Identification of novel putative causative genes and genetic marker for male sterility in Japanese cedar (Cryptomeria japonica D.Don)

Abstract

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.

Inspecting abundantly expressed genes in male strobili in sugi (Cryptomeria japonica D. Don) via a highly accurate cDNA assembly

“…Recent advances in technology are available to reveal more details on the genetics related to these loci. To more precisely identify the genetic variation or the genes related to male sterility, a functional genomic study via transcriptomics is a logical approach [6, 7], though a comprehensive genomic data of sugi is not currently available.…”

Effects of day length- and temperature-regulated genes on annual transcriptome dynamics in Japanese cedar (Cryptomeria japonica D. Don), a gymnosperm indeterminate species

“…a Roche GS-FLX system, as reported previously [26][27][28]. The NGS data (total 552.4 Mbp, approximately 1.3 million reads) were assembled into 22,250 isotigs as described in a previous report [28].…”

“…a Roche GS-FLX system, as reported previously [26][27][28]. The NGS data (total 552.4 Mbp, approximately 1.3 million reads) were assembled into 22,250 isotigs as described in a previous report [28]. SurePrint G3 Gene Expression Custom 8×60K Array probes (Agilent Technologies) consisted of three probe sets corresponding to 22,194 sequences designed using the base composition methodology of the eArray tool (Agilent Technologies) using the default settings.…”

“…These results are suggestive of evolutionary differentiation in the function of PEBP gene family members. Although we collected sequence data from various parts of trees in various developmental stages and seasons (19 libraries, approximately 3 million reads, 34,731 isotigs in total) using an NGS approach [28], no homolog of FT in Japanese cedar was identified.…”

A 3K Axiom®SNP array from a transcriptome-wide SNP resource sheds new light on the genetic diversity and structure of the iconic subtropical conifer treeAraucaria angustifolia(Bert.) Kuntze

“…[38,40–43], Cunninghamia spp. [44] and Cryptomeria japonica [45, 46]. More recently, however, with advances in technology and cost reductions, SNP arrays have become very competitive with alternative sequence based SNP genotyping methods.…”