The transcriptome profiling of the Sistani cattle and its crossbred with Montbeliarde breed

doi:10.21203/rs.3.rs-3111040/v1

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The transcriptome profiling of the Sistani cattle and its crossbred with Montbeliarde breed

https://doi.org/10.21203/rs.3.rs-3111040/v1

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Transcriptome study of the desired crossbreed and comparing it with the pure parental population is a method for evaluating and selecting cross with appropriate products, yet disease resistance, high tolerance to environmental stresses, and compatibility with the climate of the breeding tract. RNA-Sequencing (RNA-seq) technology was employed to investigate the effect of crossbreeding by the Montbeliarde cattle on the “Sistani cattle” transcriptome. Blood samples were collected from 60 cows (30 pure and 30 crossbreeds). The samples were shared together and two samples were taken from each group for sequencing (4 samples). Total RNA was extracted in the Media Teb Gene Laboratory of Iran. The mRNA selection, library preparation, and sequencing were performed at BGI Shenzhen, China on an Illumina HiSeq 2500 sequencer. After assembling the transcripts with the bovine reference genome, Cuffdiff was used to detect differential gene expression in purebred and its crossbred. In total, 45 significantly differentially expressed genes were identified (false discovery rate q < 0.05) between purebred Sistani and “Sistani×Montbeliarde” crossbreed. These genes are reported to have a role in immune response, calving, fertility, and resistance to mastitis. Besides, they may have a role in different levels of heat tolerance and disease resistance. Therefore, Sistani×Montbeliarde crossbred might be suitable for the climatic conditions of the Sistan region in Iran.

Crossbred

Differentially expressed genes

RNA sequencing

Sistani cow

There has been increased attention to crossbreeding between the indigenous cattle populations (Bos indicus) and the imported breeds (Bos Taurus) in rural areas in Iran, mainly to increase milk production in recent years. Crossbreeding is suggested as a shortcut to improving performance characteristics through adapting to harsh tropical conditions (McDougall et al., 2009; Menendez-Buxadera et al., 2016).

Sistani cattle (Bos indicus), as the only known meat-type breed in Iran, has special genetic features adapted to areas not suitable to crop agriculture (Moridi et al., 2019). In recent years, most of the area’s breeders and villagers are reluctant to continue the pure breeding of these cattle such that there has been a tendency to crossbreed with foreign breeds such as Montbeliarde, Simmental, and Holstein. Due to shrinking the free grazing land since producing concentrate feed is not economically justified, rearing local cattle breed is not profitable to farmers (Kamalzadeh et al., 2008).

Evaluating crossbreeding schemes needs to collect the performance records and some adaptive indices that are hard to measure. The transcriptome profiling and the comparison between pure parental animals and the crossbred may be an alternative method (Moridi et al., 2019). The best genetic combination from crossbreeding can be decided based on differential gene expression analysis and the desired crossbreeding goals (high productivity or higher adaptation and resistance). The application of RNA-seq was studied to investigate the genetic contribution of two Italian breeds (Maremmana and Chianina) with a different history of selection/divergence in meat production and quality by Bongiorni et al. (2016).They uncovered several differentially expressed genes that encode for proteins belonging to a family of tripartite motif proteins involved in growth, cell differentiation, and apoptosis. Therefore, this study aimed to investigate the effects of crossbreeding by the Montbeliarde cattle on the transcriptome of the Sistani cattle.

Sample collection and RNA extraction

This experiment was approved and conducted under the supervision of the Scientific-Technical Committee of Animal Science Research Institute (Karaj, Iran) with the ethic code of 2-13-13-010-960191. Sixty healthy pure and crossbred cows (pure Sistani breed (n = 30) and Sistani×Montbeliardee crossbreed (n = 30)) were selected and shared in two groups and three sample (totally six samples) from the cow farm in Zabol, Sistan province, Iran. All experimental animals, which belonged to a national crossbreeding program, were reared in the same location (Zabol city, Sistan province, Iran), farm, food, physiological, and management conditions. The samples were mixed together and three samples were taken from each group for sequencing. RNA was extracted from the blood samples by RNeasy (Qiagen) method and according to the manufacturer's protocols in the Iranian Media Gene Medicine Laboratory.

Library Preparation and Sequencing

According to the manufacturer, the mRNA selection, library preparation, and sequencing were performed at BGI Shenzhen, China on an Illumina HiSeqTM 2500 sequencer and 150bp paired-end reads specifications. The next step, Agilent 2100 Bioanalyzer and ABI StepOnePlus Real-Time PCR System were used in the quantification and qualification of the sample library during the QC steps.

Quality Control and Alignment

Quality control was done using FastQC (version 1.6; http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc). Adapter sequences were removed from reads using the cutadapt package (http://code.google.com/p/cutadapt/). Based on the bovine reference genome (ARS-UCD1.2,101) (ftp://ftp.ensembl.org/pub/release-72/fasta/bos_taurus/dna/) and the corresponding gene model annotation file (ftp://ftp.ensembl.org/pub/release-72/gtf/bos_taurus/), clean reads for each sample were mapped to the reference genome by TopHat (v2.1.1), with default settings and following the authors’ protocol [26]. Following the alignment, Cufflinks (version 2.2.1.0) was used to assemble the transcripts (Trapnell et al., 2010). Cufflinks reported the abundance of the transcripts as fragments per kilobase of transcript per million fragments sequenced, which is the normalized expression level later used by the Cuffdiff (version 2.2.1.0).

Detection of differentially expressed genes

Following the assembling of the transcripts, differential expression analysis of two conditions (pure Sistani and crossbreed Sistani×Montbeliarde) was performed using Cuffdiff (version 2.2.1.0). The Cuffdiff 2 method (Trapnell et al., 2010), implemented in Cufflinks software (Trapnell et al., 2010), was used with default settings. Differentially expressed genes were considered at a FDR (false discovery rate corrected P-values) P < 0.05. We used CummeRbund (https://bioconductor.org/packages/devel/bioc/html/cummeRbund.html) for visualizing the DEGs.

Gene ontology and KEGG pathway enrichment analysis of differentially expressed genes

As an international standardized gene functional classification system, GO offers a dynamic-updated controlled vocabulary and a strictly defined concept to describe the properties of genes and their products comprehensively. To identify the significantly enriched GO terms, we mapped all DEGs to GO terms in the GO database (http://amp.pharm.mssm.edu/Enrichr/). In this process, the FDR (P < 0.05) was used as the threshold. The Kyoto Encyclopedia of Genes and Genomes (KEGG) database is a resource for understanding high-level functions and utilities of biological systems, such as cells, organisms, and ecosystems from a molecular level. Also, it can be used to analyse large-scale Molecular datasets generated by genome sequencing and other high throughput experimental Technologies. KEGG pathway analyses were performed with the KEGG (https://www.genome.jp/kegg/kaas/).

RNA sequencing and assemble transcripts

The quality control performed using FastQC showed that the samples were of good quality based on the Phred scores (probability of incorrect base call). The analysis were carried out without trimming the reads because of the acceptable quality of the cDNA libraries and the fact that mapping algorithms use only reads that perfectly match a position on the reference genome. In total, we acquired 60575588–75529030 paired-end reads per sample. Based on Tophate2 results, the observed percentages of mapped reads to the bovine reference genome per sample were around 70.5–80.6%, and the percentages of unique aligned reads per sample were around 72.9–78.1%. The summary of reads mapping is provided in Table 1.

Table 1

Summary of read numbers based on the RNA-Seq data
Sample_name	Left reads		Right reads		Multiple mapped			Aligned pairs
	Total no.	%	Total no.	%	Total no.		%	Total no.	%
Purebred Sistani	45603282	75.3	42714026	70.5	2070372	5.5		37307542	72.9
Sistani×Montbeliardee crossbred	60851936	80.6	57053900	75.5	2091061	4.1		51621181	78.1

Differentially expressed genes between purebred Sistani and Sistani×Montbeliarde crossbred

The differentially expressed genes identified by Cuffdiff 2 are shown in Table 2. Based on Cuffdiff 2 output, 45 gene were detected as significantly differentially expressed genes (false discovery rate q < 0.05) between pure Sistani breed and Sistani×Montbeliarde crossbreed (Fig. 1).

Table 2

Differentially expressed genes between purebred Sistani and Sistani×Montbeliardee
Gene	Location	value_1	value_2	Loge2 (fold change)	test_stat	p.value	q_value
COL18A1	1:146989243–147040968	5.51	30.12	2.45	4.80	5.0e-05	0.023
MINDY3	13:30604488–30684245	24.20	86.83	1.84	3.88	1e-04	0.04
TUBB1	13:57874076–57879042	101.22	373.99	1.88555	4.07	1e-04	0.04
ENSBTAG00000017328	13:74943620–74947760	141.04	2091.53	3.89	7.76	5.0e-05	0.023
SOX13	16:1716802–1728817	24.5176	124.14	2.34	4.87	5.0e-05	0.023
STUM	16:30304539–30359147	0	4.47	inf	nan	1e-04	0.04
RGS1	16:13314191–13318292	67.04	5.44	-3.62	-5.26	5.0e-05	0.023
ENSBTAG00000046302	17:35768715–35771692	0	1.75	inf	nan	5.0–05	0.023
ENSBTAG00000048030	17:72815091–72815633	45.23	559.10	3.63	5.75	5.0e-05	0.023
PRAME	17:51374859–51380364	0	4.63	inf	nan	5.0e-05	0.023
ENSBTAG00000048145	18:63239509–63242898	0	3.79	inf	nan	1e-04	0.036
ENSBTAG00000047313	19:11490262–11492611	0	21.26	inf	nan	5.0e-05	0.023
CCL5	19:14823469–14831157	1467.47	238.43	-2.62	-5.48	5.0e-05	0.023
PPP1R1B	19:40655221–40663767	3.66	80.67	4.46	6.26	5.0e-05	0.023
WSCD1	19:26254179–26285583	0	1.39	inf	nan	5.0e-05	0.023
CXCR4	2:61582124–61585838	98.59	12.98	-2.92	-5.49	5.0e-05	0.023
DLK1	21:67274799–67283089	0	2.29	inf	nan	5.50e-05	0.002
ENSBTAG00000048268	21:71530012–71531441	67.21	558.46	3.05	5.41	5.0e-05	0.023
ENSBTAG00000047632	21:71468375–71469950	173.34	22.26	-2.96	-5.80	5.0e-05	0.023
GPg9	22:259687611 − 59688166	48.64	308.36	2.66	4.845	5.00e-05	00.023
BHLHE40	22:21492895–21498539	664.12	16.08	-2.05	-4.26	1.0e-04	0.036
ENSBTAG00000003352	23:25423550–25424597	1213.58	0	inf	nan	5.0e-05	0.023
COL11A2	23:7290454–7318840	41.07	11.11	-1.89	-4.07	5.0e-05	0.023
MPIG6B	23:27403127–27406360	47.54	237.87	2.32	4.89	5.0e-05	0.023
GLNC1	25:214005–214773	0	66.33	inf	nan	5.0e-05	0.023
SLC29A4	25:39515687–39526238	0	1.23	inf	nan	1.0e-04	0.036
IDO1	27:34686576–34699480	355.55	78.69	-2.17	-4.71	5.0e-05	0.023
ENSBTAG00000040202	29:17496571–17512594	1.49	0	inf	nan	1.0e-04	0.036
ENSBTAG00000030892	3:121412143–121413236	15.97	246.46	3.95	6.87	5.0e-05	0.023
ACOT11	3:92260762–92309036	35.63	7.54	-2.24	-4.06	1.0e-04	0.036
ENSBTAG00000030838	4:120643216–120644622	7.69	328.07	5.41	8.44	5.0e-05	0.023
VWF	5:104603431–104727301	6.96	33.41	2.26	4.75	5.0e-05	0.023
ENSBTAG00000039470	5:103132708–103261137	19.08	91.02	2.25	4.46	5.0e-05	0.023
ENSBTAG00000026531	5:103375407–103439148	14.44	62.00	2.10	4.30	5.0e-05	0.023
PF4	6:90673204–90674173	125.19	1383.75	3.47	7.068	5.0e-05	0.023
CLU	8:11043940–11061301	5.57	175.72	4.98	7.445	5.0e-05	0.023
BLK	8:7658876–7710709	51.12	176.49	1.79	3.89	1.0e-04	0.036
FHL1	X:19777798–19820952	21.49	85.48	1.99	4.04	1.0e-04	0.036
MUM1L1	X:53703693–53705778	0.62	0	inf	nan	5.0e-05	0.023
ENSBTAG00000048245	X:84070559–84080527	4.06	50.73	3.64	5.33	5.0e-05	0.023
ENSBTAG00000006383	X:126048948–126049743	443.24	41.09	-3.43	-6.43	5.0e-05	0.023
ALAS2	X:97908615–97935775	10.91	121.42	3.48	6.49	5.0e-05	0.023
ENSBTAG00000048172	X:142664999–142690152	0	4.49	inf	nan	5.0–05	0.023
ENSBTAG00000035438	X:143451490–143490945	0	1.59	inf	nan	5.0–05	0.023
ENSBTAG00000045544	X:144159055–144234222	0	3.78	inf	nan	5.0–05	0.023

Gene Ontology enrichment and pathway analysis

The GO enrichment analysis of the DEGs revealed 15 enriched pathways between pure Sistani breed and Sistani×Montbeliarde crossbreed (Table 3). Based on the result of GO enrichment, revealed only the inflammation mediated by chemokine and cytokine signalling pathway significant GO terms (FDR q < 0.05). Cytokines and chemokines play a key role in the immune response to a myriad of pathogens in species (Fig. 2).

Crossing the native breeds with the high-producing exotic cattle improves the production level of crossbreeds. The number of crossbred cattle has been increasing rapidly during the last ten years in Iran. The population of native cattle in Iran includes Sarabi, Golpayegani, Sistani, Dashtiari, Najdi and Taleshi belonging to B. indicus (Kamalzadeh et al., 2008). Although the indigenous populations show good disease resistance and are adapted to harsh environmental conditions, their milk yields are low. On the other hand, breed selection will take many generations to improve production to a desirable level (Moridi et al., 2019). Therefore, one way to achieve a significant increase in production is the implementation of crossbreeding with the high-performing breed to combine the desirable characteristics of both breeds.In this regard, we compared transcripts of pure Sistani breed and Sistani×Montbeliarde crossbreed populations to understand the effects of crossbreeding on gene expression.

In this study, two genes (i.e., PPPIR1B and ARID4A) were highly expressed in both populations (Heatmap correlation graph of expressed transcripts (Fig. 3). These genes are involved in the immune pathway and cell proliferation. The PPPIR1B (protein phosphatase 1 regulatory inhibitor subunit 1B) is involved in the cAMP signalling pathway. DARPP-32 and t-Darpp are proteins encoded by PPP1R1B (El-Rifai et al., 2002) that they are overexpressed in several cancers, including those derived from gastric, colon, breast, and lung tissues (Alam et al., 2018; Belkhiri et al., 2011). The protein encoded by the ARID4A (AT-rich interaction domain 4A) is a ubiquitously expressed nuclear protein. This protein binds directly with several other proteins to retinoblastoma protein (pRB), regulating cell proliferation.

In this study, GO enrichment analysis revealed that the differentially expressed genes are enriched in many GO terms (Table 3). This study focuses on inflammation mediated by chemokine and cytokine signalling pathway, which is observed as the highest enriched pathway compared to the other pathways in this study. Chemokines and cytokines are two immune-modulating agents and play an essential role in controlling and regulating an immune response (Horuk, 2001; Mogensen et al., 1999). The chemokine system has shown a key role in both homeostasis, such as lymphoid organogenesis and leukocyte maturation and disease mechanisms (Adema et al., 1999; Arenberg et al., 1997; Wakchaure et al., 2015).

Table 3

Summary of the Gene Ontology enrichment and pathway analysis of differentially expressed genes (DEGs) between purebred Sistani and Sistani×Montbeliarde crossbred
Pathway	Gene	p-value	FDR
Inflammation mediated by chemokine and cytokine signaling pathway	PF4, VWF, CXCR4, CCL5, RGS1	1.91e-06	3.14e-04
Integrin signaling pathway	COL11A2, ENSBTAG00000000601, ENSBTAG00000023907	1.02e02	4.19e-01
Cytoskeletal regulation by Rho GTPase	ENSBTAG00000018785	1.73e01	1.00e00
CCKR signaling map	ENSBTAG00000005574	2.61e-01	8.57e-01
Angiogenesis	ENSBTAG00000037899	3.42e-01	1.00e00
Nicotine pharmacodynamics pathway	ENSBTAG00000006035	8.60e-02	1.00e00
Blood coagulation	VWF, ENSBTAG00000014666	1.63e-03	8.91e-02
Heterotrimeric G-protein signaling pathway-Gi alpha and Gs alpha mediated pathway	ENSBTAG00000021672	2.86e-01	1.00e00
Heterotrimeric G-protein signaling pathway-Gq alpha and Go alpha mediated pathway	ENSBTAG00000021672	3.53e-01	1.00e00
Axon guidance mediated by slit/Robo	ENSBTAG00000001060	4.98e-02	1.00e00
Dopamine receptor mediated signaling pathway	ENSBTAG00000006035	1.41e-01	1.00e00
Parkinson disease	ENSBTAG00000005049	2.32e-01	1.00e00
B cell activation	ENSBTAG00000005049	1.53e-01	1.00e00
Huntington disease	ENSBTAG00000018785	5.27e-02	1.00e00
Notch signaling pathway	ENSBTAG00000037899	1.28e-01	1.00e00

We observed that PF4, vWF, CXCR4, CCL5, and RGS1 genes are deferentially expressed in the crossbreed Sistani and Montbeliarde populations. These genes are involved in the inflammation mediated by chemokine and cytokine signalling pathways and are involved in resistance to disease and inappropriate environmental conditions. The Platelet factor 4(PF4), a small cytokine belonging to the CXC chemokine family is an abundant protein stored in α- granules of megakaryocytes (MK) and platelets. PF4 plays an important role in hemostasis and this factor acts as a lineage-specific marker of megakaryocytic differentiation (Holt and Niewiarowski, 1985; Kowalska et al., 2010). PF4 as a significant player in the initiation and development of inflammatory diseases (Huo et al., 2013; Ueno et al., 2015).

Von Willebrand factor (vWF), is a glycoprotein that plays an important role in platelet adhesion and thrombosis formation. This factor specifically synthesizes endothelial cells and platelet precursors. The species-specific properties by functional characterization of bovine vWF gene promoter in the bovine endothelial cells have been demonstrated in a study by Janel et al. (1997). They reported that the sequence, which regulates the cell-specific transcription, is not conserved in the bovine counterpart. It was also determined that the cis-acting elements do not behave identically in the bovine vWF promoter.

CXCR4 (c-x-c chemokine receptor type 4) is a molecule endowed with potent chemotactic activity for lymphocytes that this gene is involved in some developmental processes, including haematopoiesis, angiogenesis, and organogenesis (Busillo and Benovic, 2007; Zou et al., 1998). This gene is highly expressed in the thymus, particularly in immature CD4 + and CD8 + cells (Zou et al., 1998). Ashley et al. (2011) reported that maternal CXCR4 was up regulated in sheep during early pregnancy due to implantation and placentation. Expression of C-X-C chemokine receptor type 4 (CXCR4) was reported in association with bovine viral diarrhea virus (BVDV) infection (Smirnova et al., 2009; Weiner et al., 2012).

CC motif chemokine ligand 5 (CCL5) is an immune-associated gene belonging to the CC chemokine family (Aldinucci et al., 2014).This gene chemotactic for monocytes, T cells, and eosinophils. It also activates eosinophils and the release of histamine from basophils. Splice variants, transcript expression, and splicingassociated SNPs of the CCL5 gene in healthy and mastitis mammary glands in Holstein cows were studied by Yang et al. (2019). Based on their results, it was determined the chemokine CCL5 was down regulated in the mammary glands in the late stages of natural mastitis infection.

Regulator of G-protein signalling 1 (RGS1) is a member of the regulator of G-protein signalling family that accelerates Gai GTPase activity and acts to down-regulate the response to sustained chemokine activation (Han et al., 2005; Moratz et al., 2004a). Rgs1 is involved in chemokine receptor signalling in both T and B cells (Gibbons et al., 2011). In particular, deletion of Rgs1 modifies the migratory behaviour of B cells within follicular areas and to increase germinal centre formation (Gibbons et al., 2011; Huang and Khatib, 2010; Moratz et al., 2004a; Moratz et al., 2004b). Also, the role of RGS1 in the control of lymphocyte homeostasis have been identified in other studies (Gibbons et al., 2011; Moratz et al., 2004a).

The consequences of cattle crossbreeding programmed on gene expression, signalling, and metabolic pathways, molecular networks, and biological functions are still indistinctive.

In conclusion, the presented study provided important information on the effect of crossbreeding by the Montbeliarde cattle on the transcriptome of the Sistani cattle. Comparing crossbred vs. purebred, integrated analysis of differential gene expression and GO enrichment analysis allowed identifying disease-associated pathways such as infection of Mammalia. These genes are involved in pathways leading to immune and transcriptional responses, and they are associated with calving, fertility, and resistance to mastitis. Moreover, these pathways may have a role in different heat tolerance levels and disease resistance in the Sistani×Montbeliarde crossbreeds.

ETHICS APPROVAL

The study was approved by the University of Zabol and Department of Biotechnology, Animal Science Research Institute of IRAN (ASIR). All participants signed written informed consent to participate.

COMPETING INTERESTS

The authors declare that they have no competing interests

FUNDING

This work was supported by the Animal Science Research Institute of IRAN (2-13-13-010-960191) and University of Zabol (IR-UOZ-4398).

ACKNOWLEDGEMEN

Analysis of the transcriptome data of this research on the server of Aarhus University. I hereby thanks from Qoutam Sahana.

Adema GJ, Hartgers F, Verstraten R, de Vries E, Marland G, Menon S, Foster J, Xu Y, Nooyen P, McClanahan T, Bacon KB, Figdor CG. (1997). A dendritic-cell-derived C-C chemokine that preferentially attracts naive T cells. Nature. 12: 387(6634): 713-717.
Alam SK, Astone M, Liu P, Hall SR, Coyle AM, Dankert EN, Hoffman DK, Zhang W, Kuang R, Roden AC, Mansfield AS, Hoeppner LH. (2018). DARPP-32 and t-DARPP promote non-small cell lung cancer growth through regulation of IKKα-dependent cell migration. Commun Biol. 1: 43.
Aldinucci D, Colombatti A. (2014). The inflammatory chemokine CCL5 and cancer progression. Mediators Inflamm. 292376.
Arenberg DA, Polverini PJ, Kunkel SL, Shanafelt A, Hesselgesser J, Horuk R, Strieter RM. (1997). The role of CXC chemokines in the regulation of angiogenesis in non-small cell lung cancer. J. Leukoc. Biol. 62(5): 554-562.
Ashley RL, Antoniazzi AQ, Anthony RV, Hansen TR. (2011). The chemokine receptor CXCR4 and its ligand CXCL12 are activated during implantation and placentation in sheep. Reprod. Biol. Endocrinol. 9: 148.
Belkhiri A, Zhu S, El-Rifai W. (2016). DARPP-32: from neurotransmission to cancer. Oncotarget. 7(14): 17631-1740.
Bongiorni S, Gruber CE, Chillemi G, Bueno S, Failla S, Moioli B, Ferrè F, Valentini A. (2016). Skeletal muscle transcriptional profiles in two Italian beef breeds, Chianina and Maremmana, reveal breed specific variation. Mol. Biol. Rep. 43(4): 253-268.
Busillo JM, Benovic JL. (2007). Regulation of CXCR4 signaling. Biochim. Biophys. Acta. 1768(4): 952-963.
El-Rifai W, Smith MF Jr, Li G, Beckler A, Carl VS, Montgomery E, Knuutila S, Moskaluk CA, Frierson HF Jr, Powell SM. (2002). Gastric cancers overexpress DARPP-32 and a novel isoform, t-DARPP. Cancer Res. 62(14): 4061-4064.
Gibbons DL, Abeler-Dörner L, Raine T, Hwang IY, Jandke A, Wencker M, Deban L, Rudd CE, Irving PM, Kehrl JH, Hayday AC. (2011). Cutting Edge: Regulator of G protein signaling-1 selectively regulates gut T cell trafficking and colitic potential. J. Immunol. 187(5): 2067-2071.
Han SB, Moratz C, Huang NN, Kelsall B, Cho H, Shi CS, Schwartz O, Kehrl JH. (2005). Rgs1 and Gnai2 regulate the entrance of B lymphocytes into lymph nodes and B cell motility within lymph node follicles. Immunity. 22(3): 343-354.
Holt JC, Niewiarowski S. (1985). Biochemistry of alpha granule proteins. Semin Hematol. 22(2): 151-163.
Horuk R. (2001). Chemokine receptors. Cytokine Growth Factor Rev. 12(4): 313-335.
Huang W, Khatib H. (2010). Comparison of transcriptomic landscapes of bovine embryos using RNA-Seq. BMC Genomics. 11: 711.
Huo Y, Schober A, Forlow SB, Smith DF, Hyman MC, Jung S, Littman DR, Weber C, Ley K. (2003). Circulating activated platelets exacerbate atherosclerosis in mice deficient in apolipoprotein E. Nat. Med. 9(1): 61-67.
Janel N, Dosne AM, Obert B, Meyer D, Kerbiriou-Nabias D. (1997). Functional characterization of bovine von Willebrand factor gene promoter in bovine endothelial cells demonstrates species-specific properties. Gene. 198(1-2): 127-134.
Kamalzadeh A, Rajabbaigy M, Kiasat A. (2008). Livestock production systems and trends in livestock industry in Iran. J. Agri. Soc. Sci. 4: 183-188.
Kowalska MA, Rauova L, Poncz M. (2010). Role of the platelet chemokine platelet factor 4 (PF4) in hemostasis and thrombosis. Thromb Res. 125(4): 292-296.
McDougall S, Parker KI, Heuer C, Compton CW. (2009). A review of prevention and control of heifer mastitis via non-antibiotic strategies. Vet. Microbiol. 134(1-2): 177-185.
Menéndez-Buxadera A, Palacios-Espinosa A, Espinosa-Villavicencio JL, Guerra-Iglesias D. (2016). Genotype Environment interactions for milk production traits in Holstein and crossbred Holstein-Zebu cattle populations estimated by a character state multibreed model. Livestock Sci. 191: 108-116.
Mogensen KE, Lewerenz M, Reboul J, Lutfalla G, Uzé G. (1999). The type I interferon receptor: structure, function, and evolution of a family business. J. Interferon Cytokine Res. 19(10): 1069-1098.
Moratz C, Harrison K, Kehrl JH. (2004a). Regulation of chemokine-induced lymphocyte migration by RGS proteins. Methods Enzymol. 389: 15-32.
Moratz C, Hayman JR, Gu H, Kehrl JH. (2004b). Abnormal B-cell responses to chemokines, disturbed plasma cell localization, and distorted immune tissue architecture in Rgs1-/- mice. Mol. Cell Biol. 24(13): 5767-5775.
Moridi M, Hosseini Moghaddam SH, Mirhoseini SZ, Bionaz M. (2019). Transcriptome analysis showed differences of two purebred cattle and their crossbreds. Italian J. Anim. Sci. 18: 70-79.
Smirnova NP, Ptitsyn AA, Austin KJ, Bielefeldt-Ohmann H, Van Campen H, Han H, van Olphen AL, Hansen TR. (2009). Persistent fetal infection with bovine viral diarrhea virus differentially affects maternal blood cell signal transduction pathways. Physiol. Genomics. 36(3): 129-139.
Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. (2010). Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28(5): 511-515.
Ueno K, Nomura Y, Morita Y, Eguchi T, Masuda K, Kawano Y. (2015). Circulating platelet-neutrophil aggregates play a significant role in Kawasaki disease. Circ. J. 79(6): 1349-1356.
Wakchaure R, Ganguly S, Para PA, Praveen PK, Kumar A, Sharma S. (2015). Development of crossbred cattle in India: a review. Int. J. Emerging. Tech. Adv. Eng. 5: 75-77.
Weiner CM, Smirnova NP, Webb BT, Van Campen H, Hansen TR. (2012). Interferon stimulated genes, CXCR4 and immune cell responses in peripheral blood mononuclear cells infected with bovine viral diarrhea virus. Res. Vet. Sci. 93(2): 1081-1088.
Yang L, Guo R, Ju Z, Wang X, Jiang Q, Liu Y, Zhao H, He K, Li J, Huang J. (2019). Production of an aberrant splice variant of CCL5 is not caused by genetic mutation in the mammary glands of mastitis‑infected Holstein cows. Mol. Med. Rep. 19(5): 4159-4166.
Zou YR, Kottmann AH, Kuroda M, Taniuchi I, Littman DR. (1999). Function of the chemokine receptor CXCR4 in haematopoiesis and in cerebellar development. Nature. 393(6685): 595-599.

No competing interests reported.

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The transcriptome profiling of the Sistani cattle and its crossbred with Montbeliarde breed

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Abstract

Figures

INTRODUCTION

MATERIAL AND METHODS

Sample collection and RNA extraction

Library Preparation and Sequencing

Quality Control and Alignment

Detection of differentially expressed genes

Gene ontology and KEGG pathway enrichment analysis of differentially expressed genes

RESULTS

RNA sequencing and assemble transcripts

Differentially expressed genes between purebred Sistani and Sistani×Montbeliarde crossbred

Gene Ontology enrichment and pathway analysis

DISCUSSION

CONCLUSION

DECLARATIONS

REFERENCES

Additional Declarations

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