An international reference consensus genetic map with 897 marker loci based on 11 mapping populations for Tetraploid Groundnut (Arachis hypogaea L.)

B. Gautami; D. Foncéka; M.K. Pandey; M.C. Moretzsohn; V. Sujay; H. Qin; Y. Hong; I. Faye; X. Chen; A. Bhanuprakash; T.M. Shah; M.V.C. Gowda; S.N. Nigam; X. Liang; D.A. Hoisington; B. Guo; D.J. Bertioli; J-F Rami; R.K. Varshney

doi:10.1371/journal.pone.0041213

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An international reference consensus genetic map with 897 marker loci based on 11 mapping populations for Tetraploid Groundnut (Arachis hypogaea L.)

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An international reference consensus genetic map with 897 marker loci based on 11 mapping populations for Tetraploid Groundnut (Arachis hypogaea L.)

B. Gautami, D. Foncéka, M.K. Pandey, M.C. Moretzsohn, V. Sujay, H. Qin, Y. Hong, I. Faye, X. Chen, A. Bhanuprakash, …

PLoS ONE, Vol.7(7), Art. e41213

2012

DOI: https://doi.org/10.1371/journal.pone.0041213

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Abstract

Only a few genetic maps based on recombinant inbred line (RIL) and backcross (BC) populations have been developed for tetraploid groundnut. The marker density, however, is not very satisfactory especially in the context of large genome size (2800 Mb/1C) and 20 linkage groups (LGs). Therefore, using marker segregation data for 10 RILs and one BC population from the international groundnut community, with the help of common markers across different populations, a reference consensus genetic map has been developed. This map is comprised of 897 marker loci including 895 simple sequence repeat (SSR) and 2 cleaved amplified polymorphic sequence (CAPS) loci distributed on 20 LGs (a01–a10 and b01–b10) spanning a map distance of 3, 863.6 cM with an average map density of 4.4 cM. The highest numbers of markers (70) were integrated on a01 and the least number of markers (21) on b09. The marker density, however, was lowest (6.4 cM) on a08 and highest (2.5 cM) on a01. The reference consensus map has been divided into 20 cM long 203 BINs. These BINs carry 1 (a10_02, a10_08 and a10_09) to 20 (a10_04) loci with an average of 4 marker loci per BIN. Although the polymorphism information content (PIC) value was available for 526 markers in 190 BINs, 36 and 111 BINs have at least one marker with >0.70 and >0.50 PIC values, respectively. This information will be useful for selecting highly informative and uniformly distributed markers for developing new genetic maps, background selection and diversity analysis. Most importantly, this reference consensus map will serve as a reliable reference for aligning new genetic and physical maps, performing QTL analysis in a multi-populations design, evaluating the genetic background effect on QTL expression, and serving other genetic and molecular breeding activities in groundnut.

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Title: An international reference consensus genetic map with 897 marker loci based on 11 mapping populations for Tetraploid Groundnut (Arachis hypogaea L.)
Authors/Creators: B. Gautami (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
D. Foncéka (Author/Creator) - Centre de Coopération Internationale en Recherche Agronomique pour le Développement
M.K. Pandey (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
M.C. Moretzsohn (Author/Creator) - Brazilian Agricultural Research Corporation
V. Sujay (Author/Creator) - University of Agricultural Sciences, Dharwad
H. Qin (Author/Creator) - Hubei Academy of Agricultural Sciences
Y. Hong (Author/Creator) - Guangdong Academy of Agricultural Sciences
I. Faye (Author/Creator) - Institut Sénégalais de Recherches Agricoles
X. Chen (Author/Creator) - Guangdong Academy of Agricultural Sciences
A. Bhanuprakash (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
M.V.C. Gowda (Author/Creator) - University of Agricultural Sciences, Dharwad
S.N. Nigam (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
X. Liang (Author/Creator) - Guangdong Academy of Agricultural Sciences
D.A. Hoisington (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
B. Guo (Author/Creator) - Agricultural Research Service
D.J. Bertioli (Author/Creator) - Universidade de Brasília
J-F Rami (Author/Creator) - Centre de Coopération Internationale en Recherche Agronomique pour le Développement
R.K. Varshney (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
Publication Details: PLoS ONE, Vol.7(7), Art. e41213
Publisher: Public Library of Science
Identifiers: 991005540332307891
Copyright: © 2012 Gautami 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: Plant Sciences
ESI research areas: Agricultural Sciences