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

Abstract

Apomixis, or asexual seed formation is prevalent in the Citrinae 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 the Citrinae, a chromosome-level genome of Hongkong kumquat (Fortunella hindsii) was assembled following a genome-wide variation map including structural variants (SVs) based on 234 Citrinae 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 Citrinae diversification. Analyses revealed that parallel evolution may explain the repeated origin of apomixis in different genera of Citrinae. Within Fortunella, we found that apomixis of some varieties originated via introgression. In apomictic Fortunella, the locus associated with apomixis contains the FhRWP gene, encoding an RWP-RK domain-containing protein previously shown to be required for nucellar embryogenesis in Citrus. We found the heterozygous SV in the FhRWP and CitRWP promoters from apomictic Citrus or Fortunella due to either two or three Miniature inverted transposon element (MITE) insertions. A transcription factor FhARID, 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 Citrinae and has potential ramifications for citrus breeding.

Genotyping by Sequencing for SNP-Based Linkage Analysis and the Development of KASPar Markers for Male Sterility and Polyembryony in Citrus

“…( Table 4 and Supplementary Table S8 ). For Fortunella and Poncirus spp., these mismatches are in accordance with the hypothesis reported by Wang et al [ 73 ], who suggest that the parallel evolution of Fortunella and Citrus has driven the evolution of apomixis in these genera in a differentiated way, resulting in the heterogeneity of genes causing polyembryony in Citrinae , a subtribe comprising Fortunella , Poncirus and Citrus genera, among others. Polyembryonic Poncirus genotypes do not have MITE insertions in the promoter region of the CitRWP gene, and it is also not expressed in nucellar ovule cells, suggesting another causal gene [ 73 , 74 ].…”

“…For Fortunella and Poncirus spp., these mismatches are in accordance with the hypothesis reported by Wang et al [ 73 ], who suggest that the parallel evolution of Fortunella and Citrus has driven the evolution of apomixis in these genera in a differentiated way, resulting in the heterogeneity of genes causing polyembryony in Citrinae , a subtribe comprising Fortunella , Poncirus and Citrus genera, among others. Polyembryonic Poncirus genotypes do not have MITE insertions in the promoter region of the CitRWP gene, and it is also not expressed in nucellar ovule cells, suggesting another causal gene [ 73 , 74 ]. Therefore, the SNP1 marker is fully validated for apomixis characterization of germplasm and hybrids of breeding projects derived from admixture between C. reticulata and C. maxima or/and C. medica , where the polyembryonic trait was inherited from the C. reticulata ancestor.…”

Pan-mitogenomics reveals the genetic basis of cytonuclear conflicts in citrus hybridization, domestication, and diversification

“…The phylogenies are incongruent in Citrinae, possibly due to introgressive hybridizations ( 47 ). There is evidence of extensive interspecific hybridization in citrus species, with Poncirus and Fortunella contributing to the gene pools of Citrus ( 34 ). As a possible explanation, the genetic information from extinct ancestors could be included in the modern species because of introgressive hybridizations that may have produced the incongruent topologies we observed between cytoplasmic and nuclear genomes.…”

“…The term “citrus” includes seven basic groups—atalantia ( Atalantia buxifolia ), poncirus ( Poncirus trifoliata ), pummelo ( Citrus maxima ), citron ( Citrus medica ), mandarin ( Citrus reticulata and Citrus unshiu ), papeda ( Citrus ichangensis ), and kumquat ( Fortunella spp. )—and four groups derived from admixtures—lemon ( Citrus limon ), sweet orange ( Citrus sinensis ), sour orange ( Citrus aurantium ), and grapefruit ( Citrus paradisi ) ( 34 , 35 ). The nuclear and chloroplast genome sequences from citrus species indicate that sweet orange, sour orange, and grapefruit are admixtures derived from pummelo and mandarin and that the nuclear genome of lemon is an admixture derived from citron, pummelo, and mandarin ( 30 , 32 ).…”

Apomictic Malus plants exhibit abnormal pollen development

“…In Pliosella , which is a subgenus of Hieracium , apomixis and the autonomous development of seeds are regulated by two independent dominant loci, LOSS OF APOMEIOSIS ( LOA ) and LOSS OF PARTHENOGENESIS ( LOP ), respectively ( Catanach et al., 2006 ; Okada et al., 2007 ; Koltunow et al., 2011 ). CitRWP , which contains an RWP-RK domain, regulates polyembryonic characters and various morphological aspects of the plant body during citrus embryogenesis ( Wang et al., 2017 ; Wang et al., 2022 ). In Zanthoxylum bungeanum , the expression of AGL11 is correlated with nucellar embryo development, and the ectopic expression of this gene can result in abnormal flower development and apomixis phenotypes in Arabidopsis ( Fei et al., 2021 ).…”