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Towards the detection of copy number variation from single sperm sequencing in cattle.
Yang, Liu; Gao, Yahui; Oswalt, Adam; Fang, Lingzhao; Boschiero, Clarissa; Neupane, Mahesh; Sattler, Charles G; Li, Cong-Jun; Seroussi, Eyal; Xu, Lingyang; Yang, Lv; Li, Li; Zhang, Hongping; Rosen, Benjamin D; Van Tassell, Curtis P; Zhou, Yang; Ma, Li; Liu, George E.
Afiliación
  • Yang L; Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA.
  • Gao Y; College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.
  • Oswalt A; Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA.
  • Fang L; Department of Animal and Avian Sciences, University of Maryland, College Park, MD, 20742, USA.
  • Boschiero C; Select Sires Inc, 11740 U.S. 42 North, Plain City, OH, 43064, USA.
  • Neupane M; MRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, EH4 2XU, UK.
  • Sattler CG; Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA.
  • Li CJ; Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA.
  • Seroussi E; Select Sires Inc, 11740 U.S. 42 North, Plain City, OH, 43064, USA.
  • Xu L; Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA.
  • Yang L; Agricultural Research Organization (ARO), Institute of Animal Science, HaMaccabim Road, P.O.B 15159, 7528809, Volcani CenterRishon LeTsiyon, Israel.
  • Li L; Innovation Team of Cattle Genetic Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
  • Zhang H; Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
  • Rosen BD; College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.
  • Van Tassell CP; College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.
  • Zhou Y; Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA.
  • Ma L; Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA.
  • Liu GE; Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
BMC Genomics ; 23(1): 215, 2022 Mar 17.
Article en En | MEDLINE | ID: mdl-35300589
ABSTRACT

BACKGROUND:

Copy number variation (CNV) has been routinely studied using bulk-cell sequencing. However, CNV is not well studied on the single-cell level except for humans and a few model organisms.

RESULTS:

We sequenced 143 single sperms of two Holstein bulls, from which we predicted CNV events using 14 single sperms with deep sequencing. We then compared the CNV results derived from single sperms with the bulk-cell sequencing of one bull's family trio of diploid genomes. As a known CNV hotspot, segmental duplications were also predicted using the bovine ARS-UCD1.2 genome. Although the trio CNVs validated only some single sperm CNVs, they still showed a distal chromosomal distribution pattern and significant associations with segmental duplications and satellite repeats.

CONCLUSION:

Our preliminary results pointed out future research directions and highlighted the importance of uniform whole genome amplification, deep sequence coverage, and dedicated software pipelines for CNV detection using single cell sequencing data.
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Texto completo: 1 Colección: 01-internacional Banco de datos: MEDLINE Asunto principal: Genoma / Variaciones en el Número de Copia de ADN Tipo de estudio: Diagnostic_studies / Prognostic_studies Límite: Animals Idioma: En Revista: BMC Genomics Asunto de la revista: GENETICA Año: 2022 Tipo del documento: Article País de afiliación: Estados Unidos
Texto completo
Imprimir
XML
PubMed Links
Buscar en Google

Texto completo: 1 Colección: 01-internacional Banco de datos: MEDLINE Asunto principal: Genoma / Variaciones en el Número de Copia de ADN Tipo de estudio: Diagnostic_studies / Prognostic_studies Límite: Animals Idioma: En Revista: BMC Genomics Asunto de la revista: GENETICA Año: 2022 Tipo del documento: Article País de afiliación: Estados Unidos