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

V. Rajaram; T. Nepolean; S. Senthilvel; R.K. Varshney; V. Vadez; R.K. Srivastava; T.M. Shah; A. Supriya; S. Kumar; B. Ramana Kumari; A. Bhanuprakash; M. Lakshmi Narasu; O. Riera-Lizarazu; C.T. Hash

doi:10.1186/1471-2164-14-159

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

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

V. Rajaram, T. Nepolean, S. Senthilvel, R.K. Varshney, V. Vadez, R.K. Srivastava, T.M. Shah, A. Supriya, S. Kumar, B. Ramana Kumari, …

BMC Genomics, Vol.14(1), Art. 159

2013

DOI: https://doi.org/10.1186/1471-2164-14-159

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Abstract

Background 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. Results 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. Conclusion 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.

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Title: Pearl millet [Pennisetum glaucum(L.) R. Br.] consensus linkage map constructed using four RIL mapping populations and newly developed EST-SSRs
Authors/Creators: V. Rajaram (Author/Creator) - Jawaharlal Nehru Technological University, Hyderabad
T. Nepolean (Author/Creator) - Indian Agricultural Research Institute
S. Senthilvel (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
R.K. Varshney (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
V. Vadez (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
R.K. Srivastava (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
T.M. Shah (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
A. Supriya (Author/Creator) - Chaudhary Charan Singh Haryana Agricultural University
S. Kumar (Author/Creator) - Anand Agricultural University
B. Ramana Kumari (Author/Creator)
A. Bhanuprakash (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
M. Lakshmi Narasu (Author/Creator)
O. Riera-Lizarazu (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
C.T. Hash (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
Publication Details: BMC Genomics, Vol.14(1), Art. 159
Publisher: BioMed Central Ltd as part of Springer Nature
Identifiers: 991005544208407891
Copyright: © 2013 Rajaram et al.
Murdoch Affiliation: Murdoch University
Language: English
Resource Type: Journal article

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Collaboration types: Domestic collaboration; International collaboration
Citation topics: 3 Agriculture, Environment & Ecology; 3.4 Crop Science; 3.4.96 QTL
Web Of Science research areas: Biotechnology & Applied Microbiology; Genetics & Heredity
ESI research areas: Molecular Biology & Genetics