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作物学报 ›› 2022, Vol. 48 ›› Issue (2): 342-352.doi: 10.3724/SP.J.1006.2022.02085

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

利用SNP标记进行水稻品种籼粳鉴定

郑向华1(), 叶俊华2(), 程朝平1, 魏兴华2, 叶新福1,*(), 杨窑龙2,*()   

  1. 1福建省农业科学院水稻研究所, 福建福州 350018
    2中国水稻研究所水稻生物学国家重点实验室, 浙江杭州 311400
  • 收稿日期:2020-12-01 接受日期:2021-04-26 出版日期:2022-02-12 网络出版日期:2021-06-16
  • 通讯作者: 叶新福,杨窑龙
  • 作者简介:郑向华, E-mail: zxhua57@126.com;
    叶俊华, E-mail: yejunhua1994@qq.com
  • 基金资助:
    本研究由福建省公益项目资助(2019R1023-3);本研究由福建省公益项目资助(2020R1023007)

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 Published:2022-02-12 Published online:2021-06-16
  • Contact: YE Xin-Fu,YANG Yao-Long
  • 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)

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摘要：

亚洲栽培稻(Oryza sativa L.)分为籼、粳2个亚种, 随着杂交水稻的发展、种间杂种优势的利用, 籼粳之间的界限变得越来越模糊。本研究利用3000份水稻种质资源信息, 通过计算约2000万个单核苷酸多态性(single nucleotide polymorphism, SNP)位点的SNP-index值, 进行籼粳特异SNP位点筛选, 最终得到4084个籼粳特异SNP位点(4k-SNP); 同时确定以籼粳指数作为水稻品种籼粳鉴定的指标。研究进一步采用大规模简单随机取样等统计分析方法对籼粳特异位点进行数据降维处理, 将4k-SNP精简至40个SNP位点(40-SNP), 用于水稻籼粳鉴定。为了验证40-SNP的籼粳鉴定效果, 本研究一方面利用水稻生产上推广的82份选育品种, 对40-SNP籼粳鉴定结果与4k-SNP鉴定结果进行比较, 结果发现40-SNP与4k-SNP得出的粳型指数非常接近, 相关系数为0.99; 另一方面利用全球6类型(indica、aus、rayada、aromatic、tropical japonica、temperate japonica)水稻品种共49份材料, 对40-SNP籼粳鉴定结果与4k-SNP及程氏指数法籼粳鉴定结果进行比较, 发现40-SNP与4k-SNP及程氏指数法籼粳鉴定结果的相关系数分别在0.98和0.86以上。这些结果证实了40-SNP对水稻品种籼粳鉴定的有效性及准确性。另外发现40-SNP对水稻6种亚群类型也有很好鉴别效果, 其中indica的粳型指数 < 0.20, aus的粳型指数在0.20~0.40, rayada和aromatic的粳型指数在0.60~0.85之间, tropical japonica的粳型指数 > 0.90, temperate japonica粳型指数最高, 基本为1.00。本研究为研究水稻籼粳分化、杂种优势利用以及水稻种子管理条例制定等方面提供了数据支撑及理论基础。

关键词: 水稻, 籼粳亚种鉴定, 籼粳指数, 籼粳杂交, SNP标记

Abstract:

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

图1

籼粳特异标记获取 A: ΔSNP-index计算方法; B: 籼粳特异标记获取流程图。"

表1

9份水稻选育品种的粳型指数与最小SNP数目"

名称
Variety name		 类型
Type		 粳型指数
Geng index		 最小SNP数
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

图2

最少SNP标记数目确定 A: 粳型指数与SNP数目的散点图; B: 粳型指数的标准差与SNP数目的曲线图; C: 利用统计分析确定最小标记数目。P值计算是通过对每5个SNP数目与相邻5个SNP数目粳型指数的标准差进行t检测而得出; 红色实线是指P = 0.05的阈值; 蓝色圆点是指-log10(P)的值; 红色方块是指每5个SNP数目-log10(P)的平均值。"

表2

40个籼粳特异SNP位点的具体信息"

编号
ID		 染色体
Chr.		 位置
Position		 粳型SNP
Geng SNP		 籼型SNP
Xian SNP		 杂合型SNP
Hybrid SNP		 ΔSNP-index SNP位置
SNP position		 突变类型
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

图3

利用82份水稻选育品种进行40-SNP与4k-SNP的粳型指数比较"

图4

利用49份全球水稻品种验证40-SNP鉴定籼粳的准确性 A: 40-SNP与4k-SNP计算得出的粳型指数相关性分析; B: 40-SNP的粳型指数与程氏指数相关性分析。"

图5

水稻6类型粳型指数分布"

图6

49份全球水稻品种籼粳成分热图"

表3

水稻六类型粳型指数方差分析"

类型
Type		 平均值±标准差
Mean ± SD		 多重比较
Multiple comparison
(LSD, P=0.05)		 多重比较
Multiple compariso
n (LSD, P=0.01)		 F值
F-value		 P值
P-value
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

表4

利用籼粳指数进行籼粳类型鉴定"

籼型指数
Xian index		 粳型指数
Geng index		 籼粳类型鉴定
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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