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ARS Home » Southeast Area » Tifton, Georgia » Crop Protection and Management Research » Research » Publications at this Location » Publication #234089
Title: A SSR-based composite genetic linkage map for the cultivated peanut (Arachis hypogaea L.)genome

Author
item HONG, Y - GUANGDONG ACADEMY, CHINA
item CHEN, X - UNIV OF GA
item LIANG, XUANQIANG - Guangdong Academy Of Agricultural Sciences
item LIU, G - GUANGDONG ACADEMY, CHINA
item ZHOU, G - GUANGDONG ACADEMY, CHINA
item LI, S - GUANGDONG ACADEMY, CHINA
item WEN, S - GUANGDONG ACADEMY, CHINA
item Holbrook, Carl - Corley
item Guo, Baozhu

Submitted to: BMC Plant Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/27/2010
Publication Date: 1/27/2010
Citation: Hong, Y., Chen, X., Liang, X., Liu, H., Zhou, G., Li, S., Wen, S., Holbrook, C., Guo, B. 2010. A SSR-based composite genetic linkage map for the cultivated peanut (Arachis hypogaea L.) genome. Biomed Central (BMC) Plant Biology. 10:17.

Interpretive Summary: Cultivated peanut is still lacking a “true” genetic map. As a result, the application of biotechnology to the improvement of the cultivated peanut has been hampered by lacking a road-map and by an inability to visualize genetic variation. Three recombinant inbred lines (RILs) populations were constructed from three crosses with one common female parental line. The four parents were screened with 1044 primer pairs designed to amplify simple sequence repeats (SSRs) makers and 901 primers produced clear products. There were 146, 124 and 64 markers were polymorphic in these populations. Three individual linkage maps were constructed from each population and a composite map was created. The composite linkage map consists of 22 composite linkage groups (LG) with 175 SSR markers (including 47 SSRs on the published AA genome map), representing the 20 chromosomes of Arachis hypogaea. The total composite map length is 885.4 cM, with an average marker density of 5.8 cM. This composite genetic map represents the “true” peanut map yet produced. The primers described in this study are PCR-based markers, which are easy to share for genetic mapping in peanuts and other legumes. All 1044 markers are provided as a supplementary material, and the three RIL populations will be made available to the public upon request for genetics analysis and linkage map improvement.

Technical Abstract: Cultivated peanut (Arachis hypogaea L.) is an allotetraploid species (AABB, 2n = 4x = 40), and is still lacking a “true” tetraploid genetic linkage map. Even though a few maps have been developed, they were constructed using diploid or interspecific tetraploid populations. The objective of this study was to construct a genetic linkage map of tetraploid cultivated peanut using simple sequence repeat (SSR) markers. Three recombinant inbred lines (RILs) populations were constructed from three crosses with one common female parental line Yueyou 13, a high yielding Spanish market type. The four parents were screened with 1044 primer pairs designed to amplify SSRs and 901 primer pairs produced clear PCR products. Of the 901 primer pairs, 146, 124 and 64 primer pairs (markers) were polymorphic in these populations, respectively. Three individual linkage maps were constructed from each population and a composite map based on 93 common loci were created using JoinMap. The composite linkage maps consist of 22 composite linkage groups (LG) with 175 SSR markers (including 47 SSRs on the published AA genome map), representing the 20 chromosomes of A. hypogaea. The total composite map length is 885.4 cM, with an average marker density of 5.8 cM. Segregation distortion in the 3 populations was 23.0%, 13.5% and 7.8% of the markers, respectively. These distorted loci tended to cluster on LG1, LG3, LG4 and LG5. There were only 15 EST-SSR markers mapped due to low polymorphism. This composite genetic linkage map represents the “true” tetraploid cultivated peanut map yet produced. The primers described in this study are PCR-based markers, which are easy to share for genetic mapping in peanuts and other legumes. Efforts are in progress to use this map and the RILs to detect quantitative trait loci (QTLs) for several important traits. All 1044 primer pairs are provided as a supplementary material, and the three RIL populations will be made available to public upon request for QTL analysis and linkage map improvement.