Evaluation of genetic differentiation and genome-wide selection signatures in Polish local sheep breeds

被引:9
|
作者
Gurgul, Artur [1 ]
Jasielczuk, Igor [1 ]
Miksza-Cybulska, Anna [2 ]
Kawecka, Aldona [2 ]
Szmatola, Tomasz [1 ,3 ]
Krupinski, Jedrzej [4 ]
机构
[1] Agr Univ Krakow, Ctr Expt & Innovat Med, Redzina 1c, PL-30248 Krakow, Poland
[2] Natl Res Inst Anim Prod, Dept Sheep & Goat Breeding, Krakowska 1, PL-32083 Balice, Poland
[3] Natl Res Inst Anim Prod, Dept Anim Mol Biol, Krakowska 1, PL-32083 Balice, Poland
[4] Natl Res Inst Anim Prod, Dept Horse Breeding, Krakowska 1, PL-32083 Balice, Poland
关键词
Sheep; Genetic diversity; Microarrays; Native; Polish; Selection signatures; HOMOZYGOSITY; ASSOCIATION; DISCOVERY; RXFP2; RUNS;
D O I
10.1016/j.livsci.2021.104635
中图分类号
S8 [畜牧、 动物医学、狩猎、蚕、蜂];
学科分类号
0905 ;
摘要
Since their domestication, sheep breeds have been a subject of artificial selection directed towards production of wool, meat and milk as well as natural selection associated with regional climates and nutritional conditions. These selection pressures created a large diversity of sheep breeds and the opportunity to study their genetic differentiation. Despite the existence of several studies on genetic variation and selection signatures in sheep, information on the genetic background and variability of local sheep populations, especially on a genome wide-level, is still incomplete. This is mostly due to the large number of local sheep breeds and populations in existence. Several of these populations are under conservative breeding because of their largely primitive character, which is not suitable for the modern intensive animal production. In this study we analysed population parameters and quantified genetic differentiation among seven Polish conserved sheep breeds or local sheep populations, namely: Black-headed (BH; n=104), Polish Merino of coloured variety (MPC; n=59), 'Old type' Merino (MPOT; n=50), Polish Mountain Sheep (PMS; n=103), Swiniarka (SW; n=100), Uhruska (UHR; n=69) and WrzosOwka (WRZ; n=90). The breeds represent mainly multipurpose production type with the emphasize on meat, wool and skin. Based on the data from OvineSNP50 BeadChip array (Illumina), we found that the genetic structures of the populations are not heavily affected, despite the bottlenecks in their recent breeding history. The only exception seems to be the SW breed in which we found very low effective population size (30.7) and high level of genomic inbreeding (17% as shown by F-ROH). Average MAF across breeds was high and ranged from 0.285 in MPC to 0.297 in PMS. The average observed heterozygosity per breed ranged from 0.378 in SW to 0.398 in UHR. The admixture patterns analysis showed that the analysed breeds have distinct genetic profiles with clear signs of common origin and admixture, similar to other worldwide sheep populations. By using F-ST statistics we also identified loci of the genome with the strongest divergence between the analysed breeds, presumably responsible for the fixed genetic differences among them which were created by artificial selection. The most pronounced of these results was selection signal at the locus of RXFP2 gene which is responsible for horn size/type in sheep. This analysis also allowed for genomic localization of genetic differences between the analysed breeds, providing a basis for further studies aimed at identification of sources of genetic variation in these sheep breeds.
引用
收藏
页数:11
相关论文
共 50 条
  • [31] A genome-wide scan for signature of positive selection in some Iranian sheep breeds.
    Manzari, Z.
    Yeghaneh, H. Mehrabani
    Nejati-Javaremi, A.
    Gholizadeh, M.
    Moradi, M. H.
    JOURNAL OF ANIMAL SCIENCE, 2016, 94 : 139 - 140
  • [32] Genetic structure of Tunisian sheep breeds as inferred from genome-wide SNP markers
    Bedhiaf-Romdhani, S.
    Baazaoui, I
    Ciani, E.
    Mastrangelo, S.
    Ben Sassi, M.
    SMALL RUMINANT RESEARCH, 2020, 191
  • [33] Genome-wide SNP analysis reveals the selection signatures of two indigenous buffalo breeds in Sichuan
    Wei Wang
    Donghui Fang
    Yi Shi
    Fang He
    Jia Gan
    Maozhong Fu
    Xiaodong Deng
    Tao Zhang
    Hongbing Shen
    Shengchao Zhong
    Yueda Aguo
    Luxi Chen
    Naza An
    Zhiguang Zhang
    Ji Yi
    Conservation Genetics Resources, 2022, 14 : 299 - 307
  • [34] Genome-wide SNP analysis reveals the selection signatures of two indigenous buffalo breeds in Sichuan
    Wang, Wei
    Fang, Donghui
    Shi, Yi
    He, Fang
    Gan, Jia
    Fu, Maozhong
    Deng, Xiaodong
    Zhang, Tao
    Shen, Hongbing
    Zhong, Shengchao
    Aguo, Yueda
    Chen, Luxi
    An, Naza
    Zhang, Zhiguang
    Yi, Ji
    CONSERVATION GENETICS RESOURCES, 2022, 14 (03) : 299 - 307
  • [35] Genome-wide screening for selection signatures in native and cosmopolitan cattle breeds reared in Türkiye
    Demir, Eymen
    Moravcikova, Nina
    Kaya, Sarp
    Kasarda, Radovan
    Bilginer, Umit
    Dogru, Huriye
    Balcioglu, Murat Soner
    Karsli, Taki
    ANIMAL GENETICS, 2023, 54 (06) : 721 - 730
  • [36] Genome-wide evaluation of copy gain and loss variations in three Afghan sheep breeds
    Moradi, Mohammad Hossein
    Mahmodi, Roqiah
    Farahani, Amir Hossein Khaltabadi
    Karimi, Mohammad Osman
    SCIENTIFIC REPORTS, 2022, 12 (01)
  • [37] Genome-wide evaluation of copy gain and loss variations in three Afghan sheep breeds
    Mohammad Hossein Moradi
    Roqiah Mahmodi
    Amir Hossein Khaltabadi Farahani
    Mohammad Osman Karimi
    Scientific Reports, 12
  • [38] Selection signatures of wool color in Gangba sheep revealed by genome-wide SNP discovery
    Zhang, Wentao
    Luosang, Cuicheng
    Yuan, Chao
    Guo, Tingting
    Wei, Caihong
    Liu, Jianbin
    Lu, Zengkui
    BMC GENOMICS, 2024, 25 (01):
  • [39] Genome-wide SNP analysis of three Azerbaijani sheep breeds
    Dotsev, Arsen V.
    Deniskova, Tatiana E.
    Bagirov, Vugar A.
    Abilov, Ahmed I.
    Reyer, Henry
    Wimmers, Klaus
    Brem, Gottfried
    Zinovieva, Natalia A.
    JOURNAL OF ANIMAL SCIENCE, 2021, 99 : 245 - 245
  • [40] Genome-Wide Analysis of Genetic Diversity and Selection Signatures in Zaobei Beef Cattle
    Shi, Liangyu
    Zhang, Pu
    Liu, Qing
    Liu, Chenhui
    Cheng, Lei
    Yu, Bo
    Chen, Hongbo
    ANIMALS, 2024, 14 (16):