Integrated consensus map of cultivated peanut and wild relatives reveals structures of the A and B genomes of Arachis and divergence of the legume genomes

Authors: SHIRASAWA, KENTA - Kazusa Dna Research Institute; BERTIOLI, DAVID - University Of Brasilia; VARSHNEY, RAJEEV - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; MORETZSOHN, MARCIO - Embrapa Genetic Resources; LEAL-BERTIOLI, SORAYA - Embrapa Genetic Resources; THUDI, MAHENDAR - University Of Brasilia; PANDEY, MANISH - University Of Brasilia; RAMI, JEAN-FRANCOIS - Centro De Cooperation Internationale En Recherche Agronomique Pour Le Development (CIRAD); FONCEKA, DANIEL - Centro De Cooperation Internationale En Recherche Agronomique Pour Le Development (CIRAD); GOWDA, MAKANAHALLY - University Of Agricultural Sciences And Veterinary Medicine - Romania; QIN, HONGDE - Hubei Academy Of Agricultural Sciences; Guo, Baozhu; HONG, YANBIN - Guangdong Academy Of Agricultural Sciences; LIANG, XUANQIANG - Guangdong Academy Of Agricultural Sciences; HIRAKAWA, HIDEKI - Kazusa Dna Research Institute; TABATA, SATOSHI - Kazusa Dna Research Institute; ISOBE, SACHIKO - Kazusa Dna Research Institute

Submitted to: DNA Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/21/2012
Publication Date: 1/12/2013
Publication URL: http://dnaresearch.oxfordjournals.org/content/early/2013/01/11/dnares.dss042.short?rss=1
Citation: Shirasawa, K., Bertioli, D.J., Varshney, R.K., Moretzsohn, M.C., Leal-Bertioli, S., Thudi, M., Pandey, M.K., Rami, J., Fonceka, D., Gowda, M., Qin, H., Guo, B., Hong, Y., Liang, X., Hirakawa, H., Tabata, S., Isobe, S. 2013. Integrated consensus map of cultivated peanut and wild relatives reveals structures of the A and B genomes of Arachis and divergence of the legume genomes. DNA Research. DOI:10.1093/dnares/dss042.

Interpretive Summary: While peanut is an important source of protein and oil and can also fix atmospheric nitrogen, the genetics and genomics of this legume lag far behind some tropical and cool-season legume crops due to a complex genome structure with challenging features, such as tetraploidy, low genetic diversity, and a relatively large genome size of 2.8 Gb. The complex, tetraploid genome structure of peanut has obstructed advances in genetics and genomics in this crop. The objective of this study was to understand the genome structure Arachis by developing a high-density integrated consensus map. Three recombinant inbred line populations derived from crosses between the A genome diploid species; the B genome diploid species; and between the AB genome tetraploids and an artificial amphidiploid, were used to construct genetic linkage maps. These maps plus 13 published maps were integrated into a consensus map covering 2,651 cM with 3,693 marker loci, which was anchored to 20 consensus linkage groups corresponding to the A and B genomes. The comparative genomics with genome sequences of pigeonpea, soybean, and model species of legume such as Lotus and Medicago truncatula revealed that the Arachis genome structure was moderately divergent from those of the other legumes. The comparative maps in legumes, integrated tetraploid consensus maps, and genome-specific diploid maps will increase the genetic and genomic understanding of Arachis, and should facilitate molecular breeding.

Technical Abstract: The complex, tetraploid genome structure of peanut (Arachis hypogaea) has obstructed advances in genetics and genomics in the species. The aim of this study is to understand the genome structure of Arachis by developing a high-density integrated consensus map. Three recombinant inbred line populations derived from crosses between the A genome diploid species, A. duranensis and A. stenosperma; the B genome diploid species, A. ipaënsis and A. magna; and between the AB genome tetraploids, A. hypogaea and an artificial amphidiploid (A. ipaënsis × A. duranensis)4×, were used to construct genetic linkage maps: 10 linkage groups (LGs) of 544 cM with 597 loci for the A genome; 10 LGs of 461 cM with 798 loci for the B genome; and 20 LGs of 1,442 cM with 1,469 loci for the AB genome. The resultant maps plus 13 published maps were integrated into a consensus map covering 2,651 cM with 3,693 marker loci which was anchored to 20 consensus LGs corresponding to the A and B genomes. The comparative genomics with genome sequences of Cajanus cajan, Glycine max, Lotus japonicus, and Medicago truncatula revealed that the Arachis genome structure was moderately divergent from those of the other legumes. The comparative maps in legumes, integrated tetraploid consensus maps, and genome-specific diploid maps will increase the genetic and genomic understanding of Arachis, and should facilitate molecular breeding.