Genotyping the world collection of oat by microsatellite markers
110 46
Keywords:
oat, world collection, genetic diversity, DNA markers,Abstract
Oat is one of the most important food and feed crops in the World. Currently the world area under the oat is less than10 million hectares and down from 13 million in 2001. Kazakhstan is one of the major oat growing countries and in 2014 the harvesting area was about 200 thousand hectares, which provided production for 226 thousand tons. In order to maintain oat supply on the World market it is required to increase efficiency of breeding projects, including based on wide use of available genetic resources. In addition, effective DNA markers are necessary for successful genetic discrimination of accessions and commercial cultivars, and for protection of intellectual rights of breeders.Therefore, the collection of oat Avena sativa L. and Аvena byzantina c. Koch.consisting from 163 accessions from Kazakhstan, Europe and America, has been studied by using polymorphic DNA microsatellite markers. In total, out of screened 29 markers, 19 markers were found to be polymorphic ones for this collection. Genetic variability of the collection was studied using PopGeneandGenAlEx 6.5 software packages. In general 86 alleles were identified for analyzed markers, which suggested 4.5 average alleles per locus and 2.6 average effective alleles. Number of alleles was varied from 2 (AM25) to 8 (AM3). Genetic indexes of Shannon and Nei were calculated both for the entire population and separate regions. Calculated values for these indexes for the entire population were 1,002 and 0,532, respectively. Most genetic variability by for Nei(0.525±0,047 и 0.521±0,052)and PIC (0.4783±0.036 и 0.4702±0.043)indexes were found for Kazakhstan and East Europe, respectively. Most informative DNA microsatellite marker was MAMA-6 (0.782), followed by MAMA-11 (0.698) and AM-1 (0.666). Phylogenetic analysis of all 163 accessions was performed by using Neighbor Joining method in MEGA 6 program. The grouping of the accessions allowed of identifying 11 separate clusters. Most of studied accessions from Kazakhstan were allocated in clusters I, III, and IV. The principal coordinate analysis (PCoA) was successfully applied to differentiate the groups of oat within studied collection. The total sum of first two coordinates in PCoA was 71.33%. It was found that North American and European accessions are genetically close to each other and far from distinct groups in Kazakhstan and South America.Obtained results could be effectively used in genotyping of commercial cultivars, in protection of intellectual rights of breeders, and for improving of oat adaptation and productivity in different regions of Kazakhstan.References
1 Stevens EJ, Armstrong KW, Bezar HJ, Griffin WB, Hampton JB (2004) “Fodder oats: an overview” in Fodder Oats: A World Overview, JM Suttie and SG Reynolds, Eds., Plant Production and Protection Series, FAO, Rome, Italy. 33:11-18.
2 Loskutov IG, Blinov EV (2013) Genetic resources for oats promising areas of selection. Works of applied botany, genetics and breeding [Geneticheskie resursy ovsa dlya perspektivnyh napravlenii selekcii. Trudy po prikladnoi botanike, genetike I selekcii] 177:42-45. (In Russian)
3 Batalova GA (2000) Oats, technology of cultivation and breeding [Oves, tehnologiya vozdelovaniya i selekciya]. Kirov. P.206. (In Russian)
4 Sartakova SV (2004) The global gene pool of oats role in addressing the priorities of selection problems in Western Siberia. The genetic resources of cultivated plants [Geneticheskie resursy kulturnyh rastenii]. St. Petersburg, Russia. P.110. (In Russian)
5 He X, Bjornstad A (2012) Diversity of North European oat analyzed by SSR, AFLP and DArT markers, Theoretical and Applied Genetics, 125(1):57-70. DOI: 10.1007/s00122-012-1816-8
6 Loskutov I.G (2009) Genetic resources oats and barley - a source of productive breeding in Russia [Geneticheskie resursy ovsa I yachmenya – istochnik rezultativnoi selekcii v Rosii]. Reports International Vavilov Conference, Russia. P.200-205. (In Russian)
7 Turuspekov Y, Sariev B, Chudinov V, Sereda G, Tokhetova L, Ortaev A, Tsygankov V, Doszhanov M, Volis S, Abugalieva S (2013) Genotype X environment interaction patterns for grain yield of spring barley in different regions of Kazakhstan, Genetics, 49(2):196-205. DOI: 10.1134/S1022795413020129
8 Zeng XQ (2015) Genetic variability in agronomic traits of a germplasm collection of hulless barley, Genet Mol Res., 28;14(4):18356-69. DOI: 10.4238/2015
9 Loskutov IG, Kovaleva ON, Blinova EV (2011) Guidelines for the study and conservation of the world collection of barley and oats [Metodicheskie ukazaniya po izucheniyu i sohraneniyu mirovoi kollekcii yachmenya i ovsa]. Russia. P.46. (In Russia)
10 State Register of Breeding Achievements Approved for use in the Republic of Kazakhstan [Gosudarstvennyi reestr selekcionnyh dostizhenii, dopushennyh k ispolzovaniyu v Respublike Kazakhstan]. Astana, Kazakhstan, 2014. P.238. (In Russia)
11 Sariev BS, Tohetova LA Abugaliyeva AI, Zhundibaev KK, Baimuratov AZ (2013) Adapted and prospective varieties of forage crops established in KazNIIZiR [Raionirovannye I perspektivnye sorta zernofurozhainyh kultur, sozdannyh v KazNIIR]. Astana, Kazakhstan. P.36. (In Russian)
12 Varieties of grain crops breeding NPC Grain Farming by Barayev AI [Sorta zernovyh kultur selekcii NPC zernovogo hozyaistva im. AI Barayeva] (2011), Catalogue. Astana, Kazakhstan. P.65. (In Russian)
13 Kaskarbaev JA (2001) Formation of the duration of the growing season of crops of oats depending on the variety, sowing date and fertilizer. Grain economy [Formirovanie prodolzhitelnosti vegetacionnogo perioda posevov ovsa v zavisimosti ot sroka poseva I udobrenii. Zernovoe hozyaistvo] 1:33-34. (In Russian)
14 Fu YB, Chong J, Fetch T, Wang ML (2007) Microsatellite variation in Avena sterilis oat germplasm, Theoretical and Applied Genetics, 114(6):1029-38. DOI 10.1007/s00122-006-0496-7
15 Montilla-Bascon G, Sanchez-Martín J, Rispail N, Rubiales D, Mur L, Langdon T, Griffiths I, Howarth C, Prats E (2013) Genetic Diversity and Population Structure Among Oat Cultivars and Landraces, Plant Molecular Biology, 31:1305–1314. DOI 10.1007/s11105-013-0598-8
16 Sood VK, Rana I, Hussain W, Chaudhary HK (2016) Genetic Diversity of Genus Avena from North Western-Himalayas Using Molecular Markers Proceedings of the National Academy of Sciences, India Section B: Biological Sciences, 86(1):151-158.
17 Wu B, Zhang Z, Chen L, He M (2012) Isolation and characterization of novel microsatellite markers for Avena sativa (Poaceae oat), American Journal of Botany, 99(2):e69-71. DOI: 10.3732/ajb.1100404
18 Sheikhehpour S, Bahraminejad S, Cheghamirza K (2014) Morphological and molecular genetic variations of oat genotypes grown in Kermanshah, Iran, Molecular Biology Reports, 41(6):4023-30. DOI: 10.1007/s11033-014-3271-x
19 Nurpeissov M, Abugaliyeva AI, Langdon T (2015) Genetic Identification of Kazakhstan Oat. Varieties Biosciences Biotechnology Research Asia, 12(3):2227-2233.
20 Abugalieva S, Ermekbaev K, Sariev B, Chudinov V, Sereda G, Turuspekov Y (2013) Genotyping and phenotyping of oat collection, 2nd Conference of Cereal Biotechnology and Breding, Budapest. P.51
21 Abugaliyeva SI, Sereda GA, Chudinov VA, Sariev BS, Turuspekov YK (2013) Analysis of agronomic characters of world collection of oats grown in three different regions of Kazakhstan. Works of applied botany, genetics and breeding [Analiz hozyaistvenno-cennyh priznakov mirovoi kollekcii ovca, vyrashennoi v treh razlichnyh regionah Kazakhstana. Trudy po prikladnoi botanike, genetike i selekcii] 171:168-174. (In Russian)
22 Abugaliyeva SI, Chudinov VA, Sereda GA, Sariev BS, Turuspekov YK (2014) Genetic and phenotypic diversity of the collection of oats (Avena sativa L.), Proceedings of the 2nd International Conference "Problems of evolution and systematics of cultivated plants" [Geneticheskoe i fenotipicheskoe raznoobrazie kollecii ovsa (Avena sativa L.), Materialy 2-oi mezhdunarodnoi konferencii "Problemy evolyucii I sistematiki kulturnyh rastenii" ] St. Petersburg, Russia. P.36. (In Russian)
23 Delaporta SL, Wood J, Hicks JB (1983) A plant DNA minipreparation. Version II, Plant Mol. Biol. Rep, P.19-21.
24 Wight CP, Yan, W, Mitchell Fetch JW, Deyl JK and Tinker NA (2010) A Set of New Simple Sequence Repeat and Avenin DNA Markers Suitable for Mapping and Fingerprinting Studies in Oat (Avena spp.), Crop Science, 50(4):1207-1218. DOI: 10.2135/cropsci2009.09.0474
25 Yeh F, Yang R, Boyle T, Ye Z (2000) Microsoft Windows-Based Freeware for Population Genetic Analysis Version 1.32 ed. Molecular Biology and Biotechnology Centre, University of Alberta, Edmonton.
26 Smouse PE, Whitehead MR, Peakall R. (2015) An informational diversity framework, illustrated with sexually deceptive orchids in early stages of speciation, Molecular Ecology Resources, 15:1375-1384. DOI 10.111/1755-0998.12422
27 Baohong G, Zhou X, Murphy JP (2003) Genetic variation within Chinese and western cultivated oat accessions. Cereal Research Communication. 31(3-4):339–346
2 Loskutov IG, Blinov EV (2013) Genetic resources for oats promising areas of selection. Works of applied botany, genetics and breeding [Geneticheskie resursy ovsa dlya perspektivnyh napravlenii selekcii. Trudy po prikladnoi botanike, genetike I selekcii] 177:42-45. (In Russian)
3 Batalova GA (2000) Oats, technology of cultivation and breeding [Oves, tehnologiya vozdelovaniya i selekciya]. Kirov. P.206. (In Russian)
4 Sartakova SV (2004) The global gene pool of oats role in addressing the priorities of selection problems in Western Siberia. The genetic resources of cultivated plants [Geneticheskie resursy kulturnyh rastenii]. St. Petersburg, Russia. P.110. (In Russian)
5 He X, Bjornstad A (2012) Diversity of North European oat analyzed by SSR, AFLP and DArT markers, Theoretical and Applied Genetics, 125(1):57-70. DOI: 10.1007/s00122-012-1816-8
6 Loskutov I.G (2009) Genetic resources oats and barley - a source of productive breeding in Russia [Geneticheskie resursy ovsa I yachmenya – istochnik rezultativnoi selekcii v Rosii]. Reports International Vavilov Conference, Russia. P.200-205. (In Russian)
7 Turuspekov Y, Sariev B, Chudinov V, Sereda G, Tokhetova L, Ortaev A, Tsygankov V, Doszhanov M, Volis S, Abugalieva S (2013) Genotype X environment interaction patterns for grain yield of spring barley in different regions of Kazakhstan, Genetics, 49(2):196-205. DOI: 10.1134/S1022795413020129
8 Zeng XQ (2015) Genetic variability in agronomic traits of a germplasm collection of hulless barley, Genet Mol Res., 28;14(4):18356-69. DOI: 10.4238/2015
9 Loskutov IG, Kovaleva ON, Blinova EV (2011) Guidelines for the study and conservation of the world collection of barley and oats [Metodicheskie ukazaniya po izucheniyu i sohraneniyu mirovoi kollekcii yachmenya i ovsa]. Russia. P.46. (In Russia)
10 State Register of Breeding Achievements Approved for use in the Republic of Kazakhstan [Gosudarstvennyi reestr selekcionnyh dostizhenii, dopushennyh k ispolzovaniyu v Respublike Kazakhstan]. Astana, Kazakhstan, 2014. P.238. (In Russia)
11 Sariev BS, Tohetova LA Abugaliyeva AI, Zhundibaev KK, Baimuratov AZ (2013) Adapted and prospective varieties of forage crops established in KazNIIZiR [Raionirovannye I perspektivnye sorta zernofurozhainyh kultur, sozdannyh v KazNIIR]. Astana, Kazakhstan. P.36. (In Russian)
12 Varieties of grain crops breeding NPC Grain Farming by Barayev AI [Sorta zernovyh kultur selekcii NPC zernovogo hozyaistva im. AI Barayeva] (2011), Catalogue. Astana, Kazakhstan. P.65. (In Russian)
13 Kaskarbaev JA (2001) Formation of the duration of the growing season of crops of oats depending on the variety, sowing date and fertilizer. Grain economy [Formirovanie prodolzhitelnosti vegetacionnogo perioda posevov ovsa v zavisimosti ot sroka poseva I udobrenii. Zernovoe hozyaistvo] 1:33-34. (In Russian)
14 Fu YB, Chong J, Fetch T, Wang ML (2007) Microsatellite variation in Avena sterilis oat germplasm, Theoretical and Applied Genetics, 114(6):1029-38. DOI 10.1007/s00122-006-0496-7
15 Montilla-Bascon G, Sanchez-Martín J, Rispail N, Rubiales D, Mur L, Langdon T, Griffiths I, Howarth C, Prats E (2013) Genetic Diversity and Population Structure Among Oat Cultivars and Landraces, Plant Molecular Biology, 31:1305–1314. DOI 10.1007/s11105-013-0598-8
16 Sood VK, Rana I, Hussain W, Chaudhary HK (2016) Genetic Diversity of Genus Avena from North Western-Himalayas Using Molecular Markers Proceedings of the National Academy of Sciences, India Section B: Biological Sciences, 86(1):151-158.
17 Wu B, Zhang Z, Chen L, He M (2012) Isolation and characterization of novel microsatellite markers for Avena sativa (Poaceae oat), American Journal of Botany, 99(2):e69-71. DOI: 10.3732/ajb.1100404
18 Sheikhehpour S, Bahraminejad S, Cheghamirza K (2014) Morphological and molecular genetic variations of oat genotypes grown in Kermanshah, Iran, Molecular Biology Reports, 41(6):4023-30. DOI: 10.1007/s11033-014-3271-x
19 Nurpeissov M, Abugaliyeva AI, Langdon T (2015) Genetic Identification of Kazakhstan Oat. Varieties Biosciences Biotechnology Research Asia, 12(3):2227-2233.
20 Abugalieva S, Ermekbaev K, Sariev B, Chudinov V, Sereda G, Turuspekov Y (2013) Genotyping and phenotyping of oat collection, 2nd Conference of Cereal Biotechnology and Breding, Budapest. P.51
21 Abugaliyeva SI, Sereda GA, Chudinov VA, Sariev BS, Turuspekov YK (2013) Analysis of agronomic characters of world collection of oats grown in three different regions of Kazakhstan. Works of applied botany, genetics and breeding [Analiz hozyaistvenno-cennyh priznakov mirovoi kollekcii ovca, vyrashennoi v treh razlichnyh regionah Kazakhstana. Trudy po prikladnoi botanike, genetike i selekcii] 171:168-174. (In Russian)
22 Abugaliyeva SI, Chudinov VA, Sereda GA, Sariev BS, Turuspekov YK (2014) Genetic and phenotypic diversity of the collection of oats (Avena sativa L.), Proceedings of the 2nd International Conference "Problems of evolution and systematics of cultivated plants" [Geneticheskoe i fenotipicheskoe raznoobrazie kollecii ovsa (Avena sativa L.), Materialy 2-oi mezhdunarodnoi konferencii "Problemy evolyucii I sistematiki kulturnyh rastenii" ] St. Petersburg, Russia. P.36. (In Russian)
23 Delaporta SL, Wood J, Hicks JB (1983) A plant DNA minipreparation. Version II, Plant Mol. Biol. Rep, P.19-21.
24 Wight CP, Yan, W, Mitchell Fetch JW, Deyl JK and Tinker NA (2010) A Set of New Simple Sequence Repeat and Avenin DNA Markers Suitable for Mapping and Fingerprinting Studies in Oat (Avena spp.), Crop Science, 50(4):1207-1218. DOI: 10.2135/cropsci2009.09.0474
25 Yeh F, Yang R, Boyle T, Ye Z (2000) Microsoft Windows-Based Freeware for Population Genetic Analysis Version 1.32 ed. Molecular Biology and Biotechnology Centre, University of Alberta, Edmonton.
26 Smouse PE, Whitehead MR, Peakall R. (2015) An informational diversity framework, illustrated with sexually deceptive orchids in early stages of speciation, Molecular Ecology Resources, 15:1375-1384. DOI 10.111/1755-0998.12422
27 Baohong G, Zhou X, Murphy JP (2003) Genetic variation within Chinese and western cultivated oat accessions. Cereal Research Communication. 31(3-4):339–346
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Ashimova, A. N., Yermekbaev, K. A., Turuspekov, Y. K., & Abugalieva, S. I. (2016). Genotyping the world collection of oat by microsatellite markers. Experimental Biology, 66(1), 134–143. Retrieved from https://bb.kaznu.kz/index.php/biology/article/view/1168
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МOLECULAR BIOLOGY AND GENETICS
