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In addition to multiple alleles at the same locus influencing traits, numerous genes or alleles at different locations may interact and influence phenotypes in a phenomenon called epistasis. For example, rabbit fur can be black or brown depending on whether the animal is homozygous dominant or heterozygous at a TYRP1 locus. However, if the rabbit is also homozygous recessive at a locus on the tyrosinase gene (TYR), it will have an unshaded coat that appears white, regardless of its TYRP1...
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Structural Variations Associated with Adaptation and Coat Color in Qinghai-Tibetan Plateau Cattle.

Xiaoting Xia1, Fuwen Wang1,2, Xiaoyu Luo1

  • 1Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.

Advanced Science (Weinheim, Baden-Wurttemberg, Germany)
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Summary

Structural variations (SVs) are key to Tibetan cattle adaptation to high altitudes. These genetic changes, including those from yak introgression, influence traits like energy metabolism and coat color.

Keywords:
cattlecoat colorgenome assemblyhigh‐altitude adaptationstructural variation

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Area of Science:

  • Genomics
  • Evolutionary Biology
  • Animal Science

Background:

  • Domesticated animals exhibit evolutionary adaptation to diverse environments.
  • Structural variations (SVs) are significant drivers of adaptation but remain understudied in Tibetan cattle.
  • Tibetan cattle have rapidly adapted to the high-altitude Qinghai-Tibetan Plateau (QTP).

Purpose of the Study:

  • To construct a de novo chromosome-level genome assembly for Tibetan cattle.
  • To identify and analyze structural variations (SVs) in high-altitude versus low-altitude cattle.
  • To investigate the role of SVs, including yak introgression, in Tibetan cattle adaptation.

Main Methods:

  • De novo chromosome-level genome assembly using long-read sequencing data.
  • Identification and analysis of 222,528 SVs and 259 SV hotspot regions.
  • Comparative analysis of SVs between 36 high-altitude and 48 low-altitude cattle populations.

Main Results:

  • A lineage-specific reference genome improved variant detection accuracy.
  • Positively selected SVs in high-altitude cattle are linked to energy metabolism, erythropoiesis, angiogenesis, and peroxisomal metabolism.
  • Identified 7293 SVs potentially introgressed from yak, including variants near the hypoxia gene EGLN1.
  • Discovered a large inversion and two translocations on chromosome 6 associated with gray coat color via KIT gene regulation.

Conclusions:

  • SVs are crucial for the evolutionary adaptation of Tibetan cattle to high-altitude environments.
  • Yak introgression contributed SVs that facilitated rapid acclimatization in Qinghai-Tibetan Plateau cattle.
  • Genetic variations, particularly SVs, underpin the unique adaptive traits of Tibetan cattle.