Aquaculture development in China has been well linked with common carp, whose origins are in Asia, and a freshwater aquatic species belonging to the Cyprinidae family. However, many genetic transformations have been done on these species strains for resistance against disease, food convection and utilization, faster growth, and becoming one of the most important species in the world for food with many strains and varieties in different parts of the world [1, 2, 3]. This species is well known in the aquaculture history of China and has helped combat food security issues, which in the past few years fish farmers in the country have embraced due to its fast growth and delicious taste [4]. The history of aquaculture development through advanced technology cannot be completed with this popular species, for which the Chinese have developed a lot of cultured systems, including the aquarium, and the strains of these species are now in large numbers worldwide as a result of their cultural history and domestication [5]. Additionally, China is known for having seven (7) more different strains than any other place in the world, the population of common carp strains has been copied numerous times through domestication in China. Likewise, the common carp strain has undergone a number of well-known genomic editing-based modifications by many researchers in China, including the following: Huanghe carp (HH): Genome-wide Identified Main Quantitative Trait Locus Related to Growth Performance of Huanghe Carp New Strain (Cyprinus carpio hacmalopterus), Oujiang color carp (OJ), Hebao red carp (HB), Songpu mirror carp (SP), Xingguo red carp (XC), and Genome-wide Identified Main QTL Related [6, 7]. In order to optimize the profit of cultured farmers, continuity in population, environmental protection and conservation, and disease prevention through resistance strain development, all this genetic diversity is created on common carp strains utilizing a variety of technologies. The common strain black carp (Cyprinus carpio var. baisenensis) from Guangxi has a history with the local Bourau people, who prefer the black color, and its sub-species color reflects the interaction between the Bourau and their surrounding environment [8]. In addition, many characteristics of these species have been linked to places of origin. This species has very unique features that make it affiliated with this place, and its selection as it is cultured in an integrated rice system helps prevent continuous flooding.
In order to manage and conserve black carp utilizing cutting-edge genetic improvement tools, it is crucial to understand their genetic diversity and genetic structure. However, the precise population genetic patterns of both freshwater and marine species may not be revealed by conventional markers. Advanced high-throughput sequencing, however, can genotype hundreds of markers on a genome-wide scale and offer a solution to this problem [9]. The genetic makeup of common carp populations and the genetics of environmental adaptability are discussed in regard to the findings of Xu et al. [10] on population genomics investigation of C. carpio utilizing high-throughput SNP genotyping of 2,198 individuals from 14 populations worldwide. Gene ontology and KEGG enrichment analysis, however, showed probable trait-related loci and genes linked to body form, scaling patterns, and skin color. These studies also revealed genes inside selective sweep regions that were discovered by genome scanning among the various ethnicities. SNPs have been employed in other fish species to examine population structure and the impacts of natural and artificial selection at the genome size and can increase the resolution of the differentiation of genetic stocks. (SNP) genotyping was utilized because, in contrast to simple sequence repeats (SSRs), it allows for cost-competitive genotyping of large samples, has universal applicability and dependability for Cyprinus species, and offers a high-throughput genotyping method for common carp genetics. SNPs make up the majority of stable genetic variation seen in genomes [11, 12]. However, SNPs that are frequently found in a gene or in a regulatory area serve as biological markers for genes that have been identified as being connected with significant attributes [13]. In light of this, the information gleaned from this study, particularly the molecular data, such as the genome-wide genetic diversity of the Common Carp Black Strain, would help to provide more thorough insights into the evolutionary biology and conservation biology of these species. According to the findings of this investigation, all samples had an average of 143,920,978 raw readings and 142,579,732 clean readings (Table 1).
Similar to this, an average effective rate of 99.07% was achieved when 42.77 GB of 66 clean bases were produced from 43.18 GB of raw bases. The GC content is 38.52%, and the Q20 and Q30 were 97.52% and 93.18%, respectively. Thus, a total of 216,881,016.9 average reads were successfully mapped to the common carp genome after mapping (Table 2), with a mapping rate of 97.23%. The average depth was 20.12, and 68.06% of the reads had coverage of at least 4X.