Copy number variation of individual cattle genomes using next-generation sequencing


Autoria(s): Bickhart, Derek M.; Hou, Yali; Schroeder, Steven G.; Alkan, Can; Cardone, Maria Francesca; Matukumalli, Lakshmi K.; Song, Jiuzhou; Schnabe, Robert D.; Ventura, Mario; Taylor, Jeremy F.; Garcia, José Fernando; Van Tasse, Curtis P.; Sonstegard, Tad S.; Eichler, Evan E.; Liu, George E.
Contribuinte(s)

Universidade Estadual Paulista (UNESP)

Data(s)

20/05/2014

20/05/2014

01/04/2012

Resumo

Copy number variations (CNVs) affect a wide range of phenotypic traits; however, CNVs in or near segmental duplication regions are often intractable. Using a read depth approach based on next-generation sequencing, we examined genome-wide copy number differences among five taurine (three Angus, one Holstein, and one Hereford) and one indicine (Nelore) cattle. Within mapped chromosomal sequence, we identified 1265 CNV regions comprising similar to 55.6-Mbp sequence-476 of which (similar to 38%) have not previously been reported. We validated this sequence-based CNV call set with array comparative genomic hybridization (aCGH), quantitative PCR (qPCR), and fluorescent in situ hybridization (FISH), achieving a validation rate of 82% and a false positive rate of 8%. We further estimated absolute copy numbers for genomic segments and annotated genes in each individual. Surveys of the top 25 most variable genes revealed that the Nelore individual had the lowest copy numbers in 13 cases (similar to 52%, chi(2) test; P-value <0.05). In contrast, genes related to pathogen- and parasite-resistance, such as CATHL4 and ULBP17, were highly duplicated in the Nelore individual relative to the taurine cattle, while genes involved in lipid transport and metabolism, including APOL3 and FABP2, were highly duplicated in the beef breeds. These CNV regions also harbor genes like BPIFA2A (BSP30A) and WC1, suggesting that some CNVs may be associated with breed-specific differences in adaptation, health, and production traits. By providing the first individualized cattle CNV and segmental duplication maps and genome-wide gene copy number estimates, we enable future CNV studies into highly duplicated regions in the cattle genome.

Formato

778-790

Identificador

http://dx.doi.org/10.1101/gr.133967.111

Genome Research. Cold Spring Harbor: Cold Spring Harbor Lab Press, Publications Dept, v. 22, n. 4, p. 778-790, 2012.

1088-9051

http://hdl.handle.net/11449/42639

10.1101/gr.133967.111

WOS:000302203800018

WOS000302203800018.pdf

Idioma(s)

eng

Publicador

Cold Spring Harbor Lab Press, Publications Dept

Relação

Genome Research

Direitos

closedAccess

Tipo

info:eu-repo/semantics/article