The construction of a high-density linkage map for identifying SNP markers that are tightly linked to a nuclear-recessive major gene for male sterility in Cryptomeria japonica D. Don

Abstract

Background: High-density linkage maps facilitate the mapping of target genes and the construction of partial linkage maps around target loci to develop markers for marker-assisted selection (MAS). MAS is quite challenging in conifers because of their large, complex, and poorly-characterized genomes. Our goal was to construct a high-density linkage map to facilitate the identification of markers that are tightly linked to a major recessive male-sterile gene (ms1) for MAS in C. japonica, a species that is important in Japanese afforestation but which causes serious social pollinosis problems.

Results: We constructed a high-density saturated genetic linkage map for C. japonica using expressed sequence-derived co-dominant single nucleotide polymorphism (SNP) markers, most of which were genotyped using the GoldenGate genotyping assay. A total of 1261 markers were assigned to 11 linkage groups with an observed map length of 1405.2 cM and a mean distance between two adjacent markers of 1.1 cM; the number of linkage groups matched the basic chromosome number in C. japonica. Using this map, we located ms1 on the 9th linkage group and constructed a partial linkage map around the ms1 locus. This enabled us to identify a marker (hrmSNP970_sf) that is closely linked to the ms1 gene, being separated from it by only 0.5 cM.

Conclusions: Using the high-density map, we located the ms1 gene on the 9th linkage group and constructed a partial linkage map around the ms1 locus. The map distance between the ms1 gene and the tightly linked marker was only 0.5 cM. The identification of markers that are tightly linked to the ms1 gene will facilitate the early selection of male-sterile trees, which should expedite C. japonica breeding programs aimed at alleviating pollinosis problems without harming productivity.

Figure 1

Two three-generation pedigrees used for linkage mapping in this study.

Figure 2

A linkage map for C. japonica derived from the YI pedigree (LG1, LG2, LG3 and LG4). Marker names are indicated to the right of the linkage groups. Centimorgan distances (Kosambi) are indicated to the left of each linkage group. Definitions for the labels ssSNP, maeSNP and hrmSNP are provided in the Materials and Methods section. The nature of the other markers is indicated by the last letter of the locus names: C, CAPS; R, RFLP; S, SSR; ES, EST-SSR; A, ALP; s, SNP.

Figure 3

A linkage map for C. japonica derived from the YI pedigree (LG5, LG6, LG7 and LG8). Marker names are indicated to the right of the linkage groups. Centimorgan distances (Kosambi) are indicated to the left of each linkage group. Definitions for the labels ssSNP, maeSNP and hrmSNP are provided in the Materials and Methods section. The nature of the other markers is indicated by the last letter of the locus names: C, CAPS; R, RFLP; S, SSR; ES, EST-SSR; A, ALP; s, SNP.

Figure 4

A linkage map for C. japonica derived from the YI pedigree (LG9, LG10 and LG11). Marker names are indicated to the right of the linkage groups. Centimorgan distances (Kosambi) are indicated to the left of each linkage group. Definitions for the labels ssSNP, maeSNP and hrmSNP are provided in the Materials and Methods section. The nature of the other markers is indicated by the last letter of the locus names: C, CAPS; R, RFLP; S, SSR; ES, EST-SSR; A, ALP; s, SNP.

Figure 5

A partial linkage map around the ms1 locus for C. japonica, derived from the TO-S pedigree. Marker names are indicated to the right of the linkage groups. Centimorgan distances (Kosambi) are indicated to the left of each linkage group. The ms1 locus is indicated in bold. The SSR and CAPS markers are indicated by the last latter of the locus names: C, CAPS; S, SSR.