Mitogenome information in cattle breeding and conservation genetics: Developments and possibilities of the SNP chip

Brajkovic, V.; Hršak, Dalibor; Bradić, L.; Turkalj, K.; Novosel, D.; Ristov, Strahil; Ajmone-Marsan, P.; Colli, L.; Cubric-Curik, V.; Sölkner, J.; Curik, I. (2023) Mitogenome information in cattle breeding and conservation genetics: Developments and possibilities of the SNP chip. Livestock Science, 275 . ISSN 18711413

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Abstract

In contrast to nuclear markers routinely used for genomic selection, mitogenome information has been underutilized for breeding and biodiversity management of cattle populations. Our main goal was to promote the efficient use of mitogenome SNPs contained in commercial high-throughput SNP arrays. In collaboration with NEOGEN Genomics (Lincoln, NE, USA), we integrated 310 SNPs into the commercial GGP Bovine 100K SNP array. In doing so, we demonstrated how mitogenome SNPs can be used in high-throughput arrays to (i) analyze population structure and diversity, (ii) classify bovine haplogroups and identify introgression and/or upgrading, (iii) screen and identify pedigree defects, (iv) impute mitogenome information on maternal lineages to increase statistical power in estimating the effects of mitogenome variation on quantitative production traits, and (v) identify deleterious mutations found in humans. In addition, we have developed protocols and pipelines integrated with the Magellan v2.0 software to enable efficient and routine use of mitogenome information in cattle breeding and genetic diversity management. Finally, we have highlighted some other interesting opportunities for the use of mitogenome information in the near future.

Item Type:	Article
Uncontrolled Keywords:	Bovine SNP chip; Cattle breeding; Diversity management; Mitochondrial DNA; Pedigree verification
Subjects:	BIOTECHNICAL SCIENCES > Agronomy
Divisions:	Division of Electronics
Projects:	Project title Project leader Project code Project type Primjena NGS metoda u procjeni genomske varijabilnosti preživača-ANAGRAMS Vlatka Čubrić Čurik IP-2018-01-8708 HRZZ Napredne metode i tehnologije u znanosti o podatcima i kooperativnim sustavima - IJ za znanost o podatcima- Sven Lončarić KK.01.1.1.01.0009-1 EK
Depositing User:	Strahil Ristov
Date Deposited:	11 Jul 2024 10:50
URI:	http://fulir.irb.hr/id/eprint/8931
DOI:	10.1016/j.livsci.2023.105299

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