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

Area of Science:

• Genomics
• Plant Biology
• Evolutionary Biology

Background:

• Apomixis (asexual seed formation) via nucellar embryony is common in citrus (Citrinae).
• Nucellar embryony allows clonal propagation but hinders hybridization and breeding.
• Understanding the genetic basis of apomixis is crucial for citrus improvement.

Purpose of the Study:

• To investigate the genetics and evolution of apomixis in Citrinae.
• To assemble a chromosome-level genome of Hongkong kumquat (Fortunella hindsii).
• To identify genetic factors contributing to nucellar embryony.

Main Methods:

• Genome-wide variation mapping including structural variants (SVs) across 234 Citrinae accessions.
• Chromosome-level genome assembly of Fortunella hindsii.
• Analysis of gene promoters, transposon insertions, and transcription factor binding.

Main Results:

• Hybrid citrus cultivars harbor deleterious mutations and SVs in heterozygous states, potentially enabling nucellar embryony.
• Apomixis origins in Citrinae likely involve parallel evolution and introgression within Fortunella.
• Apomictic Fortunella and Citrus share heterozygous SVs in FhRWP/CitRWP promoters due to MITE insertions.
• The transcription factor FhARID binds MITEs, inducing nucellar embryogenesis.

Conclusions:

• Genomic and molecular insights into apomixis in Citrinae have been elucidated.
• The findings provide a foundation for understanding apomixis evolution and its role in citrus diversification.
• This research has potential applications for advancing citrus breeding strategies.