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

[1] Diversity arrays technology (DArT) for high-throughput profiling of the hexaploid wheat genome [J].

Akbari, Mona ;

Wenzl, Peter ;

Caig, Vanessa ;

Carling, Jason ;

Xia, Ling ;

Yang, Shiying ;

Uszynski, Grzegorz ;

Mohler, Volker ;

Lehmensiek, Anke ;

Kuchel, Haydn ;

Hayden, Mathew J. ;

Howes, Neil ;

Sharp, Peter ;

Vaughan, Peter ;

Rathmell, Bill ;

Huttner, Eric ;

Kilian, Andrzej .

THEORETICAL AND APPLIED GENETICS, 2006, 113 (08) :1409-1420

[2] Detection of segregation distortion loci in triticale (x Triticosecale Wittmack) based on a high-density DArT marker consensus genetic linkage map [J].

Alheit, Katharina V. ;

Reif, Jochen C. ;

Maurer, Hans Peter ;

Hahn, Volker ;

Weissmann, Elmar A. ;

Miedaner, Thomas ;

Wuerschum, Tobias .

BMC GENOMICS, 2011, 12

[3]

Arumuganathan K., 1991, Plant Mol Biol Rep, V9, P208, DOI [10.1007/BF02672069, DOI 10.1007/BF02672069]

[4] Analysis of BAC-end sequences (BESs) and development of BES-SSR markers for genetic mapping and hybrid purity assessment in pigeonpea (Cajanus spp.) [J].

Bohra, Abhishek ;

Dubey, Anuja ;

Saxena, Rachit K. ;

Varma Penmetsa, R. ;

Poornima, K. N. ;

Kumar, Naresh ;

Farmer, Andrew D. ;

Srivani, Gudipati ;

Upadhyaya, Hari D. ;

Gothalwal, Ragini ;

Ramesh, S. ;

Singh, Dhiraj ;

Saxena, Kulbhushan ;

Kishor, P. B. Kavi ;

Singh, Nagendra K. ;

Town, Christopher D. ;

May, Gregory D. ;

Cook, Douglas R. ;

Varshney, Rajeev K. .

BMC PLANT BIOLOGY, 2011, 11

[5] Integration of physical and genetic maps of common bean through BAC-derived microsatellite markers [J].

Cordoba, Juana M. ;

Chavarro, Carolina ;

Schlueter, Jessica A. ;

Jackson, Scott A. ;

Blair, Matthew W. .

BMC GENOMICS, 2010, 11

[6] Isolation and characterization of novel microsatellite markers and their application for diversity assessment in cultivated groundnut (Arachis hypogaea) [J].

Cuc, Luu M. ;

Mace, Emma S. ;

Crouch, Jonathan H. ;

Quang, Vu D. ;

Long, Tran D. ;

Varshney, Rajeev K. .

BMC PLANT BIOLOGY, 2008, 8 (1)

[7] Development of genic-SSR markers by deep transcriptome sequencing in pigeonpea [Cajanus cajan (L.) Millspaugh] [J].

Dutta, Sutapa ;

Kumawat, Giriraj ;

Singh, Bikram P. ;

Gupta, Deepak K. ;

Singh, Sangeeta ;

Dogra, Vivek ;

Gaikwad, Kishor ;

Sharma, Tilak R. ;

Raje, Ranjeet S. ;

Bandhopadhya, Tapas K. ;

Datta, Subhojit ;

Singh, Mahendra N. ;

Bashasab, Fakrudin ;

Kulwal, Pawan ;

Wanjari, K. B. ;

Varshney, Rajeev K. ;

Cook, Douglas R. ;

Singh, Nagendra K. .

BMC PLANT BIOLOGY, 2011, 11

[8]

GAUR PM, 2005, FOCUS 2005 CHICKPEA, P8

[9] Advancing the STMS genomic resources for defining new locations on the intraspecific genetic linkage map of chickpea (Cicer arietinum L.) [J].

Gaur, Rashmi ;

Sethy, Niroj K. ;

Choudhary, Shalu ;

Shokeen, Bhumika ;

Gupta, Varsha ;

Bhatia, Sabhyata .

BMC GENOMICS, 2011, 12

[10] Development and use of genic molecular markers (GMMs) for construction of a transcript map of chickpea (Cicer arietinum L.) [J].

Gujaria, Neha ;

Kumar, Ashish ;

Dauthal, Preeti ;

Dubey, Anuja ;

Hiremath, Pavana ;

Prakash, A. Bhanu ;

Farmer, Andrew ;

Bhide, Mangla ;

Shah, Trushar ;

Gaur, Pooran M. ;

Upadhyaya, Hari D. ;

Bhatia, Sabhyata ;

Cook, Douglas R. ;

May, Greg D. ;

Varshney, Rajeev K. .

THEORETICAL AND APPLIED GENETICS, 2011, 122 (08) :1577-1589

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