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      Identification of candidate genes associated with milk yield trait in buffaloes ( Bubalus bubalis ) by restriction-site-associated DNA sequencing

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          Abstract

          ABSTRACT The objectives of our present study included the screening of single nucleotide polymorphisms (SNP) that show significant differences in allelic frequencies between two buffalo populations (Egyptian and Chinese buffaloes), categorization of functional genes associated with these SNP by gene ontology, and pathway analyses to further understand their potential values as candidate genes closely associated with milk yield trait in buffaloes. In this study, double digest restriction-site associated DNA sequencing was performed on Illumina HiSeq 2500 platform for 20 and 25 female buffaloes from Egypt and China, respectively. Approximately 118 Gb of sequencing data were obtained, and a total of 110,129 and 150,535 putative SNP were detected in Egyptian and Chinese buffaloes, respectively. Focused only on those SNP that differed significantly in allelic frequencies between the two populations, we found that genes associated with these SNP were significantly over-represented in the ionotropic glutamate receptor pathway, the endothelin signaling pathway, and the gonadotropin-releasing hormone receptor pathway, which contained a total of 29 genes. Of these, nine genes ( ADCY5, CACNA1A, CREB1, INHBA , INHBB, PIK3R1, PLCB1, PRKCE , and SMAD2 ) participating in the hormonal regulation of lactation, were considered to be promising candidate genes worthy of further investigations for favorable alleles associated with milk yield. Our results provide useful information about genetic variations in Egyptian and Chinese buffaloes. The potential influences of nine candidate genes and their associated SNP on milk yield need to be validated in more buffalo populations.

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          Most cited references49

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          PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools

          Abstract PANTHER (Protein Analysis Through Evolutionary Relationships, http://pantherdb.org) is a resource for the evolutionary and functional classification of genes from organisms across the tree of life. We report the improvements we have made to the resource during the past two years. For evolutionary classifications, we have added more prokaryotic and plant genomes to the phylogenetic gene trees, expanding the representation of gene evolution in these lineages. We have refined many protein family boundaries, and have aligned PANTHER with the MEROPS resource for protease and protease inhibitor families. For functional classifications, we have developed an entirely new PANTHER GO-slim, containing over four times as many Gene Ontology terms as our previous GO-slim, as well as curated associations of genes to these terms. Lastly, we have made substantial improvements to the enrichment analysis tools available on the PANTHER website: users can now analyze over 900 different genomes, using updated statistical tests with false discovery rate corrections for multiple testing. The overrepresentation test is also available as a web service, for easy addition to third-party sites.
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            Hormonal regulation of mammary differentiation and milk secretion.

            The endocrine system coordinates development of the mammary gland with reproductive development and the demand of the offspring for milk. Three categories of hormones are involved. The levels of the reproductive hormones, estrogen, progesterone, placental lactogen, prolactin, and oxytocin, change during reproductive development or function and act directly on the mammary gland to bring about developmental changes or coordinate milk delivery to the offspring. Metabolic hormones, whose main role is to regulate metabolic responses to nutrient intake or stress, often have direct effects on the mammary gland as well. The important hormones in this regard are growth hormone, corticosteroids, thyroid hormone, and insulin. A third category of hormones has recently been recognized, mammary hormones. It currently includes growth hormone, prolactin, PTHrP, and leptin. Because a full-term pregnancy in early life is associated with a reduction in breast carcinogenesis, an understanding of the mechanisms by which these hormones bring about secretory differentiation may offer clues to the prevention of breast cancer.
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              Prospecting major genes in dairy buffaloes

              Background Asian buffaloes (Bubalus bubalis) have an important socio-economic role. The majority of the population is situated in developing countries. Due to the scarce resources in these countries, very few species-specific biotechnology tools exist and a lot of cattle-derived technologies are applied to buffaloes. However, the application of cattle genomic tools to buffaloes is not straightforward and, as results suggested, despite genome sequences similarity the genetic polymorphisms are different. Results The first SNP chip genotyping platform designed specifically for buffaloes has recently become available. Herein, a genome-wide association study (GWAS) and gene network analysis carried out in buffaloes is presented. Target phenotypes were six milk production and four reproductive traits. GWAS identified SNP with significant associations and suggested candidate genes that were specific to each trait and also genes with pleiotropic effect, associated to multiple traits. Conclusions Network predictions of interactions between these candidate genes may guide further molecular analyses in search of disruptive mutations, help select genes for functional experiments and evidence metabolism differences in comparison to cattle. The cattle SNP chip does not offer an optimal coverage of buffalo genome, thereafter the development of new buffalo-specific genetic technologies is warranted. An annotated reference genome would greatly facilitate genetic research, with potential impact to buffalo-based dairy production. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1986-2) contains supplementary material, which is available to authorized users.
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                Author and article information

                Journal
                rbz
                Revista Brasileira de Zootecnia
                R. Bras. Zootec.
                Sociedade Brasileira de Zootecnia (Viçosa, MG, Brazil )
                1516-3598
                1806-9290
                2020
                : 49
                : e20190267
                Affiliations
                [1] Yangzhou orgnameYangzhou University orgdiv1College of Bioscience and Biotechnology China
                [3] Jiangsu orgnameYangzhou University orgdiv1Ministry of Education of China orgdiv2Joint International Research Laboratory of Agricultural & Agri-Product Safety China
                [4] Yangzhou orgnameYangzhou University orgdiv1College of Animal Science and Technology China
                [2] Beijing orgnameMinistry of Agriculture and Rural Affairs orgdiv1Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction China
                [5] Giza orgnameNational Research Center orgdiv1Genetic Engineering and Biotechnology Division orgdiv2Department of Cell Biology Egypt
                Article
                S1516-35982020000100406 S1516-3598(20)04900000406
                10.37496/rbz4920190267
                c12ca313-1017-41a0-bf8e-6d8bb96bcbef

                This work is licensed under a Creative Commons Attribution 4.0 International License.

                History
                : 13 December 2019
                : 26 May 2020
                Page count
                Figures: 0, Tables: 0, Equations: 0, References: 50, Pages: 0
                Product

                SciELO Brazil

                Categories
                Breeding and Genetics

                association,SNP screening,functional gene,pathway analysis

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