Abstract
Armeniaca sibirica L. (Rosaceae) was once an economically important species in China, but the amount of natural germplasm of A. sibirica recently declined dramatically as a consequence of habitat fragmentation and overharvesting; this species has now been listed as endangered in the China Plant Red Data Book. In this study, 72 polymorphic single nucleotide polymorphism (SNP) markers were developed in A. sibirica based on its transcriptome and characterized by genotyping 70 individuals using the SNaPshot method. The minor allele frequency varied from 0.102 to 0.516, and the observed heterozygosity, expected heterozygosity, and polymorphism information content ranged from 0.052 to 0.649, 0.186 to 0.617, and 0.105 to 0.452, respectively. Among these SNPs, seven loci deviated significantly from the Hardy–Weinberg equilibrium after Bonferroni correction (p < 0.05). These novel SNPs can be useful for future population and conservation genetics studies on this species.
This is a preview of subscription content, log in via an institution to check access.
References
Bao WQ, Wuyun TN, Wang L, Zhao H, Du HY (2016) Genetic diversity and population genetic structure of siberian apricot in Inner Mongolia. Acta Bot Boreal-Occident Sin 36:2182–2191. https://doi.org/10.7606/j.issn.1000-4025.2016.11.2182
Bao WQ, Wuyun TN, Du HY, Li TZ, Liu HM, Wang L, Bai YE (2018) Genetic diversity and population structure of Amygdalus mira in the Tibet plateau in China based on SSR markers. Sci Silvae Sin 54:30–41. https://doi.org/10.11707/j.1001-7488.20180204
Chaves CL, Blanc-Jolivet C, Sebbenn AM, Mader M, Meyer-Sand BRV, Paredes-Villanueva K, Honorio EN, Garcia-Davila C, Tysklind N, Troispoux V, Massot M, Degen B (2018) Nuclear and chloroplastic SNP markers for genetic studies of timber origin for Hymenaea trees. Conserv Genet Resour 11:329–331. https://doi.org/10.1007/s12686-018-1077-1
Excoffier L (2005) Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evol Bioinform. https://doi.org/10.1177/117693430500100003
Fan JJ, Bai JJ, Ma DM (2018) Isolation and characterization of 40 SNP in largemouth bass (Micropterus salmoides). Conserv Genet Resour. https://doi.org/10.1007/s12686-018-1076-2
Honorio Coronado EN, Blanc-Jolivet C, Mader M, García-Dávila CR, Sebbenn AM, Meyer-Sand BRV, Paredes-Villanueva K, Tysklind N, Troispoux V, Massot M, Degen B (2019) Development of nuclear and plastid SNP markers for genetic studies of Dipteryx tree species in Amazonia. Conserv Genet Resour 11:333–336. https://doi.org/10.1007/s12686-019-01081-3
Li WG, Liu S, Jiang ST, Li XL, Li G (2017) Development of 30 SNP markers for the endangered plant Taihangia rupestris based on transcriptome database and high resolution melting analysis. Conserv Genet Resour 10:775–778. https://doi.org/10.1007/s12686-017-0927-6
Meyer-Sand BRV, Blanc-Joliver C, Mader M, Paredes-Villanueva K, Tysklind N, Sebbenn AM, Guichoux E, Degen B (2017) Development of a set of SNP markers for population genetics studies of Ipe (Handroanthus sp.), a valuable tree genus from Latin America. Conserv Genet Resour 10:779–781. https://doi.org/10.1007/s12686-017-0928-5
Song C, Wuyun TN, Li H, Xu JS, Liu RQ (2015) The analysis of digital gene expression about kernel apricot flower buds at three development stages. Acta Hortic Sin 42:1559–1568. https://doi.org/10.16420/j.issn.0513-353x.2015-0176
Wang Z, Kang M, Liu HB, Gao J, Zhang ZD, Li YY, Wu RL, Pang XM (2014) High-level genetic diversity and complex population structure of Siberian apricot (Prunus sibirica L.) in China as revealed by nuclear SSR markers. PLoS ONE 9:e87381. https://doi.org/10.1371/journal.pone.0087381
Wang CD, Zhao LJ, Su CQ, Liu QG (2018) Isolation and characterization of SNPs in bighead carp. Conserv Genet Resour 10:149–152. https://doi.org/10.1007/s12686-017-0783-4
Yeh F, Yang R, Boyle T, Ye Z, Xiyan J (2000) POPGENE 32, Microsoft windows-based freeware for population genetic analysis. Molecular Biology and Biotechnology Centre, University of Alberta, Edmonton
Yin MY, Wuyun TN, Jiang ZM, Zeng J (2019) Amino acid profiles and protein quality of Siberian apricot (Prunus sibirica L.) kernels from Inner Mongolia. J For Res 18:1–7. https://doi.org/10.1007/s11676-019-00882-4
Acknowledgements
This study was funded by the Research Fund for Young Teachers of the College of Forestry of the Inner Mongolia Agricultural University (Grant Number 203-170007), High-Level Talent Introduction Project of the Inner Mongolia Agricultural University (Grant Number NDYB2017-9), Natural Science Foundation of the Inner Mongolia Autonomous Region (Grant Number 2019BS03019), and National Natural Key R&D Program of China (Grant Number 2018YFD1000606-3).
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Conflict of interest
The authors declare that they have no conflict of interest.
Additional information
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Rights and permissions
About this article
Cite this article
Bao, W., Ao, D., Wuyun, T. et al. Development and characterization of 72 SNP markers in Armeniaca sibirica based on transcriptomics. Conservation Genet Resour 12, 373–378 (2020). https://doi.org/10.1007/s12686-019-01122-x
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s12686-019-01122-x