Novel SSR Markers from BAC-End Sequences, DArT Arrays and a Comprehensive Genetic Map with 1,291 Marker Loci for Chickpea (Cicer arietinum L.)

被引：125

作者：

Thudi, Mahendar ^{[1
]}

Bohra, Abhishek ^{[1
,2
]}

Nayak, Spurthi N. ^{[1
,2
]}

Varghese, Nicy ^{[1
]}

Shah, Trushar M. ^{[1
]}

Penmetsa, R. Varma ^{[3
]}

Thirunavukkarasu, Nepolean ^{[4
]}

Gudipati, Srivani ^{[1
]}

Gaur, Pooran M. ^{[1
]}

Kulwal, Pawan L. ^{[5
]}

Upadhyaya, Hari D. ^{[1
]}

KaviKishor, Polavarapu B. ^{[2
]}

Winter, Peter ^{[6
]}

Kahl, Guenter ^{[7
]}

Town, Christopher D. ^{[8
]}

Kilian, Andrzej ^{[9
]}

Cook, Douglas R. ^{[3
]}

Varshney, Rajeev K. ^{[1
,10
]}

机构：

[1] Int Crops Res Inst Semi Arid Trop, Grain Legumes Res Program, Hyderabad, Andhra Pradesh, India

[2] Osmania Univ, Dept Genet, Hyderabad 500007, Andhra Pradesh, India

[3] Univ Calif Davis, Dept Plant Pathol, Davis, CA 95616 USA

[4] Indian Agr Res Inst, Div Genet, New Delhi 110012, India

[5] Mahatma Phule Krishi Vidyapeeth, State Level Biotechnol Ctr, Ahmednagar, India

[6] GenXPro GmbH, Frankfurt, Germany

[7] Goethe Univ Frankfurt, Frankfurt, Germany

[8] J Craig Venter Inst, Rockville, MD USA

[9] DArT Pty Ltd, Yarralumla, Australia

[10] CIMMYT, CGIAR Generat Challenge Programme, Mexico City 06600, DF, Mexico

来源：

PLOS ONE | 2011年 / 6卷 / 11期

关键词：

MICROSATELLITE MARKERS; DIVERSITY ARRAYS; LINKAGE MAP; MEDICAGO-TRUNCATULA; TECHNOLOGY DART; CONSENSUS MAP; INTEGRATION; GENOME; CONSTRUCTION; RESISTANCE;

D O I：

10.1371/journal.pone.0027275

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

Chickpea (Cicer arietinum L.) is the third most important cool season food legume, cultivated in arid and semi-arid regions of the world. The goal of this study was to develop novel molecular markers such as microsatellite or simple sequence repeat (SSR) markers from bacterial artificial chromosome (BAC)-end sequences (BESs) and diversity arrays technology (DArT) markers, and to construct a high-density genetic map based on recombinant inbred line (RIL) population ICC 4958 (C. arietinum) 6PI 489777 (C. reticulatum). A BAC-library comprising 55,680 clones was constructed and 46,270 BESs were generated. Mining of these BESs provided 6,845 SSRs, and primer pairs were designed for 1,344 SSRs. In parallel, DArT arrays with ca. 15,000 clones were developed, and 5,397 clones were found polymorphic among 94 genotypes tested. Screening of newly developed BES-SSR markers and DArT arrays on the parental genotypes of the RIL mapping population showed polymorphism with 253 BES-SSR markers and 675 DArT markers. Segregation data obtained for these polymorphic markers and 494 markers data compiled from published reports or collaborators were used for constructing the genetic map. As a result, a comprehensive genetic map comprising 1,291 markers on eight linkage groups (LGs) spanning a total of 845.56 cM distance was developed (http://cmap.icrisat.ac.in/cmap/sm/cp/thudi/). The number of markers per linkage group ranged from 68 (LG 8) to 218 (LG 3) with an average inter-marker distance of 0.65 cM. While the developed resource of molecular markers will be useful for genetic diversity, genetic mapping and molecular breeding applications, the comprehensive genetic map with integrated BES-SSR markers will facilitate its anchoring to the physical map (under construction) to accelerate map-based cloning of genes in chickpea and comparative genome evolution studies in legumes.

引用

页数：12

共 63 条

[21] Development and mapping of DArT markers within the Festuca-Lolium complex [J].

Kopecky, David ;

Bartos, Jan ;

Lukaszewski, Adam J. ;

Baird, James H. ;

Cernoch, Vladimir ;

Koelliker, Roland ;

Rognli, Odd Arne ;

Blois, Helene ;

Caig, Vanessa ;

Luebberstedt, Thomas ;

Studer, Bruno ;

Shaw, Paul ;

Dolezel, Jaroslav ;

Kilian, Andrzej .

BMC GENOMICS, 2009, 10 :473

[22]

KOROL AB, 1994, HEREDITY, V70, P254

[23] The estimation of map distances from recombination values [J].

Kosambi, DD .

ANNALS OF EUGENICS, 1943, 12 :172-175

[24] Construction of BAC and BIBAC libraries and their applications for generation of SSR markers for genome analysis of chickpea, Cicer arietinum L. [J].

Lichtenzveig, J ;

Scheuring, C ;

Dodge, J ;

Abbo, S ;

Zhang, HB .

THEORETICAL AND APPLIED GENETICS, 2005, 110 (03) :492-510

[25] DArT markers:: diversity analyses and mapping in Sorghum bicolor [J].

Mace, Emma S. ;

Xia, Ling ;

Jordan, David R. ;

Halloran, Kirsten ;

Parh, Dipal K. ;

Huttner, Eric ;

Wenzl, Peter ;

Kilian, Andrzej .

BMC GENOMICS, 2008, 9 (1)

[26] A consensus genetic map of chickpea (Cicer arietinum L.) based on 10 mapping populations [J].

Millan, T. ;

Winter, P. ;

Juengling, R. ;

Gil, J. ;

Rubio, J. ;

Cho, S. ;

Cobos, M. J. ;

Iruela, M. ;

Rajesh, P. N. ;

Tekeoglu, M. ;

Kahl, G. ;

Muehlbauer, F. J. .

EUPHYTICA, 2010, 175 (02) :175-189

[27] Cereal chromosome structure, evolution, and pairing [J].

Moore, G .

ANNUAL REVIEW OF PLANT PHYSIOLOGY AND PLANT MOLECULAR BIOLOGY, 2000, 51 :195-222

[28] A consensus genetic map of cowpea [Vigna unguiculata (L) Walp.] and synteny based on EST-derived SNPs [J].

Muchero, Wellington ;

Diop, Ndeye N. ;

Bhat, Prasanna R. ;

Fenton, Raymond D. ;

Wanamaker, Steve ;

Pottorff, Marti ;

Hearne, Sarah ;

Cisse, Ndiaga ;

Fatokun, Christian ;

Ehlers, Jeffrey D. ;

Roberts, Philip A. ;

Close, Timothy J. .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2009, 106 (43) :18159-18164

[29] Distribution of microsatellites in the genome of Medicago truncatula:: A resource of genetic markers that integrate genetic and physical maps [J].

Mun, JH ;

Kim, DJ ;

Choi, HK ;

Gish, J ;

Debellé, F ;

Mudge, J ;

Denny, R ;

Endré, G ;

Saurat, O ;

Dudez, AM ;

Kiss, GB ;

Roe, B ;

Young, ND ;

Cook, DR .

GENETICS, 2006, 172 (04) :2541-2555

[30] Integration of novel SSR and gene-based SNP marker loci in the chickpea genetic map and establishment of new anchor points with Medicago truncatula genome [J].

Nayak, Spurthi N. ;

Zhu, Hongyan ;

Varghese, Nicy ;

Datta, Subhojit ;

Choi, Hong-Kyu ;

Horres, Ralf ;

Juengling, Ruth ;

Singh, Jagbir ;

Kishor, P. B. Kavi ;

Sivaramakrishnan, S. ;

Hoisington, Dave A. ;

Kahl, Guenter ;

Winter, Peter ;

Cook, Douglas R. ;

Varshney, Rajeev K. .

THEORETICAL AND APPLIED GENETICS, 2010, 120 (07) :1415-1441

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