Uncu, A. O. (2018). High-Throughput Genomic Simple Sequence Repeat (SSR) Marker Development and Construction of a High Resolution Physical Map in Button Mushroom (Agaricus bisporus) Genome. Mantar Dergisi, 9(1), 28-35. https://doi.org/10.30708/mantar.391682

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