Sweet orange genome decoded: Somatic mutations and fruit development insights
image: Integrative analysis of candidate genetic factors affecting fruit size in sweet orange.
Credit: Horticulture Research
A pivotal study has provided unprecedented insights into the genetic architecture of sweet oranges, highlighting the critical role of somatic mutations in shaping fruit development. By constructing a haplotype-resolved genome, researchers have uncovered 10.6% novel sequences and significant genetic admixtures. Leveraging advanced phased genomics, the team identified a wealth of previously undetected somatic mutations, offering a detailed portrait of genetic mosaicism and evolutionary pressures in sweet oranges. These findings set the stage for transformative advances in citrus breeding, with the potential to enhance fruit quality and optimize agricultural practices.
Somatic mutations, including single nucleotide polymorphisms (SNPs) and insertions/deletions (InDels), are particularly prevalent in perennial and asexual crops like sweet oranges. These variations create genetic discord between homologous chromosomes, often obscured in highly heterozygous diploid genomes. Their impact on key agronomic traits and their complex inheritance make them challenging to study. However, these mutations are vital for understanding genetic diversity and phenotypic variations, underscoring the need for innovative approaches to decode their role in fruit development.
In a milestone for horticultural genomics, scientists from the Institute of Horticultural Research at the Hunan Academy of Agricultural Sciences, together with international collaborators, have unraveled these complexities. Published (DOI: 10.1093/hr/uhad268) in Horticulture Research on December 28, 2023, their study employs phased genomic analysis to reveal new genetic sequences and previously hidden somatic mutations that illuminate the intricate process of fruit development in sweet oranges.
The research team achieved a significant breakthrough by creating a high-precision haplotype-resolved genome for Citrus sinensis. Utilizing high-depth whole-genome sequencing (WGS) data from 87 sweet orange somatic varieties, they discovered 10.6% novel sequences, challenging conventional genomic assumptions. A sophisticated detection strategy unveiled a trove of hidden somatic mutations, doubling the previously known count. This approach offered an unparalleled look into genetic mosaicism and positive selection, providing new perspectives on the genetic mechanisms driving diversity and allele-specific expression during fruit development. By categorizing sweet oranges into seven major clades, the study sheds light on how heterozygous genomic variations influence key agronomic traits, paving the way for targeted breeding innovations.
"Our phased genomics approach has not only doubled the known somatic mutations in sweet oranges but also serves as a powerful tool to uncover genetic variations in highly heterozygous plants," said Dr. Peng Chen, lead researcher on the project. "This work has far-reaching implications for citrus breeding and deepens our understanding of how genetic diversity governs fruit development."
The application of phased genomics offers exciting possibilities for the future of citrus breeding. By pinpointing genetic factors that influence traits like fruit size and quality, this research could accelerate the development of superior sweet orange varieties with enhanced characteristics, such as larger fruit or improved disease resistance. These advancements promise substantial benefits for agricultural productivity and consumer satisfaction alike.
###
References
DOI
Original Source URL
https://doi.org/10.1093/hr/uhad268
Funding information
This project was supported by the National Key Research and Development Program of China (2022YFF1003100, 2019YFD1001400), the Agricultural Science and Technology Innovation Funds Project of Hunan Province (2022CX127, 2023CX71), and the Natural Science Foundation of Hunan Province (2021JJ40308).
About Horticulture Research
Horticulture Research is an open access journal of Nanjing Agricultural University and ranked number one in the Horticulture category of the Journal Citation Reports ™ from Clarivate, 2022. The journal is committed to publishing original research articles, reviews, perspectives, comments, correspondence articles and letters to the editor related to all major horticultural plants and disciplines, including biotechnology, breeding, cellular and molecular biology, evolution, genetics, inter-species interactions, physiology, and the origination and domestication of crops.