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

doi:10.3969/j.issn.1004-1524.2022.09.05

Acta Agriculturae Zhejiangensis ›› 2022, Vol. 34 ›› Issue (9): 1856-1865.DOI: 10.3969/j.issn.1004-1524.2022.09.05

• Animal Science • Previous Articles Next Articles

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

Abstract

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

CLC Number:

S965.323

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.

Figures/Tables 7

References 29

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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

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

[1]	HONG Xia, LU Jilai, QI Huijuan, CHEN Xiaoshang. Genetic diversity analysis and core collection construction of ginger (Zingiber officinale Rosc.) germplasm accessions [J]. Acta Agriculturae Zhejiangensis, 2025, 37(6): 1233-1243.
[2]	QIN Douwen, LIU Weiqiang, TIAN Jiting, JU Xiuting. Establishment of cpDNA-PCR reaction system and genetic diversity analysis of Tulipa iliensis [J]. Acta Agriculturae Zhejiangensis, 2025, 37(1): 78-89.
[3]	ZHANG Yuanyuan, FENG Juling, XIAO Jingfeng, GUAN Yu, LONG Chuer, YAO Lirong, MENG Yaxiong, SI Erjing, LI Baochun, MA Xiaole, WANG Huajun, ZHOU Xirong, LIU Meijin, WANG Juncheng. Genetic diversity and association analysis between agronomic traits and SSR markers in hulless barley [J]. Acta Agriculturae Zhejiangensis, 2024, 36(9): 1977-1989.
[4]	DONG Lili, XU Zhihao, YAN Canlong, FAN Xiaoping, JIN Zelan, WANG Zhonghua. Molecular identification and genetic relationship of different breeding populations in Fritillaria thunbergii based on phenotype and molecular markers [J]. Acta Agriculturae Zhejiangensis, 2024, 36(8): 1719-1730.
[5]	HUANG Hui, CHU Tianjiang, XIE Nan, LIU Kai. Investigation on the genetic diversity of Sarcocheilichthys sinensis from diverse geographical populations and other species within the Sarcocheilichthys genus through the analysis of mitochondrial COI sequence segments [J]. Acta Agriculturae Zhejiangensis, 2024, 36(8): 1779-1788.
[6]	MA Li, LAN Yi, XIE Bingxin, ZHOU Chunlu, LUO Shuyuan, XU Wenkun, DONG Xinxing, YAN Dawei. Study of polymorphism in the VRTN gene and its association with production traits in (Duroc×Saba)♂×[Yorkshire×(Landrace×Saba)]♀ [J]. Acta Agriculturae Zhejiangensis, 2024, 36(7): 1502-1510.
[7]	WANG Baogen, CHEN Xiaoyang, WU Jian, LI Xiao, WANG Ying, WANG Jian, WU Xiaohua, LU Zhongfu, SUN Yuyan, DONG Wenqi, LI Guojing, WU Xinyi. Genetic diversity of cowpea landraces in Zhejiang Province, China [J]. Acta Agriculturae Zhejiangensis, 2024, 36(7): 1569-1582.
[8]	ZHU Yanyu, YU Wentao, GAO Shuilian, LYU Shuiyuan, WANG Pan, JIN Wanmin, GUI Wenjing, LIN Yi, YE Naixing. The diversity of tea germplasm resources and genetic relationship of ‘Tieguanyin’-derived varieties in Anxi, Fujian, China [J]. Acta Agriculturae Zhejiangensis, 2024, 36(7): 1591-1601.
[9]	ZHANG Ting, WANG Xueyan, GUO Qinwei, LI Chaosen, LIU Huiqin, XIANG Xiaomin, WEI Jing, ZHAO Dongfeng, WAN Hongjian. Genetic diversity of pepper germplasm resources based on agronomic traits [J]. Acta Agriculturae Zhejiangensis, 2024, 36(2): 325-333.
[10]	YANG Tianwen, WANG Jing, LI Jiong, XU Binqi, CHENG Jiaowen, HONG Yu, CAO Yi, CUI Junjie. Genetic diversity analysis and fingerprint construction of Dading bitter gourd germplasm resources [J]. Acta Agriculturae Zhejiangensis, 2024, 36(1): 103-114.
[11]	WU Qian, TANG Ziyi, TIAN Shengye, HE Haiye, PAN Weiwei, WANG Junfeng, BAO Honghua, ZHANG Huijuan, JIANG Ming. Genetic diversity of Rhododendron huadingense based on SARP molecular marker [J]. Acta Agriculturae Zhejiangensis, 2024, 36(1): 127-133.
[12]	HE Yu, LIU Feng, ZHANG Tianle, LOU Bao, WEI Fuliang, YE Ting. Histological study on the effect of high temperature stress on liver tissue in Larimichthys polyactis [J]. Acta Agriculturae Zhejiangensis, 2024, 36(1): 58-66.
[13]	ZHANG Xiaoli, ZHU Linglong, LI Fuzhen, TANG Xiumei, XIA Youlin, YOU Yu, ZHONG Ruichun. Evaluation and analysis of agronomic and quality traits of 115 peanut germplasm resources [J]. Acta Agriculturae Zhejiangensis, 2023, 35(9): 2033-2044.
[14]	YUAN Ye, LIU Rui, WANG Lingyun, SHEN Meng, YE Xuelian, QUAN Xinhua, WANG Ruisen, YAO Xiangtan. Genetic diversity analysis of Trapa L. cultivars in Jiangsu and Zhejiang Provinces using SLAF-seq [J]. Acta Agriculturae Zhejiangensis, 2023, 35(8): 1773-1781.
[15]	MENG Yusha, WANG Yin, LAI Qixian, LIU Lei, XIANG Chao, WU Yonghua, ZHENG Yanran, GU Xingguo, FANG Hao, MIAO Miao, WU Liehong, TANG Yong. Assessment of genetic diversity and variety identification based on insertion site-based polymorphism (ISBP) markers developed in wild species related to sweet potato [J]. Acta Agriculturae Zhejiangensis, 2023, 35(3): 489-498.