A SSR-based composite genetic linkage map for the cultivated peanut (Arachis hypogaea L.) genome

Abstract

Background: The construction of genetic linkage maps for cultivated peanut (Arachis hypogaea L.) has and continues to be an important research goal to facilitate quantitative trait locus (QTL) analysis and gene tagging for use in a marker-assisted selection in breeding. Even though a few maps have been developed, they were constructed using diploid or interspecific tetraploid populations. The most recently published intra-specific map was constructed from the cross of cultivated peanuts, in which only 135 simple sequence repeat (SSR) markers were sparsely populated in 22 linkage groups. The more detailed linkage map with sufficient markers is necessary to be feasible for QTL identification and marker-assisted selection. The objective of this study was to construct a genetic linkage map of cultivated peanut using simple sequence repeat (SSR) markers derived primarily from peanut genomic sequences, expressed sequence tags (ESTs), and by "data mining" sequences released in GenBank.

Results: 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, and used in genotyping these RIL populations. Individual linkage maps were constructed from each of the three populations 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 maps), 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. By comparison, there were potential synteny, collinear order of some markers and conservation of collinear linkage groups among the maps and with the AA genome but not fully conservative.

Conclusion: A composite linkage map was constructed from three individual mapping populations with 175 SSR markers in 22 composite linkage groups. This composite genetic linkage map is among the first "true" tetraploid peanut maps produced. This map also consists of 47 SSRs that have been used in the published AA genome maps, and could be used in comparative mapping studies. The primers described in this study are PCR-based markers, which are easy to share for genetic mapping in peanuts. All 1044 primer pairs are provided as additional files and the three RIL populations will be made available to public upon request for quantitative trait loci (QTL) analysis and linkage map improvement.

Figure 1

Genetic linkage groups based on population Y13Zh (Yueyou 13 × Zhenzhuhei). RIL (recombinant inbred line) population Y13Zh consisted of 142 lines, derived from a cross made from the female parent Yueyou13, a Spanish type with high yield, and male parent Zhenzhuhei, a Virginia type with dark purple testa and high protein (32.4%) content. Linkage analysis was performed with JoinMap using a minimum LOD score of 3.0 and linkage maps were drawn using MapChart for Windows. Underlined markers were EST-SSRs. Markers that showed significant distortions from 1:1 segregation are indicated by *. Markers that amplified two loci are designated by an Arabic number (-1 or -2) appended to the locus name to distinguish the two loci 1 and 2 after the marker name.

Figure 2

Genetic linkage groups based on population Y13Fu (Yueyou 13 × Fu 95-5). RIL (recombinant inbred line) population Y13Fu consisted of 84 lines, derived from a cross made from the female parent Yueyou13, a Spanish type with high yield, and male parent Fu 95-5, a Spanish type with high oil content (56.2%). Linkage analysis was performed with JoinMap using a minimum LOD score of 3.0 and linkage maps were drawn using MapChart for Windows. Underlined markers were EST-SSRs. Markers that showed significant distortions from 1:1 segregation are indicated by *. Markers that amplified two loci are designated by an Arabic number (-1 or -2) appended to the locus name to distinguish the two loci 1 and 2 after the marker name.

Figure 3

Genetic linkage groups based on population Y13J11 (Yueyou 13 × J11). RIL (recombinant inbred line) population Y13J11 consisted of 136 lines, derived from the female parent Yueyou13, a Spanish type with high yield, and male parent J11, a Spanish type with reported resistance to Aspergillus flavus and aflatoxin contamination, by single seed descent from F4 to F6 generation and consisted of 136 individual lines. Linkage analysis was performed with JoinMap using a minimum LOD score of 3.0 and linkage maps were drawn using MapChart for Windows. Underlined markers were EST-SSRs. Markers that showed significant distortions from 1:1 segregation are indicated by *. Markers that amplified two loci are designated by an Arabic number (-1 or -2) appended to the locus name to distinguish the two loci 1 and 2 after the marker name.

Figure 4

A SSR-based composite linkage map of Arachis hypogaea based on three RIL populations. Based on the maps of three RIL populations, a composite map was constructed. The composite linkage maps consist of 22 composite linkage groups with 175 SSR marker loci. Linkage analysis was performed with JoinMap using a minimum LOD score of 3.0 and linkage maps were drawn using MapChart for Windows. Underlined markers were EST-SSRs. Markers that showed significant distortions from 1:1 segregation are indicated by *. Markers that amplified two loci are designated by an Arabic number (-1 or -2) appended to the locus name to distinguish the two loci 1 and 2 after the marker name.