A high-density linkage map with 2560 markers and its application for the localization of the male-sterile genes ms3 and ms4 in Cryptomeria japonica D. Don
“…The total genetic distance was close to the length of the reference map (1405 cM) for Japanese cedar, and the order of anchor markers (SSRs) in the new map also corresponded to that in reference map [ 17 ]. The average interval between markers in the new map was similar to that in reported reference maps for this species (1.1 cM/marker [ 17 ], 0.49 cM/marker [ 20 ]) and in map for other conifers (0.58-0.62 cM/marker in P. taeda, [ 36 , 37 ], 0.6 cM/marker in a consensus map for P. taeda and Pinus elliottii [ 38 ] , 0.93 cM/marker in Pinus pinaster [ 39 ], 0.92 cM/marker in a consensus map for Picea glauca and Pinus marina [ 40 ]). Fig.…”
BackgroundJapanese cedar (Cryptomeria japonica) is an important tree for Japanese forestry. Male-sterile marker development in Japanese cedar would facilitate selection of male-sterile plus trees, addressing the widespread social problem of pollinosis and facilitating the identification of heterozygotes, which are useful for breeding.ResultsThis study used next-generation sequencing for single-nucleotide polymorphism discovery in libraries constructed from several organs, including male-sterile and male-fertile strobili. The single-nucleotide polymorphisms obtained were used to construct a high-density linkage map, which enabled identification of a locus on linkage group 9 strongly correlated with male-sterile trait. Expressed sequence tags corresponding to 11 marker loci from 5 isotigs were associated with this locus within 33.4-34.5 cM. These marker loci explained 100% of the phenotypic variation. Several homologs of these sequences are associated with male sterility in rice or Arabidopsis, including a pre-mRNA splicing factor, a DEAD-box protein, a glycosyl hydrolase, and a galactosyltransferase. These proteins are thus candidates for the causal male-sterile gene at the ms-1 locus. After we used a SNaPshot assay to develop markers for marker-assisted selection (MAS), we tested F2 progeny between male-sterile and wild-type plus trees to validate the markers and extrapolated the testing to a larger plus-tree population. We found that two developed from one of the candidates for the causal gene were suitable for MAS.ConclusionsMore than half of the ESTs and SNPs we collected were new, enlarging the genomic basis for genetic research on Japanese cedar. We developed two SNP markers aimed at MAS that distinguished individuals carrying the male-sterile trait with 100% accuracy, as well as individuals heterozygous at the male-sterile locus, even outside the mapping population. These markers should enable practical MAS for conifer breeding.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4581-5) contains supplementary material, which is available to authorized users.
“…The total genetic distance was close to the length of the reference map (1405 cM) for Japanese cedar, and the order of anchor markers (SSRs) in the new map also corresponded to that in reference map [ 17 ]. The average interval between markers in the new map was similar to that in reported reference maps for this species (1.1 cM/marker [ 17 ], 0.49 cM/marker [ 20 ]) and in map for other conifers (0.58-0.62 cM/marker in P. taeda, [ 36 , 37 ], 0.6 cM/marker in a consensus map for P. taeda and Pinus elliottii [ 38 ] , 0.93 cM/marker in Pinus pinaster [ 39 ], 0.92 cM/marker in a consensus map for Picea glauca and Pinus marina [ 40 ]). Fig.…”
BackgroundJapanese cedar (Cryptomeria japonica) is an important tree for Japanese forestry. Male-sterile marker development in Japanese cedar would facilitate selection of male-sterile plus trees, addressing the widespread social problem of pollinosis and facilitating the identification of heterozygotes, which are useful for breeding.ResultsThis study used next-generation sequencing for single-nucleotide polymorphism discovery in libraries constructed from several organs, including male-sterile and male-fertile strobili. The single-nucleotide polymorphisms obtained were used to construct a high-density linkage map, which enabled identification of a locus on linkage group 9 strongly correlated with male-sterile trait. Expressed sequence tags corresponding to 11 marker loci from 5 isotigs were associated with this locus within 33.4-34.5 cM. These marker loci explained 100% of the phenotypic variation. Several homologs of these sequences are associated with male sterility in rice or Arabidopsis, including a pre-mRNA splicing factor, a DEAD-box protein, a glycosyl hydrolase, and a galactosyltransferase. These proteins are thus candidates for the causal male-sterile gene at the ms-1 locus. After we used a SNaPshot assay to develop markers for marker-assisted selection (MAS), we tested F2 progeny between male-sterile and wild-type plus trees to validate the markers and extrapolated the testing to a larger plus-tree population. We found that two developed from one of the candidates for the causal gene were suitable for MAS.ConclusionsMore than half of the ESTs and SNPs we collected were new, enlarging the genomic basis for genetic research on Japanese cedar. We developed two SNP markers aimed at MAS that distinguished individuals carrying the male-sterile trait with 100% accuracy, as well as individuals heterozygous at the male-sterile locus, even outside the mapping population. These markers should enable practical MAS for conifer breeding.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4581-5) contains supplementary material, which is available to authorized users.
“…The C. japonica population used in this study comprised 139 genotypes, which were obtained from crossing between two F 1 progenies: YI96 (female parent) and YI38 (male parent). YI96 and YI38 were obtained by crossing local varieties in the Kyushu region of Japan, 'Yabukuguri' × 'Iwao' and 'Yabukuguri' × 'Kumotooshi', respectively [37,38]. Common garden experiments were established for the 139 genotypes with three clonal replicates in two different environments in Japan: the Chiba site (35˚20 0 52.55 00 N, 140˚1 0 47.92 00 E) and the Kumamoto site (32˚41 0 58.36 00 N, 130˚45 0 17.64 00 E).…”
Section: Plant Material Common Garden Experiment Linkage Mapmentioning
Long-lived forest tree species experience a wide range of environmental conditions throughout their lifespan. Evaluation of the underlying growth and development mechanisms of these species is essential to predict tree growth under climate change. This study investigated climate sensitivity to temperature, precipitation, dry periods, and the associated genomic regions in Cryptomeria japonica, Japan's most commercially important tree. We used tree rings and common garden experiments with three clonal replicates planted in two contrasting environments in Kyushu (Kumamoto site) and Honshu (Chiba site), Japan. Tree growth showed a significant negative correlation with the dry period (>4 days) in March of the year of tree-ring formation at the Chiba site. In contrast, temperature and precipitation had little influence on tree growth. Quantitative trait locus (QTL) analysis was performed to investigate climate sensitivity to dry periods at the Chiba site, revealing 13 significant QTLs. One QTL showed a substantially large contribution to the overall climate sensitivity, accounting for 12.4% of the total phenotypic variation. The phenotypic variance explained (PVE) by other QTLs ranged from 0.9% to 2.9%, and the total PVE by all QTLs was 35.6%. These findings indicate that the tree population at the Chiba site could be vulnerable to drought in early spring and that the QTL showing the greatest impact on climate sensitivity may be closely related to genes associated with tolerance or adaptation to drought stress. The QTLs identified in this study could be useful for molecular breeding, forest management, and predicting the growth of C. japonica under a changing climate.
“…Fortunately, 23 genetically sterile male trees have already been identified [4]. Four loci ( MS1, MS2, MS3 , and MS4 ) responsible for male sterility were located in four different linkage groups (LG9, LG5, LG1, and LG4, respectively) [5]. In addition, male sterility is caused by recessive alleles.…”
21Sugi (Cryptomeria japonica D. Don) is an important conifer used for afforestation in Japan. 22 two tissue-specific libraries were compared, principal component analysis (PCA) showed that 34 there were significant differences between male strobili and leaf and bark sets. The highest three 35 upregulated transcription factors stood out as orthologs to angiosperms. The identified signature-36 like domain of the transcription factors demonstrated the accuracy of the assembly. Based on the 37 evaluation of different resources, we demonstrate that our transcriptome assembly output is 38 valuable and useful for further studies in functional genomics and evolutionary biology. 39 40
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