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

Kentaro Mishima,Makoto Takahashi,Mine Nose,So Hanaoka,Tomonori Hirao,Manabu Kurita,Miho Tamura,Atsushi Watanabe,Miyoko Tsubomura

doi:10.1186/s12864-018-4581-5

Kentaro Mishima, Makoto Takahashi + Show 7 more

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https://doi.org/10.1186/s12864-018-4581-5

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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.

Highlights

Japanese cedar (Cryptomeria japonica) is an important tree for Japanese forestry
The ms-1, ms-2, ms-3, and ms-4 loci were identified on different linkage groups (LG9, LG5, LG1, and LG4 respectively) in a high-density map [17,18,19,20,21], and adjacent markers were developed for marker-assisted selection (MAS) [18, 21]
Expressed sequence tag (EST) collection, sequencing and de novo assembly Two sequencing platforms, the Roche 454 and Illumina HiSeq system, were used to sequence 19 EST libraries constructed from multiple organs (Additional file 1); the sequencing and assembly results are summarized in Additional file 2

Summary

Introduction

Japanese 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. Mishima et al BMC Genomics (2018) 19:277 expressed sequence tags (ESTs) in male strobili and simple sequence repeats (SSRs) have been identified for linkage maps, allowing efficient use of male sterility in tree breeding [6,7,8,9,10,11,12,13,14,15,16]. The accuracy of the markers was 96.0 to 98.5% within the mapping population [18], but the markers cannot be exploited outside of this population for screening of male-sterile gene heterozygotes or cryptic carriers, which are important breeding material. The causative genes have not been discussed [17,18,19,20,21]

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