genetic diversity and population structure in nordic...
TRANSCRIPT
Objective: to lay the foundation for effective cereal breeding for disease
resistance and harvest stability in changing climatic conditions capable to meet current and future challenges in the Nordic region.
Genetic Diversity and Population Structure in Nordic Spring Barley
T. Bengtsson 1, PPP Barley Consortium 1-8, G. Backes9, A. Jahoor 1,6, J. Orabi 6 Affiliations for participants: 1 Department of Plant Breeding, Swedish University of Agricultural Sciences, Box 101, 230 53 Alnarp, Sweden, 2 Boreal Plant Breeding Ltd, Myllytie 10, 31600 Jokioinen, Finland, 3 Graminor AS, Hommelstadvegen 60, 2322 Ridabu, Norway, 4 Lantmännen Lantbruk, von Troils väg , 213 37 Malmö, Sweden, 5 Natural Resources Institute Finland (Luke), Viikinkaari 4, 00790 Helsinki, Finland, 6 Nordic Seed A/S, Kornmarken 1, 8464 Galten, Denmark, 7 Sejet Plant Breeding, Nørremarksvej 67, 8700 Horsens, Denmark, 8 The Agricultural University of Iceland, Hvanneyri, 311 Borgarnes, Iceland, 9 Organic Agricultural Sciences, Universität Kassel, Steinstr. 19, 37213 Witzenhausen, Germany. Corresponding author: [email protected], +46 (0) 40-41 53 55
Linkage Disequilibrium (LD) decay in cM
Interval of the estimated LD decay (cM) in the total population and the different sub-groups. was calculated using TASSEL 3.0 software (http.//www.maizegenetics.net) . Only intra-chromosomal comparisons were included and markers with minor allele frequency (MAF) below 0.05 were excluded. a The 95th percentile of unlinked (above 50 cM) square root transformed r2 values.
Population Structure
Analysis of molecular variance (AMOVA) for the different structure groups (p=0.001) based on the SNP marker set. Calculated using GenAlEx v. 6.5.0.1 (Peakall & Smouse 2006, 2012).
To determine population structure of the barley panel, based on SNP markers, the software package STRUCTURE v.2.3.4 based on a Bayesian clustering approach, was used (Pritchard et al. 2000). Plot generated in STRUCTURE Harvester showing Evanno´s delta K statistic for the estimation of the number of groups. ∆K over K from 2-10 with the whole SNP marker set of 6208 markers.
-20,000
-15,000
-10,000
-5,000
0,000
5,000
10,000
15,000
20,000
-20,000 -15,000 -10,000 -5,000 0,000 5,000 10,000 15,000
PC2
5.9
%)
PC1 (24.6 %)
Group I
Group II
Group III
Group IV
Group V
Group VI
Associations between structure groups revealed by principal coordinate analysis of the Nordic spring barley collection based on the SNP data. ● ; two-rowed, ▲; six-rowed. Calculated using GenAlEx v. 6.5.0.1 (Peakall and Smouse 2006, 2012).
Three groups
Six groups
Eight groups
df SS MS Est. Var. % df SS MS Est.
Var. % df SS MS Est. Var. %
Among Pops 2 46908 23454 448 9 5 259457 51891 1790 37 7 287790 41113 1875 39
Within Pops 166 717269 4321 4321 91 163 504719 3096 3096 63 161 476388 2959 2959 61
Total 168 764178 4769 100 168 764176 4886 100 168 764178 4834 100
Summary
Studying the population structure and the LD decay is prerequisite to run and understand the results of a genome-wide association study (GWAS) and to identify markers linked with traits of interest. In this study the aim was to determine the population structure and the LD decay in Nordic spring barley collection using 9k barley SNP array. The results show that the collection is divided into six sub-groups with a clear genetic structure, largely depending on the row-type, but also on geographical locations. The highest number of private alleles was found within the six-rowed lines (Group IV) and a more rapid LD decay was found in the six-rowed lines and the two-rowed lines from the northern region (Group II & VI) compared to the two-rowed lines from the southern region (Group I, III & V), indicating a more diverse genetic base for breeding in the North. A rapid LD decay was found on 2H, 4H and 7H that might be due to introduction of important traits incorporated during breeding e.g. vrs1 locus controlling the row type (2H) , mlo and the spring growth habit gene sgh1 (4H) and naked caryopsis gene nud and early flowering gene sgh3 (7H).
Chromosome
Total population
Two-rowed lines
Six-rowed lines
Group I
Group II
Group III
Group IV
Group V
Group VI
1H 0-3 5.5-9 0-3 2.5-6 0-3 2.5-6 0-3 2.5-6 0-3
2H 0-3.5 0-3.5 0-3.5 0-3.5 0-3.5 3-6.5 0-3.5 6-10 0-3.5
3H 3.5-7 10.5-14 0-3.5 7-10.5 3.5-7 0-3.5 0-3.5 3.5-7 0-3.5
4H 0-2.5 0-2.5 0-2.5 0-2.5 0-2.5 2.5-5 0-2.5 4.5-7.5 0-2.5
5H 0-4 0-4 4-8 0-4 0-4 0-3.5 4-8 8-12 0-4
6H 0-3 7.5-10.5 0-3 2.5-5.5 7.5-10.5 5-8 0-3 2.5-
5.5 0-3
7H 0-3.5 0-3.5 0-3.5 2.5-5.5 0-3.5 0-3.5 0-3.5 0-3.5 ---
Whole genome 0-4 4-8 0-4 2.5-6 0-4 4-8 0-4 4-8 0-4
Background LDa whole genome
0.202 0.159 0.194 0.158 0.232 0.184 0.194 0.200 0.315
Private alleles and genetic diversity for the breeder groups and the whole barley panel
Diversity
PPP barley field trial, Iceland 2012. Photo: Magnus Göransson
Acknowledgment: This study is a part of the Public Private Partnership (PPP) on pre-breeding initiated and financed by the Nordic Council of Ministers.
References: Botstein et al., 1980. American journal of human genetics 32:314; Earl et al., 2012. Conservation Genet Resour 4:359-361 doi:10.1007/s12686-011-9548-7; Evanno et al., 2005. Molecular ecology 14:2611-2620; Peakall & Smouse 2006. Molecular ecology notes 6:288-295; Peakall & Smouse 2012. Bioinformatics 28:2537-2539 doi:10.1093/bioinformatics/bts460; Mantel, 1967. Cancer Research 27:209-220; Pritchard et al., 2000. Genetics 155:945-959; Reif et al., 2005. Crop Science 45:1-7, Wright, 1978. University of Chicago Press .
Group
Population size
Nr of Two-rows
Nr of Six-rows
Average number of alleles per
locus
Nr of private alleles
Genetic Diversity 𝑯𝑯�
Standard deviation
of 𝑯𝑯�
I 40
40
--- 1.8 34 0.279 0.216
II
17
17
--- 1.7 6 0.252 0.363
III
30
30
--- 1.8 6 0.252 0.297
IV
45
---
45 1.8 447 0.225 0.233
V
22
22
--- 1.7 3 0.200 0.365
VI
15
15
--- 1.6 11 0.200 0.473
Total
169
124
45 0.359 0.448
P P P Public-Private Partnership in Pre-Breeding
Combining Knowledge from Field and Laboratory for Pre-Breeding in Barley