Whole Genomic EST-SSR Development Based on High-throughput Transcript Sequencing in Proso Millet (Panicum miliaceum).

Yanmiao Jiang; Haiquan Li; Jianan Zhang; Jinying Xiang; Ruhong Cheng; Guoqing Liu

doi:10.17957/IJAB/15.0531

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Whole Genomic EST-SSR Development Based on High-throughput Transcript Sequencing in Proso Millet (Panicum miliaceum).

Author(s)

Yanmiao Jiang Institute of Millet Crops, Hebei Academy of Agricultural & Forestry Sciences, 050035 Hebei, China: Key Laboratory of Minor Crops in Hebei, Shijiazhuang 050035 Hebei, China

Haiquan Li Institute of Millet Crops, Hebei Academy of Agricultural & Forestry Sciences, 050035 Hebei, China: Key Laboratory of Minor Crops in Hebei, Shijiazhuang 050035 Hebei, China

Jianan Zhang Institute of Millet Crops, Hebei Academy of Agricultural & Forestry Sciences, 050035 Hebei, China: Key Laboratory of Minor Crops in Hebei, Shijiazhuang 050035 Hebei, China

Jinying Xiang Institute of Millet Crops, Hebei Academy of Agricultural & Forestry Sciences, 050035 Hebei, China: Key Laboratory of Minor Crops in Hebei, Shijiazhuang 050035 Hebei, China

Ruhong Cheng Institute of Millet Crops, Hebei Academy of Agricultural & Forestry Sciences, 050035 Hebei, China: Key Laboratory of Minor Crops in Hebei, Shijiazhuang 050035 Hebei, China

Guoqing Liu Institute of Millet Crops, Hebei Academy of Agricultural & Forestry Sciences, 050035 Hebei, China; Key Laboratory of Minor Crops in Hebei, Shijiazhuang 050035 Hebei, China

Abstract

Proso millet (Panicum miliaceum L.) with short growing period, is highly suited to drought and semi-arid climate, and thus possesses great potential for research. In this study, 8139 Expressed Sequence Tags-simple sequence repeat (EST-SSR) makers were developed from the transcript sequencing of Proso millet cultivar Yanshu 5. Tri-type was the major type, accounting for 83.65% of all the found SSR types, followed by di-type accounting for 11.1%. CCG/CGG was the most ample repeat-motif types in Proso millet. Twenty four primer pairs of these markers were synthesized for empirical validation and 21 primers obtained targeted fragments by PCR amplification. Three of the 21 markers were polymorphic among 20 Chinese Proso millet landraces which suggested that these EST-SSR markers can be used for genetic studies. Markers developed in this work can be used for agronomic trait location, linkage map construction and molecular breeding in Proso millet in the future.

Publication Details

Page(s) 617-620

DOI 10.17957/IJAB/15.0531

Published Journal: International Journal of Agriculture and Biology, Volume: 20, Issue: 3, Year: 2018

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References

Cho , Y.,J.Chung,G.Lee,K.Ma,A.Dixit,J.Gwag,Y.Park, 2010.Development and characterization of twenty-five new polymorphic microsatellite markers in proso millet (Panicum miliaceum L.),Gen. Genomics 32 267 -273

Dixit , A.,M.Jin,J.Chung,J.Yu,H.Chung,Y.Park,E.Cho, 2005.Development of polymorphic microsatellite markers in sesame (Sesamum indicum L.),Mol. Ecol. Notes 5 736 -738

Doyle , J.,J.L.Doyle, 1987.Genomic plant DNA preparation from fresh tissue CTAB method,Phytochem. Bull. 19 11 -15

Z.,P.H.Cepková,D.Janovská,I.Viehmannová,E.Svobodová,E.F.Cusimamani,L.Milella, 2015.Comparative analysis of genetic diversity of 8 millet genera revealed by ISSR markers,Emirates J. Food Agric 27 617 -628

Geervani , P.,B.O.Eggum, 1989.Nutrient composition and protein quality of minor millets,Plant Foods Hum. Nutr 39 201 -208

Goff , S.A.,R.Darrell,L.Tien-Hung,P.Gernot,W.Ronglin,D.Molly,S.Allen,O.Paul,V.Hemant, 2005.A draft sequence of the rice genome (Oryza sativa L. ssp,Science 296 92 -100

Guo , S.,Y.Zheng,J.G.Joung,S.Liu,Z.Zhang, 2010.Transcriptome sequencing and comparative analysis of cucumber flowers with different sex types,BMC Genomics 11 384 -

Gupta , P.K.,R.K.Varshney, 2000.The development and use of microsatellite markers for genetic analysis and plant breeding with emphasis on bread wheat,Euphytica 113 163 -185

Gwag , J.G.,H.L.Jeong,H.M.A.Kyung,D.Anupam,J.P.Yong,G.C.Eun,S.K.Tae and H.L. Suk, 2006.Characterization of new microsatellite markers in mung bean, Vigna radiata (L.),Mol. Ecol. Notes 6 1132 -1134

He , C.,V.Poysa,K.Yu, 2003.Development and characterization of simple sequence repeat (SSR) markers and their use in determining relationships among Lycopersicon esculentum cultivars,Theor. Appl. Genet 106 363 -373

Hsu , C.C.,Y.L.Chung,T.C.Chen,Y.L.Lee,Y.T.Kuo,W.C.Tsai,Y.Y.Hsiao,Y.W.Chen,W.L.Wu,H.H.Chenm, 2011.An overview of the Phalaenopsis orchid genome through BAC end sequence analysis,BMC Plant Biol 11 3 -

Hu , X.,J.Wang,P.Lu,H.Zhang, 2009.Assessment of genetic diversity in broomcorn millet (Panicum miliaceum L.) using SSR markers,J. Genet. Genomics 36 491 -500

Hu , Y.G.,J.Zhu,F.Liu,Z.Zhang,Y.Chai,W.N.Song, 2008.Genetic diversity among Chinese landraces and cultivars of broomcorn millet (Panicum miliaceum) revealed by the polymerase chain reaction, 3 357 -364

Jia , X.,Z.Zhang,C.Zhang,Y.Shi,Y.Song,T.Wang,Y.Li, 2009.Development and genetic mapping of SSR markers in foxtail millet [Setaria italica,Theor. Appl. Genet 118 821 -829

Kalinova , J.,J.Moudry, 2006.Content and quality of protein in proso millet (Panicum miliaceum L.) varieties,Plant Food. Hum. Nutr 61 43 -47

Karam , D.,P.Westra,S.J.Nissen,S.M.Ward,J.Figueiredo, 2004.Genetic diversity among proso millet (Panicum miliaceum) biotypes assessed by AFLP technique,Planta Daninha 22 167 -174

Karam , D.,P.Westra,S.J.Niessen,S.M.Ward,J.E.F.Figueiredo, 2006.Assessment of silver-stained AFLP markers for studying DNA polymorphism in proso millet (Panicum miliaceum L.),Braz. J. Bot. 29 609 -615

Lagler , R.,M.Humphreys,Z.Szabo,L.Horvath,A.Bittsanszky,J.Kiss,L.Holly,L.Heszky, 2005.Morphological and molecular analysis of common millet (P. miliaceum) cultivars compared to an aDNA sample from the 15th century (Hungary),Euphytica 146 77 -85

Li , M.,Y.Yang,F.Feng,X.Li,L.Gu,Y.Tian,J.Wang,J.Wang,Z.Li,A.Chen,X.Chen,Z.Zhang, 2016.SSR development and utilization with Rehmanniaglutinosa transcriptome,Int. J. Agric. Biol 18 589 -600

Ma , K.,J.Kwag,W.Zhao,A.Dixit,G.Lee,H.Kim,N.Kim,J.Lee,J.Ji,T.Kim,Y.Park, 2009.Isolation and characteristics of eight novel polymorphic microsatellite loci from the genome of garlic (Allium sativum L.),Sci. Hortic 122 355 -361

Morgante , M.,M.Hanafey,W.Powell, 2002.Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes,Nat. Genet 30 194 -200

Mribu , H.K.,K.W.Hilu, 1994.Detection of interspecific and intraspecific variation in Panicum millets through random amplified polymorphic DNA,Theor. Appl. Genet 88 412 -416

Mun , J.H.,D.J.Kim,H.K.Choi,J.Gish,F.Debelle,J.Mudge,R.Denny,G.Endre,O.Saurat,A.M.Dudez, 2006.Distribution of microsatellites in the genome of Medicago Truncatula: a resource of genetic markers that integrate genetic and physical maps,Genetics 172 2541 -2555

Powell , W.,M.Morgante,C.Andre,M.Hanafey,J.Vogel,S.Tingey,A.Rafalski, 1996.The comparison of RFLP, RAPD, AFLP and SSR (microsatellite)markers for germplasm analysis,Mol. Breed 2 225 -238

Rajput , S.G.,T. Plyler-Harveson and D.K.,Santra, 2014.Development and Characterization of SSR Markers in Proso Millet Based on Switchgrass Genomics,Amer. J. Plant Sci. 1 175 -186

Rajput , S.G.,D.K.Santra andJ.Schnable, 2016.MappingQTLsformorpho-agronomic traits in proso millet (Panicum miliaceum L.),Mol. Breed 36 1 -18

Singh , S.,S.Gupta,A.Mani,A.Chaturvedi, 2012.Mining and gene ontology based annotation of SSR markers from expressed sequence tags of Humulus Lupulus, 8 114 -122

Wang , Y.,M.Liu,P.Lu,Z.Qiao,T.Yang,H.Li,X.Cui, 2014.Screening SSR primer for construction of genetic linkage maps of proso millet,Crops 4 32 -38

Wang , Z.,B.Fang,J.Chen,X.Zhang,Z.Luo,L.Huang,X.Chen,Y.Li, 2010.De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweet potato (Ipomoea batatas),BMC Genomics 11 726 -

You , F.M.,N.Huo,Y.Q.Gu,M.C.Luo,Y.Ma,G.R.Lazo,J.Dvorak,O.D.Angerson, 2008.BatchPrimer3: a high throughput web application for PCR and sequencing primer design,BMC Bioinform 9 253 -

Zhou , X.,L.Ren,Q.Meng,Y.Li,Y.Yu,J.Yu, 2010.The next-generation sequencing technology and application,Protein Cell 1 520 -536

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