基于线粒体Cytb基因和D-loop区的野生与养殖小黄鱼群体遗传多样性

doi:10.3969/j.issn.1004-1524.2022.09.05

浙江农业学报 ›› 2022, Vol. 34 ›› Issue (9): 1856-1865.DOI: 10.3969/j.issn.1004-1524.2022.09.05

基于线粒体Cytb基因和D-loop区的野生与养殖小黄鱼群体遗传多样性

郭丹丹(), 刘峰, 牛宝龙, 楼宝()

浙江省农业科学院水生生物研究所,浙江杭州 310021

收稿日期:2022-01-04 出版日期:2022-09-25 发布日期:2022-09-30
通讯作者: 楼宝
作者简介:*楼宝,E-mail: loubao6577@163.com
郭丹丹(1990—),女,山东滨州人,博士,助理研究员,研究方向为鱼类遗传育种。E-mail: hmguodandan@163.com
基金资助:
国家重点研发计划“蓝色粮仓科技创新”重点专项(2018YFD0901204);浙江省重点研发计划(2020C02015);浙江省重点研发计划(2021C02055)

Genetic diversity of wild and cultured populations of little yellow croaker (Larimichthys polyactis) based on mitochondrial Cytb gene and D-loop region

GUO Dandan(), LIU Feng, NIU Baolong, LOU Bao()

Institute of Hydrobiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China

Received:2022-01-04 Online:2022-09-25 Published:2022-09-30
Contact: LOU Bao

摘要/Abstract

摘要：

为研究野生与养殖小黄鱼群体的遗传多样性,基于mtDNA Cytb基因和D-loop控制区对舟山嵊泗海域(SS)和象山三门口海域(SMK)2个小黄鱼野生群体和1个养殖群体(YZ)的遗传结构与遗传分化等进行比较分析。序列分析结果显示,Cytb基因序列为841 bp,其A+T含量(50.2%)与C+G含量(49.8%)相似;D-loop区序列为629~635 bp,A+T含量(58.9%)远高于C+G含量(41.1%)。SS、SMK和YZ群体Cytb基因的单倍型数分别为26、27和12,SS和SMK群体共享2个单倍型(Hap1和Hap13),SMK和YZ群体共享1个单倍型(Hap41);SS、SMK和YZ群体D-loop区的单倍型数分别为27、30和10,SS和SMK群体共享1个单倍型(Hap4)。多样性分析结果显示,3个群体均属于高单倍型多样性(H_d>0.5),其中,SS和SMK群体单倍型多样性和核苷酸多样性高于YZ群体,表明野生群体多样性略高于养殖群体。遗传分化指数显示,2个小黄鱼野生群体间的分化程度极小,而养殖群体与野生群体间存在中度分化。遗传分化指数和AMOVA分析结果表明,群体内个体的变异是遗传变异的主要来源。Cytb基因和D-loop区序列中性检验结果中SS和SMK群体的Tajima’s D值和Fu and Li's值均为负数,且Cytb基因的Tajima’s D值和Fu and Li's值显著(P<0.05)偏离中性,表明2个野生群体有可能经历过群体扩张。单倍型系统发育树显示,SS、SMK和YZ群体均未表现出明显的地理聚集,群体间互有交叉,表明3个群体间的分化尚不明显。

关键词: 小黄鱼, 线粒体DNA, Cytb基因, D-loop区, 遗传多样性

Abstract:

In order to study the genetic diversity of wild and cultured populations of little yellow croaker (Larimichthys polyactis), the genetic structure and differentiation of two wild (SS and SMK) and one cultured (YZ) populations of little yellow croaker was analyzed based on mitochondrial DNA Cytb gene and D-loop control region. The results showed that the sequences of Cytb gene were 841 bp, with A+T (50.2%) content similar to C+G (49.8%) content. The D-loop sequences were 629-635 bp, and A+T content (58.9%) was significantly higher than C+G content (41.1%). Based on the analysis of Cytb gene, the haplotypes of SS, SMK and YZ populations were 26, 27 and 12, respectively. SS and SMK populations shared two haplotypes (hap1 and hap13), SMK and YZ populations shared one haplotypes (hap41). Based on D-loop, the haplotypes of SS, SMK and YZ populations were 27, 30 and 10, respectively, and SS and SMK populations shared one haplotype (Hap4). The diversity results showed that the haplotype diversity (H_d>0.5) of the three populations were high. In addition, the haplotype diversity and nucleotide diversity of SS and SMK populations were slightly higher than those of YZ population, indicating that the diversity of wild populations was higher than that of cultured population. The results of fixation index and AMOVA showed that the genetic variation was mainly derived from individual variation within the population, the genetic differentiation between populations of SS and SMK was small, but there was a moderate differentiation between the cultured and wild population. Neutral test analysis of SS and SMK populations showed that Tajima’s D and Fu and Li's value were both negative, and significantly (P<0.05) deviated from neutral based on Cytb gene, indicating that both wide populations have undergone a recent population expansion. The haplotype phylogenetic tree was shown that SS, SMK and YZ populations did not formed monophyletic group, which indicated that the genetic differentiation of the three populations was not significant.

Key words: Larimichthys polyactis, mitochondrial DNA, Cytb gene, D-loop region, genetic diversity

中图分类号:

S965.323

郭丹丹, 刘峰, 牛宝龙, 楼宝. 基于线粒体Cytb基因和D-loop区的野生与养殖小黄鱼群体遗传多样性[J]. 浙江农业学报, 2022, 34(9): 1856-1865.

GUO Dandan, LIU Feng, NIU Baolong, LOU Bao. Genetic diversity of wild and cultured populations of little yellow croaker (Larimichthys polyactis) based on mitochondrial Cytb gene and D-loop region[J]. Acta Agriculturae Zhejiangensis, 2022, 34(9): 1856-1865.

图/表 7

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基因Gene	群体Population	N	S	H	H_d	P_i	K	Tajima’s D	Fu and Li's
Cytb	嵊泗SS	30	40	26	0.984	0.004 85	4.078	-2.195 69^**	-2.835 55^*
	三门口SMK	30	42	27	0.993	0.005 53	4.646	-2.115 48^*	-3.012 68^*
	养殖YZ	30	22	12	0.857	0.004 29	3.600	-1.237 44	-2.089 72
	总计Total	90	74	62	0.980	0.005 07	4.258	-2.355 00^**	-4.211 26^**
D-loop	嵊泗SS	30	44	27	0.993	0.011 74	7.301	-1.377 92	-1.206 13
	三门口SMK	30	50	30	1.000	0.012 67	7.832	-1.414 35	-0.971 75
	养殖YZ	30	27	10	0.805	0.009 64	5.984	-0.437 16	-0.229 81
	总计Total	90	66	65	0.978	0.011 52	7.073	-1.572 08	-2.012 02

基因Gene	群体Population	N	S	H	H_d	P_i	K	Tajima’s D	Fu and Li's
Cytb	嵊泗SS	30	40	26	0.984	0.004 85	4.078	-2.195 69^**	-2.835 55^*
	三门口SMK	30	42	27	0.993	0.005 53	4.646	-2.115 48^*	-3.012 68^*
	养殖YZ	30	22	12	0.857	0.004 29	3.600	-1.237 44	-2.089 72
	总计Total	90	74	62	0.980	0.005 07	4.258	-2.355 00^**	-4.211 26^**
D-loop	嵊泗SS	30	44	27	0.993	0.011 74	7.301	-1.377 92	-1.206 13
	三门口SMK	30	50	30	1.000	0.012 67	7.832	-1.414 35	-0.971 75
	养殖YZ	30	27	10	0.805	0.009 64	5.984	-0.437 16	-0.229 81
	总计Total	90	66	65	0.978	0.011 52	7.073	-1.572 08	-2.012 02

Cytb								D-loop
单倍型 Haplotype	嵊泗 SS	三门口 SMK	养殖 YZ	单倍型 Haplotype	嵊泗 SS	三门口 SMK	养殖 YZ	单倍型 Haplotype	嵊泗 SS	三门口 SMK	养殖 YZ	单倍型 Haplotype	嵊泗 SS	三门口 SMK	养殖 YZ
Hap1	1	1	0	Hap34	0	1	0	Hap1	1	0	0	Hap34	0	1	0
Hap2	1	0	0	Hap35	0	1	0	Hap2	2	0	0	Hap35	0	1	0
Hap3	2	0	0	Hap36	0	1	0	Hap3	1	0	0	Hap36	0	1	0
Hap4	1	0	0	Hap37	0	2	0	Hap4	1	1	0	Hap37	0	1	0
Hap5	1	0	0	Hap38	0	1	0	Hap5	2	0	0	Hap38	0	1	0
Hap6	1	0	0	Hap39	0	1	0	Hap6	2	0	0	Hap39	0	1	0
Hap7	1	0	0	Hap40	0	1	0	Hap7	1	0	0	Hap40	0	1	0
Hap8	1	0	0	Hap41	0	1	1	Hap8	1	0	0	Hap41	0	1	0
Hap9	1	0	0	Hap42	0	1	0	Hap9	1	0	0	Hap42	0	1	0
Hap10	1	0	0	Hap43	0	1	0	Hap10	1	0	0	Hap43	0	1	0
Hap11	1	0	0	Hap44	0	1	0	Hap11	1	0	0	Hap44	0	1	0
Hap12	1	0	0	Hap45	0	1	0	Hap12	1	0	0	Hap45	0	1	0
Hap13	4	2	0	Hap46	0	1	0	Hap13	1	0	0	Hap46	0	1	0
Hap14	1	0	0	Hap47	0	1	0	Hap14	1	0	0	Hap47	0	1	0
Hap15	1	0	0	Hap48	0	1	0	Hap15	1	0	0	Hap48	0	1	0
Hap16	1	0	0	Hap49	0	1	0	Hap16	1	0	0	Hap49	0	1	0
Hap17	1	0	0	Hap50	0	1	0	Hap17	1	0	0	Hap50	0	1	0
Hap18	1	0	0	Hap51	0	1	0	Hap18	1	0	0	Hap51	0	1	0
Hap19	1	0	0	Hap52	0	0	1	Hap19	1	0	0	Hap52	0	1	0
Hap20	1	0	0	Hap53	0	0	10	Hap20	1	0	0	Hap53	0	1	0
Hap21	1	0	0	Hap54	0	0	3	Hap21	1	0	0	Hap54	0	1	0
Hap22	1	0	0	Hap55	0	0	1	Hap22	1	0	0	Hap55	0	1	0
Hap23	1	0	0	Hap56	0	0	5	Hap23	2	0	0	Hap56	0	0	1
Hap24	1	0	0	Hap57	0	0	1	Hap24	1	0	0	Hap57	0	0	12
Hap25	1	0	0	Hap58	0	0	1	Hap25	1	0	0	Hap58	0	0	4
Hap26	1	0	0	Hap59	0	0	2	Hap26	1	0	0	Hap59	0	0	1
Hap27	0	2	0	Hap60	0	0	1	Hap27	0	1	0	Hap60	0	0	5
Hap28	0	1	0	Hap61	0	0	3	Hap28	0	1	0	Hap61	0	0	1
Hap29	0	1	0	Hap62	0	0	1	Hap29	0	1	0	Hap62	0	0	1
Hap30	0	1	0					Hap30	0	1	0	Hap63	0	0	3
Hap31	0	1	0					Hap31	0	1	0	Hap64	0	0	1
Hap32	0	1	0					Hap32	0	1	0	Hap65	0	0	1
Hap33	0	1	0					Hap33	0	1	0

Cytb								D-loop
单倍型 Haplotype	嵊泗 SS	三门口 SMK	养殖 YZ	单倍型 Haplotype	嵊泗 SS	三门口 SMK	养殖 YZ	单倍型 Haplotype	嵊泗 SS	三门口 SMK	养殖 YZ	单倍型 Haplotype	嵊泗 SS	三门口 SMK	养殖 YZ
Hap1	1	1	0	Hap34	0	1	0	Hap1	1	0	0	Hap34	0	1	0
Hap2	1	0	0	Hap35	0	1	0	Hap2	2	0	0	Hap35	0	1	0
Hap3	2	0	0	Hap36	0	1	0	Hap3	1	0	0	Hap36	0	1	0
Hap4	1	0	0	Hap37	0	2	0	Hap4	1	1	0	Hap37	0	1	0
Hap5	1	0	0	Hap38	0	1	0	Hap5	2	0	0	Hap38	0	1	0
Hap6	1	0	0	Hap39	0	1	0	Hap6	2	0	0	Hap39	0	1	0
Hap7	1	0	0	Hap40	0	1	0	Hap7	1	0	0	Hap40	0	1	0
Hap8	1	0	0	Hap41	0	1	1	Hap8	1	0	0	Hap41	0	1	0
Hap9	1	0	0	Hap42	0	1	0	Hap9	1	0	0	Hap42	0	1	0
Hap10	1	0	0	Hap43	0	1	0	Hap10	1	0	0	Hap43	0	1	0
Hap11	1	0	0	Hap44	0	1	0	Hap11	1	0	0	Hap44	0	1	0
Hap12	1	0	0	Hap45	0	1	0	Hap12	1	0	0	Hap45	0	1	0
Hap13	4	2	0	Hap46	0	1	0	Hap13	1	0	0	Hap46	0	1	0
Hap14	1	0	0	Hap47	0	1	0	Hap14	1	0	0	Hap47	0	1	0
Hap15	1	0	0	Hap48	0	1	0	Hap15	1	0	0	Hap48	0	1	0
Hap16	1	0	0	Hap49	0	1	0	Hap16	1	0	0	Hap49	0	1	0
Hap17	1	0	0	Hap50	0	1	0	Hap17	1	0	0	Hap50	0	1	0
Hap18	1	0	0	Hap51	0	1	0	Hap18	1	0	0	Hap51	0	1	0
Hap19	1	0	0	Hap52	0	0	1	Hap19	1	0	0	Hap52	0	1	0
Hap20	1	0	0	Hap53	0	0	10	Hap20	1	0	0	Hap53	0	1	0
Hap21	1	0	0	Hap54	0	0	3	Hap21	1	0	0	Hap54	0	1	0
Hap22	1	0	0	Hap55	0	0	1	Hap22	1	0	0	Hap55	0	1	0
Hap23	1	0	0	Hap56	0	0	5	Hap23	2	0	0	Hap56	0	0	1
Hap24	1	0	0	Hap57	0	0	1	Hap24	1	0	0	Hap57	0	0	12
Hap25	1	0	0	Hap58	0	0	1	Hap25	1	0	0	Hap58	0	0	4
Hap26	1	0	0	Hap59	0	0	2	Hap26	1	0	0	Hap59	0	0	1
Hap27	0	2	0	Hap60	0	0	1	Hap27	0	1	0	Hap60	0	0	5
Hap28	0	1	0	Hap61	0	0	3	Hap28	0	1	0	Hap61	0	0	1
Hap29	0	1	0	Hap62	0	0	1	Hap29	0	1	0	Hap62	0	0	1
Hap30	0	1	0					Hap30	0	1	0	Hap63	0	0	3
Hap31	0	1	0					Hap31	0	1	0	Hap64	0	0	1
Hap32	0	1	0					Hap32	0	1	0	Hap65	0	0	1
Hap33	0	1	0					Hap33	0	1	0

基因 gene	群体 population	嵊泗 SS	三门口 SMK	养殖 YZ
Cytb	嵊泗SS	0.005	0.012 11	0.063 39
	三门口SMK	0.005	0.006	0.078 78
	养殖YZ	0.005	0.005	0.004
D-loop	嵊泗SS	0.011	-0.002 30	0.081 04
	三门口SMK	0.012	0.013	0.050 51
	养殖YZ	0.012	0.012	0.010

基于线粒体Cytb基因和D-loop区的野生与养殖小黄鱼群体遗传多样性

Genetic diversity of wild and cultured populations of little yellow croaker (Larimichthys polyactis) based on mitochondrial Cytb gene and D-loop region

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基因 Gene	变异来源 Source of variation	自由度 Degree of freedom	方差和 Sum of squares	变异组分 Variance components	变异贡献率 Percentage of variation/%
Cytb	群体间Among populations	2	10.767	0.110 98 Va	5.13
	群体内Within populations	87	178.700	2.054 02 Vb	94.87
	总计Total	89	189.467	2.165 00
D-loop	群体间Among populations	2	16.033	0.152 77 Va	4.26
	群体内Within populations	87	298.733	3.433 72 Vb	95.74
	总计Total	89	314.767	3.586 48

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