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A Pilot Detection and Associate Study of Gene Presence-Absence Variation in Holstein Cattle.
Boschiero, Clarissa; Neupane, Mahesh; Yang, Liu; Schroeder, Steven G; Tuo, Wenbin; Ma, Li; Baldwin, Ransom L; Van Tassell, Curtis P; Liu, George E.
Afiliación
  • Boschiero C; Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA.
  • Neupane M; Department of Veterinary Medicine, University of Maryland, College Park, MD 20742, USA.
  • Yang L; Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA.
  • Schroeder SG; Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA.
  • Tuo W; Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA.
  • Ma L; Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA.
  • Baldwin RL; Animal Parasitic Diseases Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA.
  • Van Tassell CP; Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA.
  • Liu GE; Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA.
Animals (Basel) ; 14(13)2024 Jun 28.
Article en En | MEDLINE | ID: mdl-38998033
ABSTRACT
Presence-absence variations (PAVs) are important structural variations, wherein a genomic segment containing one or more genes is present in some individuals but absent in others. While PAVs have been extensively studied in plants, research in cattle remains limited. This study identified PAVs in 173 Holstein bulls using whole-genome sequencing data and assessed their associations with 46 economically important traits. Out of 28,772 cattle genes (from the longest transcripts), a total of 26,979 (93.77%) core genes were identified (present in all individuals), while variable genes included 928 softcore (present in 95-99% of individuals), 494 shell (present in 5-94%), and 371 cloud genes (present in <5%). Cloud genes were enriched in functions associated with hormonal and antimicrobial activities, while shell genes were enriched in immune functions. PAV-based genome-wide association studies identified associations between gene PAVs and 16 traits including milk, fat, and protein yields, as well as traits related to health and reproduction. Associations were found on multiple chromosomes, illustrating important associations on cattle chromosomes 7 and 15, involving olfactory receptor and immune-related genes, respectively. By examining the PAVs at the population level, the results of this research provided crucial insights into the genetic structures underlying the complex traits of Holstein cattle.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Idioma: En Revista: Animals (Basel) Año: 2024 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: Suiza
Texto completo
Añadir a Mi BVS
Imprimir
XML
PubMed Links
Buscar en Google

Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Idioma: En Revista: Animals (Basel) Año: 2024 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: Suiza