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. 2020 Nov 3;38(3):1122–1136. doi: 10.1093/molbev/msaa279

Fig. 2.

Fig. 2.

Identification of the LINE-1 insertion in ASIP of white buffaloes. (A) Significantly higher expression of ASIP in white buffalo skin (W1, W2, and W3) than in black buffalo skin (B1, B2, and B3) revealed by RNA-seq and qPCR. Three experimental replicates of qPCR are shown separately (qPCR1, qPCR2, and qPCR3). (B) Distinct transcripts assembled from RNA-seq data of skin samples of white (blue) and black (red) buffaloes. (C) Full-length transcripts of ASIP generated using the RACE-PCR and characterization of the LINE-1 insertion in the white buffalo ASIP. The structure of a full-length LINE-1 element from cattle (L1-BT; Girardot et al. 2006) is shown as reference. (D) Schematic representation showing the chromosomal position of the LINE-1 insertion determined by soft-clipped reads analysis and the partial sequences of the LINE-1 insertion obtained by de novode novo assembling of the soft-clipped reads. (E) Genotyping the LINE-1 insertion using the allele-specific PCR and its perfect association with white coat phenotype. PCR products of wild allele (Normal; 296 bp) and mutant allele (Ins; 387 bp) are separated for six samples (S1−S6) using agarose gel electrophoresis.