DOI: 10.21776/ub.jiip.2023.033.02.09 217
Identification of the Membrane-Associated Transporter Protein (MATP) Gene Polymorphism as Candidate Mutation for Albinism in Japanese
Quail
Laksita Haniifah Pratiwi1), Ratih Dewanti1) and Muhammad Cahyadi*1,2)
1) Faculty of Animal Science, Universitas Sebelas Maret, Surakarta, Jawa Tengah 57126, Indonesia
2) Halal Research Center and Cervices (HRCS), Institute for Research and Community Service, Universitas Sebelas Maret, Surakarta, Jawa Tengah 57126, Indonesia
Submitted: 28 April 2023, Accepted: 08 August 2023
ABSTRACT: A pigmentation abnormality could be due to genetic mutation and trigger a disease related pigmentation deficiency such as albino which might be caused by mutation in membrane-associated transporter protein gene (MATP). The aim of this study was to identify polymorphism in the MATP exon 3 in Japanese quail. A total of nine Japanese quail consisting three brown plumage quail, three black plumage quail, and three albino quail were used in this study. Blood samples were used to extract the genomic Deoxyribonucleic acid (DNA) and used to amplify exon 3 regions of the MATP by polymerase chain reaction (PCR). The PCR products were then sequenced and analyzed. A total of 10 mutations were found, of which three mutations, g.4460G>A, g.4479G>A, and g.4514T>C, were within exon 3. These mutations were synonymous and non-synonymous. No specific mutation for albino was found in this study. In summary those mutations did not specifically determine albinism in Japanese quail.
Keywords: Albino; DNA sequencing; Japanese quail; MATP; Mutation
*Corresponding Author: [email protected]
DOI: 10.21776/ub.jiip.2023.033.02.09 218 INTRODUCTION
Japanese quail (Coturnix coturnix japonica) is a type of poultry that is widely raised as a producer of eggs and meat (Mokhtarzadeh et al., 2022). Brown and black plumage colors are two common colors that are often found in Japanese quails in Indonesia. The phenotype that is commonly found in nature is known as the wild-type (Clark et al., 2019). The color difference is influenced by the type and quantity of melanin pigment that is produced by melanocytes in melanosomes (Bastonini et al., 2016) and will be transferred to keratinocytes by dendritic processes (Zonunsanga, 2015).
Pigmentation is a complex trait controlled by a series of genes (Deng and Xu, 2018). Examples of genes involved in the pigmentation process include, MC1R, TPCN2, ASIP, KITLG, NCKX5, TYR, IRF4, OCA2, MATP, and TYRP1 (Ibarrola-villava et al., 2012). Mutations or commonly called changes in genetic material in these genes can cause disruption of the pigmentation process, causing diseases such as melasma, vitiligo, or albino which are inherited to their offspring. Previous studies reported that mutations within MATP may cause albinism in Medaka fish species (Fukamachi, Shimada, and Shima, 2021), human (Newton et al., 2001), mouse/rat (Du and Fisher, 2002), long haired dog (Wijesena and Schmutz, 2015), quail and chicken (Gunnarsson et al., 2007), and also several types of horses (Holl et al., 2019).
The MATP consists of seven exons and encodes a membrane-associated transporter protein (Bibi et al., 2020). The role of the MATP is to help transfer melanin pigment and maintain pH using the help of protons (Sengupta, Dutta, and Ray, 2019).
Under normal conditions, a constant pH helps copper (Cu) to bind Apo-Tyrosinase so that it becomes active tyrosine (Bin et al., 2015). Tyrosine serves as a starting material in the melanin synthesis process (Zhou and Sakamoto, 2020). Malfunction of the MATP can cause the acidity of the melanosomal membrane to be disrupted resulting in errors
in tyrosine binding (Tóth et al., 2017). As a result, the production of melanin also changes. Excess and deficiency of melanin can cause abnormalities that indicate disease (Lee, 2021). Albino is a congenital disease in which there is an absence of some or all of the pigment of the eyes, skin and hair (Kamilah et al., 2021). In quail, the disease has the potential to interfere with the eyes which is one of the quail vital organs in activities (Cornil, 2018). Previous research conducted by Gunnarsson et al. (2007) stated that albino cases in quail may be due to transversion of guanine (G) to thymine (T) at the boundary of intron 3 and exon 4 in the MATP. This mutation caused in-frame exon skipping, namely splice acceptor site.
In order to find other candidates for albino mutations in Japanese quail, this study was conducted to explore the exon 3 region of the MATP. Polymorphism identification is intended to determine genetic variation (Jin et al., 2018). Therefore, the objective of this study was to explore novel polymorphisms of the MATP as candidate of causative mutations for albinism in Japanese quail.
MATERIALS AND METHODS Materials
The materials used in this study were chemical reagents and nine blood samples of three different plumage colors of quail i.e., brown, black and albino (Figure 1) collected from samples at the Jatikuwung experimental farm, Department of Animal Science, Faculty of Agriculture, Universitas Sebelas Maret. Chemical reagents for laboratory analysis included Wizard®
Genomic DNA Purification Kit (Promega, USA), ethanol 70% for analysis, isopropanol, Taq PCR Master Mix Kit (Qiagen, Singapore), novel forward and reverse primers, nuclease free water, lambda DNA marker, bench top 100 bp marker ladder, tris acetate ethylene diamine tetraacetic acid (TAE) 1X, DNA loading dye, florosafe DNA stain, agarose gel, ziplocked plastic, plastic wrap, aluminium foil, parafilm (Bemis, USA), aquadest, aquabidest (ddH2O), and ethanol 70%.
DOI: 10.21776/ub.jiip.2023.033.02.09 219 Figure 1. Wild types and albino Japanese quail. Brown plumage quail (a) Black plumage
quail (b) Albino quail (c) The equipment used in this study was
sharp knife, sample tubes containing EDTA (Becton Dickinson, Plymouth, UK), microcentrifuge (Hettich Zentrifugen Micro 22R, German), cooler box, analytical balance (I-2000, China), incubator (Binder, German), 0.2 and 1.5 ml microtube, micropipette, micropipette rack, pipette tips, falcon tube, falcon tube rack, erlenmeyer (Duran, West German), PCR thermal cycler machine (GeneAmp® PCR System 9700, Singapore), microwave (Samsung, South Korea), electrophoresis machine (Mupid- exU®, Japan), gel documentation machine (Glite UV Gel Documentation System, Taiwan), and vortex (VM 300, Gemmy Industrial Corp, Taiwan).
Methods
Blood sample collection
Blood samples were obtained from the process of slaughtering nine quails. A total of 3 ml of blood from each quail was collected using sample tubes containing EDTA anticoagulant. The nine sample tubes were then stored at -21oC for further DNA isolation.
Extraction of DNA
The DNA extraction was carried out using blood samples according to the research procedure of Adimaka et al. (2019) which refers to the standard of the Wizard Genomic DNA Purification Kit for bloods (Promega, USA). First, the workbench and equipment to be used in laboratory activities were sterilized using alcohol to prevent contamination. Then, the blood sample in the EDTA tube was thawed and homogenized using a vortex. Each blood sample was taken as much as 20 µl using a
micropipette and put into a 1.5 ml microtube. In each microtube, 900 µl of red blood cell lysis solution was added and homogenized for 5-10 seconds. The samples were then incubated at 37°C for an hour and then centrifuged at 14,000 rpm for 20 seconds using a microcentrifuge to separate the supernatant liquid and pellets. The supernatant liquid was then removed so that only pellets were left, then 300 µl nuclei lysis and 100 µl protein precipitation solutions were added. Then the sample was homogenized for 10 seconds, then centrifuged again at 14,000 rpm for 3 minutes.
In the next step, the supernatant was transferred to a new 1.5 ml microtube and 300 µl isopropanol was added, then homogenized for 10 seconds and centrifuged again at 14,000 rpm for a minute. The supernatant was then discarded and given 300 µl 70% ethanol for analysis, then homogenized for 10 seconds and centrifuged at 14,000 rpm for a minute. The supernatant liquid was then discarded, then the microtube was drained at room temperature for 10 to 15 minutes until dry.
In the final stage, 100 µl of DNA rehydration solution was added to the tube and vortexed for 10 seconds, then incubated at 65°C for an hour. The genomic DNA was observed using the 2% agarose gel electrophoresis stained by Fluorosafe DNA stain on gel documentation system. Lambda DNA marker was used as DNA band standard size.
Amplification of the exon 3 of the MATP In the initial stage before carrying out the polymerase chain reaction (PCR)
DOI: 10.21776/ub.jiip.2023.033.02.09 220 process, primer design was carried out using
the primer3. Primers were designed based on Japanese quail sequences obtained from the National Center for Biotechnology
Information (NCBI) with accession number (NC_029547.1). The details of primer pair, target region, annealing temperature, and PCR product size are shown in Table 1.
Table 1. Primer pair targeting the exon 3 of the MATP in Japanese quail
Primer Oligonucleotide (5’-3’) Ta (oC) Target
region
Product size
F ACG GCT CTT ACC AGA CCT GA 60 Exon 3 671 bp
R TGT GCG TGT GAA AGG ACT CT
Ta is annealing temperature; F is forward primer; R is reverse primer; bp is base pair
The total volume of PCR was 25 μl which is composed of 22 μl Taq PCR Master Mix Kit, 1 μl forward primer, 1 μl reverse primer, and 1 μl DNA template. The number of PCR cycles used was 35 cycles. The PCR step started with the pre-denaturation at 94°C for 3 minutes and was followed by the denaturation at 94°C for 30 seconds. The next step was annealing at 60°C for 30 seconds and extension at 72°C for a minute.
The PCR program ended with a final extension at 72°C for 10 minutes.
The PCR results were then observed using 2% agarose gel electrophoresis stained with 2 µl of fluorosafe DNA stain for observing in the gel documentation system.
A 100 bp marker ladder was used as a DNA band standard size. The PCR results confirmed that the primer pair attached to the appropriate targeting MATP, then the sequencing process was carried out using the Sanger method at 1st BASE DNA Sequencing Division.
Data Analysis
Analysis of MATP sequences was carried out using several software such as
BioEdit, MEGA.v.7, DnaSP.v.6, and Clustal Omega. The sequence alignment process was carried out by using Clustal Omega by comparing MATP and reference sequences.
Polymorphisms found within the MATP sequences were then cross-checked using the Bio Edit software by observing nucleotide chromatograms. In addition, the value of genetic diversity and haplotype diversity (Hd) were analyzed using MEGA.v.7 and DnaSP.v.6 software.
RESULTS AND DISCUSSION Extraction of DNA
Nine samples of quail blood were extracted to obtain genomic DNA. The function of DNA extraction is to separate DNA from various other components in cells such as proteins, polysaccharides, phenolic compounds, and ribonucleic acid (RNA) (Sulassih and Santosa, 2020). The results of DNA extracted in this study showed that genomic DNA was successfully extracted which is indicated by thick and bright DNA bands (Figure 2).
Figure 2. Genomic DNA extracted from blood samples of Japanese quail visualized in 1%
agarose gels The higher the DNA concentration
shows thicker and brighter DNA bands and
vice versa. However, smears were also found in genomic DNA of this study. Setiati,
DOI: 10.21776/ub.jiip.2023.033.02.09 221 Partaya, and Hidayah (2020) reported that
the presence of stains (smears) in the visualization of the results of DNA extraction could be caused by fragmented genomic DNA or the presence of RNA contamination.
Amplification of the MATP
Amplification of the MATP exon 3 was conducted as a novel primer pair. Good quality genomic DNA which was successfully extracted previously was used as a template for PCR. The PCR products from the nine quail samples used in the study showed good results indicated by thick and bright PCR products. Farmawati, Wirajana, and Yowani (2015) stated that DNA quality affects the thickness of PCR products.
Moreover, the PCR product size was matched with the expected size which is 671 base pairs (bp) as shown in Figure 3. In the PCR, apart from the quality of DNA template, another main ingredient is needed, namely a primer pair. The success of the PCR process is determined by the ability of the primers to detect specific sequences within the genomic DNA. It is supported by the evidence that primer pairs hybridized to the specific target (Chuang et al., 2013). In addition, Lorenz (2012) explained that not unique or less specific primers produce nonspecific PCR products which are indicated by more than one PCR product sizes appearing on the agarose gel electrophoresis.
Figure 3. The PCR products targeting MATP exon 3 of Japanese quail
Identification of the MATP polymorphisms
Identification of the MATP polymorphisms among samples was carried out by DNA sequence alignment.
Sequences of the MATP of nine Japanese quail in this study were submitted to the genebank database with accession number OQ161196 to OQ161204. Those sequences along with a reference sequence (NC_029547.1) were analyzed to identify variations among samples. Huang, Shah, and Yao (2019) explained that sequence alignment aims to identify similarities between one or more sequences. Similar parts of an individual can occur as a result of evolutionary relationships (Wiltgen, 2018).
The sequence alignment results showed three graphical changes in exon positions, namely, g.4460G>A, g.4479G>A, and also g.4514T>C. Each nucleotide base has a different shape and color on the chromatogram graph, so changes in the chromatogram also indicate changes in nucleotide bases (Figure 4).
Chakraborty and Bandyopadhyay (2013) stated that if two aligned sequences have the same ancestor, the occurrence of a mismatch can be interpreted as a mutation.
Mutations indicated by single nucleotide changes (A, T, C, or G) are also called single nucleotide polymorphisms (SNP) and are associated as point mutations (Lusiastuti et al., 2015). Mutations are defined as changes that occur in an
DOI: 10.21776/ub.jiip.2023.033.02.09 222 organism's sequence (Fitzgerald and
Rosenberg, 2019). Changes in a nucleotide base can transform the amino acid composition of a protein, causing phenotypic variations and disease (Pei et al., 2020). Mutations that are expressed by genes and manifest as a phenotype are actually mutations of the coded DNA sequence (exon) because the translation of mRNA into functional protein or the
process of gene expression (Slobodin et al., 2017) requires mature mRNA. The formation of mature mRNA is obtained through the process of removing introns from the mRNA precursor so that exons can join (splicing) and form the mature mRNA (Wilkinson, Charenton, and Nagai, 2020).
Exploration of mutations in the exon 3 region of the MATP in nine samples of Japanese quail is shown in Table 2.
Figure 4. Mutations found within MATP exon 3 in Japanese quail. g.4460G>A (a).
g.4479G>A (b). g.4514T>C (c)
DOI: 10.21776/ub.jiip.2023.033.02.09 223 Table 2. Nucleotide mutations of the MATP in Japanese quail
No. Name Nucleotide
change
Location AA change Mutation
1. g.4100G>A Substitution Intron 2 2. g.4125C>T Substitution Intron 2 3. g.4230A>G Substitution Intron 2 4. g.4272C>A Substitution Intron 2 5. g.4301C>T Substitution Intron 2
6. g.4460G>A Substitution Exon 3 CCG>CCA Synonymous mutation (Pro (P)>Pro)
7. g.4479G>A Substitution Exon 3 GAC>AAC Non-synonymous (Asam aspartate /Asp (D) > Aspargarin/Asn (N) 8. g.4514T>C Substitution Exon 3 ACT>ACC Synonymous (Threonine/Thr (T) 9. g.4651C>T Substitution Intron 3
10. g.4662C>A Substitution Intron 3 AA is amino acid
Mutations were found in ten locations with details of three mutations located in exons and the others located in introns.
Nucleotide base substitutions (g.4479G>A and g.4514T>C) that occurred in the three types of Japanese quail samples (albinos, brown and black plumage quail) were a form of transitional mutation where substitution occurs between purine bases (A and G) or pyrimidine bases (C and T) (Aloqalaa et al., 2019). Another change in the exon region occurred in g.4460G>A and only occurred in black plumage quail. Moreover, the results showed that there were two types of mutations that corresponded to amino acid products, namely synonymous and nonsynonymous mutations. Mutations at position g.4460G>A cause a change in the CCG>CCA codon with a fixed amino acid, namely proline. The same mutation occurs at position g.4514T>C (ACT>ACC) which produces a fixed amino acid, namely threonine.
Mutations that only affect DNA and mRNA, and do not cause changes in amino acids are known as synonymous mutations or silent mutations (Sharma et al., 2019).
Meanwhile, nonsynonymous mutations or missense mutations are changes that occur in both the nucleotide bases and the resulting amino acids (Pires et al., 2016). This mutation occurs at position g.4479G>A, where the codon GAC>AAC causes the change of the amino acid aspartic acid (ASP) to asparagine (ASN). The emergence
of the disease can be made possible by both types of mutations, where synonymous mutations can affect the splicing process and mRNA stability (Zhang et al., 2017).
Meanwhile, nonsynonymous mutations have the potential to cause dysfunction or protein instability (Torgerson and Ochs, 2014).
Haplotype of the MATP in Japanese quail Total of 10 nucleotide variations identified in this study were then classified into several haplotype groups. The existence of haplotype groups illustrates the diversity that occurs in a population (Fakhri, Narayani, and Mahardika, 2015).
Haplotypes that are passed onto offspring function as genetic markers for certain diseases (Rusnita, 2015). The haplotype groups and nucleotide variations obtained from nine quail samples are shown in Table 3. Six haplotypes were obtained from the nine quail samples.
The first haplotype group was shown by black plumage quail sample number 40, where the sample had no difference in nucleotide bases from the quail reference sequence from NCBI. The second haplotype was spread over four samples of quail with details of the three albino quails and a brown plumage quail number 17. In addition, there was a brown plumage quail (sample number 15) which shows the form of haplotype 3, a brown plumage quail (sample number 16) as fourth haplotype group, a black plumage quail (sample number 37) as the fifth
DOI: 10.21776/ub.jiip.2023.033.02.09 224 haplotype group, and the sixth haplotype
group was shown by black plumage quail sample number 39.
In the third haplotype, the identified sample was not only the albino quail sample, but also the wild-type quail sample. This shows that the exon 3 region of the MATP
has a low specific level to be used as a marker for albinism in Japanese quail. The haplotype diversity (Hd) value of this study was 0.8444. Kusumaningrum, Sutopo, and Kurnianto (2020) stated that the haplotype diversity value between 0.5 - 1 is included in the high category.
Table 3. Haplotype of the MATP polymorphism
Haplotype Sample N
Nucleotide variaton 0
3 5
0 6 0
1 6 5
2 0 7
2 3 6
3 9 5
4 1 4
4 4 9
5 8 6
5 9 7
1 Reference, 40B 2 G C A C C G G T C C
2 15C 1 . T G . T . . . . A
3 M1, F, M2, 17C 4 A T G . . . A C T A
4 37B 1 A T G . . . A C T .
5 16C 1 . T G A . . . C . .
6 39B 1 A T G . . A . C . .
N is number of samples
The higher the haplotype value, the higher the level of genetic diversity that occurs among the population (Hendiari et al., 2020). A high level of genetic diversity can be caused by crossbreeding events between quail sample parents in the wild resulting in offspring that are not pure wild- type or albino.
CONCLUSION
Identification of polymorphisms in the exon 3 region of the MATP from Japanese quail obtained a total of 10 genetic variations with 3 mutations in the exon, namely position g.4460G>A, g.4479G>A, and g.4514T>C. Mutations observed were transitional with two types of mutations, namely synonymous and nonsynonymous mutations. The results of this study did not find any specific mutation of albino quails so that the exon 3 region of the MATP cannot specifically determine albinism in Japanese quail.
ACKNOWLEDGEMENT
The authors would like to convey gratitude to the Institute for Research and Community Service of Universitas Sebelas Maret (LPPM-UNS) for the research funding with grant ID number 00240386013892023.
REFERENCES
Adimaka, N., Rifki, M., Dewanti, R., &
Cahyadi, M. (2019). Keragaman genetik puyuh Jepang (Coturnix japonica) berdasarkan analisis sekuen DNA mitokondria gen Cytochrome-b Genetic diversity of Japanese quails (Coturnix japonica) based on complete sequence of mitochondrial DNA Cytochrome-b gene. Jurnal Ilmu-Ilmu Peternakan, 29(2), 143- 151. https://doi.org/10.21776/ub.jiip.
2019.029.02.05.
Aloqalaa, D. A., Kowalski, D. R., Blazej, P., Wnetrzak, M., Mackiewicz, D., &
Mackiewicz, P. (2019). The impact of the transversion/transition ratio on the optimal genetic code graph partition.
In BIOINFORMATICS (pp. 55-65).
https://doi.org/10.5220/00073810005 50065.
Bastonini, E., Kovacs, D., & Picardo, M.
(2016). Skin pigmentation and pigmentary disorders: focus on epidermal/dermal cross-talk. Annals of dermatology, 28(3), 279-289.
https://doi.org/10.5021/ad.2016.28.3.
279.
Bibi, N., Ullah, A., Darwesh, L., Khan, W., Khan, T., Ullah, K., & Umm-e- Kalsoom. (2020). Identification and
DOI: 10.21776/ub.jiip.2023.033.02.09 225 computational analysis of novel TYR
and SLC45A2 gene mutations in pakistani families with identical non- syndromic oculocutaneous albinism.
Frontiers in Genetics, 11, 749.
https://doi.org/10.3389/fgene.2020.00 749.
Bin, B. H., Bhin, J., Yang, S. H., Shin, M., Nam, Y. J., Choi, D. H., Shin, D. W., Lee, A. Y., Hwang, D., Cho, E. G., and Lee, T. R. (2015). Membrane- associated transporter protein (MATP) regulates melanosomal pH and influences tyrosinase activity. PLoS One, 10(6), e0129273.
https://doi.org/10.1371/journal.pone.0 129273.
Chakraborty, A., & Bandyopadhyay, S.
(2013). FOGSAA: Fast optimal global sequence alignment algorithm.
Scientific reports, 3(1), 1746. https://
doi.org/10. 1038/srep01746.
Chuang, L. Y., Cheng, Y. H., & Yang, C. H.
(2013). Specific primer design for the polymerase chain reaction.
Biotechnology letters, 35, 1541-1549.
https://doi.org/10.1007/s10529-013- 1249-8.
Clark, D. P., Pazdernik, N. J., & McGehee, M. R. (2019). Basic genetics.
Molecular Biology; Elsevier:
Amsterdam, The Netherlands, 38-62.
https://doi.org/10.1016/b978-0-12-81 3288-3.00002-1.
Cornil, C. A. (2018). The organization and activation of sexual behavior in quail.
In model animals in
neuroendocrinology: from worm to mouse to man (1st ed.) USA: John Wiley & Sons Ltd. https://doi.org/
10.1002/9781119391128.ch6.
Deng, L., & Xu, S. (2018). Adaptation of human skin color in various populations. Hereditas, 155(1), 1-12.
https://doi.org/10.1186/s41065-017-0 036-2.
Du, J., & Fisher, D. E. (2002). Identification of Aim-1 as the underwhiteMouse Mutant and Its Transcriptional Regulation by MITF. Journal of
Biological Chemistry, 277(1), 402- 406. https://doi.org/10.1074/jbc.M11 0229200.
Fakhri, F., Narayani, I., & Mahardika, I. G.
N. K. (2015). Genetic diversity of skipjack tuna (Katsuwonus pelamis) from Jembrana and Karangasem Regencies, Bali. Jurnal Biologi Udayana 19(1), 11-14. https://doi.org/
10.24843/JBIOUNUD.2015.vol19.i01 Fatmawati, D. A., Wirajana, N., & Yowani,
S. C. (2015). Perbandingan kualitas DNA dengan menggunakan Metode Boom Original dan Boom Modifikasi pada Isolat Mycobacterium tuberculosis 151. KIMIA, vol. q, 41- 45. https://doi.org/10.24843/JCHEM.
2015.v09.i01.p07.
Fitzgerald, D. M., & Rosenberg, S. M.
(2019). What is mutation? A chapter in the series: How microbes
“jeopardize” the modern synthesis.
PLoS genetics, 15(4), e1007995.
https://doi.org/10.1371/journal.pgen.1 007995.
Fukamachi, S., Shimada, A., & Shima, A.
(2001). Mutations in the gene encoding B, a novel transporter protein, reduce melanin content in medaka. Nature genetics, 28(4), 381- 385. https://doi.org/10.1038/ng584.
Gunnarsson, U., Hellström, A. R., Tixier- Boichard, M., Minvielle, F., Bed’hom, B., Ito, S., Jensen, P., Rattink, A., Vereijken, A., and Andersson, L. (2007). Mutations in SLC45A2 cause plumage color variation in chicken and Japanese quail.
Genetics, 175(2), 867-877. https://
doi.org/10.1534/genetics.106.063107.
Hendiari, I. G. A. D., Sartimbul, A., Arthana, I. W., & Kartika, G. R. A. (2020).
Keragaman genetik ikan lemuru (Sardinella lemuru) di wilayah perairan Indonesia. Acta Aquatica:
Aquatic Sciences Journal, 7(1), 28-36.
https://doi.org/10.29103/aa.v7i1.2405 Holl, H. M., Pflug, K. M., Yates, K. M., Hoefs- Martin, K., Shepard, C., Cook, D. G., Lafayette, C., and Brooks, S. A. (2019).
DOI: 10.21776/ub.jiip.2023.033.02.09 226 A candidate gene approach identifies
variants in SLC 45A2 that explain dilute phenotypes, pearl and sunshine, in compound heterozygote horses. Animal genetics, 50(3), 271-274. https://doi.
org/10.1111/age.12790.
Huang, M., Shah, N. D., & Yao, L. (2019).
Evaluating global and local sequence alignment methods for comparing patient medical records. BMC Medical Informatics and Decision Making, 19(6), 1-13. https://doi.org/
10.1186/s12911-019-0965-y.
Ibarrola-Villava, M., Hu, H. H., Guedj, M., Fernandez, L. P., Descamps, V., Basset-Seguin, N., Bagot, M., Benssussan, A., Saiag, P., Fargnoli, M. C., Peris, K., Aviles, J. A., Lluch, A., Ribas, G., and Soufir, N. (2012).
MC1R, SLC45A2 and TYR genetic variants involved in melanoma susceptibility in southern European populations: results from a meta- analysis. European journal of cancer, 48(14), 2183-2191. https://
doi.org/10.1016/j.ejca.2012.03.006.
Jin, Y., Wang, J., Bachtiar, M., Chong, S. S.,
& Lee, C. G. (2018). Architecture of polymorphisms in the human genome reveals functionally important and positively selected variants in immune response and drug transporter genes. Human genomics, 12(1), 1-13.
https://doi.org/10.1186/s40246-018- 0175-1.
Kamilah, S. N., Muslim, C., Astuti, Y. D., &
Pasaribu, M. D. (2021, June).
Phenotypic Variation in Pigmentation of Persons with Albinism in Rejang Lebong, Bengkulu. In 3rd KOBI Congress, International and National Conferences (KOBICINC 2020) (pp.
391-394). Atlantis Press. https://
doi.org/10.2991/absr.k.210621.066.
Kusumaningrum, R., Sutopo, S., &
Kurnianto, E. (2020). Genetic diversity of Sragen Black Cattle based on D-Loop gene sequencing analysis. Livestock and Animal
Research, 18(2), 124-131. https://doi.
org/10.20961/lar.v18i2.42934.
Lee, A. Y. (2021). Skin pigmentation abnormalities and their possible relationship with skin aging.
International Journal of Molecular Sciences, 22(7), 3727. https://doi.org/
10.3390/ijms22073727
Lorenz, T. C. (2012). Polymerase chain reaction: basic protocol plus troubleshooting and optimization strategies. JoVE (Journal of Visualized Experiments), (63), e3998.
https://doi.org/10.3791/3998.
Lusiastuti, A. M., Seeger, H., Sugiani, D., Mufidah, T., & Novita, H. (2015).
Deteksi polymorphisme dengan substitusi nukleotida tunggal pada Streptococcus agalactiae isolat lokal Indonesia. Media Akuakultur, 10(2), 91-95.https://doi.org/10.15578/ma.10.
2.2015.91-95.
Mokhtarzadeh, S., Nobakht, A., Mehmannavaz, Y., Palangi, V., Eseceli, H., & Lackner, M. (2022).
Impacts of continuous and intermittent use of bovine colostrum on laying Japanese quails: Egg performance and traits, blood biochemical and antioxidant status. Animals, 12(20), 2811. https://doi.org/10.3390/ani1220 2811.
Newton, J. M., Cohen-Barak, O., Hagiwara, N., Gardner, J. M., Davisson, M. T., King, R. A., & Brilliant, M. H. (2001).
Mutations in the human orthologue of the mouse underwhite gene (uw) underlie a new form of oculocutaneous albinism, OCA4. The American Journal of Human Genetics, 69(5), 981-988. https://doi.
org/10.1086/324340.
Pei, J., Kinch, L. N., Otwinowski, Z., &
Grishin, N. V. (2020). Mutation severity spectrum of rare alleles in the human genome is predictive of disease type. PLoS computational biology, 16(5), e1007775. https://doi.org/10.
1371/journal.pcbi.1007775.
DOI: 10.21776/ub.jiip.2023.033.02.09 227 Pires, D. E., Chen, J., Blundell, T. L., &
Ascher, D. B. (2016). In silico functional dissection of saturation mutagenesis: Interpreting the relationship between phenotypes and changes in protein stability, interactions and activity. Scientific reports, 6(1), 19848. https://doi.org/
10.1038/srep19848.
Rusnita, D. (2015). SNPs analysis as a tool in molecular genetics diagnostics.
Majalah Kedokteran Andalas, 38(1), 49-56. https://doi.org/10.22338/mka.
v38.i1.p49-56.2015.
Sengupta, M., Dutta, T., and Ray, K. (2019).
SLC45A2 (solute carrier family 45 member 2). Atlas of Genetics and Cytogenetics in Oncology and Haematology 23(7), 187-189.
https://doi.org/10.4267/2042/70469.
Setiati, N., & Hidayah, N. (2020, June). The use of two pairs primer for CO1 gene amplification on traded stingray at fish auction Tasik Agung Rembang.
In Journal of Physics: Conference Series (Vol. 1567, No. 3, p. 032056).
IOP Publishing. https://doi.org/10.
1088/1742-6596/1567/3/032056.
Sharma, Y., Miladi, M., Dukare, S., Boulay, K., Caudron-Herger, M., Groß, M., Backofen, R., and Diederichs, S. (2019). A pan-cancer analysis of synonymous mutations. Nature communications, 10(1), 2569. https://
doi.org/10.1038/s41467-019-10489-2.
Slobodin, B., Han, R., Calderone, V., Vrielink, J. A. O., Loayza-Puch, F., Elkon, R., & Agami, R. (2017).
Transcription impacts the efficiency of mRNA translation via co- transcriptional N6-adenosine methylation. Cell, 169(2), 326-337.
https://doi.org/10.1016/j.cell.2017.03.
031.
Sulassih, S., & Santosa, E. (2020).
Comparison of Deoxyribose Nucleic Acid Purification Methods of Mangosteen (Garcinia mangostana L.) and Its Relatives. Buletin
Agroteknologi, 1(2), 78-85. https://
doi.org/10.32663/ba.v1i2.146078 Torgerson, T. R. (2020). Genetics of primary
immune deficiencies. Stiehm's Immune Deficiencies, 133-142.
https://doi.org/10.1016/B978-0-12- 405546-9.00003-0.
Tóth, L., Fábos, B., Farkas, K., Sulák, A., Tripolszki, K., Széll, M., & Nagy, N.
(2017). Identification of two novel mutations in the SLC45A2 gene in a Hungarian pedigree affected by unusual OCA type 4. BMC Medical Genetics, 18(1), 1-4. https://doi.org/
10.1186/s12881-017-0386-7.
Wijesena, H. R., & Schmutz, S. M. (2015). A missense mutation in SLC45A2 is associated with albinism in several small long haired dog breeds. Journal of Heredity, 106(3), 285-288. https://
doi.org/10.5061/dryad.53kh1.
Wilkinson, M. E., Charenton, C., & Nagai, K.
(2020). RNA splicing by the spliceosome. Annual review of biochemistry, 89, 359-388. https://doi.
org/10.1146/annurev-biochem-09171 9-064225.
Wiltgen, M. (2018). Algorithms for structure comparison and analysis: Homology modelling of proteins (Vol. 1, pp. 38- 61). Cambridge: Elsevier. https://
doi.org/10.1016/B978-0-12-809633- 8.20484-6.
Zhang, T., Wu, Y., Lan, Z., Shi, Q., Yang, Y.,
& Guo, J. (2017). Syntool: a novel region-based intolerance score to single nucleotide substitution for synonymous mutations predictions based on 123,136 individuals. BioMed Research International, 2017. https://
doi.org/10.1155/2017/5096208 Zhou, S., & Sakamoto, K. (2020). Citric acid
promoted melanin synthesis in B16F10 mouse melanoma cells, but inhibited it in human epidermal melanocytes and HMV-II melanoma cells via the GSK3β/β-catenin signaling pathway. PLoS One, 15(12), e0243565.
DOI: 10.21776/ub.jiip.2023.033.02.09 228 https://doi.org/10.1371/journal.pone.0
243565.
Zonunsanga. (2015). Melanocytes and melanogenesis. Our Dermatology Online 6(3), 350-355. https://doi.
org/10.7241/ourd.20153.94
