High-throughput single nucleotide polymorphism genotyping reveals population structure and genetic diversity of tall fescue (Festuca arundinacea) populations
Zeynab Shahabzadeh A , Reza Darvishzadeh A * , Reza Mohammadi
B , Morad Jafari A and Hadi Alipour A *
+ Author Affiliations
- Author Affiliations
A Department of Plant Production and Genetics, Faculty of Agriculture, Urmia University, Urmia, Iran.
B Branch for Northwest & West Region, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Tabriz, Iran.
* Correspondence to: r.darvishzadeh@urmia.ac.ir, ha.alipour@urmia.ac.ir
Handling Editor: Rajeev Varshney
Crop & Pasture Science 73(9) 1070-1084 https://doi.org/10.1071/CP21311
Submitted: 4 May 2021 Accepted: 2 February 2022 Published: 28 March 2022
© 2022 The Author(s) (or their employer(s)). Published by CSIRO Publishing
Abstract
Single nucleotide polymorphisms (SNPs) are the most abundant form of genetic variation in eukaryote genomes and may be useful for selection of genetically distant parents for crossing in breeding programs. In this study, genome-wide SNPs of tall fescue (Festuca arundinacea Schreb.) were genotyped by using double-digest restriction-site-associated DNA sequencing to determine the genetic variation and differentiation among and within forage, turf and hybrid populations. After filtering, 16 036 SNPs were used to investigate genetic diversity and for structure analysis. SNP markers clearly differentiated the populations from each other. However, the hybrid population had a higher genetic similarity with the turf population than with the forage population. The results were confirmed by genetic differentiation (fixation index, Fst) and gene flow (Nm) statistics, so that low Fst and high Nm were observed between turf and hybrid groups, indicating less genetic distance and a high similarity between them. Based on the results of the weighted pair group method with arithmetic mean clustering, discriminant analysis of principal components and analysis of molecular variance, greater genetic differentiations were found among diverse turf, forage and hybrid populations, especially between turf and forage ones. In conclusion, numerous informative SNPs, natural allelic diversity-led domestication patterns, basic genetic variation statistics (e.g. Fst and heterozygosity) and population structures have multidimensional applicability for tall fescue genomics-assisted breeding.
Keywords: AMOVA, ddRAD, fixation index, genetic differentiation, gene flow, genome-wide SNPs, structure, tall fescue.
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