Single nucleotide variant detection in Jaffrabadi buffalo (Bubalus bubalis) using high-throughput targeted sequencing

Figures & data

Table 1. Details of samples and their categorization based on condition, under fertility trait, general health trait and milk production based on filed records.

Fertility trait samples			General health trait samples
Lab ID	Condition	Category	Lab ID	Condition	Category
jf1	5th lactation, calving interval less than a year	Fertile	jds1	History of FMD for last 1.2 years	Susceptible
jf2	7th lactation, calving interval less than a year	Fertile	jds2	Mastitis	Susceptible
jf3	7th lactation, calving interval less than a year	Fertile	jds3	Viral infection	Susceptible
jf4	4th lactation, calving interval less than a year	Fertile	jds4	Diarrhoea	Susceptible
ji1	Repeat breeder for last 1.5 years	Infertile	jdr1	No disease for last 3 years	Resistance
ji2	Repeat breeder for last 2 years	Infertile	jdr2	No disease for last 2 years	Resistance
ji3	True anoestrus, 6 years of age, heifer	Infertile	jdr3	No disease for last 2 years	Resistance
ji4	True anoestrus, 8 years of age, heifer	Infertile	jdr4	No disease for last 2 years	Resistance
Milk production trait samples
	Lactation no./Total yield			Lactation no./Total yield
Lab ID	(kg/lactation)	Category	Lab ID	(kg/lactation)	Category
jhp1	4/3186	High producer	jlp1	5/571	Low producer
jhp2	5/2647	High producer	jlp2	3/583	Low producer
jhp5	5/3020	High producer	jlp3	2/980	Low producer
			jlp4	3/1052	Low producer

Note: FMD = foot and mouth disease.

Table 2. Number of reads obtained after quality filtering and mapping under different trait groups.

	Total raw reads	After quality filtering	Mapped reads	Duplicate reads
Disease trait	52,732	36,951	34,093	14,440
Fertility trait	96,485	70,153	63,817	27,453
Production trait	3,903,901	1,567,560	1,446,224	91,246

Table 3. Number of single nucleotide polymorphisms (SNPs) detected in different samples of various groups.

Sample ID	DP ≥ 2^a	Sample ID	DP ≥ 2^a	Sample ID	DP ≥ 2^a
jdr1	222	jf1	3593	jhp1	22,469
jdr2	75	jf2	14,447	jhp2	2745
jdr3	103	jf3	13,743	jhp5	16,782
jdr4	189	jf4	5627	jlp1	22,140
jds1	673	jif1	2371	jlp2	22,536
jds2	1501	jif2	473	jlp3	1463
jds3	123	jif3	715	jlp4	13,453
jds4	1415	jif4	1968
jdrall	390	jfall	33,158	jhpall	31,905
jdsall	2724	jifall	4887	jlpall	39,808
common	276	common	1282	common	14,717
total	2838	total	36,763	total	56,996

Note: ^aDP ≥ 2 indicates the variant positions having a read depth of equal to or more than 2.

Figure 1. Distribution of annotated single nucleotide polymorphisms (SNPs). The highest number of SNPs was detected in the intergenic region, followed by the intron; the secondary pie chart shows the distribution of 393 SNPs detected in the exons of the genes.

Figure 2. Distribution of single nucleotide polymorphisms (SNPs) annotated in various genic regions of the 23 individuals under study: colour formatting indicates high and low values. Lower numbers are presented in dark green to light green colours, whereas yellow to red colours indicate higher numbers of SNPs.

Table 4. List of gene ontology (GO) categories with their false discovery rate (FDR) values enriched in fertility and infertility trait samples.

Category	Term	Count	FDR
Fertility trait
Molecular function	GO: 0008066 – glutamate receptor activity	8	0.015
Molecular function	GO: 0046872 – metal ion binding	171	0.048
Infertility trait
Molecular function	GO: 0005261 – cation channel activity	11	0.010
Molecular function	GO: 0022836 – gated channel activity	12	0.010
Molecular function	GO: 0005216 – ion channel activity	13	0.025
Molecular function	GO: 0022838 – substrate-specific channel activity	13	0.028
Molecular function	GO: 0015267 – channel activity	13	0.033
Molecular function	GO: 0022803 – passive transmembrane transporter activity	13	0.033
Molecular function	GO: 0046873 – metal ion transmembrane transporter activity	11	0.040

Table 5. List of top gene ontology (GO) categories with their false discovery rate (FDR) values enriched in high milk production trait samples.

Category	Term	Count	FDR
Biological process	GO: 0006468 – protein amino acid phosphorylation	54	0.003
Biological process	GO: 0006796 – phosphate metabolic process	70	0.004
Biological process	GO: 0006793 – phosphorus metabolic process	70	0.004
Biological process	GO: 0016310 – phosphorylation	59	0.007
Cellular component	GO: 0005886 – plasma membrane	107	0.015
Biological process	GO: 0030001 – metal ion transport	38	0.016
Molecular function	GO: 0004672 – protein kinase activity	50	0.016
Biological process	GO: 0006811 – ion transport	57	0.017
Molecular function	GO: 0001882 – nucleoside binding	101	0.033
Molecular function	GO: 0001883 – purine nucleoside binding	100	0.043
Molecular function	GO: 0032559 – adenyl ribonucleotide binding	95	0.049
Molecular function	GO: 0005509 – calcium ion binding	57	0.049
Molecular function	GO: 0030554 – adenyl nucleotide binding	99	0.050

Table 6. List of gene ontology (GO) categories with their false discovery rate (FDR) values enriched in low milk production trait samples.

Category	Term	Count	FDR
Molecular function	GO: 0005509 – calcium ion binding	82	0.000
Cellular component	GO: 0044459 – plasma membrane part	101	0.000
Molecular function	GO: 0022836 – gated channel activity	40	0.000
Biological process	GO: 0006816 – calcium ion transport	22	0.001
Biological process	GO: 0030001 – metal ion transport	50	0.001
Molecular function	GO: 0032559 – adenyl ribonucleotide binding	125	0.002
Biological process	GO: 0006811 – ion transport	74	0.002
Molecular function	GO: 0005216 – ion channel activity	46	0.002
Molecular function	GO: 0001882 – nucleoside binding	131	0.003
Molecular function	GO: 0022838 – substrate-specific channel activity	46	0.003
Molecular function	GO: 0005524 – ATP binding	123	0.003
Molecular function	GO: 0030554 – adenyl nucleotide binding	129	0.003
Cellular component	GO: 0005886 – plasma membrane	137	0.004
Molecular function	GO: 0015267 – channel activity	46	0.004
Molecular function	GO: 0022803 – passive transmembrane transporter activity	46	0.004
Molecular function	GO: 0001883 – purine nucleoside binding	129	0.006
Molecular function	GO: 0046873 – metal ion transmembrane transporter activity	35	0.017
Biological process	GO: 0006812 – cation transport	54	0.024
Biological process	GO: 0006468 – protein amino acid phosphorylation	63	0.042
Biological process	GO: 0007268 – synaptic transmission	19	0.044