مکان‌یابی ارتباطی صفات پومولوژیک انگور (Vitis vinifera L.) با استفاده از نشانگرهای ISSR

نوع مقاله : پژوهشی

نویسندگان

1 گروه باغبانی، دانشکده کشاورزی، دانشگاه زنجان، زنجان، ایران

2 'گروه اصلاح و بیوتکنولوژی، دانشکده کشاورزی، دانشگاه ارومیه

3 مرکز تحقیقات کشاورزی آذربایجان غربی، ارومیه

4 موسسه تحقیقات CEBAS، اسپانیا

چکیده

سابقه و هدف: انگور یکی از مهمترین محصولات باغی است که به دلیل ارزش اقتصادی، دارویی و غذایی آن به طور گسترده کشت می‌شود. با توجه به اینکه ارزش اقتصادی یک رقم به صفات مختلف آن بستگی دارد، از این رو اطلاع دقیق از رفتار ژنتیکی و شناسایی مکان‌های ژنومی پیوسته با این صفات به اصلاح ارقام کمک خواهد نمود. در این مطالعه ارتباط و پیوستگی بین نشانگرهای ISSR با برخی صفات مهم پومولوژیک مانند عملکرد و صفات کیفی ارقام انگور آذربایجان‌غربی از طریق مدل ارتباط‌یابی MLM مورد بررسی قرار گرفت.
مواد و روش‌ها: در این تحقیق از 45 رقم انگور زراعی موجود در کلکسیون مرکز تحقیقات کشاورزی و منابع طبیعی استان آذربایجان غربی استفاده گردید. صفات کیفی میوه در طی سه سال زراعی و در 10 تکرار اندازه‌گیری شدند. استخراج DNAی ژنومی بر اساس روش دویل و دویل (1987) انجام شد و از 17 نشانگر ISSR در واکنش PCR استفاده گردید. الگوی باندی حاصل، براساس وجود یا عدم وجود باند در نمونه‌ها، به صورت یک و صفر امتیازدهی شدند و ماتریس حاصل برای بررسی آنالیز آماری استفاده گردید. تجزیه مؤثر ساختار جمعیت با استفاده از روش Bayesian در نرم‌افزار Structure و شناسایی مکان‌های ژنی مرتبط با صفات مورد ارزیابی، بر اساس مدل MLM با استفاده از نرم‌افزار TASSEL انجام گرفت.
یافته‌ها: بر اساس 17 نشانگر ISSR مورد استفاده در این مطالعه، ساختار ژنتیکی جمعیت به دو زیر جمعیت فرعی (2=K) تقسیم گردید. بر اساس نتایج ارائه شده در بارپلات 20 رقم (44/44 درصد) به ساختار اول، 17 رقم (78/37 درصد) به ساختار دوم و بقیه ارقام (78/17 درصد) به گروه با ساختار مخلوط تعلق داشتند. در این بررسی از 2775 جفت مقایسه نشانگر ISSR، 72/0 درصد، LD معنی‌داری نشان دادند (P ≤ 0.01). نتایج همچنین نشان داد که 12 نشانگر(مکان ژنی) ارتباط معنی‌داری(P ≤ 0.01) با صفات مورد ارزیابی نشان دادند که از این تعداد یک مکان (UBC825-4) برای TSS، یک مکان (UBC890-2) برای pH، 2 مکان (UBC817-2 و UBC825-5) برای وزن تک بذر، 2 مکان (UBC836-7 و UBC855-2) برای تعداد بذر، 3 مکان (UBC812-3، UBC817-4 و UBC864-2) برای عرض خوشه، 2 مکان (UBC817-4 و UBC864-2) برای وزن خوشه و یک مکان (UBC826-4) برای درصد تشکیل میوه در حالت گرده‌افشانی کنترل شده شناسایی شدند.
نتیجه‌گیری: نتایج مطالعه حاضر کارایی استفاده از روش مکان‌یابی ارتباطی و مدل MLM در ارقام انگور مورد مطالعه را نشان می-دهد. برخی از مکان‌ها بین صفات مختلف مشترک بودند. شناسایی نشانگرهای مشترک اهمیت زیادی در به‌نژادی گیاهان دارد زیرا گزینش هم‌زمان چند صفت را امکان‌پذیر می‌سازند. مناطق ژنومی پیوسته با عوامل کنترل کننده صفات مورد نظر در این مطالعه می-توانند برای انتخاب به کمک نشانگر به منظور توسعه برنامه‌های مختلف اصلاح انگور استفاده شوند.

کلیدواژه‌ها

موضوعات

عنوان مقاله [English]

Association mapping for pomological traits in grape (Vitis vinifera L.) using ISSR markers

نویسندگان [English]

  • Mitra Razi 1
  • Mohammad Esmaeil Amiri 1
  • Reza Darvishzadeh 2
  • Hamed Doulati Baneh 3
  • Pedro Martinez-Gomez 4
1 Department of horticultural, Faculty of Agriculture, University of Zanjan, Zanjan, Iran
2 Department of Plant Breeding and Biotechnology,Faculty of agriculture, Urmia University
3 Research and Education Centre of West Azerbaijan Agricultural and Natural Resources Research Centre, AREEO, Urmia
4 Plant Breeding Department, CEBAS-CSIC, Murcia, Spain
چکیده [English]

Background and objectives: Grape (Vitis vinifera L.) is an important fruit crop and widely cultivated in the glob because of the nutritional, medicinal and economical values. Since the economic value of cultivar depends on different characteristics, thus detailed knowledge on genetic behavior and identification of genomic loci linked to these traits will help to improve plant cultivars. In this investigation, relation and linkage between of ISSR markers with some of pomologic traits such as yield and quality-related traits in West Azarbaijan grape cultivars was evaluated through MLM association models in Structure and TASSEL software.
Materials and Methods: 45 grape cultivars from West Azarbaijan agricultural and natural resources research germplasm bank were investigated. Berry quality traits were evaluated over three consecutive years onto 10 replications per cultivar. Genomic DNA was extracted following the Doyle and Doyle method (1987) and Polymerase chain reaction (PCR) was performed with 17 ISSR primers. Scoring of amplified fragments was performed according to present (1) or absence (0) of each band marker, and the produced binary data were served for statistical analysis. The Bayesian approach in the software package Structure was used for estimating the population structure. Identification of genomic loci linked to these traits were done with mixed linear model (MLM) in TASSEL software.
Results: Based on the 17 ISSR markers used in this study, population genetic structure subdivided into two subpopulations (K=2). Based on results in Barplot 20 cultivars (44/44%) of the studied cultivars were assigned to P1 group and 17 cultivars (37/78%) assigned to P2 group and the remaining ones (17/78%) were categorized into the mixed group. In this investigation, of 2775 ISSR markers pairs, 0.72% showed a significant level of LD (P ≤ 0.01). results showed the significant association (P ≤ 0.01) of 12 ISSR markers with genomic region controlling the studied traits. 1 locus (UBC825-4) was identified for TSS, 1 locus (UBC890-2) was identified for pH, 2 loci (UBC817-2 and UBC825-5) were identified for seed weight, 2 loci (UBC836-7 and UBC855-2) were identified for seed number, 3 loci (UBC812-3, UBC817-4 and UBC864-2) were identified for cluster width, 2 loci (UBC817-4 and UBC864-2) were identified for cluster weight and 1 locus (UBC826-4) was identified for fruit set in controlled pollination.
Conclusion: Our results suggest the importance the power and precision of MLM association mapping in grapevine. Some loci were common for more than one trait. The common markers are useful in plant improvements program because they augment efficiency of marker selection through concurrent selection for several characters.These ISSR loci identified in this study associated to quality traits may be applied in marker-assisted breeding programs for improving some important traits in grape.

کلیدواژه‌ها [English]

  • Association analysis
  • Linkage disequilibrium
  • ISSR marker
  • Population structure
  • Vitis vinifera

مراجع

1.Al-Maskri, A.H., Sajjad, M. and Khan, S.H. 2012. Association mapping: a step forward to discovering new alleles for crop improvement. Int. J. Agric. Biol.14: 153-160.
2.Ammiraju, J., Dholakia, B., Santra, D., Singh, H., Lagu, M., Tamhankar, S., Dhaliwal, H.S., Rao, V.S., Gupa, V.S. and Ranjekar, P. 2001. Identification of inter simple sequence repeat (ISSR) markers associated with seed size in wheat. Theor. Appl. Genet. 102: 5. 726-732.
3.Barnaud, A., Lacombe, T. and Doligez, A. 2006. Linkage disequilibrium in cultivated grapevine, Vitis vinifera L. Theor. Appl. Genet. 112: 708-716.
4.Barnaud, A., Laucou, V., This, P., Lacombe, T. and Doligez, A. 2010. Linkage disequilibrium in wild French grapevine, Vitis vinifera L. subsp. Silvestris. Heredity. 104: 431-437.
5.Battilana, J., Lorenzi, S., Moreira, F.M., Moreno-Sanz, P., Failla, O., Emanuelli, F. and Grando, M.S. 2013. Linkage mapping and molecular diversity at the flower sex locus in wild and cultivated grapevine reveal a prominent SSR haplotype in hermaphrodite plants. Mol. Biotechnol. 54: 1031-1037.
6.Bradbury, P.J., Zhang, Z., Kroon, D.E., Casstevens, T.M., Ramdoss, Y. and Buckler, E.S. 2007. TASSEL: software for association mapping of complextraits in diverse samples. Bioinformat.23: 2633-2635.
7.Buckler, E.S. and Thornsberry, J.M. 2002. Plant molecular diversity and applications to genomics. Curr. Opin. Plant. Biol. 5: 107-111.
8.Cabezas, J.A., Cervera, M.T., Ruiz-Garcia, L., Carreño, J. and Martínez-Zapater, J.M. 2006. A genetic analysis of seed and berry weight in grapevine. Genome. 49: 1572-85.
9.Cardon, L.R. and Palmer, L.J. 2003. Population stratification and spurious allelic association. Lancet. 361: 598-604.
10.Chitwood, D.H., Ranjan, A., Martinez, C.C., Headland, L.R., Thiem, T., Kumar, R., Covington, M.F., Hatcher, T., Naylor, D.T., Zimmerman, S., Downs, N., Raymundo, N., Buckler, E.S., Maloof, J.N., Aradhya, M., Prins, B., Li, L., Myles, S. and Sinha, N.R. 2014. A modern ampelography: a genetic basis for leaf shape and venation patterning in grape. Plant Physiol.
164: 259-272.
11.Doerge, R.W. 2002. Mapping and analysis of quantitative trait loci in experimental populations. Nat. Genet.
3: 1. 43-52.
12.Doligez, A., Bouquet, A., Danglot, Y., Lahogue, F., Riaz, S., Meredith, C.P., Edwards, J. and This, P. 2002. Genetic mapping of grapevine (Vitis vinifera L.) applied to the detection of QTLs for seedlessness and berry weight. Theor. Appl. Genet. 105: 780-95.
13.Doligez, A., Bertrand, Y., Dias, S., Grolier, M., Ballester, J., Bouquet, A. and This, P. 2010. QTLs for fertility in table grapevine (Vitis vinifera L.). Tree. Genet. Genom. 6: 413-422.
14.Doyle, J.J. and Doyle, J.L. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem. Bull. 19: 11-15.
15.Emanuelli, F., Battilana, J., Costantini, L., Le Cunff, L., Boursiquot, J.M., This, P. and Grando, M.S. 2010. A candidate gene association study on muscat flavor in grapevine (Vitis vinifera L.). BMC. Plant. Biol. 10: 241.
16.Evanno, G., Regnaut, S. and Goudet, J. 2005. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol. Ecol. 14: 2611-2620.
17.Fanizza, G., Lamaj, F., Costantini, L., Chaabane, R. and Grando, M.S. 2005. QTL analysis for fruit yield components in table grapevines (Vitis vinifera). Theor. Appl. Genet. 111: 658-664.
18.Fernandez, L., Le Cunff, L., Tello, J., Lacombe, T., Boursiquot, J.M., Fournier-Level, A., Bravo, G., Lalet, S., Torregrosa, L., This, P. and Martinez-Zapater, J.M. 2014. Haplotype diversity of VvTFL1A gene and association with cluster traits in grapevine (V. vinifera). BMC Plant Biol. 14: 209.
19.Fournier-Level, A., Le Cunff, L., Gomez, C., Doligez, A., Ageorges, A., Roux, C., Bertrand, Y., Souquet,J.M., Cheynier, V. and This, P.2009. Quantitative genetic bases of anthocyanin variation in grape (Vitis vinifera L. ssp. sativa) berry: a quantitative trait locus to quantitative trait nucleotide integrated study. Genet. 183: 1127-1139.
20.Fournier-Level, A., Huqueney, P., Verries, C., This, P. and Aqeorqes. 2011. Genetic mechanisms underlying the methylation level of anthocyanins in grape (Vitis vinifera L.). BMC Plant Biol. 15: 11. 179.
21.Grassi, F., Labra, M., Scienza, A. and Imazio, S. 2002. Chloroplast SSR markers to assess DNA diversity in wild and cultivated grapevine. Vitis. 41: 157-158.
22.Gupta, P.K., Rustgi, S. and Kulwal, P.L. 2005. Linkage disequilibrium and association studies in higher plants: Present status and future prospects. Plant. Mol. Biol. 57: 461-485.
23.Hittalmani, S., Huang, N., Courtois, B., Venuprasad, R., Shashidhar, H.E., Zhuang, J.Y., Zheng, K.L., Liu, G.F., Wang, G.C., Sidhu, J.S., Srivantaneeyakul, S., Singh, V.P., Bagali, P.G., Prasanna, H.C., McLaren, G. and Khush, G.S. 2003. Identification of QTL for growth and grain yield-related traits in rice across nine locations of Asia. Theor. Appl. Genet. 107: 679-90.
24.Houel, C., Bounon, R., Chaib, J., Guichard, C., Peros, J.P., Bacilieri, R., Dereeper, A., Canaguier, A., Lacombe, T.N., Diaye, A., Le Paslier, M.C., Vernerey, M.S., Coriton, O., Brunel, D., This, P., Torregrosa, L. and Adam-Blondon, A.F. 2010. Patterns of sequence polymorphism in the fleshless berry locus in cultivated and wild Vitis vinifera accessions. BMC. Plant. Biol. 10: 284-299.
25.Huang, Y.F., Doligez, A., Fournier-Level, A., Le Cunff, L., Bertrand,Y., Canaguier, A., Morel, C., Miralles, V., Veran, F., Souquet, J.M., Cheynier, V., Terrier, N. and This, P. 2012. Dissecting genetic architecture of grape proanthocyanidin composition through quantitative trait locus mapping. BMC. Plant. Biol. 12: 30-59.
26.Jun, T.H., Van, K., Kim, M.Y.,Lee, S.H. and Walker, D.R. 2008. Association analysis using SSR markers to find QTL for seed protein content in soybean. Euphytica. 62: 179-191.
27.Lijavetzky, D., Ruiz-Garcia, L., Cabezas, J.A., De Andres, M.T., Bravo, G., Ibanez, A., Carreno, J., Cabello, F., Ibanez, J. and Martinez-Zapater, J.M. 2006. Molecular genetics of berry colour variation in table grape. Mol. Genet. Genom. 276: 5. 427-35.
28.Lowe, K.M. and Walker, M.A. 2006. Genetic linkage map of the interspecific grape rootstock cross Ramsey (Vitis champinii) × Riparia Gloire (Vitis riparia). Theor. Appl. Genet. 112: 1582-1592.
29.Maccaferri, M., Sanguineti, M.C., Corneti, S., Ortega, J.L.A., Ben Salem, M., Bort, J., DeAmbrogio, E., del Moral, L.F.G., Demontis, A., El-Ahmed, A., Maalouf, F., Machlab, H., Martos, V., Moragues, M., Motawaj, J., Nachit, M., Nserallah, N., Ouabbou, H., Royo, C., Slama, A. and Tuberosa, R. 2008. Quantitative trait loci for grain yield and adaptation of durum wheat (Triticum durum Desf.) across a wide range of water availability. Genet. 178: 489-511.
30.Maccaferri, M., Sanguineti, M.C., Demontis, A., El-Ahmed, A., Garcia del Moral, L., Maalouf, F., Nachit, M., Nserallah, N., Ouabbou, H., Rhouma, S., Royo, C., Villegas, D. and Tuberosa, R. 2011. Association mapping in durum wheat grown across a broad range of water regimes. J. Exp. Bot. 14: 287-293.
31.Mackay, T.F., Stone, E.A. and Ayroles, J.F. 2009. The genetics of quantitative traits: challenges and prospects. Nat. Rev. Genet. 10: 8. 565-577.
32.Mauricio, R. 2001. Mapping quantitative trait loci in plants: uses and caveatsfor evolutionary biology. Nat. Genet.
2: 5. 370-381.
33.Oraguzie, N.C., Wilcox, P.L., Rikkerink, E.H.A. and de Silva, H.N. 2007. Linkage disequilibrium, Association Mapping in Plants. Springer. New York. NY. Pp: 11-39.
34.Pasam, R.K., Sharma, R., Malosetti, M., Van Eeuwijk, F.A., Haseneyer, G., Kilian, B. and Garner, A. 2012. Genome-wide association studies for agronomical traits in a world wide spring barley collection. BMC. Plant. Biol. 12: 1. 16.
35.Pritchard, J.K., Stephens, M. and Donnelly, P. 2000. Inference of population structure using multilocus genotype data. Genet. 155: 945-959.
36.Pritchard, J.K. and Donnelly, P. 2001. Casecontrol studies of association in structured or admixed populations. Theor. Popul. Biol. 60: 227-237.
37.Rafalski, A. and Morgante, M. 2004. Corn and humans: recombination and linkage disequilibrium in two genomes of similar size. Trends. Genet. 20: 103-111.
38.Reddy, M.P., Sarla, N. and Siddiq, E. 2002. Inter simple sequence repeat (ISSR) polymorphism and its application in plant breeding. Euphytica. 128: 1. 9-17.
39.Rezaeizad, A., Wittkop, B., Snowdon, R., Hasan, M., Mohammadi, V., Zali, A. and Friedt, W. 2011. Identification of QTLs for phenolic compounds in oilseed rape (Brassica napus L.) by association mapping using SSR markers. Euphytica. 177: 335-342.
40.Riaz, S., Krivanek, A.F., Xu, K., and Walker, M.A. 2006. Refined mapping of the Pierce’s disease resistance locus, PdR1, and Sex on an extended genetic map of Vitis rupestris × V. arizonica. Theor. Appl. Genet. 113: 1317-29.
41.Rostok, N., Ramsay, L., MacKenzie,K., Cardle, L. and Bhat, P.R. 2006. Recent history of artificial outcrossing facilitates whole-genome association mapping in elite inbred crop varieties. PNAS. 103: 18656-18661.
42.Semagn, K., Bjørnstad, A. and Xu, Y. 2010. The genetic dissection of quantitative traits in crops. Elec. J. Biotech. 13: 5. 1-45.
43.Spataro, G., Tiranti, B., Arcaleni, P., Bellucci, E., Attene, G., Papa, R., Spagnoletti, Z.P. and Negri, V. 2011. Genetic diversity and structure of a worldwide collection of Phaseolus coccineus L. Theor. Appl. Genet.122: 1281-1291.
44.Tello, J., Torres-Perez, R., Grimplet, J. and Ibanez, J. 2016. Association analysis of grapevine bunch traits using a comprehensive approach. Theor. Appl. Genet. 129: 227-242.
45.This, P., Lacombe, T., Cadle-Davidson, M. and Owens, C.L. 2007. Wine grape (Vitis vinifera L.) color associates with allelic variation in the domestication gene VvmybA1. Theor. Appl. Genet. 114: 4. 723-730.
46.Tuberosa, R., Gill, B.S. and Quarrie, S.A. 2002a. Cereal genomics: Ushering in a brave new world. Plant. Mol. Biol. 48: 744-755.
47.Tuberosa, R., Salvi, S., Sanguineti, M.C., Landi, P., Maccaferri, M. and Conti, S. 2002b. Mapping QTLs regulating morphophysiological traits and yield in droughtstressed maize: case studies, shortcomings and perspectives. Ann. Bot. 89: 941-963.
48.Yu, J., Arbelbide, M. and Bernardo, R. 2005. Power of in silico QTL mapping from phenotypic, pedigree and marker data in a hybrid breeding program. Theor. Appl. Genet. 110: 1061-1067.
49.Yu, J. and Buckler, E.S. 2006. Genetic association mapping and genome organization of maize. Curr. Opin. Plant. Biol. 17: 155-160.
50.Vargas, A.M., Fajardo, C., Borrego, J., De Andrés, M.T. and Ibanez, J. 2013a. Polymorphisms in VvPel associate with variation in berry texture and bunchsize in the grapevine. Aust. J. Grape. Wine Res. 19: 193-207.
51.Vargas, A.M., Le Cunff, L., This,P., Ibanez, J. and Teresa de Andres,M. 2013b. VvGAI1 polymorphisms associate with variation for berry traits in grapevine. Euphytica. 191: 1. 85-95.
52.Ward, J.A., Bhangoo, J., Fernandez-Fernandez, F., Moore, P., Swanson, J.D., Viola, R., Velasco, R., Bassil, N., Weber, C.A. and Sargent, D.J. 2013. Saturated linkage map construction in Rubus idaeus using genotyping by sequencing and genome-independent imputation. BMC Genom. 14: 2.
53.Zhang, Q., Wu, C., Ren, F., Li, Y. and Zhang, C. 2012. Association analysis of important agronomical traits of maize inbred lines with SSRs. Aust. J. Crop. Sci. 6: 1131-1138.
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دوره 26، شماره 2
شهریور 1398
صفحه 143-155

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