OMIA:002385-7950 : Reproductive seasonality in Clupea harengus (Atlantic herring)

In other species: chicken , goat , sheep , Japanese quail

Categories: Endocrine / exocrine gland phene (incl mammary gland)

Links to possible relevant human trait(s) and/or gene(s) in OMIM: 603372 (gene)

Mendelian trait/disorder: no

Mode of inheritance: Multifactorial

Considered a defect: no

Key variant known: yes

Year key variant first reported: 2021

Species-specific name: spring and autumn spawning

Species-specific description: Chen et al. (2021): “Animals living at temperate latitudes rely on the photoperiod (day length) to adapt their behaviors … to seasonal changes. Breeding at a specific time of the year, known as seasonal reproduction, ensures that offspring are born when the environment is best suited for survival (e.g. food availability and moderate climate). Organisms that reproduce during spring with increasing photoperiod … are denoted long day (LD) breeders, and those that breed during the decreasing photoperiod in autumn …, are short day (SD) breeders. …. Atlantic herring … exhibits seasonal reproduction predominantly in spring and autumn.”

Mapping: Chen et al. (2021): “Our previous whole-genome comparisons have demonstrated that there is minute genetic differentiation between spring- and autumn-spawning herring at selectively neutral loci but striking genetic differentiation at about 30 loci (Lamichhaney et al., 2012; Martinez Barrio et al., 2016; Han et al. 2020). … The most differentiated region between spring and autumn-spawning Atlantic herring overlaps TSHR (Martinez Barrio et al., 2016; Lamichhaney et al., 2017; Pettersson et al., 2019).”

Molecular basis: Chen et al. (2021): “Two non-coding SNPs, one upstream of the promoter region and the other in intron 1, and two missense mutations, Q370H and L471M, stood out as the most strongly associated with the phenotype. … We describe, two additional sequence variants distinguishing the spring and autumn haplotypes, (i) a loss of a retrotransposon sequence upstream of TSHR and (ii) a copy number polymorphism at the C terminal end of the TSHR transcript. We show using mutagenesis and transfection experiments that the L471M substitution in the spring-allele results in enhanced constitutive cAMP signalling, and the 5.2 kb retrotransposon variant upstream of TSHR near an open chromatin region may affect TSHR expression.”

Associated gene:

Symbol Description Species Chr Location OMIA gene details page Other Links
tshr thyroid stimulating hormone receptor Clupea harengus 15 NC_045166.1 (8873320..8908671) tshr Homologene, Ensembl , NCBI gene


By default, variants are sorted chronologically by year of publication, to provide a historical perspective. Readers can re-sort on any column by clicking on the column header. Click it again to sort in a descending order. To create a multiple-field sort, hold down Shift while clicking on the second, third etc relevant column headers.

WARNING! Inclusion of a variant in this table does not automatically mean that it should be used for DNA testing. Anyone contemplating the use of any of these variants for DNA testing should examine critically the relevant evidence (especially in breeds other than the breed in which the variant was first described). If it is decided to proceed, the location and orientation of the variant sequence should be checked very carefully.

Since October 2021, OMIA includes a semiautomated lift-over pipeline to facilitate updates of genomic positions to a recent reference genome position. These changes to genomic positions are not always reflected in the ‘acknowledgements’ or ‘verbal description’ fields in this table.

OMIA Variant ID Breed(s) Variant Phenotype Gene Allele Type of Variant Source of Genetic Variant Reference Sequence Chr. g. or m. c. or n. p. Verbal Description EVA ID Year Published PubMed ID(s) Acknowledgements
1339 Spring spawning tshr missense Naturally occurring variant Ch_v2.0.2 15 g.8906859C>A c.1411C>A p.(L471M) cDNA position based on transcript ENSCHAT00000005367.1 2021 34172814

Cite this entry

Nicholas, F. W., Tammen, I., & Sydney Informatics Hub. (2021). OMIA:002385-7950: Online Mendelian Inheritance in Animals (OMIA) [dataset].


Note: the references are listed in reverse chronological order (from the most recent year to the earliest year), and alphabetically by first author within a year.

2021 Chen, J., Bi, H., Pettersson, M.E., Sato, D.X., Fuentes-Pardo, A.P., Mo, C., Younis, S., Wallerman, O., Jern, P., Molés, G., Gómez, A., Kleinau, G., Scheerer, P., Andersson, L. :
Functional differences between TSHR alleles associate with variation in spawning season in Atlantic herring. Commun Biol 4:795, 2021. Pubmed reference: 34172814. DOI: 10.1038/s42003-021-02307-7.
2020 Han, F., Jamsandekar, M., Pettersson, M.E., Su, L., Fuentes-Pardo, A.P., Davis, B.W., Bekkevold, D., Berg, F., Casini, M., Dahle, G., Farrell, E.D., Folkvord, A., Andersson, L. :
Ecological adaptation in Atlantic herring is associated with large shifts in allele frequencies at hundreds of loci. Elife 9, 2020. Pubmed reference: 33274714. DOI: 10.7554/eLife.61076.
2019 Pettersson, M.E., Rochus, C.M., Han, F., Chen, J., Hill, J., Wallerman, O., Fan, G., Hong, X., Xu, Q., Zhang, H., Liu, S., Liu, X., Haggerty, L., Hunt, T., Martin, F.J., Flicek, P., Bunikis, I., Folkvord, A., Andersson, L. :
A chromosome-level assembly of the Atlantic herring genome-detection of a supergene and other signals of selection. Genome Res 29:1919-1928, 2019. Pubmed reference: 31649060. DOI: 10.1101/gr.253435.119.
2017 Lamichhaney, S., Fuentes-Pardo, A.P., Rafati, N., Ryman, N., McCracken, G.R., Bourne, C., Singh, R., Ruzzante, D.E., Andersson, L. :
Parallel adaptive evolution of geographically distant herring populations on both sides of the North Atlantic Ocean. Proc Natl Acad Sci U S A 114:E3452-E3461, 2017. Pubmed reference: 28389569. DOI: 10.1073/pnas.1617728114.
2016 Martinez Barrio, A., Lamichhaney, S., Fan, G., Rafati, N., Pettersson, M., Zhang, H., Dainat, J., Ekman, D., Höppner, M., Jern, P., Martin, M., Nystedt, B., Liu, X., Chen, W., Liang, X., Shi, C., Fu, Y., Ma, K., Zhan, X., Feng, C., Gustafson, U., Rubin, C.J., Sällman Almén, M., Blass, M., Casini, M., Folkvord, A., Laikre, L., Ryman, N., Ming-Yuen Lee, S., Xu, X., Andersson, L. :
The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing. Elife 5, 2016. Pubmed reference: 27138043. DOI: 10.7554/eLife.12081.
2013 Nakane, Y., Ikegami, K., Iigo, M., Ono, H., Takeda, K., Takahashi, D., Uesaka, M., Kimijima, M., Hashimoto, R., Arai, N., Suga, T., Kosuge, K., Abe, T., Maeda, R., Senga, T., Amiya, N., Azuma, T., Amano, M., Abe, H., Yamamoto, N., Yoshimura, T. :
The saccus vasculosus of fish is a sensor of seasonal changes in day length. Nat Commun 4:2108, 2013. Pubmed reference: 23820554. DOI: 10.1038/ncomms3108.
2012 Lamichhaney, S., Martinez Barrio, A., Rafati, N., Sundström, G., Rubin, C.J., Gilbert, E.R., Berglund, J., Wetterbom, A., Laikre, L., Webster, M.T., Grabherr, M., Ryman, N., Andersson, L. :
Population-scale sequencing reveals genetic differentiation due to local adaptation in Atlantic herring. Proc Natl Acad Sci U S A 109:19345-50, 2012. Pubmed reference: 23134729. DOI: 10.1073/pnas.1216128109.

Edit History

  • Created by Imke Tammen2 on 14 Aug 2021
  • Changed by Imke Tammen2 on 14 Aug 2021