Genetic diversity analysis of different age of a Dalian population of the Manila clam<i>Ruditapes philippinarum</i>by EST-SSR

Zhifei, 虞志飞 Yu; Xiwu, 闫喜武 Yan; Yuehuan, 张跃环 Zhang; Fei, 杨霏 Yang; Feng, 杨凤 Yang; Guofan, 张国范 Zhang

doi:10.5846/stxb201105150625

Cited by 4 publications

(6 citation statements)

References 3 publications

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“…The more reasonable explanation for this is probably due to seeds’ transplantation by local farmers among different culture regions. In recent decades, there is considerable translocation of clam seeds cultivated in Fujian province (south) to culture sites in Shandong and Liaoning provinces (north) [ 4 , 20 , 21 ]. Therefore, the artificial breeding and culture of clams may increase the gene flow of clams, resulting in the low genetic differentiation between northern and southern populations, as evidenced by our present results.…”

Section: Discussionmentioning

confidence: 99%

“…The small N e values may be caused by inadvertent selection of the best offspring produced by a few parents and asymmetric reproduction [ 58 ]. Despite this, the accumulation of inbreeding might have some negative effects on survival rates of clams in these populations with small N e values [ 21 , 22 ]. Thus, it is essential to recover the local populations by the conservation programs (e.g., broodstock management and controlled spawning) to maintain a minimum viable population to maintain the evolutionary potential [ 59 , 60 ].…”

Section: Discussionmentioning

confidence: 99%

“…Eleven pairs of microsatellite markers with stable amplification were selected from the previous reports [ 20 , 21 ]. The basic information for primer sequences and PCR conditions is shown in Table 2 .…”

Section: Methodsmentioning

confidence: 99%

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Population Genetics of Manila Clam (Ruditapes philippinarum) in China Inferred from Microsatellite Markers

Zheng

Zhang

et al. 2023

Biology

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The Manila clam (Ruditapes philippinarum) is one of the most commercially important bivalves along the coast of China. With the continuous expansion of clam farming scale, it may lead to some serious problems, including loss of genetic variation, inbreeding depression, and reduced effective population size (Ne). In the present study, eleven microsatellite markers were used to investigate the genetic diversity and differentiation among 13 clam populations along the coast of China. As a result, 150 alleles were detected according to the genotyping results of eleven microsatellite loci. The observed heterozygosity (Ho) was estimated to be ranging from 0.437 to 0.678, while the expected heterozygosity (He) was calculated to be varying from 0.587 to 0.700. Fst values between populations ranged from 0.0046-0.1983. In particular, the Laizhou population had the highest genetic variability, which was significantly different from the others (all Fst values > 0.1). For all the clam populations, there was no significant linear regression between genetic and geographic distance, indicating that these populations do not follow a pattern of isolation by distance (IBD). Genetic structure was estimated according to NJ, principal coordinates (PCoA), and structure-based clustering. Estimates of effective population size range from dozens to thousands among different populations, based on linkage-disequilibrium and molecular coancestry methods. The results reveal the genetic diversity of clams and verify the hypothesis that clam population differentiation may be influenced by the mode of southern breeding and northern culture, providing guiding information for natural resource conservation and genetic breeding of clams.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Population Genetics of Manila Clam (Ruditapes philippinarum) in China Inferred from Microsatellite Markers

Zheng

Zhang

et al. 2023

Biology

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“…A possible explanation for this is that clam seeds’ transplantation among different culture regions may serve as the main contributor for the genetic homogeneity. In recent decades, a large number of clam seeds produced in southern China have been transferred to different culture regions in northern China [ 47 , 48 ]. For R. philippinarum , the mode of southern breeding and northern culture may increase the gene flow of clams, resulting in low genetic differentiation between northern and southern populations [ 24 , 25 , 40 , 47 ].…”

Section: Discussionmentioning

confidence: 99%

Genetic and Haplotype Diversity of Manila Clam Ruditapes philippinarum in Different Regions of China Based on Three Molecular Markers

Wei,

Zheng,

Wang

et al. 2023

Animals

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China has the largest production yield of Manila clam Ruditapes philippinarum in the world. Most of the clam seeds for aquaculture are mainly derived from artificial breeding in southern China, likely resulting in the loss of genetic variation and inbreeding depression. To understand the genetic and haplotype diversity of R. philippinarum, 14 clam populations sampled from different regions of China were analyzed by three molecular markers, including COI, 16SrRNA and ITS. Based on the results of the COI and ITS genes, the 14 populations showed a moderate to high level of genetic diversity, with an average haplotype diversity of 0.9242 and nucleotide diversity of 0.05248. AMOVA showed that there was significant genetic differentiation among all populations (mean FST of the total population was 0.4534). Pairwise FST analysis showed that genetic differentiation reached significant levels between Laizhou and other populations. Two Laizhou populations showed great divergence from other populations, forming an independent branch in the phylogenetic tree. The shared haplotypes Hap_2 and Hap_4 of COI appeared most frequently in most clam populations. In contrast, 16SrRNA analysis of the clam populations revealed the dominated haplotype Hap_2, accounting for 70% of the total number of individuals. The haplotype diversity of the Laizhou population (Laizhou shell-wide (KK) and Laizhou dock (LZMT)) was relatively higher than other populations, showing multiple unique haplotypes (e.g., Hap_40, Hap_41 and Hap_42). These findings of genetic and haplotype diversity of clam populations provide guiding information for genetic resource conservation and genetic improvement of the commercially important R. philippinarum.

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“…Genetic diversity parameters of each geographic population, including the observed number of alleles, effective number of alleles, Nei’s diversity index, Shannon’s information index, total gene diversity, intrapopulation gene diversity, the coefficient of gene differentiation, and gene flow [ 41 ], were calculated using POPGENE 32 (version 1.32) [ 42 ]. The NTSYS-pc (version 2.0) software was used to calculate the genetic similarity coefficient [ 43 ].…”

Section: Methodsmentioning

confidence: 99%

Development of Simple Sequence Repeat Markers and Genetic Diversity Evaluation of Mycocentrospora acerina in Yunnan Province, China

Wang,

Yang,

Huang

et al. 2023

JoF

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Round spot is a destructive disease that limits of Panax notoginseng production in China. However, the genetic diversity of its etiological agent Mycocentrospora acerina has yet to be studied. In this work, firstly, we developed 32 M. acerina polymorphic microsatellite markers using MISA and CERVUS 3.0 and selected 14 for further analysis. Then, we studied the genetic diversity of 187 isolates collected from P. notoginseng round spot using simple sequence repeat markers and polyacrylamide gel electrophoresis. The genetic diversity ranged from 0.813 to 0.946, with 264 alleles detected at the 14 microsatellite loci. The expected average heterozygosity was 0.897.

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Genetic diversity analysis of different age of a Dalian population of the Manila clamRuditapes philippinarumby EST-SSR

Abstract: Genetic diversity analysis of different age of a Dalian population of the Manila clam Ruditapes

Cited by 4 publications

References 3 publications

Population Genetics of Manila Clam (Ruditapes philippinarum) in China Inferred from Microsatellite Markers

Population Genetics of Manila Clam (Ruditapes philippinarum) in China Inferred from Microsatellite Markers

Genetic and Haplotype Diversity of Manila Clam Ruditapes philippinarum in Different Regions of China Based on Three Molecular Markers

Development of Simple Sequence Repeat Markers and Genetic Diversity Evaluation of Mycocentrospora acerina in Yunnan Province, China

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