Two evolutionary histories in one nucleus: genome remodeling and allelic regulation underlying heterosis in hybrid oil palm
- 1State Key Laboratory of Tropical Crop Breeding, Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences
Abstract
Oil palm (Elaeis) is the primary source of global vegetable oil. Interspecific hybrids of Elaeis exhibit pronounced heterosis by integrating two distinct subgenomes into a single nucleus, effectively combining the high yield of African oil palm (E. guineensis) with the high unsaturated fatty acid content and disease resistance of American oil palm (E. oleifera). However, the genetic basis underlying heterosis is still unclear. Here, we combine phased genome assembly, comparative genomics, evolutionary genomics and haplotype-aware transcriptomics to unravel the genetic architecture of heterosis of hybrid oil palm. We assemble the highly heterozygous F1 genome ('Reyou 40', 3.75% heterozygosity) into a complete 1.73 Gb T2T haplotype (HapG) and a 1.84 Gb near-T2T haplotype (HapO with17 gaps). Despite 91.56% sequence identity, HapG and HapO diverged in LTR-RT occurrence and PAV affected genes, showing complementary biases in lipid metabolism and stress responses, respectively. Evolutionary genomics revealed that ancient WGDs preserved the palm family. Whereas lineage-specific lipid-related gene expansions in oil palm. Six ancient introgressed regions (~64 Mb) in HapG were reshaped by transposable elements and tandem duplication, showing an enrichment of genes related to resistance and lipid metabolism. Transcriptomically, 82.2% of allelic gene pairs maintained balanced expression, accompanied by parental functional complementarity and dosage buffering, revealing a potential regulatory basis for coordinating parental genetic differences in the hybrid genome. These haplotype-resolved genomic resources offer vital targets for understanding heterosis and accelerating oil palm molecular breeding.
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BibTeX
@misc{su2026evolutionary,
title = {{Two evolutionary histories in one nucleus: genome remodeling and allelic regulation underlying heterosis in hybrid oil palm}},
author = {X. Su and Y. Peng and X. Yang and F. Zhang and Q. Xu and Z. Ma and Y. Dong and L. Zhou and H. Xue and X. Cao and Z. Zou and Y. Wang and Y. Zhou and X. Zeng},
howpublished = {bioRxiv},
year = {2026},
month = aug,
doi = {10.64898/2026.08.27.747553},
url = {https://www.biorxiv.org/content/10.64898/2026.08.27.747553v1},
note = {CC BY},
}
RIS
TY - UNPB
TI - Two evolutionary histories in one nucleus: genome remodeling and allelic regulation underlying heterosis in hybrid oil palm
AU - X. Su
AU - Y. Peng
AU - X. Yang
AU - F. Zhang
AU - Q. Xu
AU - Z. Ma
AU - Y. Dong
AU - L. Zhou
AU - H. Xue
AU - X. Cao
AU - Z. Zou
AU - Y. Wang
AU - Y. Zhou
AU - X. Zeng
PY - 2026
DA - 2026/08/27
PB - bioRxiv
DO - 10.64898/2026.08.27.747553
UR - https://www.biorxiv.org/content/10.64898/2026.08.27.747553v1
AB - Oil palm (Elaeis) is the primary source of global vegetable oil. Interspecific hybrids of Elaeis exhibit pronounced heterosis by integrating two distinct subgenomes into a single nucleus, effectively combining the high yield of African oil palm (E. guineensis) with the high unsaturated fatty acid content and disease resistance of American oil palm (E. oleifera). However, the genetic basis underlying heterosis is still unclear. Here, we combine phased genome assembly, comparative genomics, evolutionary genomics and haplotype-aware transcriptomics to unravel the genetic architecture of heterosis of hybrid oil palm. We assemble the highly heterozygous F1 genome ('Reyou 40', 3.75% heterozygosity) into a complete 1.73 Gb T2T haplotype (HapG) and a 1.84 Gb near-T2T haplotype (HapO with17 gaps). Despite 91.56% sequence identity, HapG and HapO diverged in LTR-RT occurrence and PAV affected genes, showing complementary biases in lipid metabolism and stress responses, respectively. Evolutionary genomics revealed that ancient WGDs preserved the palm family. Whereas lineage-specific lipid-related gene expansions in oil palm. Six ancient introgressed regions (~64 Mb) in HapG were reshaped by transposable elements and tandem duplication, showing an enrichment of genes related to resistance and lipid metabolism. Transcriptomically, 82.2% of allelic gene pairs maintained balanced expression, accompanied by parental functional complementarity and dosage buffering, revealing a potential regulatory basis for coordinating parental genetic differences in the hybrid genome. These haplotype-resolved genomic resources offer vital targets for understanding heterosis and accelerating oil palm molecular breeding.
ER -