Genome-wide genetic diversity of the Common Carp Black Strain (Cyprinus carpio var. baisenensis)

Abstract

Abstract The black strain of common carp (Cyprinus carpio var. baisenensis) is known for its black skin and is one of the key strains of common carp cultured in the integrated rice-agriculture system, as well as a non-escape property under torrential floods. The common carp black strain, Huanghe carp, and Songpu carp were collected and re-sequenced for SNP-based research using three techniques. Quality control was performed, and UCSC-known genes were used to annotate genes and regions in the genome. The average raw reads of 143,920,978 were separated from the average 142,579,732 clean reads with an average effective rate of 99.07%, where the total number of SNPs was 264,39902, with 62,855 in the 1 kb upstream region and 63,553 in the 1 kb downstream region. The common carp black strain's mean Tajima D values were 3.304, compared to 2.266 for other common carp black strains. Due to mutations and the size of its population, the common carp black strain had a higher number of Tajima "D" values.