Genomic insights into the diversity of rice cultivars developed in Heilongjiang Province, China

Yuhan ZHOU; Naixin LIU; Jiaqi YANG; Baicui CHEN; Chengxin LI; Fanshan BU; Sanling WU; Ziqi ZHOU; Qingtao YU; Qingyao SHU

doi:10.1631/jzus.B2400339

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Research Article | Updated：2026-03-18

Genomic insights into the diversity of rice cultivars developed in Heilongjiang Province, China
Genomic insights into the diversity of rice cultivars developed in Heilongjiang Province, China
中国黑龙江省水稻品种多样性的基因组学特征研究
Journal of Zhejiang University-SCIENCE B Vol. 27, Issue 3, Pages: 264-279(2026)
Affiliations：

1.State Key Laboratory of Rice Biology & Breeding, Zhejiang Provincial Key Laboratory of Crop Germplasm Innovation and Utilization, the Advanced Seed Institute, Zhejiang University, Hangzhou 310058, China
2.Beet Quality Inspection and Test Center Ministry of Agriculture and Rural Affairs, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin 150080, China
3.Harbin Academy of Agricultural Sciences, Harbin 150080, China
4.Analysis Center of Agrobiology and Environmental Sciences, Faculty of Agriculture, Life and Environment Sciences, Zhejiang University, Hangzhou 310058, China
Funds：
DOI：10.1631/jzus.B2400339
CLC：
CSTR：
Received：05 July 2024，

Revised：2024-10-21，

Online First：17 December 2025，

Published：18 March 2026
Accepted：

周宇涵,刘乃新,杨家琪等.中国黑龙江省水稻品种多样性的基因组学特征研究[J].浙江大学学报（英文版）（B辑：生物医学和生物技术）,2026,27(03):264-279.

Yuhan ZHOU, Naixin LIU, Jiaqi YANG, et al. Genomic insights into the diversity of rice cultivars developed in Heilongjiang Province, China[J]. Journal of Zhejiang University-SCIENCE B, 2026, 27(3): 264-279.
周宇涵,刘乃新,杨家琪等.中国黑龙江省水稻品种多样性的基因组学特征研究[J].浙江大学学报（英文版）（B辑：生物医学和生物技术）,2026,27(03):264-279. DOI： 10.1631/jzus.B2400339.

Yuhan ZHOU, Naixin LIU, Jiaqi YANG, et al. Genomic insights into the diversity of rice cultivars developed in Heilongjiang Province, China[J]. Journal of Zhejiang University-SCIENCE B, 2026, 27(3): 264-279. DOI： 10.1631/jzus.B2400339.

摘要

随着全球人口快速增长与可持续农业需求日益增加，改进水稻育种策略迫在眉睫，尤其是在中国的主要水稻生产省份——黑龙江省，该省以优质温带粳稻而闻名。因此，本研究对黑龙江省优良水稻品种开展了系统的基因组学分析。通过对包括由哈尔滨农科院育成的14个哈粳稻系列品种在内的376个代表性水稻品种的全基因组重测序数据分析，共鉴定出490万个单核苷酸多态性和98万个插入缺失变异，为认识遗传多样性与种群结构提供了全面的视角。进一步按育种年份将376个水稻品种划分为五个亚组，其中2010年后育成的品种分别归类于HLJ-IV-1和HLJ-IV-2亚组，二者表现出显著的遗传分化。通过基因组选择信号分析，鉴定到

OsACBP5

、

Os4CL5

和

GFR1

等基因在不同亚群中均受到选择，反映出其在选育广谱抗病性和增强分蘖能力的品种方面的重要性。此外，为了识别哈粳稻系列品种的优劣势，本研究还对香气化合物及其相关基因

OsODC

和

OsBadh2

进行了深入分析，发现哈粳稻7号中具有优势的长粒基因

OsGL3.1

单倍型。研究还探讨了通过引入

sd1

基因来降低株高的潜力。综上，本研究结果有望为加速优良水稻品种培育、提升水稻

的感官特性和营养价值提供重要参考。

Abstract

Amid the rapid increase of the global population and the quest for sustainable agriculture

the need for enhanced rice breeding strategies has become increasingly pronounced

particularly in Heilongjiang

China’s foremost rice-producing province

renowned for its premium temperate

japonica

rice. Here

we conducted an extensive genomic investigation of the elite rice cultivars developed in Heilongjiang Province. Using whole-genome re-sequencing of a total of 376 representative cultivars from Heilongjiang

of which 14 were developed by a single research group

we identified 4.9 million

single nucleotide polymorphisms (SNPs) and 0.98 million insertions and deletions (InDels)

offering a comprehensive perspective on genetic diversity and population structure. We classified the 376 rice cultivars into five subgroups based on their breeding years. Recently bred cultivars

assigned to subgroups HLJ-IV-1 and HLJ-IV-2

showed notable genetic differentiation. Through a selective sweep analysis

significant genomic variation in genes such as

OsACBP5

Os4CL5

and

GFR1

was pinpointed

reflecting a concerted effort in selecting for broad-spectrum disease resistance and enhanced tillering capacity. Furthermore

to identify the strengths and areas for improvement within those series

we conducted an exhaustive analysis of aromatic compounds and their corresponding genes

OsODC

and

OsBadh2

as well as the advantageous long-grain gene

OsGL3.1

haplotype within Hagengdao7. Additionally

strategies for reducing plant height through the introduction of the

sd1

gene have been elucidated. With a commitment to expediting the development of superior rice cultivars

our discoveries are poised to raise the sensory attributes and nutritional profile of rice

thereby bolstering the resilience and sustainability of global food systems.

关键词

Keywords

references

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