Home About Browse Search
Svenska


Insights Into the Genetic Diversity of Nordic Red Clover (Trifolium pratense) Revealed by SeqSNP-Based Genic Markers

Osterman, Johanna and Hammenhag, Cecilia and Ortiz, Rodomiro and Geleta, Mulatu Dida (2021). Insights Into the Genetic Diversity of Nordic Red Clover (Trifolium pratense) Revealed by SeqSNP-Based Genic Markers. Frontiers in Plant Science. 12 , 748750
[Research article]

[img] PDF
4MB

Abstract

Red clover (Trifolium pratense) is one of the most important fodder crops worldwide. The knowledge of genetic diversity among red clover populations, however, is under development. This study provides insights into its genetic diversity, using single nucleotide polymorphism (SNP) markers to define population structure in wild and cultivated red clover. Twenty-nine accessions representing the genetic resources available at NordGen (the Nordic gene bank) and Lantmännen (a Swedish agricultural company with a red clover breeding program) were used for this study. Genotyping was performed via SeqSNP, a targeted genotype by sequencing method that offers the capability to target specific SNP loci and enables de novo discovery of new SNPs. The SNPs were identified through a SNP mining approach based on coding sequences of red clover genes known for their involvement in development and stress responses. After filtering the genotypic data using various criteria, 623 bi-allelic SNPs, including 327 originally targeted and 296 de novo discovered SNPs were used for population genetics analyses. Seventy-one of the SNP loci were under selection considering both Hardy-Weinberg equilibrium and pairwise FST distributions. The average observed heterozygosity (HO), within population diversity (HS) and overall diversity (HT) were 0.22, 0.21 and 0.22, respectively. The tetraploids had higher average HO (0.35) than diploids (0.21). The analysis of molecular variance (AMOVA) showed low but significant variation among accessions (5.4%; P < 0.001), and among diploids and tetraploids (1.08%; P = 0.02). This study revealed a low mean inbreeding coefficient (FIS = −0.04) exhibiting the strict outcrossing nature of red clover. As per cluster, principal coordinate and discriminant analyses, most wild populations were grouped together and were clearly differentiated from the cultivated types. The cultivated types of red clover had a similar level of genetic diversity, suggesting that modern red clover breeding programs did not negatively affect genetic diversity or population structure. Hence, the breeding material used by Lantmännen represents the major genetic resources in Scandinavia. This knowledge of how different types of red clover accessions relate to each other and the level of outcrossing and heterozygosity will be useful for future red clover breeding.

Authors/Creators:Osterman, Johanna and Hammenhag, Cecilia and Ortiz, Rodomiro and Geleta, Mulatu Dida
Title:Insights Into the Genetic Diversity of Nordic Red Clover (Trifolium pratense) Revealed by SeqSNP-Based Genic Markers
Series Name/Journal:Frontiers in Plant Science
Year of publishing :2021
Volume:12
Article number:748750
Number of Pages:18
ISSN:1664-462X
Language:English
Publication Type:Research article
Article category:Scientific peer reviewed
Version:Published version
Copyright:Creative Commons: Attribution 4.0
Full Text Status:Public
Subjects:(A) Swedish standard research categories 2011 > 4 Agricultural Sciences > 401 Agricultural, Forestry and Fisheries > Agricultural Science
(A) Swedish standard research categories 2011 > 4 Agricultural Sciences > 404 Agricultural Biotechnology > Genetics and Breeding
(A) Swedish standard research categories 2011 > 4 Agricultural Sciences > 404 Agricultural Biotechnology > Plant Biotechnology
Keywords:DAPC, gene targeting markers, heterozygosity:loci under selection:population structure:red clover, SeqSNP
URN:NBN:urn:nbn:se:slu:epsilon-p-114125
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-p-114125
Additional ID:
Type of IDID
DOI10.3389/fpls.2021.748750
ID Code:26079
Faculty:LTV - Fakulteten för landskapsarkitektur, trädgårds- och växtproduktionsvetenskap
Department:(LTJ, LTV) > Department of Plant Breeding (from 130101)
Deposited By: SLUpub Connector
Deposited On:08 Nov 2021 11:25
Metadata Last Modified:08 Nov 2021 11:31

Repository Staff Only: item control page

Downloads

Downloads per year (since September 2012)

View more statistics

Downloads
Hits