# Phenotype of White Sika Deer Due to SCF Gene Structural Variation
## 3 Results
### Analysis of SCF Genotype and Phenotype in White Sika Deer Family  
In the family atlas of white sika deer (Figure 3a), the maternal (F), paternal (D), and grandfather's (C) faces all had white spots, whereas the remainder (E, G, and H) had normal phenotypes. The electrophoresis chart (Figure 3(b1)) showed that the control (A) had primer amplification bands of SCF-2, SCF-3, and SCF-4, as well as of SCF-1, but the size of the bands did not match; thus, SCF-1 could not be amplified normally. The information on primer positions is shown in the Figure 3 (b2). The mutant group (B, white sika deer) had SCF-1 amplification bands, but no SCF-2, SCF-3, and SCF-4 amplification bands. According to the family map and genotype analysis (Table 2), it was found that the individual genotypes of C, D, and F were heterozygous (SCF789/SCF1-9), and their coat  
\begin{table}
\begin{tabular}{c c c c c} \hline \hline
**Genes** & **AF** & **Mutation Position** & **Chromosome** & **Type** \\ \hline CIITA & 0.819079 & exon10:c.C1209T:p.S403S & MHL\_chr10 & Synonymous SNV \\ CIITA & 0.8125 & exon10:c.C1644T:p.S548S & MHL\_chr10 & Synonymous SNV \\ AP3B1 & 0.9471831 & exon23c:A2754G:p.O918Q & MHL\_chr12 & Synonymous SNV \\ ICAT & 0.822368 & exon2:c.C268G:p.P90A & MHL\_chr14 & Nonsynonymous SNV \\ LYST & 0.832237 & exon9:c.C166T:p.S556L & MHL\_chr15 & Nonsynonymous SNV \\ HPS3 & 0.834507 & exon9:c.G1590A:p.A530A & MHL\_chr19 & Synonymous SNV \\ GSK3-ß & 0.835526 & exon10:c.G1047A:p.L349L & MHL\_chr19 & Synonymous SNV \\ DKK3 & 0.888158 & exon4:c.G510A:p.P170P & MHL\_chr1 & Synonymous SNV \\ DKK3 & 0.9205298 & exon4:c.G5137C:p.C17C & MHL\_chr1 & Synonymous SNV \\ EPG5 & 0.9276316 & exon11:c.C217T:P70P & MHL\_chr27 & Synonymous SNV \\ EPG5 & 0.9337748 & exon27:c.A4762G:p.S1588G & MHL\_chr27 & Nonsynonymous SNV \\ EPG5 & 0.807947 & exon29:c.C5040T:p.D1680D & MHL\_chr27 & Synonymous SNV \\ EPG5 & 0.9342105 & exon32c.T5643C:p.V1881V & MHL\_chr27 & Synonymous SNV \\ TYRP1 & 0.838816 & exon10:c.C137T:p.S46F & MHL\_chr29 & Nonsynonymous SNV \\ WRN & 0.809211 & exon12c.T1529C:p.I510T & MHL\_chr32 & Nonsynonymous SNV \\ SLC38A8 & 0.894737 & exon1:c.C24T:p.GS & MHL\_chr4 & Synonymous SNV \\ SLC38A8 & 0.888158 & exon67c.C696T:p.H232H & MHL\_chr4 & Synonymous SNV \\ HPS4 & 0.9212329 & exon9:c.G813A:p.A271A & MHL\_chr5 & Synonymous SNV \\ VPS33A & 0.886986 & exon6:c.G735T:p.T245T & MHL\_chr5 & Synonymous SNV \\ SCF & - & c.16444201-16454300 & MHL\_chr3 & CNV \\ \hline \hline \end{tabular}
\end{table}
Table 1: Mutant genes information.  
color phenotypes were normal except for white patches on their faces. Genotypes E, G, and H were consistent with that of A (SCF1-9/SCF1-9), and the coat color phenotype was normal. The genotype of the white sika deer (B) was homozygous (SCF789/SCF789), and its coat color phenotype was snow white.  
Figure 3: (**a**) Genetic atlas of the white sika deer family. (**b1**) Electrophrogram: A (control); B–H (individual deer corresponding to Figure 3a). Primer amplification positions corresponded to Figure 3(b2). (**b2**) Location of exons and amplification regions of the SCF gene, along with the mutation regions (dashed areas), in sika deer. (**b3**) Sequence comparison.  
Figure 2: (**A**): HE staining of coat follicle sections: normal (upper); white (below). (**B**) L-DOPA staining: normal (upper); white (bottom).