Structural variation and parallel evolution of apomixis in citrus during domestication and diversification

Abstract

Apomixis, or asexual seed formation, is prevalent in <i>Citrinae</i> via a mechanism termed nucellar or adventitious embryony. Here, multiple embryos of a maternal genotype form directly from nucellar cells in the ovule and can outcompete the developing zygotic embryo as they utilize the sexually derived endosperm for growth. Whilst nucellar embryony enables the propagation of clonal plants of maternal genetic constitution, it is also a barrier to effective breeding through hybridization. To address the genetics and evolution of apomixis in <i>Citrinae</i>, a chromosome-level genome of the Hongkong kumquat (<i>Fortunella hindsii</i>) was assembled following a genome-wide variation map including structural variants (SVs) based on 234 <i>Citrinae</i> accessions. This map revealed that hybrid citrus cultivars shelter genome-wide deleterious mutations and SVs into heterozygous states free from recessive selection, which may explain the capability of nucellar embryony in most cultivars during <i>Citrinae</i> diversification. Analyses revealed that parallel evolution may explain the repeated origin of apomixis in different genera of <i>Citrinae</i>. Within <i>Fortunella</i>, we found that apomixis of some varieties originated via introgression. In apomictic <i>Fortunella</i>, the locus associated with apomixis contains the <i>FhRWP</i> gene, encoding an RWP-RK domain-containing protein previously shown to be required for nucellar embryogenesis in <i>Citrus</i>. We found the heterozygous SV in the <i>FhRWP</i> and <i>CitRWP</i> promoters from apomictic <i>Citrus</i> and <i>Fortunella</i>, due to either two or three miniature inverted transposon element (MITE) insertions. A transcription factor, <i>FhARID</i>, encoding an AT-rich interaction domain-containing protein binds to the MITEs in the promoter of apomictic varieties, which facilitates induction of nucellar embryogenesis. This study provides evolutionary genomic and molecular insights into apomixis in <i>Citrinae</i> and has potential ramifications for citrus breeding.