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United States Department of Agriculture

Agricultural Research Service

Research Project: GENETIC AND GENOMIC APPROACHES TO IMPROVE PEANUT AND CORN RESISTANCE TO DISEASE AND AFLATOXIN CONTAMINATION

Location: Crop Protection and Management Research

Title: An international reference consensus genetic map with 897 marker loci based on 11 mapping populations for tetraploid groundnut (Arachis hypogaea L.)

Authors
item Gautami, Bhimana -
item Fonceka, Daniel -
item Pandey, Manish -
item Moretzsohn, Marcio -
item Sujay, Venkataswamy -
item Qin, Hongde -
item Hong, Yanbin -
item Faye, Issa -
item Chen, Xianoping -
item Bhanuprakash, Amindala -
item Shah, Trushar -
item Gowda, Makanahally -
item Nigam, Shyam -
item Liang, Xuanqiang -
item Hoisington, Dave -
item Guo, Baozhu
item Bertioli, David -
item Rami, Jean-Francois -
item Varshney, Rajeev -

Submitted to: PLoS One
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: June 18, 2012
Publication Date: July 18, 2012
Citation: Gautami, B., Fonceka, D., Pandey, M.K., Moretzsohn, M.C., Sujay, V., Qin, H., Hong, Y., Faye, I., Chen, X., Bhanuprakash, A., Shah, T.M., Gowda, M., Nigam, S.N., Liang, X., Hoisington, D.A., Guo, B., Bertioli, D.J., Rami, J., Varshney, R.K. 2012. An international reference consensus genetic map with 897 marker loci based on 11 mapping populations for tetraploid groundnut (Arachis hypogaea L.). PLoS One. 7(7):e41213.

Interpretive Summary: Peanut or groundnut is the fourth largest oilseed crop in the world and is cultivated in more than 100 countries with the annual production of 35.5 million tones. Dense genetic linkage maps are cornerstones for wide spectrum of genetics and breeding applications such as linkage mapping or association analysis based trait mapping, marker-assisted breeding, map-based cloning and physical map alignment. In general, it is possible to map only limited number of molecular markers in a given mapping population due to polymorphism constraints. Subsequently, with an objective to increase the number of mapped marker loci, genetic maps developed for different mapping populations are used for developing a consensus map. As a result, 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 reference consensus map has been divided into 20 cM long 203 BINs. 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.

Technical 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.

Last Modified: 9/22/2014
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