Fig. 4: Ancestry of apomixis alleles and two subspecies of mainland Asian mandarins (C. reticulata).

a Diversity of the apomixis alleles in mandarins and inter-specific mandarin hybrids. The ancestral allele does not have the MITE transposon insertion in the promoter of the CitRKD1 gene regulating citrus apomixis. Derived alleles with the MITE insertion are dominant for the nucellar embryony phenotype. Four MITE haplotypes in two haplogroups (H1=H1A and H1B; H2=H2A and H2B) are observed among sequenced mandarins and hybrids with each black line denoting a segregating SNP. Listed next to each MITE allele type are representative citrus accessions containing that allele. b Genetic ancestry of the citrus polyembryonic locus (200 kb region flanking CitRKD1 gene). Fifty-five accessions derived from six  progenitor species are analyzed with ADMIXTURE⁶⁸ and the eight-population (K=8) structure is presented with additional figures shown in Supplementary Fig. 8. (PU=pummelo, CI=citron, RK=C. ryukyuensis, IC=Ichang papeda, FO=Fortunella (kumquat), MA= common mandarin, h1 and h2 have mangshanyeju ancestry). Accessions with h1 ancestry contain MITE H1A or H1B, whereas those with h2 ancestry have MITE H2A or H2B. MS1 and MS2 are two mangshanyeju accessions. All sequenced polyembryonic accessions carry the dominant allele with the MITE insertion and have mangshanyeju ancestry at this locus, whereas monoembryonic accessions have common mandarin but not mangshanyeju ancestry. c Genome-wide local ancestry inference of mainland East Asian citrus with four ancestral populations including two subspecies of C. reticulata (MS, MA). Population code as in Fig. 1b. This figure complements Fig. 3b by considering 21 accessions without C. ryukyuensis ancestry. Note that the apomixis locus is located near the end of chromosome 1 (based on the Clementine reference sequence) which exhibits extensive MS admixture in common mandarins relative to other chromosomes. MS admixture is widespread in all sequenced mandarins. Two wild mandarins (M01=Daoxian wild mandarin and clonal relatives, M04=Suanpangan) show hybrid ancestry with nearly equal contribution from MS and MA. Source data underlying Fig. 4b and c are provided as a Source Data file.