Exome-wide comparative analyses revealed differentiating genomic regions for performance traits in Indian native buffaloes

Figures & data

Table 1. Summary of sequence data of all four buffalo breeds.

		Raw Reads			Trimmed Reads
Breeds	Reads	Average GC (%)	Length (bp)	Total sequences (Millions)	Average GC (%)	Length (bp)	Total sequences (Millions)
Chhattisgarhi_1	R1	54	159	65.8	54	146	63.4
	R2	54	159	65.8	54	146	63.4
Chhattisgarhi_2	R1	54	159	86.7	54	147	83.5
	R2	54	159	86.7	54	147	83.5
Chhattisgarhi_3	R1	53	159	96.7	54	146	93.2
	R2	54	159	96.7	54	146	93.2
Chilika _1	R1	52	159	85	52	150	81.4
	R2	52	159	85	52	150	81.4
Chilika_2	R1	51	159	49.7	51	150	47.6
	R2	51	159	49.7	51	150	47.6
Chilika_3	R1	50	159	32.7	50	150	30.8
	R2	50	159	32.7	50	150	30.8
Chilika_4	R1	51	159	50.9	51	150	48.6
	R2	51	159	50.9	51	150	48.6
Gojri_1	R1	53	159	68.8	54	147	66.4
	R2	53	159	68.8	54	147	66.4
Gojri_2	R1	54	159	76.7	54	148	73.8
	R2	54	159	76.7	54	148	73.8
Gojri_3	R1	53	159	85.8	54	147	82.8
	R2	53	159	85.8	54	147	82.8
Murrah_1	R1	52	159	62.2	52	149	60
	R2	52	159	62.2	52	149	60
Murrah_2	R1	52	159	62	52	149	60
	R2	52	159	62	52	149	60
Murrah_3	R1	51	159	75.1	51	150	72.1
	R2	51	159	75.1	51	150	72.1
Murrah_4	R1	51	159	75.1	51	150	72.1
	R2	51	159	75.1	51	150	72.1

Table 2. Summary of sequencing and mapping results of all four buffalo breeds.

Sample	Total reads	Mapped reads
Chhattisgarhi_1	127014478	99.60%
Chhattisgarhi_2	167143508	99.00%
Chhattisgarhi_3	186567775	99.09%
Chilika_1	162948392	99.24%
Chilika_2	95355400	99.08%
Chilika_3	61663798	99.21%
Chilika_4	97368928	99.27%
Gojri_1	133068276	98.99%
Gojri_2	147901772	98.92%
Gojri_3	165897460	98.88%
Murrah_1	120117156	99.01%
Murrah_2	89003072	98.87%
Murrah_3	144494497	99.08%
Murrah_4	157245880	99.05%

Figure 1. (a) Venn diagram depicting common and unique InDels in all four breeds of buffalo. (b) Exome-wide probability of InDels detection in four breeds of buffalo. The content of the buffalo reference genome sequence was represented by the outermost circle. Proceeding from outer to inner of the circle showed the exome-wide spreading of InDels in Chhattisgarhi, Gojri, Murrah, and Chilika, respectively.

Figure 2. Population structure and relationships of Chhattisgarhi, Chilika, Gojri and Murrah buffaloes. (a) The optimal number of clusters present in the analyzed buffalo germplasms was estimated using the Evanno technique employing estimates of the number of sub-populations (K) using various statistics. (b) Buffalo breeds model-based clustering with K = 2 to 4 using the STRUCTURE programme. (c) Using principal component analysis (PCA), the comparison of PC1 and PC2 and PC3 is shown.

Figure 3. Summary statistics for population genetics. (a) Histogram showing frequency of different nucleotide diversity values throughout chromosome. Summary statistics for population genetics. (b) Box plots displaying distribution of nucleotide diversity, measured exome-wide across 100-kb windows in all four breeds. (c) Histogram showing frequency of different Tajima’s D values throughout exome.

Table 3. The summary of nucleotide diversity in all four buffalo breed populations.

Breeds	Nucleotide diversity
	Mean ± SE
Chhattisgarhi	0.000006692 ± 0.000000094^b
Chilika	0.000006694 ± 0.00000009^b
Gojri	0.000006152 ± 0.000000095^a
Murrah	0.000006557 ± 0.000000087^b

Note: Different capital letters in the same column indicate significant differences between populations (p < 0.01), while the same letters indicate no significant differences.

Figure 4. Whole exome distribution of ZF_ST values estimated in 100-kb sliding windows with 25-kb increments in all four breeds of buffalo.

Table 4. Summary of genes identified for performance traits in all four studied breeds.

Breeds	Performance traits
	Milk yield	Milk composition	Fertility	Adaptation
				Salinity	High-altitude	Immunity
Chhattisgarhi	CAMSAP3	CLCN1, CASP2
Chilika		NUDT3		RPS28, HMGA1, GRM4, KCNA3		LCN2
Gojri			DBI		APBB2, TH, CTU1, ALKBH8, INS, IGF2, CALD1, HABP2
Murrah		LPAR6, FADS1	PTGER3, PARVG			ITGB1BP1

Figure 5. (a) Summary of the top 10 GO-slim biological processes into which the candidate genes were classified. (b) Network analysis of genes identified in present study in all four breeds.

Table 5. Top 10 genes based on the number of interactions identified in the STRING database.

Gene symbol	Number of interactions
STXBP2	10
XAB2	9
TRAPPC5	8
PCP2	7
FCER2	6
RETN	6
INS	5
RPS28	5
FEN1	5
MCEMP1	4