Fine mapping of the male-sterile genes (MS1, MS2, MS3, and MS4) and development of SNP markers for marker-assisted selection in Japanese cedar (Cryptomeria japonica D. Don).

Yoichi Hasegawa,Yoshinari Moriguchi,Junji Iwai,Saneyoshi Ueno,Kentaro Uchiyama,Tokuko Ujino-Ihara,Satoko Totsuka,Tetsuji Hakamata,Asako Matsumoto,Chunxian Chen

doi:10.1371/journal.pone.0206695

Abstract

Pollinosis caused by Japanese cedar (Cryptomeria japonica) is a widespread social problem in Japan. To date, 23 male-sterile C. japonica trees have been selected in Japan to address pollinosis, from which four male-sterility loci (MS1, MS2, MS3, and MS4) have been identified from test crossing results. For efficient breeding of male-sterile C. japonica trees, more male-sterile individuals and individuals heterozygous for male-sterile genes are required. Therefore, we aimed to develop DNA markers for marker-assisted selection of four types of male-sterile genes from populations without a family structure. First, for four families exhibiting segregation of each male-sterile locus (MS1, MS2, MS3, and MS4), genome-wide single-nucleotide polymorphism and insertion/deletion (indel) genotyping was performed using the Axiom myDesign Targeted Genotyping Array method. Four high-density linkage maps for mapping the MS1, MS2, MS3, and MS4 families were constructed, which included 4923, 1722, 1896, and 2247 markers, respectively. In these maps, 15, 4, 2, and 2 markers were located 0.0, 3.3, 1.1, and 0.0 cM from the MS1, MS2, MS3, and MS4 loci, respectively. Second, for the markers located 0.0 cM from a male-sterile locus (i.e., MS1 and MS4), to clarify the most tightly linked markers, we calculated the prediction rate of male-sterile gene genotypes from marker genotypes for 78 trees. The markers with the highest prediction rates were AX-174127446 (0.95) for MS1 and AX-174121522 (1.00) for MS4. The AX-174121522 marker was considered to be suitable for selecting trees homozygous or heterozygous for the MS4 gene from plus-trees without a pollination test, which requires a large amount of time and effort. The nearest markers to the male-sterile loci found in this study may facilitate the isolation of male-sterile genes in C. japonica via combination with the draft genomic sequence that is currently being collated.

Highlights

Marker-assisted selection (MAS) is a breeding approach used to select individuals with desirable traits based on the genotypes of markers tightly linked to target genes, as has been reported for barley [1] and grape [2]
We developed a large number of new single-nucleotide polymorphism (SNP) and insertion/deletion markers and constructed four high-density linkage maps exhibiting consistent marker order including the MS1, MS2, MS3, and MS4 genes
10,808 (F1O7 family), 11,442 (S1-2 family), 10,882 (S5HK7 family), and 10,913 (S8HK5 family) of the 73,434 markers on the Axiom array were successfully genotyped in this study (Table 2)

Summary

Introduction

Marker-assisted selection (MAS) is a breeding approach used to select individuals with desirable traits based on the genotypes of markers tightly linked to target genes, as has been reported for barley [1] and grape [2]. The main advantage of MAS is that it reduces the time required for breeding cycles This is especially attractive for tree species with longer generation times than other crop species. C. japonica is the most important forestry species in Japan, with outstanding features such as easy processes for cutting/propagation and artificial promotion of flowering, wide adaptability to the environment, rapid growth, straight bole, and soft wood with a pleasant color and scent. It covers an area of 4.5 million hectares, accounting for 44% of all Japanese artificial forests [5]

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Results