Aquarium, I+R+D

The Genetics Behind the Coloration of Koi and Carp

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By Milthon Lujan

Koi Fish Specimens. Source: Rouyer noelle
Koi Fish Specimens. Source: Rouyer noelle

The dazzling variety of colors that adorn koi and carp has captivated humans for centuries. But what exactly determines these vibrant hues? Scientists are unraveling the genetic code behind this fascinating diversity, paving the way for future advancements in breeding and understanding fish evolution.

A team of researchers from Nanjing Agricultural University (China), the Freshwater Fisheries Research Center of Chinese Academy of Fishery Sciences, and Jiangsu Qi Hong Ecological Agriculture Development Co., Ltd (China) used restriction site-associated DNA sequencing (2d-RAD) to determine the distribution characteristics of single nucleotide polymorphisms (SNPs) in eight common carp strains: six koi lines—Kohaku (Hb), Taisho (Dz), Showa (Zh), Golden (Hj), Matsukawabake (Sch), and Five-color (Ws)—and two genetically improved carp lines, the FFRC No. 2 strain (Fr) and the red FFRC strain (Hfr). They then used SNP markers to resolve genetic information about the population structure and skin color formation of these strains.

The Rich Heritage of Chinese Carp

China has a long history of carp cultivation, with various carp varieties such as the Yellow River carp and the colorful Oujiang carp. Among them, the FFRC No. 2 strain (Fr) stands out for its rapid growth, excellent body shape, and high survival rate, making it a popular choice for aquaculture.

The Challenge of Koi Breeding

While the FFRC strain thrives in aquaculture, the ornamental koi industry faces challenges. Koi come in over 100 color variations, but inbreeding and improper breeding techniques threaten the quality of these prized fish. Additionally, China heavily relies on imported koi germplasm from Japan, limiting its role in the ornamental fish market.

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The Science of Fish Colors

Fish body color plays a crucial role in their evolution and classification. Several factors influence this color palette, including:

  • Genetics: This is the most important factor determining the pattern for color formation.
  • Nutrition: Diet plays a role in providing pigments and precursors for color development.
  • Hormones: Physiological hormones can influence color expression.
  • Environment: Breeding conditions, such as light and temperature, can also affect coloration.

Unraveling the Koi Code

To address these challenges, researchers are using a powerful tool called 2d-RAD sequencing. This technique allows scientists to identify and analyze single nucleotide polymorphisms (SNPs), small variations in a fish’s DNA. By studying these variations, researchers can:

  • Measure Genetic Diversity: This study analyzed eight carp populations, including koi and FFRC carp, to understand their genetic makeup and relationships.
  • Identify Color-Related Genes: Researchers identified specific SNPs related to skin color differentiation in koi carp. These genes are responsible for processes such as melanin synthesis (browns and blacks) and carotenoid metabolism (yellows and oranges).
  • Develop Molecular Markers: By identifying SNPs associated with desired skin color traits, researchers can develop breeding tools to select for specific colors and patterns.

Decoding the Carp Family Tree

The study revealed distinct genetic fingerprints for each carp strain, with most individuals clustering into separate groups. This analysis provided valuable insights into the genetic diversity within these strains. Interestingly, carp strains like FFRC No. 2, Matsukawabake, and Five-color showed higher genetic diversity, while others like Taisho and Kohaku showed lower diversity.

Genes and Coloration: A Roadmap for Future Breeding

By comparing the genetic composition of different strains, researchers identified significant variations related to skin color formation. This analysis identified specific genes associated with:

  • Melanin Synthesis: Genes such as ephrinb2, slc22a23, herc2, and ephb2 were related to melanin production, a pigment responsible for black and brown tones.
  • Carotenoid Metabolism: Genes like oca2, bcmo1, and bco2 influence the processing of carotenoids, pigments responsible for vibrant reds, oranges, and yellows.
  • Circadian Rhythm: The gene cipc was linked to the body’s internal clock, which may play a role in regulating color.
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Impact for Koi Carp Aquaculture

This innovative research provides a wealth of information about the genetic basis of carp and koi coloration. This knowledge can be used to:

  • Maintain and Improve Koi Germplasm: Genetic diversity is crucial for healthy and vibrant fish populations. Understanding the genetic makeup of koi allows breeders to maintain and enhance existing strains.
  • Develop New Color Varieties: By selecting for specific color-related genes, breeders can create new and stunning koi varieties with desired patterns and hues.
  • Reduce Dependence on Imports: China can leverage its rich carp germplasm, combined with genetic knowledge, to develop high-quality domestic koi strains.

This study marks a significant leap in understanding the fascinating world of carp and koi coloration. By uncovering the secrets hidden within their genes, researchers are paving the way for a future filled with even more vibrant and diverse carp varieties.

The study was funded by the Jiangsu Agricultural Science and Technology Innovation Fund, Central Public Interest Scientific Institution Basal Research Fund, Chinese Academy of Fishery Sciences, National Natural Science Foundation of China, among others.

Mingkun Luo
Wuxi Fisheries College, Nanjing Agricultural University, Wuxi
Jiangsu 214081, China

Zaijie Dong
Wuxi Fisheries College, Nanjing Agricultural University, Wuxi
Jiangsu 214081, China

Shi, X., Zhu, W., Guo, J., Lin, K., Fu, J., Wang, L., Dong, Y., Luo, M., & Dong, Z. (2024). Genome-wide association study reveals candidate genes critical for skin pigmentation in common carp (Cyprinus carpio) strains including koi. Aquaculture, 590, 741075.