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作物学报 ›› 2026, Vol. 52 ›› Issue (10): 2864-2874.doi: 10.3724/SP.J.1006.2026.62010

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

长江下游粳稻主导品种的基因组解析与籼型片段渗入分析

叶俊华1(), 谢玲娟1, 闫影1, 王凯1, 杨航1, 张丽霞1, 时振英1, 胡泽军1, 曹黎明1, 周锋利2,*(), 吴书俊1,*()   

  1. 1 上海市农业科学院作物育种栽培研究所 / 农业农村部粮油作物种质创新与遗传改良重点实验室(部省共建) / 上海市农业遗传育种重点实验室, 上海 201403
    2 上海市嘉定区农业技术推广服务中心, 上海 201800
  • 收稿日期:2026-03-30 接受日期:2026-07-15 出版日期:2026-10-12 网络出版日期:2026-07-23
  • 通讯作者: 周锋利, E-mail: sharpzhou@126.com;吴书俊, E-mail: wushujun@saas.sh.cn
  • 作者简介:叶俊华, E-mail: yejunhua@saas.sh.cn
  • 基金资助:
    上海市农业科技创新项目(T2025311);上海市农业科学院AI赋能农业专项(AI-A-2025-001);上海市水稻产业技术体系(202503)

Genomic analysis of dominant japonica/geng rice varieties in the lower Yangtze River Region and analysis of indica/xian introgression segments

Ye Jun-Hua1(), Xie Ling-Juan1, Yan Ying1, Wang Kai1, Yang Hang1, Zhang Li-Xia1, Shi Zhen-Ying1, Hu Ze-Jun1, Cao Li-Ming1, Zhou Feng-Li2,*(), Wu Shu-Jun1,*()   

  1. 1 Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences / Key Laboratory of Germplasm Innovation and Genetic Improvement of Grain and Oil Crops (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs / Key Laboratory of Agricultural Genetics and Breeding of Shanghai, Shanghai 201403, China
    2 Shanghai Jiading District Agricultural Technology Extension Service Center, Shanghai 201800, China
  • Received:2026-03-30 Accepted:2026-07-15 Published:2026-10-12 Published online:2026-07-23
  • Contact: Zhou Feng-Li, E-mail: sharpzhou@126.com;Wu Shu-Jun, E-mail: wushujun@saas.sh.cn
  • Supported by:
    Shanghai Agricultural Science and Technology Innovation Program(T2025311);Al-Empowered Agriculture Project of Shanghai Academy of Agricultural Sciences(AI-A-2025-001);Agriculture Research System of Shanghai, China(202503)

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摘要：

长江下游地区是我国重要的粳稻产区, 解析该区域主导品种的遗传背景、籼型血缘渗入特征及重要性状的基因型构成, 对于优异种质资源的高效利用与分子设计育种具有重要意义。本研究对长江下游8份代表性常规粳稻主导品种进行了全基因组测序(平均测序深度为19.8×), 系统开展了亲缘关系评估、基因组籼型渗入片段鉴定及重要功能基因的基因型剖析, 并对优质高产品种沪软1212进行了系谱溯源分析。结果表明, 8份供试品种在粳稻群体中具有较好的遗传多样性和代表性。全基因组解析表明, 籼型渗入片段在供试品种的粳稻遗传背景中呈不规则的碎片化分布, 片段总长在品种间变幅较大(0~4.9 Mb), 其中沪早粳193和秀水134的籼型片段渗入量最多; 这些籼稻来源片段中注释到的基因显著富集于抗病、耐逆及生物量积累等通路。基因型分析表明, 主导品种在品质(ALK和Waxy)、耐逆(HAN1、OsPP15、qLTG3-1)及抗条纹叶枯病(STV11)基因上已基本实现优异等位基因的高度聚合, 但在抗稻瘟病及病毒性、细菌性病害上还存在进一步遗传改良潜力; 在主要农艺性状方面, 供试品种携带的优异等位基因分布频率整体较低。系谱溯源表明, 优质品种沪软1212的遗传背景主要源自亲本南粳46 (39.71%), 还整合了来自亲本金丰的多个产量相关优异基因型, 以及大华香粳的籼型渗入片段。本研究在基因组水平上揭示了长江下游8份代表性粳稻主导品种的籼型片段渗入特征与重要性状优异等位基因的分布, 为今后高产优质粳稻的分子设计育种及种质资源的高效利用提供了重要的遗传信息。

关键词: 粳稻, 主导品种, 基因组, 籼型渗入, 长江下游

Abstract:

The lower Yangtze River Region is a major production area for japonica/geng rice in China. Understanding the genetic architecture, indica/xian introgression patterns, and functional genotypes of dominant varieties is essential for accelerating molecular design breeding and germplasm improvement. In this study, whole-genome sequencing, with an average depth of 19.8×, was performed on eight dominant japonica/geng rice varieties from this region to systematically evaluate their genetic relationships, genome-wide indica-type introgression segments, and key functional alleles. Pedigree traceability was further examined using the high-quality variety Huruan 1212 as an example. The results showed that the eight varieties maintained high genetic diversity and representativeness. Genome-wide analysis indicated that indica-type introgression segments were irregularly distributed across the genome, with total lengths ranging from 0 to 4.9 Mb. Notably, Huzaogeng 193 and Xiushui 134 carried the largest number of introgression segments. These indica-derived segments were significantly enriched in pathways associated with disease resistance, stress tolerance, and biomass accumulation. Genotypic analysis revealed that although these varieties had successfully incorporated favorable alleles related to grain quality (ALK and Waxy), stress tolerance (HAN1, OsPP15, and qLTG3-1), and stripe leaf blight resistance (STV11), clear genetic gaps remained. In particular, resistance to rice blast and bacterial diseases still requires further improvement, and the frequencies of favorable alleles for major agronomic traits remain relatively low. Pedigree tracing of Huruan 1212 showed that its genetic background was mainly derived from Nangeng 46, accounting for 39.71%, while also incorporating yield-related genotypes from Jinfeng and indica-derived segments from Dahuaxianggeng. Collectively, these genomic insights provide an important foundation for the molecular breeding of high-yielding and high-quality japonica/geng rice varieties.

Key words: japonica/geng, dominant varieties, genome, indica/xian-type introgression, the lower Yangtze River Region

表1

供试粳稻品种的株型和穗型性状差异显著性分析"

性状
Trait		 银香38
YX38		 南粳46
NG46		 松香粳1018
SXG1018		 松早香1号
SZX1		 沪早粳193
HZG193		 沪软1212
HR1212		 秀水134
XS134		 沪粳137
HG137
PH (cm) 109.2±0.8 b 104.8±1.1 c 100.0±3.4 e 81.8±1.8 g 86.6±1.3 f 111.8±2.1 a 103.0±2.6 cd 100.6±1.1 de
EPN 9.8±0.8 b 8.4±1.7 bc 9.6±2.0 bc 7.6±0.6 c 9.4±1.8 bc 12.0±2.2 a 8.0±1.9 bc 8.6±1.5 bc
PL (cm) 18.5±1.3 bcd 17.7±1.4 cde 17.5±1.3 de 18.4±1.0 bcd 20.9±1.0 a 17.0±0.4 e 19.08±1.6 bc 19.2±0.7 b
PBN 12.2±1.1 b 13.0±0.7 ab 12.6±2.1 ab 14.0±1.4 a 12.6±1.5 ab 13.0±0.7 ab 12.6±1.1 ab 12.4±0.6 ab
SBN 27.0±7.0 ab 24.0±2.2 b 24.4±2.6 b 12.6±6.8 c 26.2±1.9 ab 26.2±2.6 ab 31.0±7.5 a 27.0±4.6 ab
GNPP 177.2±28.5 bc 169.2±9.5 bcd 164.6±9.1 cd 148.6±25.5 d 192.6±22.9 ab 174.2±10.2 bcd 204.0±26.9 a 191.4±18.5 ab
SSR (%) 87.5±5.2 c 92.2±2.9 ab 89.0±5.9 bc 93.0±1.7 ab 89.0±2.3 bc 96.1±2.2 a 90.5±4.0 bc 86.0±3.0 c
TGW (g) 23.4±1.7 d 26.5±0.9 b 26.0±0.1 b 27.2±1.3 b 24.1±1.2 cd 24.0±0.9 cd 30.0±1.0 a 25.6±2.0 bc
HD (d) 93 105 108 85 88 101 103 102

表2

供试粳稻品种的蒸煮食味品质相关性状差异显著性分析"

性状
Trait		 银香38
YX38		 南粳46
NG46		 松香粳1018
SXG1018		 松早香1号
SZX1		 沪早粳193
HZG193		 沪软1212
HR1212		 秀水134
XS134		 沪粳137
HG137
AC (%)
 5.70±
0.04 f		 8.80±
0.26 e		 9.30±
0.57 e		 11.40±
0.28 c		 9.90±
0.25 d		 11.37±
0.12 c		 17.56±
0.13 b		 18.83±
0.31 a
GC (mm)
 95.00±
2.00 a		 84.00±
2.00 c		 85.50±
0.50 bc		 86.50±
0.50 b		 86.50±
0.50 b		 85.00±
0.00 bc		 70.00±
0.00 e		 80.00±
0.00 d
PC (%)
 7.56±
0.21 b		 6.10±
0.02 e		 6.21±
0.12 e		 8.35±
0.02 a		 8.47±
0.04 a		 6.32±
0.09 e		 6.63±
0.03 d		 7.13±
0.13 c
BDV (cp)
 2309.50±
28.00 a		 1818.00±
75.00 d		 1979.50±
33.00 bc		 1867.00±
75.00 cd		 1867.50±
36.00 cd		 2002.00±
52.00 b		 1046.00±
75.00 e		 1147.50±
6.00 e
SBV (cp)
 -1863.50±
52.00 f		 -1251.50±
66.00 d		 -1441.50±
39.00 e		 -1180.50±
77.00 cd		 -1088.00±
31.00 c		 -1420.00±
48.00 e		 36.00±
37.00 a		 -87.00±
3.00 b
CSV (cp)
 446.00±
24.00 f		 566.50±
9.00 de		 538.00±
6.00 e		 686.50±
2.00 c		 779.50±
5.00 b		 582.00±
4.00 d		 1082.00±
37.00 a		 1060.50±
9.00 a

图1

供试粳稻品种间的遗传亲缘关系分析 A: 基于200份广泛来源温带粳稻品种背景的主成分分析。红色代表8份供试品种, 蓝色代表背景品种; 不同形状表示品种的选育地区。SH: 中国上海; JS: 中国江苏; ZJ: 中国浙江; NEC: 中国东北地区; Other: 中国其他地区; JP: 日本。B: 8份供试粳稻品种的系统发生树; 热图显示各品种全基因组中粳稻(蓝色)与籼稻(橙色)成分的渗入比例。SXG1018: 松香粳1018; SZX1: 松早香1号; HZG193: 沪早粳193; XS134: 秀水134; HG137: 沪粳137; YX38; 银香38; NG46: 南粳46; HR1212: 沪软1212。"

图2

供试粳稻品种间的籼型渗入片段对比 A: 8份粳稻品种籼型渗入区段的UpSet图分析。柱状图代表各品种基因组中籼型片段的总数(以10 kb为检测单位); 黑点及连线代表不同品种间共有的籼型渗入区段。B: 8份粳稻品种的籼和粳遗传组分在12条染色体上的分布。圆环由外向内(V1-V8)依次代表品种: 松香粳1018、松早香1号、沪早粳193、秀水134、沪粳137、银香38、沪软1212和南粳46。橙色代表籼型渗入片段, 蓝色代表粳型背景片段。最外圈标注了相应籼型区域包含的重要功能基因。"

附图1

8份粳稻品种的全基因组籼粳组分鉴定结果 每个bin长度为10 kb且互不重叠。SXG1018: 松香粳1018; SZX1: 松早香1号; HZG193: 沪早粳193; XS134: 秀水134; HG137: 沪粳137; YX38: 银香38; NG46: 南粳46; HR1212: 沪软1212。"

图3

8份粳稻品种重要功能基因的优异等位基因分布 缩写同图1。"

图4

沪软1212的遗传组成溯源 A: 沪软1212的育种系谱及其亲本的基因组贡献率。JF: 金丰; DHXG: 大华香粳; NG46: 南粳46; HR1212: 沪软1212。不同颜色分别代表亲本特异性遗传区段或多亲本共有遗传区段。B: 亲本遗传组分在沪软1212染色体上的分布。配色方案与图A一致。C: 沪软1212第5号染色体上籼型渗入片段的来源追溯(上图)及对应区域的rIBD值(下图)。上图中3种颜色的曲线分别代表3个亲本, 其中, 蓝色代表大华香粳, 绿色和红色分别代表金丰和南粳46。下图中虚线为籼型片段判定的阈值线, 高于此线被界定为来自籼稻的渗入片段。"

图5

基于主导品种基因组剖析的分子设计育种范式"

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