The red bayberry genome and genetic basis of sex determination

Abstract

Morella rubra, red bayberry, is an economically important fruit tree in south China. Here, we assembled the first high-quality genome for both a female and a male individual of red bayberry. The genome size was 313-Mb, and 90% sequences were assembled into eight pseudo chromosome molecules, with 32 493 predicted genes. By whole-genome comparison between the female and male and association analysis with sequences of bulked and individual DNA samples from female and male, a 59-Kb region determining female was identified and located on distal end of pseudochromosome 8, which contains abundant transposable element and seven putative genes, four of them are related to sex floral development. This 59-Kb female-specific region was likely to be derived from duplication and rearrangement of paralogous genes and retained non-recombinant in the female-specific region. Sex-specific molecular markers developed from candidate genes co-segregated with sex in a genetically diverse female and male germplasm. We propose sex determination follow the ZW model of female heterogamety. The genome sequence of red bayberry provides a valuable resource for plant sex chromosome evolution and also provides important insights for molecular biology, genetics and modern breeding in Myricaceae family.

Keywords: Morella rubra; genome; sex-determining region; sex-linked marker.

Figure 1

Red bayberry flower and fruit. a and b, female flower. c, male flowers. d to g, the fruits of red bayberry cultivars Y2012‐145, Xiazhihong, Biqi and Dongkui respectively.

Figure 2

Genome evolution and comparative analysis in the red bayberry genome. (a) Phylogenetic analysis of red bayberry and other sequenced plants. Actinidia chinensis was used as outgroup. (b) Syntenies among red bayberry (pseudochromosomes 1–8), peach (chromosome 1–8) and silver birch (chromosome 1–14).

Figure 3

Identification of female‐specific region (FSR) and sex‐determination ZW model in red bayberry. (a) A female‐specific genomic region was found on chromosome 8 based on BSA reads from male and female samples (BSA‐M and BSA‐F respectively). (b) Schematic alignment of the boundary scaffolds from both W (based on female) and Z (based on male) chromosome around the FSR by BLASTN, a gap of 1.4 kb was filled between S_5204 and S_2925a by nested PCR amplification. (c) ZW model of chromosome 8 and the candidate genes in the female‐specific region.

Figure 4

Genomic structure comparison between the putative genes in FSR and corresponding paralogous genes leading to development of sex‐linked markers. (a) The schematic gene structures and repetitive sequence in FSR and their paralogous. The red boxes are repetitive sequence around the genes, green boxes are exons, the blue box a UTR region, dash lines link similar regions of the female‐specific gene and paralogous present in different scaffolds. (b) Sex‐linked markers derived from three candidate genes. I and IV, co‐dominant sex‐linked markers derived from MrCPS2 and MrFT2 in female and male M. rubra. II and III dominant female‐specific markers from MrSAUR2 and MrFT2.

Figure 5

Female and male floral bud development and expression profiles of four female‐specific candidate genes. (a) Morphology and cross‐sectional images of female and male flower initiation and development from July to February. (b) Quantitative expression level of four female‐specific candidate genes: MR8G025874.1 (MrCPS2), ent‐copalyl diphosphate synthase. MR8G025877.1 (MrASP2) is SUMO protease; MR8G025878.1 (MrSAUR2), SAUR‐like auxin‐responsive protein family; MR8G025880.1 (MrFT2) predicated as FLOWERING LOCUS T ( FT ) gene.