The red bayberry genome and genetic basis of sex determination.

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.

Construction of an anchoring SSR marker genetic linkage map and detection of a sex-linked region in two dioecious populations of red bayberry.

Red bayberry (Morella rubra) is an evergreen fruit tree found in southern China whose whole-genome sequence has recently been published. We updated the linkage map of the species by adding 118 SSR markers and the female-specific marker MrFT2_BD-SEX. The integrated map included eight linkage groups and spanned 491 cM. Eleven sex-associated markers were identified, six of which were located in linkage group 8, in agreement with the previously reported location of the sex-determining region. The MrFT2_BD-SEX marker was genotyped in 203 cultivated accessions. Among the females of the accessions, we found two female-specific alleles, designated W-b (151 bp) and W-d (129 bp). We previously found that 'Dongkui', a female cultivar, could produce viable pollen (we refer to such plants 'Dongkui-male') and serve as the paternal parent in crosses. The genotypes of the MrFT2_BD-SEX marker were W-b/Z in 'Biqi' and W-d/Z in 'Dongkui-male'. The progeny of a cross between these parents produced a 3:1 female (W-) to male (ZZ) ratio and the expected 1:1:1:1 ratio of W-b/W-d: W-b/Z: W-d/Z: Z/Z. In addition, the flowering and fruiting phenotypes of all the F1 progeny fit their genotypes. Our results confirm the existence of ZW sex determination and show that the female phenotype is controlled by a single dominant locus (W) in a small genomic region (59 kb and less than 3.3 cM). Furthermore, we have produced a homozygous "super female" (WW) that should produce all-female offspring in the F2 generation, providing a foundation for commercial use and presenting great potential for use in modern breeding programs.

Development of 107 SSR markers from whole genome shotgun sequences of Chinese bayberry (Myrica rubra) and their application in seedling identification.

Chinese bayberry (Myrica rubra Sieb. et Zucc.) is one of the important subtropical fruit crops native to the South of China and Asian countries. In this study, 107 novel simple sequence repeat (SSR) molecular markers, a powerful tool for genetic diversity studies, cultivar identification, and linkage map construction, were developed and characterized from whole genome shotgun sequences. M13 tailing for forward primers was applied as a simple method in different situations. In total, 828 alleles across 45 accessions were detected, with an average of 8 alleles per locus. The number of effective alleles ranged from 1.22 to 10.41 with an average of 4.08. The polymorphic information content (PIC) varied from 0.13 to 0.89, with an average of 0.63. Moreover, these markers could also be amplified in their related species Myrica cerifera (syn. Morella cerifera) and Myrica adenophora. Seventy-eight SSR markers can be used to produce a genetic map of a cross between 'Biqi' and 'Dongkui'. A neighbor-joining (NJ) tree was constructed to assess the genetic relationships among accessions, and the elite accessions 'Y2010-70', 'Y2012-140', and 'Y2012-145', were characterized as potential new genotypes for cultivation.