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Acta Agronomica Sinica ›› 2026, Vol. 52 ›› Issue (10): 2864-2874.doi: 10.3724/SP.J.1006.2026.62010

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS • Previous Articles     Next Articles

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 Online:2026-10-12 Published: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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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

Table 1

Statistical analysis of plant architecture and panicle traits in the tested japonica rice varieties"

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

Table 2

Statistical analysis of traits related to cooking and eating quality in the tested japonica rice varieties"

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

Fig. 1

Genetic relationship analysis of the tested japonica rice varieties A: principal component analysis based on 200 diverse temperate japonica rice varieties. Red and blue points represent the eight tested varieties and background varieties, respectively; different shapes indicate breeding regions. SH: Shanghai, China; JS: Jiangsu, China; ZJ: Zhejiang, China; NEC: Northeast China; Other: other regions of China; JP: Japan. B: phylogenetic tree of the eight tested japonica rice varieties; heatmap shows the genome-wide proportions of japonica, shown in blue, and indica, shown in orange, components in each variety. SXG1018: Songxianggeng 1018; SZX1: Songzaoxiang 1; HZG193: Huzaogeng 193; XS134: Xiushui 134; HG137: Hugeng 137; YX38: Yinxiang 38; NG46: Nangeng 46; HR1212: Huruan 1212."

Fig. 2

Comparison of indica-type introgression segments among the tested japonica rice varieties A: UpSet plot showing indica-type introgression segments across the eight japonica rice varieties. The vertical bar chart indicates the total number of indica-type segments in each genome, calculated in 10-kb units; black dots and connecting lines indicate introgression segments shared among specific combinations of varieties. B: chromosomal distribution of indica and japonica genetic components across the 12 chromosomes of the eight varieties. Concentric rings from outside to inside, V1-V8, represent Songxianggeng 1018 (SXG1018), Songzaoxiang 1 (SZX1), Huzaogeng 193 (HZG193), Xiushui 134 (XS134), Hugeng 137 (HG137), Yinxiang 38 (YX38), Huruan 1212 (HR1212), and Nangeng 46 (NG46), respectively. Orange and blue blocks indicate indica introgression segments and japonica background segments, respectively. The outermost circle highlights key functional genes located within the corresponding indica-type regions."

Fig. S1

Characterization of indica/japonica genomic components in eight japonica rice varieties The genome was scanned with non-overlapping 10-kb bins. SXG1018: Songxianggeng 1018; SZX1: Songzaoxiang 1; HZG193: Huzaogeng 193; XS134: Xiushui 134; HG137: Hugeng 137; YX38: Yinxiang 38; NG46: Nangeng 46; HR1212: Huruan 1212."

Fig. 3

Distribution of favorable alleles for key functional genes among the eight japonica rice varieties Abbreviations are the same as those given in Fig. 1."

Fig. 4

Pedigree-based tracing of the genetic composition of Huruan 1212 A: pedigree of Huruan 1212 (HR1212) and genomic contribution ratios from its parents. JF: Jinfeng; DHXG: Dahuaxianggeng; NG46: Nangeng 46; HR1212: Huruan 1212. Different colors represent parent-specific genetic segments or shared genetic segments derived from multiple parents. B: chromosomal distribution of parental genetic components in the HR1212 genome. The color scheme is consistent with that in panel A. C: ancestry tracing of indica introgression segments on chromosome 5, shown in the upper panel, and the corresponding relative identity-by-descent (rIBD) values, shown in the lower panel. In the upper panel, curves in three colors represent the three parents, where blue represents DHXG, and green and red represent JF and NG46, respectively. In the lower panel, the dashed horizontal line represents the threshold for identifying indica-type segments, and regions above this threshold are defined as indica-type introgressions."

Fig. 5

Molecular design breeding paradigm based on dominant variety genome analysis"

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