Phylogeny, Genetic Relationships and Population Structure of Five Italian Local Chicken Breeds

Figures & data

Figure 1. Geographical sampling areas.

Figure 2. Median-Joining network tree for the twelve haplotypes of Italian chicken breeds and the nine reference sequences by Liu et al. (2006) based on the polymorphic sites of the mitochondrial D-loop region. Circled areas are proportional to the haplotype frequencies.

Figure 3. Neighbour-joining tree obtained from the Reynolds’ genetic distances among five Italian chicken breeds (1000 bootstraps). Bootstrap values above 50% are shown at each node. AN, Ancona; LI, Livornese bianca; MO, Modenese; RO, Romagnola; VA, Valdarnese bianca; WLA, white egg layer line A; LSS, white egg layer experimental line; BLA, brown egg layer line A; BLC, brown egg layer line C; BRDA, broiler dam line A; BRSA, broiler sire line A.

Figure 4. STRUCTURE cluster analysis of the samples. AN, Ancona; LI, Livornese bianca; MO, Modenese; RO, Romagnola; VA, Valdarnese bianca; WLA, white egg layer line A; LSS, white egg layer experimental line; BLA, brown egg layer line A; BLC, brown egg layer line C; BRDA, broiler dam line A; BRSA, broiler sire line A.

Table 1. Microsatellite loci, chromosomal position, size range and number of alleles observed at each locus.

Locus	Chr	Size range(bp)	Na	Locus	Chr	Size range (bp)	Na
MCW0248	1	215-223	2	MCW0078	5	135-145	4
MCW0111	1	98-114	7	MCW0081	5	112-135	8
ADL0268	1	104-116	4	MCW0014	6	164-182	7
MCW0020	1	179-185	4	MCW0183	7	296-326	8
MCW0206	2	223-249	6	ADL0278	8	114-124	4
MCW0034	2	220-242	11	MCW0067	10	174-184	5
MCW0222	3	220-226	4	ADL0112	10	122-132	4
MCW0103	3	266-270	2	MCW0216	13	141-147	4
MCW0016	3	144-184	7	MCW0104	13	178-226	9
LEI0166	3	356-366	3	MCW0123	14	80-94	7
MCW0037	3	154-158	3	MCW0330	17	258-290	4
MCW0295	4	88-106	6	MCW0165	23	114-118	3
LEI0094	4	247-285	11	MCW0069	26	158-170	7
MCW0098	4	261-265	3

Table 2. mtDNA diversity indices of the five Italian chicken breeds.

	N	π	nh	Hd	S
Ancona	10	0.0000±0.0000	1	0.0000±0.0000	0
Livornese	10	0.0097±0.0018	3	0.6390±0.1260	11
Modenese	10	0.0045±0.0027	3	0.6000±0.1310	10
Romagnola	10	0.0007±0.0004	3	0.3780±0.1810	2
Valdarnese	10	0.0029±0.0003	5	0.8440±0.0800	4
Overall	50	0.0045±0.0013	12	0.7250±0.0650	18

N, number of used sequences; π, nucleotide diversity; nh, number of haplotypes; Hd, haplotype diversity; S, number of segregation sites.

Table 3. Nucleotide polymorphisms observed in the D-loop region of 50 chicken sequences.

	N	167	199	210	212	217	225	243	246	256	261	264	281	296	306	310	315	330	342	347	439	446	492
Ref. sequence		T	T	C	G	T	C	C	C	C	T	C	G	T	C	T	C	C	G	A	C	C	C
Ancona	10	.	.	.	.	C	.	.	.	.	.	.	A	C	T	.	.	.	A	.	.	T	.
Livornese bianca	1	C	.	T	.	.	T	T	.	T	C	.	A	C	T	.	.	.	A	.	.	.	.
Livornese bianca	3	.	.	.	A	.	.	T	T	T	C	.	A	C	T	C	T	.	A	.	.	.	.
Livornese bianca	6	.	.	.	.	C	.	T	.	.	.	.	A	C	T	.	.	.	A	.	.	T	.
Modenese	1	C	.	T	.	.	T	T	.	T	C	.	A	C	T	C	.	.	A	.	.	.	.
Modenese	3	.	.	.	.	C	.	.	.	.	.	T	A	C	T	.	.	.	A	.	.	T	.
Modenese	6	.	.	.	.	C	.	.	.	.	.	.	A	C	T	.	.	.	A	.	.	T	.
Romagnola	1	.	C	.	.	C	.	.	.	.	.	.	A	C	T	.	.	.	A	.	.	T	.
Romagnola	1	.	.	.	.	C	.	.	.	.	.	.	A	C	T	.	.	.	A	G	.	T	.
Romagnola	8	.	.	.	.	C	.	.	.	.	.	.	A	C	T	.	.	.	A	.	.	T	.
Valdarnese	1	.	.	.	.	C	.	.	.	.	.	.	.	C	T	.	.	.	A	.	.	T	.
Valdarnese	1	.	.	.	.	C	.	.	.	.	.	.	A	C	T	.	.	.	A	.	.	T	.
Valdarnese	1	.	.	.	.	C	.	.	.	.	.	.	A	C	T	.	.	T	A	.	.	T	.
Valdarnese	2	.	.	.	.	C	.	.	.	.	.	.	A	C	T	.	.	.	.	.	.	T	.
Valdarnese	2	.	.	.	.	C	.	.	.	.	.	.	.	C	T	.	.	.	A	.	.	T	.
Valdarnese	3	.	.	.	.	C	.	.	T	.	.	.	A	C	T	.	.	.	A	.	.	T	.

N, number of sequences. Vertically oriented numbers indicate the nucleotide position. Only mutated sites are reported in the table. Dots (.) indicate identity with the reference sequence (GenBank accession number NC007236; Nishibori et al., 2005).

Table 4. Results from the hierarchical AMOVA in the five Italian chicken breeds, obtained from mtDNA data.

Source of variation	df	Sum of square	Variance components	Percentage of variation	FST	P
Between breeds	4	21.40	0.449	32.17	0.322	0.001
Within breeds	44	41.70	0.948	67.83

df, degrees of freedom.

Table 5. Chicken breeds studied, sample size of each breed, mean number of observed alleles, mean observed and expected heterozygosity, and inbreeding coefficient per breed.

	Sample size	MNA±SD	HO±SD	HE±SD	FIS
Ancona	30	3.26±1.10	0.39±0.017	0.48±0.041	0.19244^a
Livornese bianca	30	3.11±0.97	0.40±0.019	0.45±0.036	0.10920^a
Modenese	23	2.63±0.93	0.39±0.020	0.39±0.040	-0.00902
Romagnola	24	3.59±1.45	0.47±0.020	0.50±0.040	0.07704
Valdarnese	30	3.67±1.11	0.53±0.018	0.53±0.039	0.00006
Mean value		3.25±0.42	0.43±0.06	0.47±0.05	0.07394

MNA, mean number of observed alleles; HO, mean observed; HE expected heterozygosity; F_IS, inbreeding coefficient.

^aSignificantly different from zero (P<0.05).

Table 6. Overall population, between-population and within-population inbreeding coefficients and their standard errors of the Italian and commercial populations.

Population	FIT±SE	FST±SE	FIS±SE
Italian	0.285±0.026^**	0.225±0.019^**	0.077±0.027^**
Commercial	0.374±0.025^**	0.354±0.025^**	0.030±0.014^*
Overall	0.349±0.017^**	0.314±0.015^**	0.051±0.015^**

F_IT, overall population; F_ST, between-population; F_IS, within-population inbreeding coefficients; F-statistics for the commercial lines was calculated according the genotyping data taken from previous studies using the same microsatellite loci which were made available for this project (Muchadeyi et al., 2007, Mtileni et al., 2011).

^*P<0.05;

^**P<0.01.

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