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Acta Agronomica Sinica ›› 2022, Vol. 48 ›› Issue (2): 342-352.doi: 10.3724/SP.J.1006.2022.02085


Xian-geng identification by SNP markers in Oryza sativa L.

ZHENG Xiang-Hua1(), YE Jun-Hua2(), CHENG Chao-Ping1, WEI Xing-Hua2, YE Xin-Fu1,*(), YANG Yao-Long2,*()   

  1. 1Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350018, Fujian, China
    2State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 311400, Zhejiang, China
  • Received:2020-12-01 Accepted:2021-04-26 Online:2022-02-12 Published:2021-06-16
  • Contact: YE Xin-Fu,YANG Yao-Long E-mail:zxhua57@126.com;yejunhua1994@qq.com;yexinfu@126.com;yangxiao182@126.com
  • Supported by:
    This study was supported by the Public Welfare Project of Fujian Province(2019R1023-3);This study was supported by the Public Welfare Project of Fujian Province(2020R1023007)


Asian cultivated rice (Oryza sativa L.) is divided into two subspecies of xian and geng. With the development of hybrid rice and utilization of interspecific heterosis, the boundaries between xian and geng are becoming more and more vague. In this study, based on the SNP-index value of 20 million single nucleotide polymorphism (SNP) loci from 3000 rice germplasm resources, we captured 4084 xian-geng specific SNP loci named as 4k-SNP and used the xian-geng index as an indicator for xian-geng identification. Furthermore, the 4k-SNP was reduced to 40-SNP (40 SNP loci) for indica/japonica identification by using the statistical analysis methods such as large-scale simple random sampling based on the dimensionality reduction algorithms. To verify the effectiveness of 40-SNP on xian-geng identification, 82 bred varieties were used in this study to compare the results of 40-SNP xian-geng identification and 4k-SNP identification. The result showed that the geng index obtained from 40-SNP and 4k-SNP were very close, and the correlation coefficient was 0.99. Moreover, a total of 49 varieties, belonging to six subgroups (indica, aus, rayada, aromatic, tropical japonica, and temperate japonica), were used to compare the xian-geng identification results of 40-SNP with those of 4k-SNP and Cheng’s index. And the correlation coefficients of xian-geng identifications between 40-SNP and 4k-SNP as well as between 40-SNP and Cheng’s index were above 0.98 and 0.86, respectively. These results verified the validity and accuracy of 40-SNP on xian-geng identification in Oryza sativa L. In addition, 40-SNP also had a good distinguishability for the six subgroups in rice, and the xian-geng index of indica, aus, rayada, aromatic, tropical japonica, and, temperate japonica was less than 0.20, 0.20-0.40, 0.60-0.85, more than 0.90, and 1.00, respectively. This study provides the data and theoretical basis for the differentiation of xian-geng and the utilization of heterosis and, formulation of seed management regulations.

Key words: rice (Oryza sativa L.), xian-geng identification, xian-geng index, crossing between xian-geng, SNP markers

Fig. 1

Acquisition of special xian-geng markers A: the calculation method of ΔSNP-index; B: the flow chart of specific xian-geng markers acquisition."

Table 1

Geng index and minimum number of SNPs in nine bred varieties"

Variety name
Geng index
Minimum number of SNPs
楚粳27 Chujing 27 粳稻 Japonica 0.933 35
秀水03 Xiushui 03 粳稻 Japonica 0.967 40
南粳46 Nanjing 46 粳稻 Japonica 0.979 35
扬两优6号 Yangliangyou 6 籼稻 Indica 0.052 35
丰两优1号 Fengliangyou 1 籼稻 Indica 0.088 40
荆两优10号 Jingliangyou 10 籼稻 Indica 0.050 45
甬优12 Yongyou 12 籼粳交 Indica-japonica hybridization 0.518 40
甬优1512 Yongyou 1512 籼粳交 Indica-japonica hybridization 0.466 35
甬优9号 Yongyou 9 籼粳交 Indica-japonica hybridization 0.514 40

Fig. 2

Determination of minimum number of SNPs A: scatter chart of geng index of different SNPs with 1000 repetitions; B: curve chart of standard deviation of geng index of different SNPs; C: statistical analysis for determining minimum SNPs. P-value was calculated from the t-test between the standard deviation of every five continuous SNP numbers and that of next five continuous SNP numbers. Red line indicates the threshold of P-value (P = 0.05), blue point indicates -log10(P) value, and red square indicates the average -log10(P) value of each five SNP numbers."

Table 2

Information of 40 xian-geng specific SNPs"

Geng SNP
Xian SNP
Hybrid SNP
ΔSNP-index SNP位置
SNP position
Mutation type
IG1 1 12,556,378 A T A/T 0.757 Exonic 非同义突变 Non-synonymous SNV
IG2 1 17,768,964 C A C/A 0.715 Downstream
IG3 1 22,381,235 T G T/G 0.709 UTR3
IG4 1 28,913,384 C T C/T 0.746 Exonic 非同义突变 Non-synonymous SNV
IG5 2 12,079,928 A G A/G 0.752 Exonic 非同义突变 Non-synonymous SNV
IG6 2 20,225,356 T G T/G 0.749 Upstream
IG7 2 29,516,322 C G C/G 0.747 Exonic 非同义突变 Non-synonymous SNV
IG8 2 33,038,088 C A C/A 0.755 Exonic 非同义突变 Non-synonymous SNV
IG9 3 2,936,058 G A G/A 0.737 Intronic
IG10 3 3,461,333 T C T/C 0.730 Intergenic
IG11 3 4,109,581 C T C/T 0.745 Exonic 非同义突变 Non-synonymous SNV
IG12 3 32,716,455 A C A/C 0.793 Upstream
IG13 4 12,290,320 A G A/G 0.745 Exonic 非同义突变 Non-synonymous SNV
IG14 4 20,612,989 C T C/T 0.745 Intergenic
IG15 4 24,973,823 T C T/C 0.717 Exonic 非同义突变 Non-synonymous SNV
IG16 5 21,148,417 A C A/C 0.727 Upstream
IG17 5 25,953,822 C G C/G 0.788 UTR3
IG18 6 12,025,192 A G A/G 0.787 Downstream
IG19 6 20,502,262 G A G/A 0.769 Exonic 非同义突变 Non-synonymous SNV
IG20 6 31,049,929 C T C/T 0.702 Exonic 非同义突变 Non-synonymous SNV
IG21 7 8,962,741 C A C/A 0.736 Intergenic
IG22 7 14,923,259 A G A/G 0.778 Exonic 同义突变 Synonymous SNV
IG23 7 17,,136,369 T C T/C 0.722 Exonic 非同义突变 Non-synonymous SNV
IG24 7 28,782,595 C T C/T 0.740 Intronic
IG25 8 14,427,488 C A C/A 0.751 Intergenic
IG26 8 18,825,519 A G A/G 0.726 Exonic 非同义突变 Non-synonymous SNV
IG27 8 21,801,474 G A G/A 0.791 Upstream
IG28 8 28,268,656 T C T/C 0.749 Exonic 非同义突变 Non-synonymous SNV
IG29 9 3,099,717 T C T/C 0.794 Exonic 非同义突变 Non-synonymous SNV
IG30 9 4,396,038 C T C/T 0.732 Intergenic
IG31 9 14,812,651 T C T/C 0.756 Exonic 非同义突变 Non-synonymous SNV
IG32 9 16,775,838 G A G/A 0.743 Intergenic
IG33 10 14,820,587 T C T/C 0.782 Downstream
IG34 10 20,325,921 G A G/A 0.796 Downstream
IG35 10 21,759,092 G A G/A 0.723 Exonic 非同义突变 Non-synonymous SNV
IG36 11 808,969 A G A/G 0.761 Intergenic
IG37 11 5,533,977 G A G/A 0.737 Exonic 非同义突变 Non-synonymous SNV
IG38 12 18,352,099 C G C/G 0.746 Exonic 非同义突变 Non-synonymous SNV
IG39 12 24,494,788 A C A/C 0.736 Intronic
IG40 12 27,263,526 G T G/T 0.750 Upstream

Fig. 3

Comparison of geng index between 40-SNP and 4k-SNP in 82 bred rice varieties"

Fig. 4

Accuracy of xian-geng identification for 40-SNP in 49 global rice varieties A: correlation analysis of geng index between 40-SNP and 4k-SNP; B: correlation analysis between geng index calculated by 40-SNP and Cheng’s index."

Fig. 5

Geng index distribution of six types of rice varieties aro: aromatic; aus: aus; ind: indica; ray: rayada; tej: temperate japonica; trj: tropical japonica."

Fig. 6

Heat map of xian-geng components of 49 rice varieties"

Table 3

ANOVA analysis of six types of rice varieties"

Mean ± SD
Multiple comparison
(LSD, P=0.05)
Multiple compariso
n (LSD, P=0.01)
tej 0.998 ± 0.005 a A 2.43 < 0.001
trj 0.953 ± 0.039 b A
aro 0.765 ± 0.077 c B
ray 0.676 ± 0.036 c B
aus 0.277 ± 0.082 d C
ind 0.030 ± 0.050 e D

Table 4

Identification of xian and gene subspecies using xian-geng index"

Xian index
Geng index
Xian and geng subspecies identification
≥ 0.6 ≤ 0.4 籼稻 Indica
0.4-0.6 0.4-0.6 中间型 Intermediate type
≤ 0.4 ≥ 0.6 粳稻 Japonica
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