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Development of 49 novel microsatellite markers from Next-generation sequencing data and a robust method for parentage tests in the emu (Dromaius novaehollandiae).

Development of 49 novel microsatellite markers from Next-generation sequencing data and a robust method for parentage tests in the emu (Dromaius novaehollandiae).

Authors :
Koshiishi Y
Uchiyama H
Murata-Okubo M
Tanaka K
Kameyama Y
Hirayama H
Wada K
Source :
Gene [Gene] 2021 Feb 15; Vol. 769, pp. 145238. Date of Electronic Publication: 2020 Oct 15.
Publication Year :
2021

Abstract

The emu is a useful and new breed of poultry, but their genetic improvement has not advanced yet due to their very recent domestication. Pedigree information is difficult to record because of their complex reproduction system (polyandry). To identify parent-offspring relationships in the emu, parentage test based on polymorphic DNA markers have to be developed. In this study, we isolated more than 25,000 microsatellite (simple sequence repeat, SSR) regions from Next-generation sequencing data via the QDD pipeline and developed 49 SSR markers with polymorphism in the Japanese farmed emu. The dinucleotide motifs, (AC) <subscript>n</subscript> , (AT) <subscript>n</subscript> and (AG) <subscript>n</subscript> , were the most frequently detected and were found on 10,167 (38.55%), 8,114 (30.76%) and 4,796 (18.18%) contigs, respectively. Forty-nine novel SSR markers were characterized in 20 individuals and showed N <subscript>A</subscript> ranged from 2 to 12, with an average of 4.2. H <subscript>E</subscript> /H <subscript>O</subscript> ranged from 0.389/0.071 to 0.702/1.000 with an average of 0.601/0.515. PIC value ranged from 0.059 to 0.886 with an average of 0.528, and 17 of 49 markers showed a higher polymorphism than 0.500. Thirty-four individuals were genotyped using 12 markers, and CERVUS simulations based on genotype showed that parents of all offspring were identified with 0.9995-1.0 probability. Thus, 49 novel SSR markers and a robust method for parentage test for the Japanese emu were developed.<br /> (Copyright © 2020 Elsevier B.V. All rights reserved.)

Details

Language :
English
ISSN :
1879-0038
Volume :
769
Database :
MEDLINE
Journal :
Gene
Publication Type :
Academic Journal
Accession number :
33068676
Full Text :
https://doi.org/10.1016/j.gene.2020.145238