Assessing the genetic diversity conserved in the Norwegian live poultry genebank

Figures & data

Table 1. Number of genotyped individuals after quality control.

Line	Abbrev.	# Individuals	# Males	# Females
Jærhøns	JH	19	5	14
Rokohoens	RK	20	5	15
Norbrid 1	NB1	20	5	15
Norbrid 4	NB4	18	5	13
Norbrid 7	NB7	18	4	14
Norbrid 8	NB8	17	5	12
Barred Plymouth Rock	TPR	19	5	14
Red Rhode Island	RRI	19	4	15
Lohmann white	LMW	18	0	18
Lohmann brown	LMB	19	0	19
Total		187	38	149

Note: The total number of individuals as well as number of females and males of the eight genetic lines from the live poultry gene bank at Hvam and the two commercial production lines, Lohmann white and brown, are listed.

Table 2. An overview of the genetic lines in the Synbreed data set (Weigend et al. 2014).

Origin	Type	Lines
Asia	Long-tailed breeds	PHxx, SAsch, YOwr
	Game type and related breeds	ASrb, IKxx, Maxx, OFrbx, SHsch
	Asian type breeds	BHrg, BHwsch, COsch, DLIa, MRschk, NHbr, NHL68, ORge, PRgp, ROro, SNwsch, TOgh, WYsschs, WYw
	Crested breeds	SEsch, Sew
	Bantam breeds	CHgesch, CHschw, KSgw, OHgh, OHsh, ZCsch, ZCw
Europe	Intermediate type breeds	ARsch, ARwi, DOxx, VWco, VWcoE
	Mediterranean type breeds	ITrh, ITsch, KAsch, LER11, LEw, Misch
	Northwest-European breeds	AKxx, BKschg, BLxx, BSsch, DSgp, FRgew, HAsI, KRsch, KRw, LAco, OMsschg, RHrh, RHsch, THsch, WTs
	Crested breeds	APsscht, HOxx, PAxx
	Bantam breeds	ABwa, BAsch, DZgh, FZgpo, FZsch, GBxx, SBgschs, SBsschs
Wild	Gallus gallus gallus	GGg
	Gallus gallus spadiceus	GGsc
Line abbreviations
Bwa – Barbue d'Anvers quail AKxx – Carlise Old English Game any colour APsscht – Appenzeller Pointed Hood silver spangled ARsch – Rumpless Araucana black ARwi – Rumpless Araucana black breasted red ASrb – Aseel red mottled BAsch – Rosecomb Bantam black BHrg – Brahma gold BHwsch – Brahma light BKschg – Bergische Crower BLxx – Brakel silver BSsch – Berg-Schlotter black CHgesch – Japanese Bantam black tailed buff CHschw – Japanese Bantam black mottled COsch – Cochin black DLIa – German Faverolles salmon DOxx – Dorking any colour DSgp – German Grey Chickens cuckoo DZgh – German Bantam gold partridge FRgew – Frisian Fowl chamois penciled FZgpo – Booted Bantam millefleur FZsch – Booted Bantam black GBxx – Barbue du Grubbe any color HAsl – Hamburgh silver spangled HOxx – Poland White Crested black IKxx – Indian Game dark ITrh – Leghorn brown ITsch – Leghorn black KAsch – Castilians black KRsch – Creeper black KRw – Creeper white KSgw – Ko Shamo black-red LAco – Lakenvelder black and white LER11 – White Leghorn line R11 LEw – White Leghorn Maxx – Malay black red Misch – Minorca black		MRschk – Marans copper black NHbr – New Hampshire red NHL68 – New Hampshire line 68 OFrbx – Orloff red spangled OHgh – Ohiki red duckwing OHsh – Ohiki silver duckwing OMsschg – East Friesian Gulls silver pencilled ORge – Orpington buff PAxx – Poland any color PHxx – Phoenix golden or golden duckwing PRgp – Plymouth Rocks barred RHrh – Rhinelander Chicken brown RHsch – Rhinelander Chicken black ROro – Rhode Island Red red SAsch – Sumatra black SBgschs – Sebright Bantam golden SBsschs – Sebright Bantam silver SEsch – Silkies black SEw – Silkies white SHsch – Shamo black SNwsch – Sundheimer light THsch – Thuringian Bearded Chicken black TOgh – Toutenkou black breasted red VWco – Vorwerk buff columbian VWcoE – Vorwerk conservation program WTs – Westphalian Chicken silver WYsschs – Wyandotte silver laced WYw – Wyandotte white YOwr – Y okohama red saddled white ZCsch – Pekin Bantam black ZCw – Pekin Bantam white Ggg – Gallus gallus gallus Gsc – Gallus gallus spadiceus

Table 3. Genotyping quality controls performed in PLINK1.9. Filtering was carried out on the lines with >2 individuals per line, i.e. lines from the Norwegian genebank plus the commercial Lohmann lines.

Filter	# SNPs left	# SNPs removed
Initial data set	580,961	0
Duplicate probe sets	580,917	44
Deviation from HWE p < 0.001 and SNP missing call rates within lines (>10%) and overall (>9%)	481,748	99,169
Minor allele count <1	457,684	24,064
Only autosomes	448,723	8961

Table 4. Number of lines, individuals and SNPs in the final data sets used in the different analyses.

Final data sets	# Lines	# Males	# Females	# SNPS	Analyses
Genebank
Full	8	38	112	448,723	G-matrix, Ne
International
Full	80	108	219	448,718	Core set
LD-pruned, 2 per line	80	78	82	133,118	PCA
LD-pruned, Genebank + Lohmann	10	38	149	42,016	Fst, Admixture

Figure 1. Heatmap presenting the 8 × 8 genomic relationship matrix with average genomic relationships within and between the lines at the Norwegian gene bank. A lighter shade reflects higher relationship estimates. The ordering of the lines follows the clustering in the dendrogram.

Table 5. Means and standard deviations of the genomic inbreeding coefficient (F) and observed heterozygosity (Ho) within the genetic lines at the genebank.

Genetic line	# Ind	Mean (F) ± SD	Ho
Jærhøns	19	0.70 ± 0.02	0.30
Norbrid 1	20	0.64 ± 0.02	0.36
Norbrid 4	18	0.68 ± 0.02	0.32
Norbrid 7	18	0.59 ± 0.03	0.41
Norbrid 8	17	0.63 ± 0.03	0.37
Rokohoens	20	0.64 ± 0.03	0.36
Red Rhode Island	19	0.54 ± 0.03	0.46
Barred Plymouth Rock	19	0.65 ± 0.01	0.35

Figure 2. Graphic presentation of the matrix containing genomic relationships within and between lines in the International data set. Colour is dependent on the genomic relationship estimate, where a lighter colour towards yellow reflects a higher relationship estimate. The ordering of the lines is decided by the clustering in the dendrogram.

Table 6. Relative loss of genetic diversity when a line is lost from the genebank data set and priority ranking for conservation of genetic diversity.

Set(S)	Div(S)	% Lost	Priority
Genebank	0.6962
Genebank – 1
Jærhøns	0.6926	0.52	6
Rokohoens	0.6934	0.41	7
Norbrid 1	0.6894	0.97	4
Norbrid 4	0.6941	0.30	8
Norbrid 7	0.6804	2.27	1
Norbrid 8	0.6907	0.79	5
Red Rhode Island	0.6890	1.03	3
Barred Plymouth Rock	0.6867	1.37	2

Notes: Div(S) is the genetic diversity in a set S (5). Losses are calculated relative to genetic diversity in the full set.

Table 7. The relative gain in genetic diversity when a gene bank line is added to the core set consisting of the international set excluding the genebank lines.

Set(S)	Div(S)	% Gained	Priority
Core Set (International excluding genebank)	0.726855
Core Set + 1
Jærhøns	0.726904	0.0067	8
Rokohoens	0.727092	0.0326	4
Norbrid1	0.727203	0.0478	3
Norbrid4	0.727010	0.0213	6
Norbrid7	0.727529	0.0925	1
Norbrid8	0.727008	0.0210	7
Red Rhode Island	0.727084	0.0314	5
Barred Plymouth Rock	0.727300	0.0611	2

Notes: Priority ranking for conservation of genetic diversity. Div(S) is the genetic diversity in a set S (5).

Table 8. The Relative gain in genetic diversity when a gene bank line is added to the core set consisting of the international set excluding the Lohmann and genebank lines.

Set(S)	Diversity(S)	% Gained	Priority
Core set (International excluding genebank and Lohmann lines)	0.71621
Genebank + 1
Jærhøns	0.71630	0.013	8
Rokohoens	0.71668	0.065	6
Norbrid 1	0.71755	0.187	4
Norbrid 4	0.71658	0.052	7
Norbrid 7	0.72098	0.661	1
Norbrid 8	0.71861	0.334	2
Red Rhode Island	0.71757	0.189	3
Barred Plymouth Rock	0.71670	0.068	5

Notes: Priority ranking for conservation of genetic diversity. Div(S) is the genetic diversity in a set S (5).

Table 9. Pair-wise Fst values between 10 chicken lines based on the LD-pruned Genebank + Lohmann data set.

	JH	LMB	LMW	NB1	NB4	NB7	NB8	RK	RRI	TPR
JH
LMB	0.413
LMW	0.447	0.346
NB1	0.487	0.376	0.299
NB4	0.505	0.394	0.401	0.440
NB7	0.518	0.231	0.445	0.475	0.497
NB8	0.532	0.262	0.456	0.490	0.512	0.445
RK	0.466	0.364	0.367	0.403	0.382	0.464	0.477
RRI	0.473	0.248	0.403	0.435	0.454	0.388	0.327	0.421
TPR	0.534	0.367	0.466	0.497	0.520	0.480	0.491	0.484	0.426

Notes: The lower half of the matrix shows the Fst values, while the top half shows the 95% lower and upper bound confidence intervals calculated from bootstrapping. All p-values <0.0001.

Figure 3. Individual ancestry estimates for the eight Norwegian genebank lines and the two commercial crossbred layer lines based on an LD-pruned data set for K=2, 6, 9 and 10. Mean similarity score and mean Log-Likelihood value of the 50 replicate runs is given. Each bar represents an individual and genetic lines, labelled at the bottom, are separated by black lines. Colours correspond to the 2, 6, 9 or 10 different presumed ancestries.

Figure 4. Plot of principal component (PC) 1 against PC 2 based on an LD-pruned data set for two individuals of 80 genetic lines. Individuals are coloured according to the type of their breed/line. The Norwegian genebank lines are marked in a separate light blue colour.

Figure 5. NeighborNet of the eight Norwegian genebank lines and the two commercial crossbred layer lines based on population (line) level Fst values. The main split separates white from brown egg layers.

Figure 6. Effective population size estimates 13 generations ago, the most recent generation possible to estimate, for all gene bank lines.

Figure 7. Historical effective population size levels from 30 to 13 generations ago for all the gene bank lines.

Weigend, S., Janßen-Tapken, U., Erbe, M., Baulain, U., Weigend, A., Sölkner, J. & Simianer, H. (2014). Genome-wide analyses of genetic diversity and phylogenetic relationships in the Synbreed Chicken Diversity Panel. In Proceedings XIV (Stavanger), pp. 164–176.

 Google Scholar

Data availability

The data that support the findings of this study are available from the corresponding author, CB, upon reasonable request.