Comparison of genetic diversity and population structure of eight Macrobrachium nipponense populations in China based on D-loop sequences

Zhang, Wenyi; Jiang, Sufei; Salumy, Khamis Rabii; Xuan, Zhongya; Xiong, Yiwei; Jin, Shubo; Gong, Yongsheng; Wu, Yan; Qiao, Hui; Fu, Hongtuo

doi:10.1016/j.aqrep.2022.101086

Cited by 8 publications

(17 citation statements)

References 27 publications

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“…The pairwise F ST value was considerably lower than the genetic differentiation index of the eight populations in China (Zhang et al, 2022). This might be due to frequent interaction between these populations given the relatively short geographical distance separating them.…”

Section: Discussionmentioning

confidence: 75%

Genetic diversity and structure assessment ofMacrobrachium nipponensepopulations: implications for the protection and management of genetic resources

Xiong

Jiang

Zhang

et al. 2023

Aquat. Living Resour.

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This article presents a study of D-loop sequences to characterize the genetic diversity of wild Macrobrachium nipponense populations in Yixing natural waters including two reservoirs (Hengshan reservoir, HS; Youche reservoir, YC), 3 brooks (Linjin Dang, LJD; Magong Dushan Dang, MDD; Yangshan Dang, YSD) and 3 shallow lakes (Dongjiu lake, DJ; Xijiu lake, XJ; Tuanjiu lake, XJ), and compared the genetic differentiation and population structure with wild populations of Taihu Lake (TH), Yangtze River (YZ), and the main local artificially bred varieties “Taihu No. 2” (TH-2). A 747 bp D-loop sequence fragment was amplified in 321 individuals and the results exhibited a higher content of A+T (80.03%) than C+G (19.97%). A total of 110 haplotypes were identified. The h and π value proved the diversity of these populations was at the same level with high genetic diversity. TH-2 and YZ showed remarkable diversity, and XJ is even better. Fst estimates suggested that YZ and TH-2 were significant differentiation with other Yixing populations (P < 0.05). Three populations from shallow lake (DJ, XJ and TJ) displayed significant differentiated with the left Yixing ones (P < 0.05). The pairwise genetic distance, as well as haplotype network results, also suggested that all these 11 populations did not diverge at the species level (<15%). The P values of Tajima's D and Fu Fs were relatively greater than 0.1 (P > 0.1) and the nucleotide mismatch distribution analysis showed multiple peaks, giving a conclusion that the populations did not exhibited expansion. All these results suggested that TH-2 and YZ have remarkable diversity, and the germplasm resources and genetic diversity of M. nipponense in Yixing are very good and are suitable for original materials of breeding.

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Section: Discussionmentioning

confidence: 75%

Genetic diversity and structure assessment ofMacrobrachium nipponensepopulations: implications for the protection and management of genetic resources

Xiong

Jiang

Zhang

et al. 2023

Aquat. Living Resour.

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“…Genetic diversity is an important basis for the evaluation of population germplasm resources (Zhang et al, 2022). Further, genetic diversity is the basis of species adaptability and evolution, and there is a positive linear relationship between intraspecific genetic diversity and the adaptability of the species to the environment (Cruz et al, 2013).…”

Section: Discussionmentioning

confidence: 99%

“…(Javonillo et al, 2010;Lei et al, 2010;Zhang et al, 2015). Therefore, mtDNA is widely used in various research fields, such as DNA structure and gene expression (Yang et al, 2022), taxonomic resolution and species identification (Krzywinski et al, 2011;Zhu et al, 2017), species evolution and phylogenetic distribution (Sharma et al, 2020;Sun CH et al, 2021;Staden et al, 2022;Yang et al, 2022), and population genetics (Gissi et al, 2008;Fang et al, 2021;Zhang et al, 2022). To date, the classification about P. leptocephalus is still disputed.…”

Section: Introductionmentioning

confidence: 99%

“…Mitochondrial markers are important indicators of species structure and genetic diversity, and are widely used in genetic relationship analysis, germplasm identification, and population genetic structure analysis (Liu et al, 2021;Pan et al, 2021;Emelianova et al, 2022;Sultana et al, 2022;Zhang et al, 2022). Among the most common mitochondrial genes used in detecting genetic diversity and population structure, the mtDNA cytochrome c oxidase subunit I (COI) gene represent useful genetic marker and its easily amplified (Folmer et al, 1994).…”

Section: Introductionmentioning

confidence: 99%

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Comparison genetic diversity and population structure of four Pseudaspius leptocephalus populations in Heilongjiang River Basin based on mitochondrial COI gene

et al. 2023

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The Pseudaspius leptocephalus is a unique fish in the Heilongjiang River Basin and has important economic and ecological value. In the present study, the complete mitochondrial genome of P. leptocephalus were determined, and COI partial sequences of 85 individuals from Erguna river (EH), Mohe (MH), Fuyuan (FY), Hulan (HL) were used to evaluated the genetic diversity of four populations of P. leptocephalus in Heilongjiang River Basin. The mitogenome is 16,607 bp in length and contained one D-loop, 2 rRNA, 13 PCG, and 22 tRNA. 4 variable sites and 5 haplotypes were detected in 705 bp COI, and 705 bp COI exhibited a lower content of C + G (45.95%) than A + T (54.05%). The nucleotide diversity (π) and haplotype diversity (h) indices ranged from 0.00027 (HL) to 0.00065 (EH and FY) and from 0.192 (HL) to 0.462 (EH), respectively. The genetic distance within the population and between populations ranged from 0.0006554 to 0.0002728 and from 0.0003541 to 0.0006974, respectively. Pairwise values of FST and Nm showed that there was moderate genetic differentiation between EH population and other populations and individuals between EH population and other populations can mate randomly (0.15 > FST > 0.05, Nm > 4). Significant negative values of neutrality tests (P < 0.05) indicated that MH and FY populations may had experienced population expansion, but mismatch distribution analysis suggested that all populations have remained basically stable. These results provide strong basis for the protection and utilization of P. leptocephalus germplasm resources, and provide valuable information for the population structure and genetic diversity of P. leptocephalus.

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“…Even more, farmers use the remaining prawns as parents for the following year and continue to breed the next generation. This led to widespread and severe breed degradation by the end of the 1990s, mainly manifesting as early maturation, individual miniaturization, commodity rate decrease and disease increase [4]. The breed degradation led to a significant benefit decline and an increased risk and seriously restricted the development of prawn aquaculture [5].…”

Section: Introductionmentioning

confidence: 99%

Genetic diversity and Population structure assessment of 22 wild Macrobrachium nipponense populations across China: Implications for genetic resources protection and population management

Jiang

Xiong

Zhang

et al. 2022

Preprint

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Macrobrachium nipponense, is an important economic indigenous prawn in China, which is widely distributed in freshwater in China, Japan and Southeast Asia. In this study, D-loop region sequences was used to investigate the genetic diversity and population structure of 22 wild populations of M. nipponense through China, containing the major rivers and lakes of China. Totally 475 valid D-loop sequences from 22 populations with a length of 1110bp were obtained, and 348 variation sites and 221 haplotypes were detected. A total of 221 haplotypes were defined in 22 populations. Hap48 was the dominant haplotype, accounting for about 13%. The haplotype diversity (h) was ranged from 0.1630 (BN) ~1.0000 (AR) and the nucleotide diversity π value ranged from 0.001164 (MR) ~ 0.037168 (NR). The pairwise genetic differentiation index (FST) ranged from 0.00344 to 0.91243 and most pair-wised FST was significant (P < 0.05). The lowest FST was displayed in MR and JLR population and the highest was between NDR and NR. The phylogenetic tree of genetic distance based on UPGMA showed that all populations were divided into two branches. The DC, NDR, JLR and MR populations were clustered into one branch. The neutral test and mismatch distribution results showed that M. nipponense populations were not experienced expanding and kept a steady increase. Taken together, a joint resources protection and management strategy for M. nipponense have been suggested based on the results of this study for its sustainable use.

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Comparison of genetic diversity and population structure of eight Macrobrachium nipponense populations in China based on D-loop sequences

Cited by 8 publications

References 27 publications

Genetic diversity and structure assessment ofMacrobrachium nipponensepopulations: implications for the protection and management of genetic resources

Genetic diversity and structure assessment ofMacrobrachium nipponensepopulations: implications for the protection and management of genetic resources

Comparison genetic diversity and population structure of four Pseudaspius leptocephalus populations in Heilongjiang River Basin based on mitochondrial COI gene

Genetic diversity and Population structure assessment of 22 wild Macrobrachium nipponense populations across China: Implications for genetic resources protection and population management

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