Development and cross-species/genera transferability of microsatellite markers discovered using 454 genome sequencing in chokecherry (Prunus virginiana L.)
Tóm tắt
Từ khóa
Tài liệu tham khảo
Agarwal M, Shrivastava N, Padh H (2008) Advances in molecular marker techniques and their applications in plant sciences. Plant Cell Rep 27:617–631
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410
Aranzana MJ, Mas JG, Carbo J, Arús P (2002) Development and variability of microsatellite markers in peach. Plant Breed 121:87–92
Canli FA (2004) Development of a second generation genetic linkage map for sour cherry using SSR markers. Pak J Biol Sci 7:1676–1683
Cardle L, Ramsay L, Milbourne D, Macaulay M, Marshall D, Waugh R (2000) Computational and experimental characterization of physically clustered simple sequence repeats in plants. Genetics 156:847–854
Castillo A, Budak H, Martin AC, Dorado G, Borner A, Roder M, Hernandez P (2010) Interspecies and intergenus transferability of barley and wheat D-genome microsatellite markers. Ann Appl Biol 156:347–356
Cavagnaro PF, Senalik DA, Yang L, Simon PW, Harkins TT, Kodria CD, Huang S (2010) Genome-wide characterization of simple sequence repeats in cucumber (Cucumis sativus L.). BMC Genomics 11:569–586
Cipriani G, Lot G, Huang WG, Marrazzo MT, Peterlunger E, Testolin R (1999) AC/GT and AG/CT microsatellite repeats in peach (Prunus persica (L.) Batsch): isolation, characterization and cross-species amplification in Prunus. Theor Appl Genet 99:65–72
Csencsics D, Brodeck S, Holderegger R (2010) Cost-effective, species-specific microsatellite development for the endangered dwarf bulrush (Typha minima) using next-generation sequencing technology. J Hered 101:789–793
Decroocq V, Fave MG, Hagen L, Bordenave L, Decroocq S (2003) Development and transferability of apricot and grape EST microsatellite markers across taxa. Theor Appl Genet 106:912–922
Gasic K, Han Y, Kerbundit S, Shulaev V, Iezzoni AF, Stover EW, Bell RL, Wisniewski ME (2009) Characteristics and transferability of new apple EST-derived SSRs to other Rosaceae species. Mol Breed 23:397–411
Gupta PK, Rustgi S, Sharma S, Singh R, Kumar N, Balyan HS (2003) Transferable EST-SSR markers for the study of polymorphism and genetic diversity in bread wheat. Mol Genet Genomics 270:315–323
Hagen LS, Chaib J, Fad B, Decrocq V, Bouchet P, Lambert P, Audergon JM (2004) Genomic and cDNA microsatellite from apricot (Prunus armeniaca L.). Mol Ecol Notes 4:432–434
Hayden MJ, Sharp PJ (2001) Sequence-tagged microsatellite profiling (STMP): a rapid technique for developing SSR markers. Nucleic Acids Res 29:e43
Holton TA, Christopher JT, McClure L, Harker N, Henry RJ (2002) Identification and mapping of polymorphic SSR markers from expressed gene sequences of barley and wheat. Mol Breed 9:63–71
Ince AG, Karaca M, Onus AN (2010) Polymorphic microsatellite markers transferable across Capsicum species. Plant Mol Biol Rep 28:285–291
Jun TH, Michel AP, Mian MAR (2011) Development of soybean aphid genomic SSR markers using next generation sequencing. Genome 54:360–367
Kalia RK, Rai MK, Kalia S, Singh R, Dhawan AK (2011) Microsatellite markers: an overview of the recent progress in plants. Euphytica 177:309–334
Lee S, Wen J (2001) A phylogenetic analysis of Prunus and the Amygdaloideae (Rosaceae) using ITS sequences of nuclear ribosomal DNA. Am J Bot 88:150–160
Lewers KS, Styan SMN, Hokanson SC (2005) Strawberry Gen-Bank-derived and genomic simple sequence repeat (SSR) markers and their utility with strawberry, blackberry, and red and black raspberry. J Am Soc Hort Sci 130:102–115
Lodhi MA, Ye GN, Weeden NF, Reisch BI (1994) A simple and efficient method for DNA extraction from grapevine cultivars, Vitis species and Ampelopsis. Plant MolBiol Rep 12:6–13
Luro FL, Constantino G, Terol J, Argout X, Allario T, Wincker P, Talon M, Ollitrault P, Morillon R (2008) Transferability of the ESR-SSRs developed on Nules clementine (Citrus clementine Hort ex Tan) to other Citrus species and their effectiveness for genetic mapping. BMC Genomics 9:287
Mardis ER (2008) The impact of next-generation sequencing technology on genetics. Trends Genet 24:133–141
Mnejja M, Garcia-Mas J, Howad W, Arús P (2005) Development and transportability across Prunus species of 42 polymorphic almond microsatellites. Mol Ecol Notes 5:531–535
Mnejja M, Garcia-Mas J, Audergon JM, Arús P (2010) Prunus microsatellite marker transferability across rosaceous crops. Tree Gen Genomes 6:689–700
Morgante M, Hanafey M, Powell W (2002) Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. Nat Genet 30:194–200
Olmstead JW, Sebolt AM, Cabrera A, Sooriyapathirana SS, Hammar S, Iriarte G, Wang D, Chen CY, van der Knaap E, Iezzoni AF (2008) Construction of an intra-specific sweet cherry (Prunus avium L.) genetic linkage map and syteny analysis with the Prunus reference map. Tree Genet Genomes 4:897–910
Parida SK, Kalia SK, Sunita K, Dalal V, Hemaprabha G, Selvi A, Pandit A, Singh A, Gaikwad K, Sharma TR, Srivastava PS, Singh NK, Mohapatra T (2009) Informative genomic microsatellite markers for efficient genotyping applications in sugarcane. Theor Appl Genet 118:327–338
Park YH, Ahn SG, Choi YM, Oh HJ, Ahn DC, Kim JG, Kang JS, Choi YW, Jeong BR (2010) Rose (Rosa hybrid L.) EST-derived microsatellite markers and their transferability to strawberry (Fragaria spp.). Sci Hort 125:733–739
Qi X, Cui F, Yu L, Ding A, Li J, Chen G, Wang H (2010) Molecular tagging wheat powdery mildew resistance gene Pm21 by EST-SSR and STS markers. Molecular Plant Breeding 1(4). doi: 10.5376/mpb.2010.01.0004
Rehder A (1940) Manual of cultivated trees and shrubs, 2nd edn. McMillan, New York, pp 452–481
Sim SC, Yu JK, Jo YK, Sorrells ME, Jung G (2009) Transferability of cereal EST-SSR markers to ryegrass. Genome 52:431–437
Singh RK, Singh RB, Singh SP, Sharma ML (2011) Identification of sugarcane microsatellites associated to sugar content in sugarcane and transferability to other cereal genomes. Euphytica 182:335–354
Song Q, Jia G, Zhu Y, Grant D, Nelson RT, Hwang EY, Hyten DL, Cregan PB (2010) Abundance of SSR motifs and development of candidate polymorphic SSR makers (BARCSOYSSR_1.0) in soybean. Crop Sci 50:1950–1957
Tang J, Gao Y, Jia J (2006) Homologous analysis of SSR- ESTs and transferability of wheat SSR-EST markers across barley, rice, and maize. Euphytica 151:87–93
Tangphatsornruang S, Somta P, Uthaipaisanwong P, Chanprasert J, Sangsrakru D, Seehalk W, Sommanas W, Tragoonrung S, Srinives P (2009) Characterization of microsatellites and gene contents from genome shotgun sequences of mungbean (Vigna radiata (L.) Wilczek). BMC Plant Biol 9:137–148
Temnykh S, DeClerck G, Lukashova A, Lipovich L, Cartinhour S, McCouch S (2001) Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations and genetic marker potential. Genome Res 11:1441–1452
Tuskan GA, Gunter LE, Yang ZK, Yin T, Sewell MM, DiFazio SP (2004) Characterization of microsatellites revealed by genomic sequencing of Populus trichocarpa. Can J For Res 34:85–93
Wang Z, Li J, Luo Z, Huang L, Chen X, Fang B, Li Y, Chen J, Zhang X (2011) Characterization and development of EST-derived SSR markers in cultivated sweet potato (Ipomoea batatas). BMC Plant Biol 11:139
Wen M, Wang H, Xia Z, Zou M, Lu C, Wang W (2010) Development of EST-SSR and genomic-SSR markers to assess genetic diversity in Jatropha curcas L. BMC Res Notes 3:42
Yamamoto T, Kimura T, Shoda M, Ban Y, Hayashi T, Matsuta N (2002) Development of microsatellite markers in the Japanese pear (Pyrus pyrifolia Nakai). MolEcol Notes 2:14–16
Yonemaru J, Ando T, Mizubayashi T, Kasugo S, Matsumoto T, Yano M (2009) Development of genome-wide simple sequence repeat markers using whole-genome shotgun sequences of sorghum (Sorghum bicolor (L.) Moench). DNA Res 16:187–193
Yu F, Wang BH, Feng SP, Wang JY, Li WG, Wu YT (2011) Development, characterization, and cross-species/genera transferability of SSR markers for rubber tree (Hevea brasiliensis). Plant Cell Rep 30:335–344
Zalapa JE, Cuevas H, Zhu H, Steffan S, Senalik D, Zeldin E, McCown B, Harbut R, Simon P (2012) Using next-generation sequencing approaches to isolate simple sequence repeat (SSR) loci in the plant science. Am J Bot 99:193–208