Open Access Open Badges Research article

Pearl millet [Pennisetum glaucum (L.) R. Br.] consensus linkage map constructed using four RIL mapping populations and newly developed EST-SSRs

Vengaldas Rajaram12, Thirunavukkarasu Nepolean13, Senapathy Senthilvel14, Rajeev K Varshney1, Vincent Vadez1, Rakesh K Srivastava1, Trushar M Shah1, Ambawat Supriya15, Sushil Kumar16, Basava Ramana Kumari1, Amindala Bhanuprakash1, Mangamoori Lakshmi Narasu2, Oscar Riera-Lizarazu17 and Charles Thomas Hash18*

Author Affiliations

1 International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Andhra Pradesh 502 324, India

2 Centre for Biotechnology, IST, JNTUH, Kukatpally, Hyderabad, Andhra Pradesh, 500 085, India

3 Division of Genetics, Indian Agricultural Research Institute, New Delhi, 110 012, India

4 Department of Crop Improvement, Directorate of Oilseeds Research, Hyderabad, 500 030, India

5 Department of Biotechnology, College of Basic Sciences and Humanities, Chaudhary Charan Singh Haryana Agricultural University, Hisar, Haryana, 125 004, India

6 Centre of Excellence in Biotechnology, Anand Agricultural University, Anand, Gujarat, 388 110, India

7 Department of Crop and Soil Sciences, Oregon State University, Corvallis, Oregon, 97331, USA

8 International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), ICRISAT Sahelian Center, Niamey, BP 12404, Niger

For all author emails, please log on.

BMC Genomics 2013, 14:159  doi:10.1186/1471-2164-14-159

Published: 9 March 2013



Pearl millet [Pennisetum glaucum (L.) R. Br.] is a widely cultivated drought- and high-temperature tolerant C4 cereal grown under dryland, rainfed and irrigated conditions in drought-prone regions of the tropics and sub-tropics of Africa, South Asia and the Americas. It is considered an orphan crop with relatively few genomic and genetic resources. This study was undertaken to increase the EST-based microsatellite marker and genetic resources for this crop to facilitate marker-assisted breeding.


Newly developed EST-SSR markers (99), along with previously mapped EST-SSR (17), genomic SSR (53) and STS (2) markers, were used to construct linkage maps of four F7 recombinant inbred populations (RIP) based on crosses ICMB 841-P3 × 863B-P2 (RIP A), H 77/833-2 × PRLT 2/89-33 (RIP B), 81B-P6 × ICMP 451-P8 (RIP C) and PT 732B-P2 × P1449-2-P1 (RIP D). Mapped loci numbers were greatest for RIP A (104), followed by RIP B (78), RIP C (64) and RIP D (59). Total map lengths (Haldane) were 615 cM, 690 cM, 428 cM and 276 cM, respectively. A total of 176 loci detected by 171 primer pairs were mapped among the four crosses. A consensus map of 174 loci (899 cM) detected by 169 primer pairs was constructed using MergeMap to integrate the individual linkage maps. Locus order in the consensus map was well conserved for nearly all linkage groups. Eighty-nine EST-SSR marker loci from this consensus map had significant BLAST hits (top hits with e-value ≤ 1E-10) on the genome sequences of rice, foxtail millet, sorghum, maize and Brachypodium with 35, 88, 58, 48 and 38 loci, respectively.


The consensus map developed in the present study contains the largest set of mapped SSRs reported to date for pearl millet, and represents a major consolidation of existing pearl millet genetic mapping information. This study increased numbers of mapped pearl millet SSR markers by >50%, filling important gaps in previously published SSR-based linkage maps for this species and will greatly facilitate SSR-based QTL mapping and applied marker-assisted selection programs.

EST-SSR markers; EST; Linkage map; Consensus map; Drought stress; Pearl millet; Synteny