Fig. 4: Identification of male-specific chromosomal region in Cycas.
From: The Cycas genome and the early evolution of seed plants
a, Manhattan plot of GWAS analysis of sex differentiation in 31 male and 31 female Cycas samples. The red horizontal dashed line represents the Bonferroni-corrected threshold for genome-wide significance (α = 0.05). P values were calculated from a mixed linear model association of SNPs. Association analyses were performed once with a population of 31 male and 31 female individuals. b, Ratio of π, FST and difference of pooled heterozygosity (ΔHp) within a 100-kb sliding window between the female and male sequences. Colour represents values from low (blue) to high (red). c, Genome alignment of the MSY scaffolds with the corresponding female-specific region on chromosome 8. Scaffolds are separated by grey dashed lines. Red lines represent alignments >5 kb on the forward strand, and blue lines represent those on the reverse strand. Pink boxes in a–c represent the most differentiated regions between the sex chromosomes. d, Photographs of microsporophyll and megasporophyll of C. panzhihuaensis. Bar, 1 cm. e, Sex-specific expression of MADS-Y (CYCAS_034085) and CYCAS_010388 in male and female reproductive organs. Microsporophyll tissues were collected before meiosis (BFm), during prophase (Prophase), after meiosis (AFm) and before pollination (BFp); female tissues were collected at 0, 7, 11 and 21 days post-pollination. f, Phylogeny of MADS-Y homologues across land plants. Genes from MSY and autosomes are marked on the right, and those from Selaginella and Physcomitrium are used as outgroups. Numbers above branches represent bootstrap scores from IQ-TREE. g, Molecular genotyping of male and female cycad samples from Cycas debaoensis, Macrozamia lucida and Zamia furfuracea using primers specific to homologues of MADS-Y and CYCAS_010388.
