PMEL p.Leu18del dilutes coat color of Kumamoto sub-breed of Japanese Brown cattle

Identification and Expression Patterns of Critical Genes Related to Coat Color in Cashmere Goats

Background/Objectives: Research on cashmere goat coat color is crucial for optimizing cashmere goat breeds and increasing their economic value. To identify key genes associated with the formation of cashmere goat coat color and to provide molecular markers for breeding purposes, three healthy, 3-year-old does with similar weights and distinct coat colors-white, black, and light brown-were selected. Methods: Skin samples were collected for transcriptome sequencing, and bioinformatics methods were applied to screen for differentially expressed genes (DEGs) in the skin of cashmere goats with varying coat colors. Real-time fluorescence quantitative PCR (qRT-PCR) and immunofluorescence were subsequently conducted to examine the expression patterns of these DEGs. Results: The results showed that a total of 1153 DEGs were identified across the three groups of cashmere goats. According to GO and KEGG analyses, these DEGs were involved in key biological processes and structures, such as the melanin biosynthetic process (GO:0042438), melanosome membrane (GO:0033162), and melanin biosynthesis from tyrosine (GO:0006583). Employing Cytoscape, a gene interaction network was plotted, highlighting a compact network of DEGs associated with coat color formation. Critical genes identified included TYRP1, TYR, DCT, ASIP, PMEL, LOC102180584, MLANA, TSPAN10, TRPM1, CLDN16, AHCY, LOC106503350, and LOC102175263. qRT-PCR and fluorescence immunohistochemistry further determined that TYRP1, TYR, DCT, and PMEL expression levels were high in black goats (BGs), while ASIP and AHCY expression levels were high in white goats (WGs). The expression levels of these six genes in light brown goats (RGs) were intermediate between those in BGs and WGs. Conclusions:TYRP1, TYR, DCT, and PMEL were believed to play pivotal roles in the formation of black coat color, while ASIP and AHCY regulated the formation of white coat color in cashmere goats.

Transcriptomic and Metabolomic Analyses Reveal Molecular Regulatory Networks for Pigmentation Deposition in Sheep

Domestic animals have multiple phenotypes of skin and coat color, which arise from different genes and their products, such as proteins and metabolites responsible with melanin deposition. However, the complex regulatory network of melanin synthesis remains to be fully unraveled. Here, the skin and tongue tissues of Liangshan black sheep (black group) and Liangshan semi-fine-wool sheep (pink group) were collected, stained with hematoxylin-eosin (HE) and Masson-Fontana, and the transcriptomic and metabolomic data were further analyzed. We found a large deposit of melanin granules in the epidermis of the black skin and tongue. Transcriptome and metabolome analysis identified 744 differentially expressed genes (DEGs) and 443 differentially expressed metabolites (DEMs) between the pink and black groups. Gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analyses revealed the DEGs and DEMs were mainly enriched in the pathways of secondary metabolic processes, melanin biosynthesis processes, melanin metabolism processes, melanosome membranes, pigment granule membranes, melanosome, tyrosine metabolism, and melanogenesis. Notably, we revealed the gene ENSARG00020006042 may be a family member of YWHAs and involved in regulating melanin deposition. Furthermore, several essential genes (TYR, TYRP1, DCT, PMEL, MLANA, SLC45A2) were significantly associated with metabolite prostaglandins and compounds involved in sheep pigmentation. These findings provide new evidence of the strong correlation between prostaglandins and related compounds and key genes that regulate sheep melanin synthesis, furthering our understanding of the regulatory mechanisms and molecular breeding of pigmentation in sheep.

PMEL p.L18del associates with beef quality of Kumamoto sub-breed of Japanese Brown cattle

Japanese Brown cattle is the second most popular breed among Wagyu breeds and raised mainly in Kumamoto and Kochi Prefectures. Typical coat color of the Kumamoto sub-breed is solid brown, but individuals with diluted coat color are sometimes born. We previously detected four SNPs in PMEL gene and identified p.L18del as the causative polymorphism of this diluted phenotype. The current study examined the association between the SNPs in PMEL gene and carcass traits of the Kumamoto sub-breed. Our association analysis revealed that p.L18del had significant effects on BMS (p = 0.0263), meat brightness (p = 0.0179), meat firmness (p = 0.0102), and meat texture (p = 0.0252) and that del allele of this SNP might be useful to improve these carcass traits.

Genome-Wide Association Analysis Identifies the PMEL Gene Affecting Coat Color and Birth Weight in Simmental × Holstein

Coat color and birth weight, as easily selected traits in cattle, play important roles in cattle breeding. Therefore, we carried out a genome-wide association study on birth weight and coat color to identify loci or potential linkage regions in 233 Simmental × Holstein crossbred beef cattle. The results revealed that nine SNPs were significantly associated with coat color (rs137169378, rs110022687, rs136002689, Hypotrichosis_PMel17, PMEL_1, rs134930689, rs383170073, rs109924971, and rs109146332), and these were in RNF41, ZC3H10, ERBB3, PMEL, and OR10A7 on BTA5. Interestingly, rs137169378, rs110022687, rs136002689, Hypotrichosis_PMel17, and PMEL_1 showed strong linkage disequilibrium (r2 > 0.8) and were significantly associated with coat color. Notably, Hypotrichosis_PMel17 and PMEL_1 were located in the gene PMEL (p = 2.22 × 10-18). Among the five significant SNPs associated with coat color, the birth weight of heterozygous individuals (AB) was greater than that of homozygous individuals (AA). Notably, the birth weight of heterozygous individuals with Hypotrichosis_PMel17 and PMEL_1 genotypes was significantly greater than that of homozygous individuals (0.01 < p < 0.05). Interestingly, the two loci were homozygous in black/white individuals and heterozygous in gray/white individuals, and the birth weight of heterozygous brown/white individuals (43.82 ± 5.25 kg) was greater than that of homozygous individuals (42.58 ± 3.09 kg). The birth weight of calves with the parental color (41.95 ± 3.53 kg) was significantly lower than that of calves with a non-parental color (43.54 ± 4.78 kg) (p < 0.05), and the birth weight of gray/white individuals (49.40 ± 7.11 kg) was the highest. Overall, PMEL appears to be a candidate gene affecting coat color in cattle, and coat color may have a selective effect on birth weight. This study provides a foundation for the breeding of beef cattle through GWAS for coat color and birth weight.

Production of light-coloured, low heat-absorbing Holstein Friesian cattle by precise embryo-mediated genome editing

CONTEXT

Genome editing enables the introduction of beneficial sequence variants into the genomes of animals with high genetic merit in a single generation. This can be achieved by introducing variants into primary cells followed by producing a live animal from these cells by somatic cell nuclear transfer cloning. The latter step is associated with low efficiencies and developmental problems due to incorrect reprogramming of the donor cells, causing animal welfare concerns. Direct editing of fertilised one-cell embryos could circumvent this issue and might better integrate with genetic improvement strategies implemented by the industry.

METHODS

In vitro fertilised zygotes were injected with TALEN editors and repair template to introduce a known coat colour dilution mutation in the PMEL gene. Embryo biopsies of injected embryos were screened by polymerase chain reaction and sequencing for intended biallelic edits before transferring verified embryos into recipients for development to term. Calves were genotyped and their coats scanned with visible and hyperspectral cameras to assess thermal energy absorption.

KEY RESULTS

Multiple non-mosaic calves with precision edited genotypes were produced, including calves from high genetic merit parents. Compared to controls, the edited calves showed a strong coat colour dilution which was associated with lower thermal energy absorbance.

CONCLUSIONS

Although biopsy screening was not absolutely accurate, non-mosaic, precisely edited calves can be readily produced by embryo-mediated editing. The lighter coat colouring caused by the PMEL mutation can lower radiative heat gain which might help to reduce heat stress.

IMPLICATIONS

The study validates putative causative sequence variants to rapidly adapt grazing cattle to changing environmental conditions.

Causative alleles for chondrodysplastic dwarfism, factor XI deficiency, and factor XIII deficiency in the Kumamoto sub-breed of Japanese Brown cattle

Japanese Brown cattle are the second most popular Wagyu breed, and the Kumamoto sub-breed shows better daily gain and carcass weight. One of the breeding objectives for this sub-breed is to reduce genetic defects. Chondrodysplastic dwarfism and factor VIII deficiency have been identified as genetic diseases in the Kumamoto sub-breed. Previously, we detected individuals in the Kumamoto sub-breed with causative alleles of genetic diseases identified in Japanese Black cattle. In the current study, 11 mutations responsible for genetic diseases in the Wagyu breeds were analyzed to evaluate the risk of genetic diseases in the Kumamoto sub-breed. Genotyping revealed the causative mutations of chondrodysplastic dwarfism, factor XI deficiency, and factor XIII deficiency and suggested the appearance of affected animals in this sub-breed. DNA testing for these diseases is needed to prevent economic loses in beef production using the Kumamoto sub-breed.