Assessing major genes allele frequencies and the genetic diversity of the native Aosta cattle female population

Figures & data

Figure 1. A) Graphical representation of Principal Component Analysis (PCA) result for the three breeds (ARP, ABC and ACH): Principal component 1 (PC_1) vs Principal Component 2 (PC_2) are plotted; B) Graphical representation of Principal Component Analysis (PCA) result limited to ABC and ACH: Principal component 1 (PC_1) vs Principal Component 2 (PC_2) are plotted; C) Aosta breeds Wright’s fixation index - F_ST.

Figure 2. Effective population size (Ne) per generation ago for the ARP and ABCH breeds.

Table 1. Minimum (MIN), maximum (MAX), and average (AVG) values for inbreeding coefficients calculated for the Aosta population.

Inbreeding coefficients	ABCH			ARP
	MIN	MAX	AVG (sd)	MIN	MAX	AVG (sd)
FHOM	−0.078	0.169	0.001 (0.02)	−0.123	0.208	−0.003 (0.03)
FROH*	0.007	0.220	0.056 (0.02)	0.005	0.250	0.064 (0.02)
FROH class ≤2 Mbp	0.007	0.220	0,056 (0.02)	0.005	0.250	0,064 (0,02)
FROH class 2-4 Mbp	0.001	0.172	0,030 (0.02)	0.001	0.209	0,037 (0,02)
FROH class 4-8 Mbp	0.002	0.109	0,012 (0.01)	0.002	0.160	0,016 (0.01)
FROH class 8-16 Mbp	0.003	0.049	0,006 (0.01)	0.003	0.085	0,007 (0.01)
FROH class ≥16 Mbp	0.006	0.009	0,007 (0)	0.006	0.016	0,008 (0)

*F_ROH calculated considering five Runs of Homozygosity (ROH) length (in Mbp) classes.

Table 2. Minimum (MIN), maximum (MAX), and average number (AVG) and length (in bps) of Runs of Homozygosity (ROH) identified in the Aosta population.

	ROH statistics
	N				Length
Breed	Total	Min	Max	Avg (sd)	Min	Max	Avg
ABCH	74,237	11	179	68 (16)	1,000,004	23,005,964	2,023,899
ARP	156,711	9	183	74 (17)	1,000,000	26,380,269	2,125,789

*Average calculated per breed on total ROH length covered for each sample’s genome.

Figure 3. Manhattan plots of the SNPs incidence. Red lines threshold represents the top 1% of SNP defining the ROH_islands.

Table 3. ROH_Islands identified in the ARP breed, with genes mapped in the ROH and associated QTL.

Breed	Chr	From	To	Genes	QTL*
ARP	2	61057756	61281214	CXCR4
ARP	2	61300454	61404353	DARS
ARP	5	18259786	18430163	KITLG	KITLG: Eye area pigmentation (QTL:21151)
ARP	6	69700321	69804132	PDGFRA
ARP	6	69826263	71305377	KIT, KDR, SRD5A3, TMEM165, CLOCK, PDCL2, NMU, EXOC1L, EXOC1	KIT: Eye area pigmentation (QTL:21154; QTL:21160), Somatic cell count (QTL:31634; QTL:31635); KDR: Bovine respiratory disease susceptibility (QTL:137210);
ARP	23	512811	1270657	KHDRBS2	KHDRBS2: Calving ease (maternal) (QTL:51867), Calving ease (QTL:51877), Dairy form (QTL:51868), Daughter pregnancy rate (QTL:51869), Foot angle (QTL:51870), Length of productive life (QTL:51874), Milk fat percentage (QTL:51871), Milk fat yield (QTL:51872), Milk protein percentage (QTL:51875), Net merit (QTL:51873), Rear leg placement - side view (QTL:51876), Somatic cell score (QTL:51878), Stillbirth (QTL:51879), Strength (QTL:51880), Teat length (QTL:51881)

*QTL (Quantitative Trait Loci) annotated in the Animal QTL Database for Cattle (https://www.animalgenome.org/cgi-bin/QTLdb/BT/index).

Table 4. ROH_Islands identified in the ABCH breed, with genes mapped in the ROH and associated QTL.

Breed	Chr	from	to	Genes	QTL*
ABCH	5	17,120,900	18,390,837	C5H12orf50, C5H12orf29, CEP290, TMTC3, KITLG	KITLG: Eye area pigmentation (QTL:21151)
ABCH	6	79,502,698	80,269,768	TECRL
ABCH	19	26,897,393	27,496,286	ASGR2, ASGR1, DLG4, ACADVL, DVL2, PHF23, GABARAP, CTDNEP1, ELP5, CLDN7, SLC2A4, YBX2, EIF5A, GPS2, NEURL4, ACAP1, KCTD11, TMEM95, TNK1, PLSCR3, TMEM256, NLGN2, SPEM1, SPEM2, TMEM102, FGF11, CHRNB1, ZBTB4, SLC35G6, POLR2A, TNFSF12, TNFSF13, SENP3, EIF4A1, CD68, MPDU1, SOX15, FXR2, SAT2, SHBG, ATP1B2, TP53, WRAP53, EFNB3, DNAH2	ACADVL: Bovine respiratory disease susceptibility (QTL:160277); ATP1B2: 305-day milk yield (QTL:14129; QTL:14128), Average daily milk yield (QTL:14134; QTL:14132; QTL:14133), Body temperature (QTL:14130), Milk fat percentage (QTL:14126), Milk protein percentage (QTL:14127), Red blood cell Na+/K + ATPase activity (QTL:14135; QTL:14136), Red blood cell potassium level (QTL:14131)
ABCH	21	497,917	2,006,266	MKRN3, MAGEL2, NDN, SNRPN, SNURF

*QTL (Quantitative Trait Loci) annotated in the Animal QTL Database for Cattle (https://www.animalgenome.org/cgi-bin/QTLdb/BT/index).

Table 5. Genotypic frequencies for milk proteins and the lactoferrin loci.

Milk traits
Trait	Chr	Genotype	Frequency
			ABCH	ARP
α-S1-casein	6	AA	0.644	0.903
		AG	0.314	0.094
		GG	0.042	0.002
β-casein^#	6	A2A2	0,302	0,363
		A2B	0,270	0,023
		A2C	0,000	0,004
		A2E	0,000	0,000
		A2I	0,115	0,131
		A1A1	0,010	0,070
		A1A2	0,109	0,309
		A1B	0,061	0,013
		A1I	0,021	0,065
		BB	0,055	0,000
		BC	0,000	0,000
		BI	0,046	0,007
		II	0,011	0,014
β-lactoglobulin	11	AA	0.100	0.074
		AB	0.411	0.388
		BB	0.489	0.538
K-casein	6	AA	0.352	0.133
		AB	0.490	0.475
		BB	0.158	0.392
Lactoferrin*	22	GG	0.066	0.074
		AG	0.409	0.398
		AA	0.525	0.528

^#The β-casein gene variants have been identified considering the genotypes at the following SNPrs, as suggested by (Chessa et al. 2020): rs433954503, rs43703013, rs43703012, rs109299401, rs43703011, rs721259074 and rs3423226649.

*SNP markers on the GGP Bovine 100K.

Table 6. Genotypic frequencies at loci related to meat quality traits.

Meat traits
Trait	Chr	Genotype	Frequency
			ABCH	ARP
Calpain_316	29	GG	0.853	0.871
		GC	0.137	0.121
		CC	0.010	0.007
Calpain_4751	29	TT	0.307	0.546
		TC	0.502	0.385
		CC	0.190	0.069
CAST_2870*	7	GG	0.143	0.110
		AG	0.478	0.472
		AA	0.379	0.418
CAST_2959*	7	GG	0.005	0.037
		AG	0.105	0.296
		AA	0.890	0.667
Leptin 2FB	4	CC	0.340	0.588
		CT	0.489	0.361
		TT	0.171	0.051
UoGCAST1	7	GG	0.427	0.271
(CAST_282*)		GC	0.443	0.510
		CC	0.130	0.219

*SNP on the GGP Bovine 100K at the Calpastatin (CAST) gene.

Table 7. Genotypic frequencies for fertility traits.

Fertility
Trait^#	Chr	Genotype	Frequency
			ABCH	ARP
COQ9	18	AA	0.343	0.160
rs109301586*		AG	0.508	0.470
		GG	0.149	0.370
MH1	19	CC	0.958	0.997
		CT	0.042	0.003
		TT	0.000	0.000
PKP2-988*	5	DD	0.065	0.161
		DI	0.357	0.469
		II	0.578	0.370
STAT3_25402*	19	GG	0.034	0.018
		GT	0.283	0.258
		TT	0.683	0.724
STAT3_19069*	19	CC	0.027	0.019
		CT	0.247	0.254
		TT	0.726	0.727
STAT5_13244*	19	CC(GG)	0.059	0.020
(STAT5_13516*)		CT(GT)	0.339	0.262
		TT(TT)	0.602	0.718
STAT5_13319*	19	AA	0.001	0.000
		AG	0.080	0.004
		GG	0.919	0.996

*SNP markers on the GGP Bovine 100K.

^#Coenzyme Q9 (COQ9) (rs109301586); Montbéliarde Haplotype 1 (MH1); plakophilin 2 (PKP2_988). I → insertion; D → Deletion; Signal transducer and activator of transcription (STAT).

Chessa S, Gattolin S, Cremonesi P, Soglia D, Finocchiaro R, Van Kaam J-T, Marusi M, Civati G. 2020. The effect of selection on casein genetic polymorphisms and haplotypes in Italian Holstein cattle. Ital J Anim Sci. 19(1):833–839. doi: 10.1080/1828051X.2020.1802356.

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Data availability statement

The data supporting the conclusions of this manuscript are included in the Supplementary Materials.