Fig. 4

Single embryo and endosperm sequencing reveals two classes of aneuploidy. In each panel, the upper dot plot represents CNV by the log₂(CNR) value, CNV is identified if continuous and dispersed obviously Log₂(CNR) values between large segments ( > 10 Mb) are observed. The lower dot plot represents the genetic background SNP-ratio by log₂(RGR) value, which means paternal genome deletion if the value is >0, in contrast, maternal genome deletion if the value is <0. The upper and lower figure of each panel is referring to the same sample. a The normal euploid embryo (embryo 1). A total of 71 embryos and 80 endosperms were identified as euploid. b The complete haploid embryo (embryo 16), in which CAU5-derived chromosomes are eliminated. A total of seven (embryos 16, 19, 21, 32, 38, 45, and 73) were identified as haploid. c One incompletely haploid embryo (embryo 44), in which fragments of chromosomes 1, 7, 8, and 9 remain. d Chromosome 5 of one embryo (embryo 69), in which the CAU5-derived fragments were lost. e Chromosome 1 of one embryo (embryo 78), in which the Zheng58-derived fragments were lost. f Chromosome 4 of one endosperm (endosperm 13), in which the Zheng58-derived fragments were lost. The blue and red spots represent CNVs in odd and even chromosomes, respectively. The black triangles point to centromeres. In the CNV plots, the green, black, and yellow lines around spots indicate haploidy, diploidy, and triploidy, respectively. In the SNP-ratio plots, the blue and red shadings indicate paternal and maternal deletions, respectively