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Yao H, Pan Z, Ma W, Zhao Z, Su Z, Yang J. Whole-Genome Resequencing Analysis of the Camelus bactrianus (Bactrian Camel) Genome Identifies Mutations and Genes Affecting Milk Production Traits. Int J Mol Sci 2024; 25:7836. [PMID: 39063078 PMCID: PMC11277051 DOI: 10.3390/ijms25147836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 07/09/2024] [Accepted: 07/16/2024] [Indexed: 07/28/2024] Open
Abstract
Milk production is an important trait that influences the economic value of camels. However, the genetic regulatory mechanisms underlying milk production in camels have not yet been elucidated. We aimed to identify candidate molecular markers that affect camel milk production. We classified Junggar Bactrian camels (9-10-year-old) as low-yield (<1.96 kg/d) or high-yield (>2.75 kg/d) based on milk production performance. Milk fat (5.16 ± 0.51 g/100 g) and milk protein (3.59 ± 0.22 g/100 g) concentrations were significantly lower in high-yielding camels than those in low-yielding camels (6.21 ± 0.59 g/100 g, and 3.93 ± 0.27 g/100 g, respectively) (p < 0.01). There were no apparent differences in gland tissue morphology between the low- and high-production groups. Whole-genome resequencing of 12 low- and 12 high-yield camels was performed. The results of selection mapping methods, performed using two methods (FST and θπ), showed that 264 single nucleotide polymorphism sites (SNPs) overlapped between the two methods, identifying 181 genes. These genes were mainly associated with the regulation of oxytocin, estrogen, ErbB, Wnt, mTOR, PI3K-Akt, growth hormone synthesis/secretion/action, and MAPK signaling pathways. A total of 123 SNPs were selected, based on significantly associated genomic regions and important pathways for SNP genotyping, for verification in 521 additional Bactrian camels. This analysis showed that 13 SNPs were significantly associated with camel milk production yield and 18 SNPs were significantly associated with camel milk composition percentages. Most of these SNPs were located in coding regions of the genome. However, five and two important mutation sites were found in the introns of CSN2 (β-casein) and CSN3 (κ-casein), respectively. Among the candidate genes, NR4A1, ADCY8, PPARG, CSN2, and CSN3 have previously been well studied in dairy livestock. These observations provide a basis for understanding the molecular mechanisms underlying milk production in camels as well as genetic markers for breeding programs aimed at improving milk production.
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Affiliation(s)
- Huaibing Yao
- Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830017, China; (H.Y.); (Z.Z.)
- Xinjiang Camel Industry Engineering Technology Research Center, Urumqi 830017, China
| | - Zhangyuan Pan
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China;
| | - Wanpeng Ma
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi 830052, China; (W.M.); (Z.S.)
| | - Zhongkai Zhao
- Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830017, China; (H.Y.); (Z.Z.)
- Xinjiang Camel Industry Engineering Technology Research Center, Urumqi 830017, China
| | - Zhanqiang Su
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi 830052, China; (W.M.); (Z.S.)
| | - Jie Yang
- Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830017, China; (H.Y.); (Z.Z.)
- Xinjiang Camel Industry Engineering Technology Research Center, Urumqi 830017, China
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Mota-Rojas D, Napolitano F, Chay-Canul A, Ghezzi M, Braghieri A, Domínguez-Oliva A, Bragaglio A, Álvarez-Macías A, Olmos-Hernández A, De Rosa G, García-Herrera R, Lendez P, Pacelli C, Bertoni A, Barile VL. Anatomy and Physiology of Water Buffalo Mammary Glands: An Anatomofunctional Comparison with Dairy Cattle. Animals (Basel) 2024; 14:1066. [PMID: 38612305 PMCID: PMC11011071 DOI: 10.3390/ani14071066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 03/19/2024] [Accepted: 03/28/2024] [Indexed: 04/14/2024] Open
Abstract
The present review aims to analyze the anatomical and physiological characteristics of the mammary gland and udders of water buffalo by making an anatomofunctional comparison with dairy cattle. It will also discuss the knowledge generated around the physiological regulation of milk ejection in the water buffalo. It was found that buffalo's average udder depth and width is approximately 20 cm smaller than Bos cattle. One of the main differences with dairy cattle is a longer teat canal length (around 8.25-11.56 cm), which highly influences buffalo milking. In this sense, a narrower teat canal (2.71 ± 0.10 cm) and thicker sphincter muscle are associated with needing higher vacuum levels when using machine milking in buffalo. Moreover, the predominant alveolar fraction of water buffalo storing 90-95% of the entire milk production is another element that can be related to the lower milk yields in buffalo (when compared to Bos cattle) and the requirements for prolonged prestimulation in this species. Considering the anatomical characteristics of water buffalo's udder could help improve bubaline dairy systems.
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Affiliation(s)
- Daniel Mota-Rojas
- Neurophysiology, Behavior and Animal Welfare Assessment, DPAA, Universidad Autónoma Metropolitana (UAM), Mexico City 04960, Mexico
| | - Fabio Napolitano
- Scuola di Scienze Agrarie, Forestali, Alimentari ed Ambientali, Università degli Studi della Basilicata, 85100 Potenza, Italy
| | - Alfonso Chay-Canul
- División Académica de Ciencias Agropecuarias, Universidad Juárez Autónoma de Tabasco, Villahermosa 86040, Mexico
| | - Marcelo Ghezzi
- Anatomy Area, Faculty of Veterinary Sciences (FCV), Universidad Nacional del Centro de la Provincia de Buenos Aires (UNCPBA), University Campus, Tandil 7000, Argentina
| | - Ada Braghieri
- Scuola di Scienze Agrarie, Forestali, Alimentari ed Ambientali, Università degli Studi della Basilicata, 85100 Potenza, Italy
| | - Adriana Domínguez-Oliva
- Neurophysiology, Behavior and Animal Welfare Assessment, DPAA, Universidad Autónoma Metropolitana (UAM), Mexico City 04960, Mexico
| | - Andrea Bragaglio
- Research Centre for Engineering and Food Processing, Council for Agricultural Research and Agricultural Economy Analysis (CREA), Via Milano 43, 24047 Treviglio, Italy
| | - Adolfo Álvarez-Macías
- Neurophysiology, Behavior and Animal Welfare Assessment, DPAA, Universidad Autónoma Metropolitana (UAM), Mexico City 04960, Mexico
| | - Adriana Olmos-Hernández
- Division of Biotechnology—Bioterio and Experimental Surgery, Instituto Nacional de Rehabilitación-Luis Guillermo Ibarra Ibarra (INR-LGII), Mexico City 14389, Mexico
| | - Giuseppe De Rosa
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy
| | - Ricardo García-Herrera
- División Académica de Ciencias Agropecuarias, Universidad Juárez Autónoma de Tabasco, Villahermosa 86040, Mexico
| | - Pamela Lendez
- Faculty of Veterinary Sciences (FCV), Universidad Nacional del Centro de la Provincia de Buenos Aires, CIVETAN, UNCPBA-CICPBA-CONICET (UNCPBA), University Campus, Tandil 7000, Argentina
| | - Corrado Pacelli
- Scuola di Scienze Agrarie, Forestali, Alimentari ed Ambientali, Università degli Studi della Basilicata, 85100 Potenza, Italy
| | - Aldo Bertoni
- Neurophysiology, Behavior and Animal Welfare Assessment, DPAA, Universidad Autónoma Metropolitana (UAM), Mexico City 04960, Mexico
| | - Vittoria Lucia Barile
- Research Centre for Animal Production and Aquaculture, Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria (CREA), Via Salaria 31, 00015 Monterotondo, Italy
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Jourshari MG, Shadparvar AA, Ghavi Hossein-Zadeh N, Rafeie F, Banabazi MH, Johansson AM. Genome-wide association study on abdomen depth, head width, hip width, and withers height in native cattle of Guilan (Bos indicus). PLoS One 2023; 18:e0289612. [PMID: 37595009 PMCID: PMC10437930 DOI: 10.1371/journal.pone.0289612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 07/22/2023] [Indexed: 08/20/2023] Open
Abstract
Native breeds in any country are a national capital, and their preservation is of great importance. Native Cattle of Guilan (NCG) is one of the few pure native breeds in Iran and the West Asia region. During the last decade, NCG population has decreased by more than 40%. This study aimed to identify significant single nucleotide polymorphisms (SNPs) and candidate genes associated with meat production traits in NCG using a genome-wide association study (GWAS). The blood and hair samples were collected from 72 NCG individuals and genotyped using the Illumina Bovine SNP50 chip. The results of the genomic scan showed that several SNPs were associated with abdominal depth, head width, hip width, and withers height in NCG. Several candidate genes were identified, including multiple epidermal growth factor-like domains 11 (MEGF11), Methionine Sulfoxide Reductase A (MSRA), chondroitin sulfate synthase 3 (CHSY3), Cyclin-Dependent Kinase 7 (CDK7), and Parkin (PRKN) genes, which are involved in muscle growth, meat tenderness, differentiation of fat cells, fat metabolism, and adipogenesis. These genes can contribute to meat quantity and quality in NCG. This study provided valuable insights into the genetics of NCG and the identification of effective genes associated with meat production traits. The results of this study could be used for the preservation and sustainable use of this breed of native cattle, as an important genetic resource in Iran.
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Affiliation(s)
| | - Abdol Ahad Shadparvar
- Department of Animal Science, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran
| | | | - Farjad Rafeie
- Department of Agricultural Biotechnology, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran
| | - Mohammad Hossein Banabazi
- Department of Biotechnology, Animal Science Research Institute of IRAN (ASRI), Agricultural Research, Education & Extension Organization (AREEO), Karaj, Iran
- Department of Animal Breeding and Genetics (HGEN), Centre for Veterinary Medicine and Animal Science (VHC), Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Anna Maria Johansson
- Department of Animal Breeding and Genetics (HGEN), Centre for Veterinary Medicine and Animal Science (VHC), Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
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Mishra DC, Bhati J, Yadav S, Avashthi H, Sikka P, Jerome A, Balhara AK, Singh I, Rai A, Chaturvedi KK. Comparative expression analysis of water buffalo ( Bubalus bubalis) to identify genes associated with economically important traits. Front Vet Sci 2023; 10:1160486. [PMID: 37252384 PMCID: PMC10213454 DOI: 10.3389/fvets.2023.1160486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 04/11/2023] [Indexed: 05/31/2023] Open
Abstract
The milk, meat, skins, and draft power of domestic water buffalo (Bubalus bubalis) provide substantial contributions to the global agricultural economy. The world's water buffalo population is primarily found in Asia, and the buffalo supports more people per capita than any other livestock species. For evaluating the workflow, output rate, and completeness of transcriptome assemblies within and between reference-free (RF) de novo transcriptome and reference-based (RB) datasets, abundant bioinformatics studies have been carried out to date. However, comprehensive documentation of the degree of consistency and variability of the data produced by comparing gene expression levels using these two separate techniques is lacking. In the present study, we assessed the variations in the number of differentially expressed genes (DEGs) attained with RF and RB approaches. In light of this, we conducted a study to identify, annotate, and analyze the genes associated with four economically important traits of buffalo, viz., milk volume, age at first calving, post-partum cyclicity, and feed conversion efficiency. A total of 14,201 and 279 DEGs were identified in RF and RB assemblies. Gene ontology (GO) terms associated with the identified genes were allocated to traits under study. Identified genes improve the knowledge of the underlying mechanism of trait expression in water buffalo which may support improved breeding plans for higher productivity. The empirical findings of this study using RNA-seq data-based assembly may improve the understanding of genetic diversity in relation to buffalo productivity and provide important contributions to answer biological issues regarding the transcriptome of non-model organisms.
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Affiliation(s)
- Dwijesh Chandra Mishra
- ICAR-Indian Agricultural Statistics Research Institute, Indian Council of Agricultural Research (ICAR), PUSA, New Delhi, India
| | - Jyotika Bhati
- ICAR-Indian Agricultural Statistics Research Institute, Indian Council of Agricultural Research (ICAR), PUSA, New Delhi, India
| | - Sunita Yadav
- ICAR-Indian Agricultural Statistics Research Institute, Indian Council of Agricultural Research (ICAR), PUSA, New Delhi, India
| | - Himanshu Avashthi
- ICAR-Indian Agricultural Statistics Research Institute, Indian Council of Agricultural Research (ICAR), PUSA, New Delhi, India
| | - Poonam Sikka
- ICAR-Central Institute for Research on Buffaloes, Indian Council of Agricultural Research (ICAR), Hisar, India
| | - Andonissamy Jerome
- ICAR-Central Institute for Research on Buffaloes, Indian Council of Agricultural Research (ICAR), Hisar, India
| | - Ashok Kumar Balhara
- ICAR-Central Institute for Research on Buffaloes, Indian Council of Agricultural Research (ICAR), Hisar, India
| | - Inderjeet Singh
- ICAR-Central Institute for Research on Buffaloes, Indian Council of Agricultural Research (ICAR), Hisar, India
| | - Anil Rai
- ICAR-Indian Agricultural Statistics Research Institute, Indian Council of Agricultural Research (ICAR), PUSA, New Delhi, India
| | - Krishna Kumar Chaturvedi
- ICAR-Indian Agricultural Statistics Research Institute, Indian Council of Agricultural Research (ICAR), PUSA, New Delhi, India
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Zhang XX, An ZG, Niu KF, Chen C, Ye TZ, Shaukat A, Yang LG. Evaluation of type traits in relation to production, and their importance in early selection for milk performance in dairy buffaloes. Animal 2022; 16:100653. [DOI: 10.1016/j.animal.2022.100653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 09/09/2022] [Accepted: 09/12/2022] [Indexed: 11/29/2022] Open
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Valente GF, Ferraz GAES, Santana LS, Ferraz PFP, Mariano DDC, dos Santos CM, Okumura RS, Simonini S, Barbari M, Rossi G. Mapping Soil and Pasture Attributes for Buffalo Management through Remote Sensing and Geostatistics in Amazon Biome. Animals (Basel) 2022; 12:ani12182374. [PMID: 36139234 PMCID: PMC9495005 DOI: 10.3390/ani12182374] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/22/2022] [Accepted: 09/06/2022] [Indexed: 11/16/2022] Open
Abstract
The mapping of pastures can serve to increase productivity and reduce deforestation, especially in Amazon Biome regions. Therefore, in this study, we aimed to explore precision agriculture technologies for assessing the spatial variations of soil pH and biomass indicators (i.e., Dry Matter, DM; and Green Matter, GM). An experiment was conducted in an area cultivated with Panicum maximum (Jacq.) cv. Mombaça in a rotational grazing system for dairy buffaloes in the eastern Amazon. Biomass and soil samples were collected in a 10 m × 10 m grid, with a total of 196 georeferenced points. The data were analyzed by semivariogram and then mapped by Kriging interpolation. In addition, a variability analysis was performed, applying both the Normalized Difference Vegetation Index (NDVI) and Normalized Difference Water Index (NDWI) derived from satellite remote sensing data. The Kriging mapping between DM and pH at 0.30 m depth demonstrated the best correlation. The vegetative index mapping showed that the NDVI presented a better performance in pastures with DM production above 5.42 ton/ha−1. In contrast, DM and GM showed low correlations with the NDWI. The possibility of applying a variable rate within the paddocks was evidenced through geostatistical mapping of soil pH. With this study, we contribute to understanding the necessary premises for utilizing remote sensing data for pasture variable analysis.
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Affiliation(s)
- Gislayne Farias Valente
- Agricultural Engineering Department, Federal University of Lavras, P.O. Box 3037, Lavras 37200-900, MG, Brazil
| | | | - Lucas Santos Santana
- Agricultural Engineering Department, Federal University of Lavras, P.O. Box 3037, Lavras 37200-900, MG, Brazil
| | | | - Daiane de Cinque Mariano
- Department of Agronomy, Federal Rural University of the Amazon—UFRA, P.O. Box 3017, Parauapebas 68515-000, PA, Brazil
| | | | - Ricardo Shigueru Okumura
- Department of Agronomy, Federal Rural University of the Amazon—UFRA, P.O. Box 3017, Parauapebas 68515-000, PA, Brazil
| | - Stefano Simonini
- Department of Agriculture, Food, Environment and Forestry (DAGRI), University of Florence, Via San Bonaventura 13, 50145 Florence, Italy
| | - Matteo Barbari
- Department of Agriculture, Food, Environment and Forestry (DAGRI), University of Florence, Via San Bonaventura 13, 50145 Florence, Italy
| | - Giuseppe Rossi
- Department of Agriculture, Food, Environment and Forestry (DAGRI), University of Florence, Via San Bonaventura 13, 50145 Florence, Italy
- Correspondence:
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Genome-Wide Association Study Identifies Candidate Genes Associated with Feet and Leg Conformation Traits in Chinese Holstein Cattle. Animals (Basel) 2021; 11:ani11082259. [PMID: 34438715 PMCID: PMC8388412 DOI: 10.3390/ani11082259] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/24/2021] [Accepted: 07/28/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Feet and leg problems are among the major reasons for dairy cows leaving the herd, as well as having direct association with production and reproduction efficiency, health (e.g., claw disorders and lameness) and welfare. Hence, understanding the genetic architecture underlying feet and conformation traits in dairy cattle offers new opportunities toward the genetic improvement and long-term selection. Through a genome-wide association study on Chinese Holstein cattle, we identified several candidate genes associated with feet and leg conformation traits. These results could provide useful information about the molecular breeding basis of feet and leg traits, thus improving the longevity and productivity of dairy cattle. Abstract Feet and leg conformation traits are considered one of the most important economical traits in dairy cattle and have a great impact on the profitability of milk production. Therefore, identifying the single nucleotide polymorphisms (SNPs), genes and pathways analysis associated with these traits might contribute to the genomic selection and long-term plan selection for dairy cattle. We conducted genome-wide association studies (GWASs) using the fixed and random model circulating probability unification (FarmCPU) method to identify SNPs associated with bone quality, heel depth, rear leg side view and rear leg rear view of Chinese Holstein cows. Phenotypic measurements were collected from 1000 individuals of Chinese Holstein cattle and the GeneSeek Genomic Profiler Bovine 100 K SNP chip was utilized for individual genotyping. After quality control, 984 individual cows and 84,906 SNPs remained for GWAS work; as a result, we identified 20 significant SNPs after Bonferroni correction. Several candidate genes were identified within distances of 200 kb upstream or downstream to the significant SNPs, including ADIPOR2, INPP4A, DNMT3A, ALDH1A2, PCDH7, XKR4 and CADPS. Further bioinformatics analyses showed 34 gene ontology terms and two signaling pathways were significantly enriched (p ≤ 0.05). Many terms and pathways are related to biological quality, metabolism and development processes; these identified SNPs and genes could provide useful information about the genetic architecture of feet and leg traits, thus improving the longevity and productivity of Chinese Holstein dairy cattle.
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E Silva AGM, de Lima SCG, de Oliveira PD, Moraes MDS, Guimarães CMC, da Silva JAR, Garcia AR, Nahúm BDS, Neres LDS, Noronha GN, Lourenço Júnior JDB. Production, chemical composition, and fatty acid profile of milk from buffaloes fed with cupuaçu (Theobroma grandiflorum) cake and murumuru (Astrocaryum murumuru) cake in the Eastern Amazon. Anim Sci J 2021; 92:e13576. [PMID: 34173304 DOI: 10.1111/asj.13576] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 10/30/2020] [Accepted: 11/24/2020] [Indexed: 01/20/2023]
Abstract
The objective was to evaluate the effect of concentrate supplementation using by-products of the Amazonian industry on milk production, milk composition, and milk fatty acid profile of dairy buffaloes. Twelve lactating buffaloes (544.5 ± 35.6 kg, 6.4 ± 2.2 years old, 59 ± 6 days in milk) were allotted in a pasture of Mombaça grass and managed under rotational grazing (4 days occupancy/28 days rest). A 3 × 3 Latin square was adopted, and each animal alternately received three supplementary treatments based on corn bran + soybean meal or cupuaçu cake or murumuru cake for 21 days per treatment. Murumuru cake increased the levels of lauric acid and myristic acid in the milk (p < 0.05). Murumuru cake reduced the unsaturated fatty acid contents in the milk compared with animals fed control diet or cupuaçu cake (24.27% vs. 25.24% vs. 25.08%). The n-6/n-3 ratio was 2.6, 1.97, and 2.0 in the control, cupuaçu, and murumuru groups, respectively. Based on this parameter, cakes made from cupuaçu as well as murumuru could be considered to be adequate for inclusion in dairy water buffalo feed. However, the murumuru cake addition requires some caution because its use induces the secretion of higher levels of lauric and myristic fatty acids that are related to human cardiovascular disease.
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Affiliation(s)
| | | | - Pedro Danilo de Oliveira
- Postgraduate Program in Food Science and Technology, Federal University of Pará (UFPA), Belém, Brazil
| | | | - Célia Maria Costa Guimarães
- Animal Science Department, Federal Institute of Education, Science, and Technology (IFPA), Castanhal, Brazil
| | | | | | | | - Lilaine de Sousa Neres
- Postgraduate Program in Animal Science, Federal University of Pará (UFPA), Belém, Brazil
| | - Gerlane Nunes Noronha
- Postgraduate Program in Animal Science, Federal University of Pará (UFPA), Belém, Brazil
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Lázaro SF, Tonhati H, Oliveira HR, Silva AA, Nascimento AV, Santos DJA, Stefani G, Brito LF. Genomic studies of milk-related traits in water buffalo (Bubalus bubalis) based on single-step genomic best linear unbiased prediction and random regression models. J Dairy Sci 2021; 104:5768-5793. [PMID: 33685677 DOI: 10.3168/jds.2020-19534] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 01/02/2021] [Indexed: 01/14/2023]
Abstract
Genomic selection has been widely implemented in many livestock breeding programs, but it remains incipient in buffalo. Therefore, this study aimed to (1) estimate variance components incorporating genomic information in Murrah buffalo; (2) evaluate the performance of genomic prediction for milk-related traits using single- and multitrait random regression models (RRM) and the single-step genomic best linear unbiased prediction approach; and (3) estimate longitudinal SNP effects and candidate genes potentially associated with time-dependent variation in milk, fat, and protein yields, as well as somatic cell score (SCS) in multiple parities. The data used to estimate the genetic parameters consisted of a total of 323,140 test-day records. The average daily heritability estimates were moderate (0.35 ± 0.02 for milk yield, 0.22 ± 0.03 for fat yield, 0.42 ± 0.03 for protein yield, and 0.16 ± 0.03 for SCS). The highest heritability estimates, considering all traits studied, were observed between 20 and 280 d in milk (DIM). The genetic correlation estimates at different DIM among the evaluated traits ranged from -0.10 (156 to 185 DIM for SCS) to 0.61 (36 to 65 DIM for fat yield). In general, direct selection for any of the traits evaluated is expected to result in indirect genetic gains for milk yield, fat yield, and protein yield but also increase SCS at certain lactation stages, which is undesirable. The predicted RRM coefficients were used to derive the genomic estimated breeding values (GEBV) for each time point (from 5 to 305 DIM). In general, the tuning parameters evaluated when constructing the hybrid genomic relationship matrices had a small effect on the GEBV accuracy and a greater effect on the bias estimates. The SNP solutions were back-solved from the GEBV predicted from the Legendre random regression coefficients, which were then used to estimate the longitudinal SNP effects (from 5 to 305 DIM). The daily SNP effect for 3 different lactation stages were performed considering 3 different lactation stages for each trait and parity: from 5 to 70, from 71 to 150, and from 151 to 305 DIM. Important genomic regions related to the analyzed traits and parities that explain more than 0.50% of the total additive genetic variance were selected for further analyses of candidate genes. In general, similar potential candidate genes were found between traits, but our results suggest evidence of differential sets of candidate genes underlying the phenotypic expression of the traits across parities. These results contribute to a better understanding of the genetic architecture of milk production traits in dairy buffalo and reinforce the relevance of incorporating genomic information to genetically evaluate longitudinal traits in dairy buffalo. Furthermore, the candidate genes identified can be used as target genes in future functional genomics studies.
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Affiliation(s)
- Sirlene F Lázaro
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907; Department of Animal Science, College of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, 14884-900, SP, Brazil
| | - Humberto Tonhati
- Department of Animal Science, College of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, 14884-900, SP, Brazil
| | - Hinayah R Oliveira
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907; Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, N1G 2W1, ON, Canada
| | - Alessandra A Silva
- Department of Animal Science, College of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, 14884-900, SP, Brazil
| | - André V Nascimento
- Department of Animal Science, College of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, 14884-900, SP, Brazil
| | - Daniel J A Santos
- Department of Animal and Avian Science, University of Maryland, College Park 20742
| | - Gabriela Stefani
- Department of Animal Science, College of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, 14884-900, SP, Brazil
| | - Luiz F Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907.
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Vanvanhossou SFU, Scheper C, Dossa LH, Yin T, Brügemann K, König S. A multi-breed GWAS for morphometric traits in four Beninese indigenous cattle breeds reveals loci associated with conformation, carcass and adaptive traits. BMC Genomics 2020; 21:783. [PMID: 33176675 PMCID: PMC7656759 DOI: 10.1186/s12864-020-07170-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 10/20/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Specific adaptive features including disease resistance and growth abilities in harsh environments are attributed to indigenous cattle breeds of Benin, but these breeds are endangered due to crossbreeding. So far, there is a lack of systematic trait recording, being the basis for breed characterizations, and for structured breeding program designs aiming on conservation. Bridging this gap, own phenotyping for morphological traits considered measurements for height at withers (HAW), sacrum height (SH), heart girth (HG), hip width (HW), body length (BL) and ear length (EL), including 449 cattle from the four indigenous Benin breeds Lagune, Somba, Borgou and Pabli. In order to utilize recent genomic tools for breed characterizations and genetic evaluations, phenotypes for novel traits were merged with high-density SNP marker data. Multi-breed genetic parameter estimations and genome-wide association studies (GWAS) for the six morphometric traits were carried out. Continuatively, we aimed on inferring genomic regions and functional loci potentially associated with conformation, carcass and adaptive traits. RESULTS SNP-based heritability estimates for the morphometric traits ranged between 0.46 ± 0.14 (HG) and 0.74 ± 0.13 (HW). Phenotypic and genetic correlations ranged from 0.25 ± 0.05 (HW-BL) to 0.89 ± 0.01 (HAW-SH), and from 0.14 ± 0.10 (HW-BL) to 0.85 ± 0.02 (HAW-SH), respectively. Three genome-wide and 25 chromosome-wide significant SNP positioned on different chromosomes were detected, located in very close chromosomal distance (±25 kb) to 15 genes (or located within the genes). The genes PIK3R6 and PIK3R1 showed direct functional associations with height and body size. We inferred the potential candidate genes VEPH1, CNTNAP5, GYPC for conformation, growth and carcass traits including body weight and body fat deposition. According to their functional annotations, detected potential candidate genes were associated with stress or immune response (genes PTAFR, PBRM1, ADAMTS12) and with feed efficiency (genes MEGF11 SLC16A4, CCDC117). CONCLUSIONS Accurate measurements contributed to large SNP heritabilities for some morphological traits, even for a small mixed-breed sample size. Multi-breed GWAS detected different loci associated with conformation or carcass traits. The identified potential candidate genes for immune response or feed efficiency indicators reflect the evolutionary development and adaptability features of the breeds.
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Affiliation(s)
| | - Carsten Scheper
- Institute of Animal Breeding and Genetics, Justus-Liebig-University Gießen, Gießen, Germany
| | - Luc Hippolyte Dossa
- School of Science and Technics of Animal Production, Faculty of Agricultural Sciences, University of Abomey-Calavi, Cotonou, Benin
| | - Tong Yin
- Institute of Animal Breeding and Genetics, Justus-Liebig-University Gießen, Gießen, Germany
| | - Kerstin Brügemann
- Institute of Animal Breeding and Genetics, Justus-Liebig-University Gießen, Gießen, Germany
| | - Sven König
- Institute of Animal Breeding and Genetics, Justus-Liebig-University Gießen, Gießen, Germany.
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