Genetics analysis based on mitochondrial COⅠ sequences in five cultured populations of red-claw crayfish (Cherax quadricarinatus)

doi:10.3969/j.issn.1004-1524.2021.08.05

Acta Agriculturae Zhejiangensis ›› 2021, Vol. 33 ›› Issue (8): 1385-1392.DOI: 10.3969/j.issn.1004-1524.2021.08.05

• Animal Science • Previous Articles Next Articles

Genetics analysis based on mitochondrial COⅠ sequences in five cultured populations of red-claw crayfish (Cherax quadricarinatus)

LIU Shili¹^,²(), BIAN Yuling¹^,², JIA Yongyi¹, CHI Meili¹, LI Fei¹, ZHENG Jianbo¹, CHENG Shun¹, GU Zhimin¹^,^*()

1. Key Laboratory of Healthy Freshwater Aquaculture, Ministry of Agriculture and Rural Affairs / Key Laboratory of Freshwater Aquatic Animal Genetic and Breeding of Zhejiang Province, Zhejiang Institute of Freshwater Fisheries, Huzhou 313001, China
2. Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai 201306, China

Received:2020-09-16 Online:2021-08-25 Published:2021-08-27
Contact: GU Zhimin

Abstract

Abstract:

Cherax quadricarinatus is native to Australia with good breeding prospects. In the present study, the genetic diversity and structure of five cultured populations of Cherax quadricarinatus were evaluated based on mitochondrial COⅠ sequences, to provide basic data for scientific introduction, variety selection, and germplasm resource protection. The results showed that the complete sequence of the mitochondrial COⅠ region was 1 534 bp, of which 24 were variation sites, accounting for 1.6% of the analysis sites. In the 24 variation sites, 22 were parsimony-informative sites, and the average transversion ratio was 6.14. The content of (A+T) (58.7%) was higher than that of (G+C) (41.3%). A total of 35 haplotypes were defined in 143 individuals. Zhejiang, Hainan, and Taiwan cultured populations had some shared haplotypes (COⅠ-01, COⅠ-02, and COⅠ-03), and these three haplotypes were dominant also. The haplotype diversity of Jiangsu cultured population (0.739) was the lowest, while the highest was found in Anhui cultured population (0.881). The haplotype diversity index and nucleotide diversity index of whole samples were 0.896 and 0.004 65, respectively. The genetic distance between different cultured populations varied from 0.002 63 to 0.006 81, and the genetic distance between Zhejiang and Hainan cultured populations was the closest, while the genetic distance between Hainan and Anhui cultured populations was the furthest. The genetic differentiation coefficient within populations was 0.342 1 (P<0.01), indicating genetic differentiation within populations. The genetic diversity of the five cultured populations of C. quadricarinatus was different, indicating that there was some gene exchange among populations. These results provided molecular biological basis for the rational development and utilization of the germplasm resources of C. quadricarinatus.

Key words: Cherax quadricarinatus, genetic diversity, genetic structure

CLC Number:

S931.5
Q347

LIU Shili, BIAN Yuling, JIA Yongyi, CHI Meili, LI Fei, ZHENG Jianbo, CHENG Shun, GU Zhimin. Genetics analysis based on mitochondrial COⅠ sequences in five cultured populations of red-claw crayfish (Cherax quadricarinatus)[J]. Acta Agriculturae Zhejiangensis, 2021, 33(8): 1385-1392.

Figures/Tables 7

References 15

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来源Origin	A	G	T	C	A+T	C+G
浙江Zhejiang	27.0	16.5	31.7	24.8	58.7	41.3
海南Hainan	27.0	16.5	31.7	24.8	58.7	41.3
台湾Taiwan	27.0	16.6	31.7	24.8	58.6	41.4
江苏Jiangsu	27.0	16.6	31.7	24.7	58.7	41.3
安徽Anhui	26.9	16.7	31.7	24.7	58.6	41.4
总体Total	27.0	16.6	31.7	24.8	58.7	41.3

来源Origin	A	G	T	C	A+T	C+G
浙江Zhejiang	27.0	16.5	31.7	24.8	58.7	41.3
海南Hainan	27.0	16.5	31.7	24.8	58.7	41.3
台湾Taiwan	27.0	16.6	31.7	24.8	58.6	41.4
江苏Jiangsu	27.0	16.6	31.7	24.7	58.7	41.3
安徽Anhui	26.9	16.7	31.7	24.7	58.6	41.4
总体Total	27.0	16.6	31.7	24.8	58.7	41.3

单倍型 Haplotype	浙江 Zhejiang	海南 Hainan	台湾 Taiwan	江苏 Jiangsu	安徽 Anhui	总计 Total	序列号 Accession No.
COⅠ-01	13	12	8	0	0	33	MT966719
COⅠ-02	9	10	1	0	0	20	MT966720
COⅠ-03	4	2	6	11	0	23	MT966721
COⅠ-04	2	0	0	0	0	2	MT966722
COⅠ-05	1	6	1	0	0	8	MT966723
COⅠ-06	1	0	1	0	0	2	MT966724
COⅠ-07	1	0	0	0	0	1	MT966725
COⅠ-08	1	0	0	0	0	1	MT966726
COⅠ-09	1	0	0	0	0	1	MT966727
COⅠ-10	0	3	1	0	0	4	MT966728
COⅠ-11	0	2	0	0	0	2	MT966729
COⅠ-12	0	1	1	0	0	2	MT966730
COⅠ-13	0	1	0	0	0	1	MT966731
COⅠ-14	0	1	0	0	0	1	MT966732
COⅠ-15	0	0	2	0	0	2	MT966733
COⅠ-16	0	0	2	0	0	2	MT966734
COⅠ-17	0	0	1	0	1	2	MT966735
COⅠ-18	0	0	1	0	0	1	MT966736
COⅠ-19	0	0	1	0	0	1	MT966737
COⅠ-20	0	0	1	0	0	1	MT966738
COⅠ-21	0	0	0	5	0	5	MT966739
COⅠ-22	0	0	0	3	0	3	MT966740
COⅠ-23	0	0	0	3	0	3	MT966741
COⅠ-24	0	0	0	2	0	2	MT966742
COⅠ-25	0	0	0	0	6	6	MT966743
COⅠ-26	0	0	0	0	5	5	MT966744
COⅠ-27	0	0	0	0	1	1	MT966745
COⅠ-28	0	0	0	0	1	1	MT966746
COⅠ-29	0	0	0	0	1	1	MT966747
COⅠ-30	0	0	0	0	1	1	MT966748
COⅠ-31	0	0	0	0	1	1	MT966749
COⅠ-32	0	0	0	0	1	1	MT966750
COⅠ-33	0	0	0	0	1	1	MT966751
COⅠ-34	0	0	0	0	1	1	MT966752
COⅠ-35	0	0	0	0	1	1	MT966753

单倍型 Haplotype	浙江 Zhejiang	海南 Hainan	台湾 Taiwan	江苏 Jiangsu	安徽 Anhui	总计 Total	序列号 Accession No.
COⅠ-01	13	12	8	0	0	33	MT966719
COⅠ-02	9	10	1	0	0	20	MT966720
COⅠ-03	4	2	6	11	0	23	MT966721
COⅠ-04	2	0	0	0	0	2	MT966722
COⅠ-05	1	6	1	0	0	8	MT966723
COⅠ-06	1	0	1	0	0	2	MT966724
COⅠ-07	1	0	0	0	0	1	MT966725
COⅠ-08	1	0	0	0	0	1	MT966726
COⅠ-09	1	0	0	0	0	1	MT966727
COⅠ-10	0	3	1	0	0	4	MT966728
COⅠ-11	0	2	0	0	0	2	MT966729
COⅠ-12	0	1	1	0	0	2	MT966730
COⅠ-13	0	1	0	0	0	1	MT966731
COⅠ-14	0	1	0	0	0	1	MT966732
COⅠ-15	0	0	2	0	0	2	MT966733
COⅠ-16	0	0	2	0	0	2	MT966734
COⅠ-17	0	0	1	0	1	2	MT966735
COⅠ-18	0	0	1	0	0	1	MT966736
COⅠ-19	0	0	1	0	0	1	MT966737
COⅠ-20	0	0	1	0	0	1	MT966738
COⅠ-21	0	0	0	5	0	5	MT966739
COⅠ-22	0	0	0	3	0	3	MT966740
COⅠ-23	0	0	0	3	0	3	MT966741
COⅠ-24	0	0	0	2	0	2	MT966742
COⅠ-25	0	0	0	0	6	6	MT966743
COⅠ-26	0	0	0	0	5	5	MT966744
COⅠ-27	0	0	0	0	1	1	MT966745
COⅠ-28	0	0	0	0	1	1	MT966746
COⅠ-29	0	0	0	0	1	1	MT966747
COⅠ-30	0	0	0	0	1	1	MT966748
COⅠ-31	0	0	0	0	1	1	MT966749
COⅠ-32	0	0	0	0	1	1	MT966750
COⅠ-33	0	0	0	0	1	1	MT966751
COⅠ-34	0	0	0	0	1	1	MT966752
COⅠ-35	0	0	0	0	1	1	MT966753

群体 Population	样本数 Sample number	变异位点数 Number of variable sites	单倍型数 Number of haplotypes	单倍型多样性 Haplotype diversity	核苷酸多样性 Nucleotide diversity	Tajima's D	Fu's Fs
浙江 Zhejiang	33	16	9	0.771	0.003 14	0.737	1.281
海南 Hainan	38	15	9	0.814	0.001 88	-0.613	-0.312
台湾 Taiwan	27	20	13	0.872	0.005 20	1.908	-0.233
江苏 Jiangsu	24	11	5	0.739	0.003 21	2.275	4.562
安徽 Anhui	21	16	12	0.881	0.003 63	0.928	-1.972
总体 Total	143	24	35	0.896	0.004 65	1.817	-6.685

Genetics analysis based on mitochondrial COⅠ sequences in five cultured populations of red-claw crayfish (Cherax quadricarinatus)

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来源 Origin	浙江 Zhejiang	海南 Hainan	台湾 Taiwan	江苏 Jiangsu	安徽 Anhui
浙江 Zhejiang	—	0.042 77	0.147 91	0.376 17	0.466 51
海南 Hainan	0.002 63	—	0.318 57	0.565 22	0.617 28
台湾 Taiwan	0.004 90	0.005 08	—	0.095 63	0.217 40
江苏 Jiangsu	0.005 11	0.005 68	0.004 69	—	0.331 04
安徽 Anhui	0.006 33	0.006 81	0.005 71	0.005 13	—

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