Open Access Research article

Construction of a consensus linkage map for red clover (Trifolium pratense L.)

Sachiko Isobe1*, Roland Kölliker2, Hiroshi Hisano15, Shigemi Sasamoto1, Tshyuko Wada1, Irina Klimenko3, Kenji Okumura4 and Satoshi Tabata1

Author Affiliations

1 Kazusa DNA Research Institute, Kazusa-Kamatari 2-6-7, Kisarazu, Chiba, 292-0818, Japan

2 Agroscope Reckenholz-Tänikon Research Station ART, Reckenholzstr. 191, 8046 Zurich, Switzerland

3 All-Russian Williams Fodder Crop Research Institute, 141055 Lugovaya, Moscow Region, Russia

4 National Agricultural Research Institute for Hokkaido Region, Hitsujigaoka 1, Toyohira, Sapporo, 062-8555, Japan

5 Samuel Robert Noble Foundation. 2510 Sam Noble Pky. Ardmore, OK, 73401, USA

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BMC Plant Biology 2009, 9:57  doi:10.1186/1471-2229-9-57

Published: 14 May 2009



Red clover (Trifolium pratense L.) is a major forage legume that has a strong self-incompatibility system and exhibits high genetic diversity within populations. For several crop species, integrated consensus linkage maps that combine information from multiple mapping populations have been developed. For red clover, three genetic linkage maps have been published, but the information in these existing maps has not been integrated.


A consensus linkage map was constructed using six mapping populations originating from eight parental accessions. Three of the six mapping populations were established for this study. The integrated red clover map was composed of 1804 loci, including 1414 microsatellite loci, 181 amplified fragment length polymorphism (AFLP) loci and 204 restriction fragment length polymorphism (RFLP) loci, in seven linkage groups. The average distance between loci and the total length of the consensus map were 0.46 cM and 836.6 cM, respectively. The locus order on the consensus map correlated highly with that of accession-specific maps. Segregation distortion was observed across linkage groups. We investigated genome-wide allele frequency in 1144 red clover individuals using 462 microsatellite loci randomly chosen from the consensus map. The average number of alleles and polymorphism information content (PIC) were 9.17 and 0.69, respectively.


A consensus genetic linkage map for red clover was constructed for the first time based on six mapping populations. The locus order on the consensus map was highly conserved among linkage maps and was sufficiently reliable for use as a reference for genetic analysis of random red clover germplasms.