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Article ; Online: Identification of candidate genes associated with milk production and mastitis based on transcriptome-wide association study.

Hosseinzadeh, Sevda / Rafat, Seyed Abbas / Javanmard, Arash / Fang, Lingzhao

2024 Volume 55, Issue 3, Page(s) 430–439

Abstract: Genetic research for the assessment of mastitis and milk production traits simultaneously has a long history. The main issue that arises in this context is the known existence of a positive correlation between the risk of mastitis and lactation ... ...

Abstract	Genetic research for the assessment of mastitis and milk production traits simultaneously has a long history. The main issue that arises in this context is the known existence of a positive correlation between the risk of mastitis and lactation performance due to selection. The transcriptome-wide association study (TWAS) approach endeavors to combine the expression quantitative trait loci and genome-wide association study summary statistics to decode complex traits or diseases. Accordingly, we used the farmgtex project results as a complete bovine database for mastitis and milk production. The results of colocalization and TWAS approaches were used for the detection of functional associated candidate genes with milk production and mastitis traits on multiple tissue-based transcriptome records. Also, we used the david database for gene ontology to identify significant terms and associated genes. For the identification of interaction networks, the genemania and string databases were used. Also, the available z-scores in TWAS results were used for the calculation of the correlation between tissues. Therefore, the present results confirm that LYNX1, DGAT1, C14H8orf33, and LY6E were identified as significant genes associated with milk production in eight, six, five, and five tissues, respectively. Also, FBXL6 was detected as a significant gene associated with mastitis trait. CLN3 and ZNF34 genes emerged via both the colocalization and TWAS approaches as significant genes for milk production trait. It is expected that TWAS and colocalization can improve our perception of the potential health status control mechanism in high-yielding dairy cows.
MeSH term(s)	Animals ; Mastitis, Bovine/genetics ; Cattle/genetics ; Female ; Transcriptome ; Lactation/genetics ; Quantitative Trait Loci ; Milk/metabolism ; Genome-Wide Association Study/veterinary
Language	English
Publishing date	2024-04-09
Publishing country	England
Document type	Journal Article
ZDB-ID	632766-7
ISSN	1365-2052 ; 0268-9146 ; 0268-9154
ISSN (online)	1365-2052
ISSN	0268-9146 ; 0268-9154
DOI	10.1111/age.13422
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Article: Detection of chicken and fat adulteration in minced lamb meat by VIS/NIR spectroscopy and chemometrics methods

Kazemi, Amir / Mahmoudi, Asghar / Veladi, Hadi / Javanmard, Arash

International journal of food engineering. 2022 June 30, v. 18, no. 7

2022

Abstract: Meat fraud has been changed to an important challenge to both industry and governments because of the public health issue. The main purpose of this research was to inspect the possibility of using VIS/NIR spectroscopy, combined with chemometric ... ...

Abstract	Meat fraud has been changed to an important challenge to both industry and governments because of the public health issue. The main purpose of this research was to inspect the possibility of using VIS/NIR spectroscopy, combined with chemometric techniques to detect the adulteration of chicken meat and fat in minced lamb meat. 180 samples of pure lamb, chicken and fat and adulterated samples at different levels: 5, 10, 15 and 20% (w/w) were prepared and analyzed after pre-processing techniques. In order to remove additive and multiplicative effects in spectral data, derivatives and scatter-correction preprocessing methods were applied. Principle Component Analysis (PCA) as unsupervised method was applied to compress data. Moreover, Support Vector Machine (SVM) and Soft Independent Modeling Class Analogies (SIMCA) as supervised methods was applied to estimate the discrimination power of these models for nine and three class datasets. The best classification results were 56.15 and 80.70% for classification of nine class and three class datasets respectively with SVM model. This study shows the applicability of VIS/NIR combined with chemometrics to detect the type of fraud in minced lamb meat.
Keywords	adulterated products ; chemometrics ; chicken meat ; chickens ; data collection ; fraud ; industry ; minced lamb ; models ; near-infrared spectroscopy ; principal component analysis ; public health ; spectral analysis ; support vector machines
Language	English
Dates of publication	2022-0630
Size	p. 525-535.
Publishing place	De Gruyter
Document type	Article
ZDB-ID	2207267-6
ISSN	1556-3758 ; 2194-5764
ISSN (online)	1556-3758
ISSN	2194-5764
DOI	10.1515/ijfe-2021-0333
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Article ; Online: Supplementation of broiler chicken diets with bovine lactoferrin improves growth performance, histological parameters of jejunum and immune‐related gene expression

Olyayee, Majid / Javanmard, Arash / Janmohammadi, Hossein / Kianfar, Ruhollah / Alijani, Sadegh / Mir Ghelenj, Seyed Ali

Journal of Animal Physiology and Animal Nutrition. 2023 Jan., v. 107, no. 1 p.200-213

2023

Abstract: The aim of this study was to investigate the influence of dietary supplementation of bovine lactoferrin (bLF) on growth performance, carcass traits, histomorphology of jejunum, immune function and hepatic and splenic gene expression of interferon‐gamma ( ... ...

Abstract	The aim of this study was to investigate the influence of dietary supplementation of bovine lactoferrin (bLF) on growth performance, carcass traits, histomorphology of jejunum, immune function and hepatic and splenic gene expression of interferon‐gamma (IFN‐γ) and interleukine‐2 (IL‐2) in broiler chickens. A total of 240 one‐day‐old Ross 308 male broiler chickens were randomly allotted into six dietary treatments with four replicate pens (10 chicks per pen) and fed experimental diet in 3 feeding phases (starter: d 0–10, grower: d 11–24 and finisher: d 25–42). The experimental treatments were (1) corn–soya bean meal‐based basal diet (control), (2–5) basal diet supplemented with 200, 400, 600, 800 mg/kg bLF, respectively, and (6) basal diet supplemented with 200 mg/kg oxytetracycline (OTC). The average body weight gain (ABWG) of broilers fed 800 mg/kg bLF was 8.48% higher than those fed a corn–soybean meal‐based diet during the starter period (d 0–10) (linear effect, p = 0.002; quadratic effect, p = 0.24). Average daily feed intake (ADFI) and the feed conversion ratio (FCR) were not affected (p>0.05) by bLF supplementation. At 42 days of age, the breast meat percentage and carcass yield of broilers fed 800 mg/kg bLF compared with the control group significantly increased by 9.51% and 6.03% respectively (p < 0.05). Compared with the chicks fed the control diet, the chicks fed diets supplemented with bLF had higher villus height, muscle thickness and villus surface area (p > 0.05). Dietary bLF inclusion increased the total immunoglobulin (IgT) titre against sheep red blood cells (SRBCs) antigen (linear effect, p = 0.031; quadratic effect, p = 0.035) and improved the phytohaemagglutinin‐P (PHA‐P)‐skin test of broilers. Compared with the control, bLF enhanced the gene expression of IFN‐γ in spleen (p = 0.048, linear effect, p = 0.009; quadratic effect, p = 0.093) and liver (p = 0.012, linear effect, p = 0.008; quadratic effect, p = 0.01) and IL‐2 expression in spleen (p = 0.021, linear effect, p = 0.026; quadratic effect, p = 0.103). The bLF supplementation had no effect on IL‐2 gene expression in liver (p > 0.05, linear effect, p = 0.213; quadratic effect, p = 0.159). In conclusion, we found that supplementation of broiler diets with 800 mg/kg bLF can improve the growth performance, carcass yield, cell‐mediated and antibody‐mediated immune responses and enhance the IL‐2 and IFN‐γ gene expression of broilers.
Keywords	antigens ; beans ; blood ; body weight changes ; breast meat ; broiler chickens ; carcass yield ; dietary supplements ; experimental diets ; feed conversion ; feed intake ; gene expression ; growth performance ; histology ; immune response ; immunoglobulins ; interferon-gamma ; interleukin-2 ; jejunum ; lactoferrin ; liver ; males ; muscles ; oxytetracycline ; sheep ; spleen ; surface area ; villi
Language	English
Dates of publication	2023-01
Size	p. 200-213.
Publishing place	John Wiley & Sons, Ltd
Document type	Article ; Online
Note	JOURNAL ARTICLE
ZDB-ID	232729-6
ISSN	0931-2439
ISSN	0931-2439
DOI	10.1111/jpn.13683
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Article: Selective genotyping to implement genomic selection in beef cattle breeding.

Esrafili Taze Kand Mohammaddiyeh, Maryam / Rafat, Seyed Abbas / Shodja, Jalil / Javanmard, Arash / Esfandyari, Hadi

Frontiers in genetics

2023 Volume 14, Page(s) 1083106

Abstract: Genomic selection (GS) plays an essential role in livestock genetic improvement programs. In dairy cattle, the method is already a recognized tool to estimate the breeding values of young animals and reduce generation intervals. Due to the different ... ...

Abstract	Genomic selection (GS) plays an essential role in livestock genetic improvement programs. In dairy cattle, the method is already a recognized tool to estimate the breeding values of young animals and reduce generation intervals. Due to the different breeding structures of beef cattle, the implementation of GS is still a challenge and has been adopted to a much lesser extent than dairy cattle. This study aimed to evaluate genotyping strategies in terms of prediction accuracy as the first step in the implementation of GS in beef while some restrictions were assumed for the availability of phenotypic and genomic information. For this purpose, a multi-breed population of beef cattle was simulated by imitating the practical system of beef cattle genetic evaluation. Four genotyping scenarios were compared to traditional pedigree-based evaluation. Results showed an improvement in prediction accuracy, albeit a limited number of animals being genotyped (i.e., 3% of total animals in genetic evaluation). The comparison of genotyping scenarios revealed that selective genotyping should be on animals from both ancestral and younger generations. In addition, as genetic evaluation in practice covers traits that are expressed in either sex, it is recommended that genotyping covers animals from both sexes.
Language	English
Publishing date	2023-03-17
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2606823-0
ISSN	1664-8021
ISSN	1664-8021
DOI	10.3389/fgene.2023.1083106
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Article ; Online: Changes in the gene expression profile of the mammary gland lipogenic enzymes in Saanen goats in response to dietary fats.

Javaheri Barfourooshi, Hoda / Sadeghipanah, Hassan / Asadzadeh, Nader / Seyedabadi, Hamidreza / Borazjani, Marjan / Javanmard, Arash

Veterinary medicine and science

2023 Volume 9, Issue 2, Page(s) 945–956

Abstract: Background: The second half of the first pregnancy is a critical period in the growth and development of the mammary gland. The use of functional compounds during this period may positively impact livestock performance.: Objectives: In this study, ... ...

Abstract	Background: The second half of the first pregnancy is a critical period in the growth and development of the mammary gland. The use of functional compounds during this period may positively impact livestock performance. Objectives: In this study, changes in lipogenic enzyme gene expression in the mammary gland of Saanen goats in response to different dietary fat sources were analysed. Methods: Goats from four groups (10 each) received these diets from the last two months of pregnancy through four months of lactation: C-, no added fat (negative control group), C+, with saturated palm oil (positive control group), SB, with roasted soybeans (omega-6 group) and FS, with extruded flaxseed (omega-3 group). The fat content was about 4% of dry matter. Milk yield, milk fatty acid profile, milk health index (HI) and gene expression of four lipogenic enzymes in mammary tissue were measured. Results: The FS group had significantly higher milk production with lower omega-6 to omega-3, monounsaturated to polyunsaturated, and total saturated fatty acids compared to other groups. The shorter and longer than16-carbon chain of total milk fatty acid indicates significantly higher values for the C- and C+ groups, respectively. The milk HI for the SB group was significantly higher. The gene expression profile for acetyl-coenzyme A carboxylase was higher in the C- group than other experimental groups. Conclusions: The results show that manipulation of the diet with unsaturated fat supplements improved milk production, synthesis of milk fat and molecular expression of lipogenic enzymes in mammary tissue in primiparous Saanen goats.
MeSH term(s)	Female ; Animals ; Dietary Fats/metabolism ; Transcriptome ; Dietary Supplements ; Fatty Acids/metabolism ; Goats/physiology
Chemical Substances	Dietary Fats ; Fatty Acids
Language	English
Publishing date	2023-01-03
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2819409-3
ISSN	2053-1095 ; 2053-1095
ISSN (online)	2053-1095
ISSN	2053-1095
DOI	10.1002/vms3.1062
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Article ; Online: A critical review of the recent concept of artificial mechanical uterus design in relation to the maternal microbiome: An Update to past researches.

Nami, Yousef / Haghshenas, Babak / Javanmard, Arash / Samari, Mahya / Mohammadi, Nahid / Oroojalian, Fatemeh / Mokhtarzadeh, Ahad

Journal of reproductive immunology

2023 Volume 156, Page(s) 103828

Abstract: The microbiome in the female reproductive tract plays an essential role in immune modulation and reproductive health. However, various microbes become established during pregnancy, the balance of which plays a crucial role in embryonic development and ... ...

Abstract	The microbiome in the female reproductive tract plays an essential role in immune modulation and reproductive health. However, various microbes become established during pregnancy, the balance of which plays a crucial role in embryonic development and healthy births. The contribution of disturbances in the microbiome profile to embryo health is poorly understood. A better understanding of the relationship between reproductive outcomes and the vaginal microbiota is needed to optimize the chances of healthy births. In this regards, microbiome dysbiosis refers to conditions in which the pathways of communication and balance within the normal microbiome are imbalanced due to the intrusion of pathogenic microorganisms into the reproductive system. This review summarizes the current state of knowledge on the natural human microbiome, with a focus on the natural uterine microbiome, mother-to-child transmission, dysbiosis, and the pattern of microbial change in pregnancy and parturition, and reviews the effects of artificial uterus probiotics during pregnancy. These effects can be studied in the sterile environment of an artificial uterus, and microbes with potential probiotic activity can be studied as a possible therapeutic approach. The artificial uterus is a technological device or biobag used as an incubator, allowing extracorporeal pregnancy. Establishing beneficial microbial communities within the artificial womb using probiotic species could modulate the immune system of both the fetus and the mother. The artificial womb could be used to select the best strains of probiotic species to fight infection with specific pathogens. Questions about the interactions and stability of the most appropriate probiotics, as well as dosage and duration of treatment, need to be answered before probiotics can be a clinical treatment in human pregnancy.
MeSH term(s)	Pregnancy ; Female ; Humans ; Dysbiosis ; Infectious Disease Transmission, Vertical ; Uterus ; Microbiota ; Vagina
Language	English
Publishing date	2023-02-03
Publishing country	Ireland
Document type	Journal Article ; Review
ZDB-ID	424421-7
ISSN	1872-7603 ; 0165-0378
ISSN (online)	1872-7603
ISSN	0165-0378
DOI	10.1016/j.jri.2023.103828
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Article: Rapid identification and quantification of intramuscular fat adulteration in lamb meat with VIS–NIR spectroscopy and chemometrics methods

Kazemi, Amir / Mahmoudi, Asghar / Veladi, Hadi / Javanmard, Arash / Khojastehnazhand, Mostafa

Journal of food measurement & characterization. 2022 June, v. 16, no. 3

2022

Abstract: Meat adulteration can be one of the main reasons of human’s healthy and safety problems. Therefore resolving this problem is a significant issue in food industry. VIS–NIR spectroscopy in this work was used as nondestructive technique to classify and ... ...

Abstract	Meat adulteration can be one of the main reasons of human’s healthy and safety problems. Therefore resolving this problem is a significant issue in food industry. VIS–NIR spectroscopy in this work was used as nondestructive technique to classify and evaluate the quantity of intramuscular fat in minced lamb meat. There were totally 110 samples and every sample weighed 10 gr. adulterated samples were prepared manually with 5%, 10%, 15%, and 20% (w/w) adulteration levels. Principle Component Analysis and Linear Discriminant Analysis (LDA) models were applied with different preprocessing methods to separate unadulterated and adulterated samples in to two and five class datasets. The best results of LDA model was 86.2% and 100% accuracy with Savitzky–Golay smoothing preprocessing for five and two class datasets, respectively. Partial Least Squares Regression model was built under cross-validation and external validation testing to quantify the adulteration level of samples. The best outcome of this model was with SNV with Correlation Coefficient of prediction Rₚ² = 76.51% and root mean square error of prediction RMSEP = 0.76. Then Ultraviolet–Visible-Near infrared spectroscopy can be used safely as non-destructive technique for detection of adulteration in meat industry.
Keywords	adulterated products ; chemometrics ; data collection ; discriminant analysis ; food industry ; humans ; infrared spectroscopy ; intramuscular fat ; livestock and meat industry ; measurement ; minced lamb ; models ; nondestructive methods ; prediction ; principal component analysis
Language	English
Dates of publication	2022-06
Size	p. 2400-2410.
Publishing place	Springer US
Document type	Article
ZDB-ID	2754612-3
ISSN	2193-4134 ; 2193-4126
ISSN (online)	2193-4134
ISSN	2193-4126
DOI	10.1007/s11694-022-01352-y
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Article ; Online: The pattern of runs of homozygosity and genomic inbreeding in world-wide sheep populations.

Nosrati, Maryam / Asadollahpour Nanaei, Hojjat / Javanmard, Arash / Esmailizadeh, Ali

Genomics

2021 Volume 113, Issue 3, Page(s) 1407–1415

Abstract: Genome-wide pattern of runs of homozygosity (ROH) across ovine genome can provide a useful resource for studying diversity and demography history in sheep. We analyzed 50 k SNPs chip data of 2536 animals to identify pattern, distribution and level of ... ...

Abstract	Genome-wide pattern of runs of homozygosity (ROH) across ovine genome can provide a useful resource for studying diversity and demography history in sheep. We analyzed 50 k SNPs chip data of 2536 animals to identify pattern, distribution and level of ROHs in 68 global sheep populations. A total of 60,301 ROHs were detected in all breeds. The majority of the detected ROHs were <16 Mb and the average total number of ROHs per individual was 23.8 ± 13.8. The ROHs greater than 1 Mb covered on average 8.2% of the sheep autosomes, 1% of which was related to the ROHs with 1-4 Mb of length. The mean sum of ROH length in two-thirds of the populations was less than 250 Mb ranging from 21.7 to near 570 Mb. The level of genomic inbreeding was relatively low. The average of the inbreeding coefficients based on ROH (F
MeSH term(s)	Animals ; Cattle ; Genome ; Genomics ; Genotype ; Homozygote ; Inbreeding ; Polymorphism, Single Nucleotide ; Sheep/genetics ; Swine
Language	English
Publishing date	2021-03-08
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	356334-0
ISSN	1089-8646 ; 0888-7543
ISSN (online)	1089-8646
ISSN	0888-7543
DOI	10.1016/j.ygeno.2021.03.005
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Article ; Online: Supplementation of broiler chicken diets with bovine lactoferrin improves growth performance, histological parameters of jejunum and immune-related gene expression.

Olyayee, Majid / Javanmard, Arash / Janmohammadi, Hossein / Kianfar, Ruhollah / Alijani, Sadegh / Mir Ghelenj, Seyed Ali

Journal of animal physiology and animal nutrition

2022

Abstract	The aim of this study was to investigate the influence of dietary supplementation of bovine lactoferrin (bLF) on growth performance, carcass traits, histomorphology of jejunum, immune function and hepatic and splenic gene expression of interferon-gamma (IFN-γ) and interleukine-2 (IL-2) in broiler chickens. A total of 240 one-day-old Ross 308 male broiler chickens were randomly allotted into six dietary treatments with four replicate pens (10 chicks per pen) and fed experimental diet in 3 feeding phases (starter: d 0-10, grower: d 11-24 and finisher: d 25-42). The experimental treatments were (1) corn-soya bean meal-based basal diet (control), (2-5) basal diet supplemented with 200, 400, 600, 800 mg/kg bLF, respectively, and (6) basal diet supplemented with 200 mg/kg oxytetracycline (OTC). The average body weight gain (ABWG) of broilers fed 800 mg/kg bLF was 8.48% higher than those fed a corn-soybean meal-based diet during the starter period (d 0-10) (linear effect, p = 0.002; quadratic effect, p = 0.24). Average daily feed intake (ADFI) and the feed conversion ratio (FCR) were not affected (p>0.05) by bLF supplementation. At 42 days of age, the breast meat percentage and carcass yield of broilers fed 800 mg/kg bLF compared with the control group significantly increased by 9.51% and 6.03% respectively (p < 0.05). Compared with the chicks fed the control diet, the chicks fed diets supplemented with bLF had higher villus height, muscle thickness and villus surface area (p > 0.05). Dietary bLF inclusion increased the total immunoglobulin (IgT) titre against sheep red blood cells (SRBCs) antigen (linear effect, p = 0.031; quadratic effect, p = 0.035) and improved the phytohaemagglutinin-P (PHA-P)-skin test of broilers. Compared with the control, bLF enhanced the gene expression of IFN-γ in spleen (p = 0.048, linear effect, p = 0.009; quadratic effect, p = 0.093) and liver (p = 0.012, linear effect, p = 0.008; quadratic effect, p = 0.01) and IL-2 expression in spleen (p = 0.021, linear effect, p = 0.026; quadratic effect, p = 0.103). The bLF supplementation had no effect on IL-2 gene expression in liver (p > 0.05, linear effect, p = 0.213; quadratic effect, p = 0.159). In conclusion, we found that supplementation of broiler diets with 800 mg/kg bLF can improve the growth performance, carcass yield, cell-mediated and antibody-mediated immune responses and enhance the IL-2 and IFN-γ gene expression of broilers.
Language	English
Publishing date	2022-02-01
Publishing country	Germany
Document type	Journal Article
ZDB-ID	232729-6
ISSN	1439-0396 ; 0044-3565 ; 0931-2439
ISSN (online)	1439-0396
ISSN	0044-3565 ; 0931-2439
DOI	10.1111/jpn.13683
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Article: Variation and frequency of supernumerary teats, litter size, histological features and the fibroblast growth factor 2 (FGF-2) gene expression pattern in goats

Ghaffarilaleh, Vahid / Javanmard, Arash / Saberivand, Adel / Asadzadeh, Nader / Masoudi, Reza / Barfourooshi, Hoda Javaheri / Rashidi, Amir / Eghbalsaied, Shahin

Theriogenology. 2022 Feb., v. 179

2022

Abstract: Historically, female domestic goats carrying multiple kids are mostly unable to express sufficient nursing ability due to a limited number of functional teats. Therefore, the functional teat is an important component in prolific goat breeding, and plays ... ...

Abstract	Historically, female domestic goats carrying multiple kids are mostly unable to express sufficient nursing ability due to a limited number of functional teats. Therefore, the functional teat is an important component in prolific goat breeding, and plays a key role in the future health of their kids. With this motivation, we wanted to investigate the phenotypic features, litter size, histology of adult female mammary glands, and the gene expression profile of the fibroblast growth factor 2 (FGF-2) gene in goats. To illustrate this, the initial dataset of the current study consists of an electronic questionnaire that includes 697 individuals (548 does and 149 bucks) of five endemic and three exotic goats from 2015 to 2020 in different geographic areas of Iran, from 59 Markhoz (MARG), 50 Azari (AZAR), 73 Busheri (BUSH), 69 Sarbisheh (SARB), 165 Mahabadi (MOHA) indigenous goats and also exotic breeds, including 183 Saanen (SANN), 39 Alpine (ALPN), and 59 Boer (BORE) goats. The results of this study confirmed that MOHA goats (4.16%), BORE (4.43%) and SANN goat breeds (5.75%) have larger litter sizes. Interestingly, the evidence gathering when SNTs occurred showed that both the BUSH and BORE goat breeds had the highest frequency of SNTs. Moreover, under the same physiological and lactation conditions, there was no statistically significant difference in histological features between the three compared does class consist of the two teats, SNTs, and four functional teats. In addition, the results of the gene expression profile significantly highlight the FGF-2 gene pattern in two teat groups compared to other SNT groups (P < 0.01). In summary, this scenario can be used to generate further research and facts on responsible candidate genes, the variations in teat numbers in goats, examining both the incidence of SNT and litter size.
Keywords	Saanen ; adults ; data collection ; females ; fibroblast growth factor 2 ; gene expression ; gene expression regulation ; genes ; goats ; histology ; lactation ; litter size ; motivation ; phenotype ; questionnaires ; Iran
Language	English
Dates of publication	2022-02
Size	p. 141-148.
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	189232-0
ISSN	1879-3231 ; 0093-691X
ISSN (online)	1879-3231
ISSN	0093-691X
DOI	10.1016/j.theriogenology.2021.11.016
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