罗氏沼虾不同育种群体遗传多样性研究

唐琼英; 谢巨洪; 夏正龙; 蔡缪荧; 吴云明; 白鹿淮; 杜厚宽; 李景芬; 杨国梁

doi:10.7541/2020.127

罗氏沼虾不同育种群体遗传多样性研究

1.
湖州师范学院浙江省水生生物资源养护与开发技术研究重点实验室, 中国水产科学研究院水生动物繁育与营养重点实验室, 湖州 313000
2.
江苏数丰水产种业有限公司, 高邮 225654

基金项目: 国家重点研发计划“蓝色粮仓科技创新”重点专项(2018YFD0901300); 农业农村部现代农业产业技术体系专项(CARS-48); 浙江省农业(水产)新品种选育重大科技专项(2016C02055-2-1); 2019年度国家级大学生创新创业训练计划项目(201910347039)资助

详细信息

作者简介:
唐琼英(1976—), 女, 博士, 副研究员; 主要从事水产动物遗传育种研究。E-mail: tangqy@zjhu.edu.cn

通信作者:
杨国梁, 研究员; 主要从事水产动物遗传育种研究。E-mail: ygl0572@163.com

中图分类号: Q346⁺.5
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出版历程
- 收稿日期: 2020-02-20
- 修回日期: 2020-07-09
- 网络出版日期: 2020-08-19
- 发布日期: 2020-09-29

GENETIC DIVERSITY OF THE BREEDING POPULATIONS OF GIANT FRESHWATER PRAWN MACROBRACHIUM ROSENBERGII

1.
Zhejiang Provincial Key Laboratory of Aquatic Resources Conservation and Development; Key Laboratory of Aquatic Animal Genetic Breeding and Nutrition, Chinese Academy of Fishery Sciences; College of Life Science, Huzhou University, Huzhou 313000, China
2.
Jiangsu Shufeng Prawn Breeding Co. LTD, Gaoyou 225654, China

Funds: Supported by the National Key R&D Programme of China for Blue Granary (2018YFD0901300); China Agriculture Research System (CARS-48); Special Funds for Major Science and Technology of Breeding New Agriculture (aquatic) Varieties in Zhejiang Province (2016C02055-2-1); the National Students’ Innovation and Entrepreneurship Training Program (201910347039)

Corresponding author:

摘要

摘要: 为深入了解罗氏沼虾(Macrobrachium rosenbergii)不同种质资源的遗传背景, 研究采用微卫星标记和线粒体基因相结合, 对罗氏沼虾4个育种群体, 即选育3代的数丰核心群体(SF)、引进的正大群体(ZD)、正大和数丰杂交的群体(ZDS)、正大子代和数丰杂交的群体(ZD2S)的遗传多样性进行了研究。150个个体的微卫星分析结果显示, 7个微卫星位点均表现出高度多态性(PIC>0.5), 4个群体平均的等位基因数(N_a)、期望杂合度(H_e)和多态信息含量(PIC)分别为19.43、0.8980和0.8867。SF群体的平均H_e (0.874)和PIC (0.854)最高, ZD2S的H_e (0.863)和PIC (0.834)其次, ZDS群体的H_e (0.798)和PIC (0.761)最低。4个群体间的遗传分化指数(F_ST)为0.04166—0.10438, 处于中低水平的遗传分化, 其中, ZD和ZDS的遗传分化最大, F_ST为0.10438。线粒体COⅠ和12S rRNA基因组合序列分析结果显示, 149个个体共识别27个单倍型, 平均单倍型多样性(H_d)和核苷酸多样性(π)分别为0.846和0.00313。在4个群体中, ZD2S群体的H_d值最高, 其次为SF群体, ZDS的最低; 对于π值, SF群体的最高, 其次为ZD2S群体, ZD群体的则最低, 该结果与微卫星的结果基本一致。但基于线粒体基因的群体间遗传分化较小, F_ST值为–0.02226—0.07310, 小于微卫星估计的结果。微卫星和线粒体基因一致表明, SF和ZD2S两个群体均保持着较高的遗传多样性, 具有进一步选育的潜力。
- 罗氏沼虾 /
- 微卫星标记 /
- COⅠ /
- 12S rRNA /
- 遗传多样性 /
- 育种
Abstract: To learn the genetic background of the giant freshwater prawn (Macrobrachium rosenbergii), four different breeding populations, including Shufeng nucleus breeding population selected for three generations (SF), introduced Zhengda population (ZD), hybrid population between the introduced Zhengda population and Shufeng population (ZDS), and hybrid population between the progeny of the introduced Zhengda population and Shufeng population (ZD2S), were investigated by using both microsatellite loci and mitochondrial COⅠand 12S rRNA genes as molecular markers. The microsatellite data of 150 individuals revealed that all the seven loci had high diversity with PIC>0.5. The average number of alleles (N_a), expected heterozygosity (H_e) and polymorphism information content (PIC) were 19.43, 0.8980 and 0.8867, respectively. Among seven loci of four populations, the average H_e (0.874) and PIC (0.854) of the SF were the highest, followed by H_e (0.863) and PIC (0.834) of the ZD2S, and the lowest H_e (0.798) and PIC (0.761) of the ZDS. The pairwised genetic differentiation indices (F_ST) among the four populations was 0.04166—0.10438, suggesting low to moderate genetic differentiations. The F_ST between ZD and ZDS was the highest with a value of 0.10438. Based on the concatenated mitochondrial COⅠ and 12S rRNA gene sequences, 149 individuals contained 27 haplotypes, with the average haplotype diversity (H_d) and nucleotide diversity (π) of 0.846 and 0.00313, respectively. Among four populations, the H_d of the ZD2S was the highest, followed by the SF, and ZDS was the lowest. For the π values, the SF was the highest, followed by ZD2S, and ZD was the lowest, which was generally consistent with the genetic diversity results analyzed based on microsatellite data. However, the genetic differentiation among four populations based on mitochondrial genes was low with F_ST values of –0.02226—0.07310, which is much lower than those based on microsatellite. These results indicated that both SF and ZD2S maintain high genetic diversity and have the potential for further selective breeding of Macrobrachium rosenbergii.
- Macrobrachium rosenbergii /
- Microsatellite loci /
- COⅠ /
- 12S rRNA /
- Genetic diversity /
- Breeding

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图 1 罗氏沼虾COⅠ和12S rRNA基因组合序列单倍型间的聚类分析

节点处的数值代表支持率, 括弧中代表对应单倍型包含的种群

Figure 1. Phylogenetic tree for the combined COⅠ and 12S rRNA sequence haplotypes of Macrobrachium rosenbergii

Values at the nodes correspond to the support values, and the populations included by the corresponding haplotype are listed in the parentheses

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表 1 用于本研究的微卫星引物相关信息

Table 1 Primers used in the present study

位点Locus	引物序列Primer sequence (5′—3′)	退火温度T_m	片段大小Size range (bp)	来源Resource
6CT55	FAM-CAGCTCTAACCTGATTGAAAGAC	55	220—264	钟丹丹等^[3]
	GCAGGCATTATCGTTACTTCTCC	55	220—264	钟丹丹等^[3]
12AG57	HEX-GGAACAAATGAAGACTTGGATGC	57.6	232—294	钟丹丹等^[3]
	CTCTCTCTCCCTCAAGGTGTTGG	57.6	232—294	钟丹丹等^[3]
27AG62	FAM-CAACTCTATGTTTCGGCATTTGG	62	224—276	孙成飞等^[8]
	GGGGAATTTTACCGATGTTTCTG	62	224—276	孙成飞等^[8]
28GT62	HEX-CCACCTACCGTACATTCCCAAAC	62	203—291	孙成飞等^[8]
	CGGGGCGACTTTTAGTATCGAC	62	203—291	孙成飞等^[8]
29AG62	FAM-CAAGGCTCGTGTCTCTTGTTTC	62	274—322	孙成飞等^[8]
	GCTTGTACTTGTTCAGCTTTTGC	62	274—322	孙成飞等^[8]
47AAG54	HEX-AAGAGGATTTGGAGCGATTGG	54	169—229	本研究
	CTGAGTAAGATACGACGCCTTC	54	169—229	本研究
50AG54	FAM-GTAATGAACAGCACGAAAAGGAAG	54	274—322	本研究
	TCTGCGTTATTTTGAGTTTGGTATG	54	274—322	本研究

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表 2 各微卫星位点在4个罗氏沼虾育种群体中的遗传多样性参数

Table 2 Genetic diversity parameters of each microsatellite locus in the four breeding populations of Macrobrachium rosenbergii

位点Locus	所有群体All stocks				SF (n=60)				ZD (n=30)
位点Locus	N_a	H_o	H_e	PIC	N_a	H_o	H_e	PIC	N_a	H_o	H_e	PIC
12AG57	19	0.460	0.879	0.867	17	0.350	0.858	0.837	13	0.400	0.900	0.874
47AAG54	14	0.873	0.891	0.878	13	0.867	0.851	0.827	9	0.800	0.818	0.782
27AG62	18	0.386	0.878	0.864	14	0.549	0.857	0.836	10	0.200	0.817	0.779
29AG62	24	0.813	0.919	0.910	19	0.717	0.907	0.892	14	0.867	0.897	0.871
50AG54	20	0.604	0.908	0.898	16	0.508	0.872	0.851	11	0.867	0.847	0.814
28GT62	21	0.456	0.904	0.893	15	0.424	0.882	0.863	17	0.367	0.899	0.874
6CT55	20	0.711	0.907	0.897	16	0.683	0.890	0.873	10	0.567	0.772	0.737
平均值Mean	19.439	0.615	0.898	0.887	15.71	0.585	0.874	0.854	12.00	0.581	0.850	0.819

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位点Locus	ZDS (n=30)				ZD2S (n=30)
位点Locus	N_a	H_o	H_e	PIC	N_a	H_o	H_e	PIC
12AG57	10	0.600	0.755	0.718	14	0.600	0.867	0.842
47AAG54	8	1.000	0.848	0.812	12	0.833	0.865	0.835
27AG62	5	0.182	0.555	0.499	10	0.448	0.816	0.781
29AG62	16	0.900	0.910	0.887	20	0.867	0.937	0.917
50AG54	11	0.567	0.880	0.852	12	0.567	0.875	0.846
28GT62	9	0.767	0.840	0.803	12	0.300	0.877	0.849
6CT55	8	0.900	0.801	0.756	9	0.724	0.806	0.770
平均值Mean	9.57	0.702	0.798	0.761	12.71	0.620	0.863	0.834
注: 表中各遗传多样性参数简写如下, N_a. 等位基因数; H_o. 观察杂合度; H_e. 期望杂合度; PIC. 多态信息含量Note: the abbreviation of the genetic diversity parameters as the following. N_a. number of alleles; H_o. observed heterozygosity; H_e. expected heterozygosity; PIC. polymorphism information content

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表 3 基于微卫星位点的罗氏沼虾各育种群体间遗传分化指数

Table 3 Genetic differentiation index (F_ST) of the breeding populations of Macrobrachium rosenbergii based on SSR

	ZDS	ZD2S	SF	ZD
ZDS	0.00000
ZD2S	0.06451^**	0.00000
SF	0.05520^**	0.04166^**	0.00000
ZD	0.10438^**	0.06539^**	0.07281^**	0.00000
注: 表示P≤0.01Note: represents P≤0.01

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表 4 罗氏沼虾育种群体线粒体COⅠ、12S rRNA基因及两个基因组合序列的遗传多样性参数

Table 4 Genetic diversity parameters of mitochondrial COⅠ, 12S rRNA and their concatenated gene sequences in each breeding population of Macrobrachium rosenbergii

群体Population	COⅠ				12S rRNA				COⅠ+ 12S rRNA
群体Population	N	H	H_d	π	N	H	H_d	π	N	H	H_d	π
ZDS	19	3	0.205	0.00193	28	2	0.138	0.00086	29	5	0.594	0.001
ZD2S	26	5	0.603	0.00455	26	4	0.637	0.00197	30	11	0.876	0.0035
ZD	25	2	0.080	0.00006	28	3	0.500	0.00078	30	7	0.713	0.0004
SF	47	5	0.530	0.00512	55	10	0.598	0.00293	60	19	0.835	0.0042
总计Total	117	9	0.425	0.00371	137	12	0.660	0.00230	149	27	0.846	0.0031
注: 表中各参数简写如下, N. 样本数; H. 单倍型数; H_d. 单倍型多样性; π. 核苷酸多样性Note: the abbreviation of each parameter as the following. N. sample size; H. number of haplotype; H_d. haplotype diversity; π. nucleotidae diversity

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表 5 罗氏沼虾各育种群体COⅠ和12S rRNA基因组合序列单倍型在各群体中的分布

Table 5 Distribution of combined COⅠ and 12S rRNA sequence haplotypes in each breeding population of Macrobrachium rosenbergii

单倍型 Haplotype	ZDS	ZD2S	SF	ZD	总个体数 Total	相对频率Relative frequency (%)
Hap1	10	2		3	15	10.07
Hap2	16	5	2	6	29	19.46
Hap3				1	1	0.67
Hap4			1		1	0.67
Hap5		1			1	0.67
Hap6		9	22	15	46	30.87
Hap7			1		1	0.67
Hap8			1		1	0.67
Hap9		2	9	2	13	8.72
Hap10				1	1	0.67
Hap11		3	1		4	2.68
Hap12			1		1	0.67
Hap13			1		1	0.67
Hap14	1				1	0.67
Hap15			2		2	1.34
Hap16			1		1	0.67
Hap17			1		1	0.67
Hap18			1		1	0.67
Hap19		2			2	1.34
Hap20	1	2	3		6	4.03
Hap21			1		1	0.67
Hap22			6		6	4.03
Hap23	1	2	4	2	9	6.04
Hap24		1			1	0.67
Hap25		1			1	0.67
Hap26			1		1	0.67
Hap27			1		1	0.67
总个体数Total	29	30	60	30	149	100

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表 6 基于COⅠ和12S rRNA基因组合序列的罗氏沼虾育种群体间遗传分化指数

Table 6 Genetic differentiation index (F_ST) of the breeding populations of Macrobrachium rosenbergii based on the combined COⅠ and 12S rRNA sequences

	ZDS	ZD	ZD2S	SF
ZDS	0
ZD	0.03899	0
ZD2S	0.07310^*	–0.02226	0
SF	0.01419	–0.01611	–0.00472	0
注: 表示P≤0.05Note: represents P≤0.05

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