Fig 1.
Geographic illustration of the six indigenous cattle breeds collected in Sichuan Province, China.
The two-letter abbreviations for every breed are defined in the main text. Please note that this map was created by the authors and is intended for illustrative purposes only.
Fig 2.
SNP calling and statistical metrics.
The call rates of SNPs (A) were first revealed among 55 samples after our hard filtering. The per-site coverage depth of reads was compared among SNPs derived from chromosomes and unanchored contigs (B). The density distributions among 30 chromosomes (C) and substitution types (D) are illustrated. The bin size in (C) was set to 0.2 M for counting SNPs.
Fig 3.
The frequencies of minor alleles for known and novel SNPs (A). Density distribution of nucleotide diversity (π) and polymorphism information content (PIC) for all SNPs (B).
Table 1.
Overview of genetic diversity within each breed.
Fig 4.
Genetic structure among the six populations.
The matrix (A) shows the pairwise Wright’s FST values in the lower triangular area and FIS values in diagonal cells. The IBS distance-based multidimensional scaling plot of 55 samples is shown in (B).