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

BackgroundHigh-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.ResultsWe 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.ConclusionsUsing 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.

Annotated genetic linkage maps of Pinus pinaster Ait. from a Central Spain population using microsatellite and gene based markers

“…Near 94% of the markers could be assigned to LGs and 60% could be positioned in the final maps (Table 1, Figure 1, Figure 2 and Additional file 3). The lower percentage of markers positioned when compared with other highly saturated maps [46] is due to the use of SAMPLs only scoring in one of the mapping progenies, as revealed by the low percentage of positioned SAMPLs (Table 1). When we discard SAMPLs scored only in one or the two mapping progenies, the percentage of SAMPL markers positioned in the parental maps increases to 65.3% for C14 and 72.1% for C15.…”

“…Moreover, new technologies have been developed for high throughput detection and genotyping of SNPs reducing the cost of assays [41,42]. Thus, highly saturated genetic linkage maps can be constructed even for species with large and un-sequenced genomes like conifers [21,43-46]. …”

Genome scanning for detecting adaptive genes along environmental gradients in the Japanese conifer, Cryptomeria japonica

“…Sixty-four of these loci Genome scan for adaptive genes in Cryptomeria japonica Y Tsumura et al were successfully mapped on the C. japonica linkage map, and their distribution was studied ( Figure 5, Moriguchi et al, 2012). The numbers of mapped outlier loci in each LG varied substantially.…”

“…The figure shows plots of marker position (based on 1255 mapped SNPs or the other DNA markers; Moriguchi et al, 2012) in cumulative centiMorgans (cM) versus (a) Bayes factor (log 10 ), as determined by BayeScan analysis, (b) the probability that the locus is an outlier as judged by the F ST -based test (Beaumont and Nichols, 1996) and (c) F-statistic value, F ST . Vertical dashed lines demarcate the 11…”

Genetics and Genomics of Tree Architecture

“…Similar examples of gene or miRNA atlas can be found in fruit trees, for their response to water stress (Bassett et al, 2014;Eldem et al, 2012) or during winter dormancy (Falavigna et al, 2014). These genomic resources combined with high-density genetic maps constructed for many forest tree species as in eucalyptus (Kullan et al, 2011;Neves, Mamani, Alfenas, Kirst, & Grattapaglia, 2011), maritime pine (Chancerelle et al, 2013), P. abies (Lind et al, 2014), Populus (Berlin, Lagercrantz, von Arnold, € Ost, & R€ onnberg-W€ astljung, 2010; Muchero et al, 2015), Cryptomeria japonica (Moriguchi et al, 2012), constitute a major basis to study the genetic determinants involved in the architectural development of trees. A recent study reported two high-resolution genetic maps constructed using a SNPs array genotyped on a large size pedigree , which has been useful to identify putative candidate genes underlying QTLs (Bartholomé, Mabiala, et al, 2015).…”