Haplotype-resolved genome assembly of the diploid Rosa chinensis provides insight into the mechanisms underlying key ornamental traits

Xiaoni Zhang; Quanshu Wu; Lan Lan; Dan Peng; Huilin Guan; Kaiqing Luo; Manzhu Bao; Mohammed Bendahmane; Xiaopeng Fu; Zhiqiang Wu

doi:10.1186/s43897-024-00088-1

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Haplotype-resolved genome assembly of the diploid Rosa chinensis provides insight into the mechanisms underlying key ornamental traits

Journal article

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Haplotype-resolved genome assembly of the diploid Rosa chinensis provides insight into the mechanisms underlying key ornamental traits

Xiaoni Zhang, Quanshu Wu, Lan Lan, Dan Peng, Huilin Guan, Kaiqing Luo, Manzhu Bao, Mohammed Bendahmane, Xiaopeng Fu and Zhiqiang Wu

Molecular horticulture, Vol.4(1), 14

2024

DOI: https://doi.org/10.1186/s43897-024-00088-1

PMID: 38622744

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Abstract

Rosa chinensis

Haplotype-resolved genome

Petal colour

Flower development

Roses are consistently ranked at the forefront in cut flower production. Increasing demands of market and changing climate conditions have resulted in the need to further improve the diversity and quality of traits. However, frequent hybridization leads to highly heterozygous nature, including the allelic variants. Therefore, the absence of comprehensive genomic information leads to them making it challenging to molecular breeding. Here, two haplotype-resolved chromosome genomes for Rosa chinensis 'Chilong Hanzhu' (2n = 14) which is high heterozygous diploid old Chinese rose are generated. An amount of genetic variation (1,605,616 SNPs, 209,575 indels) is identified. 13,971 allelic genes show differential expression patterns between two haplotypes. Importantly, these differences hold valuable insights into regulatory mechanisms of traits. RcMYB114b can influence cyanidin-3-glucoside accumulation and the allelic variation in its promoter leads to differences in promoter activity, which as a factor control petal color. Moreover, gene family expansion may contribute to the abundance of terpenes in floral scents. Additionally, RcANT1, RcDA1, RcAG1 and RcSVP1 genes are involved in regulation of petal number and size under heat stress treatment. This study provides a foundation for molecular breeding to improve important characteristics of roses.

Details

Title: Haplotype-resolved genome assembly of the diploid Rosa chinensis provides insight into the mechanisms underlying key ornamental traits
Authors/Creators: Xiaoni Zhang - Huazhong Agricultural University
Quanshu Wu - Huazhong Agricultural University
Lan Lan - Agricultural Genomics Institute at Shenzhen
Dan Peng - Agricultural Genomics Institute at Shenzhen
Huilin Guan - Huazhong Agricultural University
Kaiqing Luo - Agricultural Genomics Institute at Shenzhen
Manzhu Bao - Huazhong Agricultural University
Mohammed Bendahmane - Huazhong Agricultural University
Xiaopeng Fu - Huazhong Agricultural University
Zhiqiang Wu - Huazhong Agricultural University
Publication Details: Molecular horticulture, Vol.4(1), 14
Publisher: BioMed Central Ltd unless otherwise stated. Part of Springer Nature
Grant note: KIMA-ZDKY2022004 / Major Scientific Research Tasks, Kunpeng Institute of Modern Agriculture at Foshan 2019YFD1000403 / the National key research and development program of China 2021YFD1200205-03 / Key Technologies Research and Development Program KIMA-QD2022004 / The Scientific Research Foundation for Principle Investigator, Kunpeng Institute of Modern Agriculture at Foshan
Identifiers: 991005656566707891
Murdoch Affiliation: Murdoch University
Language: English
Resource Type: Journal article

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