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Wanapat M, Dagaew G, Sommai S, Matra M, Suriyapha C, Prachumchai R, Muslykhah U, Phupaboon S. The application of omics technologies for understanding tropical plants-based bioactive compounds in ruminants: a review. J Anim Sci Biotechnol 2024; 15:58. [PMID: 38689368 PMCID: PMC11062008 DOI: 10.1186/s40104-024-01017-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Accepted: 02/29/2024] [Indexed: 05/02/2024] Open
Abstract
Finding out how diet impacts health and metabolism while concentrating on the functional qualities and bioactive components of food is the crucial scientific objective of nutritional research. The complex relationship between metabolism and nutrition could be investigated with cutting-edge "omics" and bioinformatics techniques. This review paper provides an overview of the use of omics technologies in nutritional research, with a particular emphasis on the new applications of transcriptomics, proteomics, metabolomics, and genomes in functional and biological activity research on ruminant livestock and products in the tropical regions. A wealth of knowledge has been uncovered regarding the regulation and use of numerous physiological and pathological processes by gene, mRNA, protein, and metabolite expressions under various physiological situations and guidelines. In particular, the components of meat and milk were assessed using omics research utilizing the various methods of transcriptomics, proteomics, metabolomics, and genomes. The goal of this review is to use omics technologies-which have been steadily gaining popularity as technological tools-to develop new nutritional, genetic, and leadership strategies to improve animal products and their quality control. We also present an overview of the new applications of omics technologies in cattle production and employ nutriomics and foodomics technologies to investigate the microbes in the rumen ecology. Thus, the application of state-of-the-art omics technology may aid in our understanding of how species and/or breeds adapt, and the sustainability of tropical animal production, in the long run, is becoming increasingly important as a means of mitigating the consequences of climate change.
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Affiliation(s)
- Metha Wanapat
- Tropical Feed Resources Research and Development Center (TROFREC), Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Gamonmas Dagaew
- Tropical Feed Resources Research and Development Center (TROFREC), Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Sukruthai Sommai
- Tropical Feed Resources Research and Development Center (TROFREC), Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Maharach Matra
- Tropical Feed Resources Research and Development Center (TROFREC), Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Chaichana Suriyapha
- Tropical Feed Resources Research and Development Center (TROFREC), Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Rittikeard Prachumchai
- Department of Animal Science, Faculty of Agricultural Technology, University of Technology Thanyaburi, Rajamangala Pathum Thani, 12130, Thailand
| | - Uswatun Muslykhah
- Tropical Feed Resources Research and Development Center (TROFREC), Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Srisan Phupaboon
- Tropical Feed Resources Research and Development Center (TROFREC), Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen, 40002, Thailand.
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2
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Abbasi-Moshaii B, Moradi MH, Yin T, Rahimi-Mianji G, Nejati-Javaremi A, König S. Genome-wide scan for selective sweeps identifies novel loci associated with resistance to mastitis in German Holstein cattle. J Anim Breed Genet 2023; 140:92-105. [PMID: 35988016 DOI: 10.1111/jbg.12737] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 08/02/2022] [Indexed: 12/13/2022]
Abstract
Domestication and selection significantly changed phenotypic and behavioural traits in modern domestic animals. In this study, to identify the genomic regions associated with mastitis, genomic data of German Holstein dairy cattle were analysed. The samples were genotyped using the Bovine 50 K SNP chip. For each defined healthy and sick group, 133 samples from 13,276 genotyped dairy cows were selected based on mastitis random residual effects. Grouping was done to infer selection signatures based on XP-EHH statistic. The results revealed that for the top 0.01 percentile of the obtained XP-EHH values, five genomic regions on chromosomes 8, 11, 12, 14 and 26 of the control group, and four regions on chromosomes 3, 4 (two regions) and 22 of the case group, have been under selection. Also, consideration of the top 0.1 percentile of the XP-EHH values, clarified 21 and 15 selective sweeps in the control and case group, respectively. This study identified some genomic regions containing potential candidate genes associated with resistance and susceptibility to mastitis, immune system and inflammation, milk traits, udder morphology and different types of cancers. In addition, these regions overlap with some quantitative trait loci linked to clinical mastitis, immunoglobulin levels, somatic cell score, udder traits, milk fat and protein, milk yield, milking speed and veterinary treatments. It is noteworthy that we found two regions in the healthy group (on chromosomes 12 and 14) with strong signals, which were not described previously. It is likely that future research could link these identified genomic regions to mastitis. The results of the current study contribute to the identification of causal mutations, genomic regions and genes affecting mastitis incidence in dairy cows.
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Affiliation(s)
- Bita Abbasi-Moshaii
- Institute of Animal Breeding and Genetics, Justus-Liebig University Giessen, Giessen, Germany.,Department of Animal Science and Fisheries, Sari Agricultural Science and Natural Resources University, Sari, Iran
| | | | - Tong Yin
- Institute of Animal Breeding and Genetics, Justus-Liebig University Giessen, Giessen, Germany
| | - Ghodratollah Rahimi-Mianji
- Department of Animal Science and Fisheries, Sari Agricultural Science and Natural Resources University, Sari, Iran
| | - Ardeshir Nejati-Javaremi
- Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Sven König
- Institute of Animal Breeding and Genetics, Justus-Liebig University Giessen, Giessen, Germany
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3
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Zhu Y, Bu D, Ma L. Integration of Multiplied Omics, a Step Forward in Systematic Dairy Research. Metabolites 2022; 12:metabo12030225. [PMID: 35323668 PMCID: PMC8955540 DOI: 10.3390/metabo12030225] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 02/22/2022] [Accepted: 02/23/2022] [Indexed: 02/07/2023] Open
Abstract
Due to their unique multi-gastric digestion system highly adapted for rumination, dairy livestock has complicated physiology different from monogastric animals. However, the microbiome-based mechanism of the digestion system is congenial for biology approaches. Different omics and their integration have been widely applied in the dairy sciences since the previous decade for investigating their physiology, pathology, and the development of feed and management protocols. The rumen microbiome can digest dietary components into utilizable sugars, proteins, and volatile fatty acids, contributing to the energy intake and feed efficiency of dairy animals, which has become one target of the basis for omics applications in dairy science. Rumen, liver, and mammary gland are also frequently targeted in omics because of their crucial impact on dairy animals’ energy metabolism, production performance, and health status. The application of omics has made outstanding contributions to a more profound understanding of the physiology, etiology, and optimizing the management strategy of dairy animals, while the multi-omics method could draw information of different levels and organs together, providing an unprecedented broad scope on traits of dairy animals. This article reviewed recent omics and multi-omics researches on physiology, feeding, and pathology on dairy animals and also performed the potential of multi-omics on systematic dairy research.
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Affiliation(s)
- Yingkun Zhu
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China;
- School of Agriculture & Food Science, University College Dublin, Belfield, D04 V1W8 Dublin, Ireland
| | - Dengpan Bu
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China;
- Joint Laboratory on Integrated Crop-Tree-Livestock Systems of the Chinese Academy of Agricultural Sciences (CAAS), Ethiopian Institute of Agricultural Research (EIAR), and World Agroforestry Center (ICRAF), Beijing 100193, China
- Correspondence: (D.B.); (L.M.)
| | - Lu Ma
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China;
- Correspondence: (D.B.); (L.M.)
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4
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Gurgul A, Jasielczuk I, Semik-Gurgul E, Szmatoła T, Majewska A, Sosin-Bzducha E, Bugno-Poniewierska M. Diversifying selection signatures among divergently selected subpopulations of Polish Red cattle. J Appl Genet 2019; 60:87-95. [PMID: 30685825 PMCID: PMC6373403 DOI: 10.1007/s13353-019-00484-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 01/11/2019] [Accepted: 01/15/2019] [Indexed: 01/11/2023]
Abstract
Polish Red cattle is one of the few indigenous breeds of European red cattle which is characterized by several desired features, such as high disease resistance, good health, longevity, good fertility, and high nutritional value of milk. Currently, Polish Red cattle population is a subject of two independent breeding programs: (i) improvement program and (ii) genetic resources conservation program. The aim of the improvement program is the genetic progress in terms of milk production and body conformation traits, while the conservation program mainly focuses on protection of the genetic resources of Polish Red cattle and preservation of the existing, original gene pool. By the analysis of FST genetic distances across genome-wide SNP panel, we detected diversifying selection signatures among these two subpopulations and indicated (among others) the significance of DGAT1 and FGF2 genes for milk production traits in these cattle. We also found that among genes being presumably under selection in terms of milk production, there are genes responsible, for example, for mammary gland development (e.g., SOSTDC1, PYGO2, MED1, and CCND1) and immune system response (e.g., IL10RA, IL12B, and IL21). The most important finding of this study is that the most pronounced genetic differences between the analyzed populations were associated with β-defensin genes (e.g., DEFB1, DEFB4A, DEFB5, DEFB7, DEFB10, DEFB13, EBD, BNBD-6, and LAP) located within so-called bovine cluster D on BTA27. The β-defensins are expressed mainly in the mammary gland and are antimicrobial peptides against the Gram-negative and Gram-positive bacteria, viruses, and other unicellular parasites. This suggests that antimicrobial resistance of mammary gland is of high importance during selection towards increased milk production and that genes responsible for this process are selected together with increasing levels of productivity.
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Affiliation(s)
- Artur Gurgul
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083, Balice, Poland.
| | - I Jasielczuk
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083, Balice, Poland
| | - E Semik-Gurgul
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083, Balice, Poland
| | - T Szmatoła
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083, Balice, Poland
| | - A Majewska
- Department of Cattle Breeding, National Research Institute of Animal Production, Krakowska 1, 32-083, Balice, Poland
| | - E Sosin-Bzducha
- Department of Nutrition Physiology, National Research Institute of Animal Production, Krakowska 1, 32-083, Balice, Poland
| | - M Bugno-Poniewierska
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083, Balice, Poland.,University of Agriculture in Krakow, Institute of Veterinary Sciences, Mickiewicza 24/28, 30-059, Kraków, Poland
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Weller JI, Bickhart DM, Wiggans GR, Tooker ME, O'Connell JR, Jiang J, Ron M, VanRaden PM. Determination of quantitative trait nucleotides by concordance analysis between quantitative trait loci and marker genotypes of US Holsteins. J Dairy Sci 2018; 101:9089-9107. [PMID: 30031583 DOI: 10.3168/jds.2018-14816] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Accepted: 05/19/2018] [Indexed: 12/14/2022]
Abstract
Experimental designs that exploit family information can provide substantial predictive power in quantitative trait nucleotide discovery projects. Concordance between quantitative trait locus genotype as determined by the a posteriori granddaughter design and marker genotype was determined for 30 trait-by-chromosomal segment effects segregating in the US Holstein population with probabilities of <10-20 to accept the null hypotheses of no segregating gene affecting the trait within the chromosomal segment. Genotypes for 83 grandsires and 17,217 sons were determined by either complete sequence or imputation for 3,148,506 polymorphisms across the entire genome; 471 Holstein bulls had a complete genome sequence, including 64 of the grandsires. Complete concordance was obtained only for stature on chromosome 14 and daughter pregnancy rate on chromosome 18. For each quantitative trait locus, effects of the 30 polymorphisms with highest concordance scores for the analyzed trait were computed by stepwise regression for predicted transmitting abilities of 26,750 bulls with progeny test and imputed genotypes. Effects for stature on chromosome 11, daughter pregnancy rate on chromosome 18, and protein percentage on chromosome 20 met 3 criteria: complete or almost complete concordance, nominal significance of the polymorphism effect after correction for all other polymorphisms, and marker coefficient of determination >40% of total multiple-regression coefficient of determination for the 30 polymorphisms with highest concordance. An intronic variant marker on chromosome 5 at 93,945,738 bp explained 7% of variance for fat percentage and 74% of total multiple-marker regression variance but was concordant for only 24 of 30 families. The missense polymorphism Phe279Tyr in GHR at 31,909,478 bp on chromosome 20 was confirmed as the causative mutation for fat and protein concentration. For effect on fat percentage on chromosome 14, 12 additional missense polymorphisms were found that had almost complete concordance with the suggested causative polymorphism (missense mutation Ala232Glu in DGAT1). The only polymorphism found likely to improve predictive power for genomic evaluation of dairy cattle was on chromosome 15; that polymorphism had a frequency of 0.45 for the allele with economically positive effects on all production traits.
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Affiliation(s)
- J I Weller
- Institute of Animal Sciences, ARO, The Volcani Center, Rishon LeZion 7505101, Israel; USDA, Agricultural Research Service, Animal Genomics and Improvement Laboratory, Beltsville, MD 20705-2350.
| | - D M Bickhart
- USDA, Agricultural Research Service, Animal Genomics and Improvement Laboratory, Beltsville, MD 20705-2350; USDA, Agricultural Research Service, Cell Wall Biology and Utilization Laboratory, Madison, WI 53706
| | - G R Wiggans
- USDA, Agricultural Research Service, Animal Genomics and Improvement Laboratory, Beltsville, MD 20705-2350
| | - M E Tooker
- USDA, Agricultural Research Service, Animal Genomics and Improvement Laboratory, Beltsville, MD 20705-2350
| | - J R O'Connell
- University of Maryland School of Medicine, Baltimore 21201
| | - J Jiang
- Department of Animal and Avian Sciences, University of Maryland, College Park 20742
| | - M Ron
- Institute of Animal Sciences, ARO, The Volcani Center, Rishon LeZion 7505101, Israel
| | - P M VanRaden
- USDA, Agricultural Research Service, Animal Genomics and Improvement Laboratory, Beltsville, MD 20705-2350
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Cardoso DF, de Albuquerque LG, Reimer C, Qanbari S, Erbe M, do Nascimento AV, Venturini GC, Scalez DCB, Baldi F, de Camargo GMF, Mercadante MEZ, do Santos Gonçalves Cyrillo JN, Simianer H, Tonhati H. Genome-wide scan reveals population stratification and footprints of recent selection in Nelore cattle. Genet Sel Evol 2018; 50:22. [PMID: 29720080 PMCID: PMC5930444 DOI: 10.1186/s12711-018-0381-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 02/20/2018] [Indexed: 12/11/2022] Open
Abstract
Background This study aimed at (1) assessing the genomic stratification of experimental lines of Nelore cattle that have experienced different selection regimes for growth traits, and (2) identifying genomic regions that have undergone recent selection. We used a sample of 763 animals genotyped with the Illumina BovineHD BeadChip, among which 674 animals originated from two lines that are maintained under directional selection for increased yearling body weight and 89 animals from a control line that is maintained under stabilizing selection. Results Multidimensional analysis of the genomic dissimilarity matrix and admixture analysis revealed a substantial level of population stratification between the directional selection lines and the stabilizing selection control line. Two of the three tests used to detect selection signatures (FST, XP-EHH and iHS) revealed six candidate regions with indications of selection, which strongly indicates truly positive signals. The set of identified candidate genes included several genes with roles that are functionally related to growth metabolism, such as COL14A1, CPT1C, CRH, TBC1D1, and XKR4. Conclusions The current study identified genetic stratification that resulted from almost four decades of divergent selection in an experimental Nelore population, and highlighted autosomal genomic regions that present patterns of recent selection. Our findings provide a basis for a better understanding of the metabolic mechanism that underlies the growth traits, which are modified by selection for yearling body weight. Electronic supplementary material The online version of this article (10.1186/s12711-018-0381-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Diercles F Cardoso
- Department of Animal Science, Faculty of Agrarian and Veterinary Sciences, Sao Paulo State University, Jaboticabal, SP, Brazil.
| | - Lucia Galvão de Albuquerque
- Department of Animal Science, Faculty of Agrarian and Veterinary Sciences, Sao Paulo State University, Jaboticabal, SP, Brazil.,National Counsel of Technological and Scientific Development (CNPq), Brasília, DF, Brazil
| | - Christian Reimer
- Animal Breeding and Genetics Group, Department of Animal Sciences, University of Goettingen, Goettingen, Germany
| | - Saber Qanbari
- Animal Breeding and Genetics Group, Department of Animal Sciences, University of Goettingen, Goettingen, Germany
| | - Malena Erbe
- Animal Breeding and Genetics Group, Department of Animal Sciences, University of Goettingen, Goettingen, Germany.,Institute for Animal Breeding, Bavarian State Research Center for Agriculture, Grub, Germany
| | - André V do Nascimento
- Department of Animal Science, Faculty of Agrarian and Veterinary Sciences, Sao Paulo State University, Jaboticabal, SP, Brazil
| | - Guilherme C Venturini
- Department of Animal Science, Faculty of Agrarian and Veterinary Sciences, Sao Paulo State University, Jaboticabal, SP, Brazil
| | - Daiane C Becker Scalez
- Department of Animal Science, Faculty of Agrarian and Veterinary Sciences, Sao Paulo State University, Jaboticabal, SP, Brazil
| | - Fernando Baldi
- Department of Animal Science, Faculty of Agrarian and Veterinary Sciences, Sao Paulo State University, Jaboticabal, SP, Brazil.,National Counsel of Technological and Scientific Development (CNPq), Brasília, DF, Brazil
| | - Gregório M Ferreira de Camargo
- Department of Animal Science, Faculty of Agrarian and Veterinary Sciences, Sao Paulo State University, Jaboticabal, SP, Brazil
| | - Maria E Zerlotti Mercadante
- National Counsel of Technological and Scientific Development (CNPq), Brasília, DF, Brazil.,APTA Beef Cattle Center, Institute of Animal Science, Sertãozinho, SP, Brazil
| | | | - Henner Simianer
- Animal Breeding and Genetics Group, Department of Animal Sciences, University of Goettingen, Goettingen, Germany
| | - Humberto Tonhati
- Department of Animal Science, Faculty of Agrarian and Veterinary Sciences, Sao Paulo State University, Jaboticabal, SP, Brazil.,National Counsel of Technological and Scientific Development (CNPq), Brasília, DF, Brazil
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7
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Li S, Wang Q, Lin X, Jin X, Liu L, Wang C, Chen Q, Liu J, Liu H. The Use of "Omics" in Lactation Research in Dairy Cows. Int J Mol Sci 2017; 18:ijms18050983. [PMID: 28475129 PMCID: PMC5454896 DOI: 10.3390/ijms18050983] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 04/17/2017] [Accepted: 04/25/2017] [Indexed: 02/07/2023] Open
Abstract
“Omics” is the application of genomics, transcriptomics, proteomics, and metabolomics in biological research. Over the years, tremendous amounts of biological information has been gathered regarding the changes in gene, mRNA and protein expressions as well as metabolites in different physiological conditions and regulations, which has greatly advanced our understanding of the regulation of many physiological and pathophysiological processes. The aim of this review is to comprehensively describe the advances in our knowledge regarding lactation mainly in dairy cows that were obtained from the “omics” studies. The “omics” technologies have continuously been preferred as the technical tools in lactation research aiming to develop new nutritional, genetic, and management strategies to improve milk production and milk quality in dairy cows.
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Affiliation(s)
- Shanshan Li
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Quanjuan Wang
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Xiujuan Lin
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Xiaolu Jin
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Lan Liu
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Caihong Wang
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Qiong Chen
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Jianxin Liu
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Hongyun Liu
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China.
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Cohen-Zinder M, Asher A, Lipkin E, Feingersch R, Agmon R, Karasik D, Brosh A, Shabtay A. FABP4 is a leading candidate gene associated with residual feed intake in growing Holstein calves. Physiol Genomics 2016; 48:367-76. [PMID: 26993365 DOI: 10.1152/physiolgenomics.00121.2015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 03/09/2016] [Indexed: 01/08/2023] Open
Abstract
Ecological and economic concerns drive the need to improve feed utilization by domestic animals. Residual feed intake (RFI) is one of the most acceptable measures for feed efficiency (FE). However, phenotyping RFI-related traits is complex and expensive and requires special equipment. Advances in marker technology allow the development of various DNA-based selection tools. To assimilate these technologies for the benefit of RFI-based selection, reliable phenotypic measures are prerequisite. In the current study, we identified single nucleotide polymorphisms (SNPs) associated with RFI phenotypic consistency across different ages and diets (named RFI 1-3), using DNA samples of high or low RFI ranked Holstein calves. Using targeted sequencing of chromosomal regions associated with FE- and RFI-related traits, we identified 48 top SNPs significantly associated with at least one of three defined RFIs. Eleven of these SNPs were harbored by the fatty acid binding protein 4 (FABP4). While 10 significant SNPs found in FABP4 were common for RFI 1 and RFI 3, one SNP (FABP4_5; A<G substitution), in the promoter region of the gene, was significantly associated with all three RFIs. As the three RFI classes reflect changing diets and ages with concomitant RFI phenotypic consistency, the above polymorphisms and in particular FABP4_5, might be considered possible markers for RFI-based selection for FE in the Holstein breed, following a larger-scale validation.
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Affiliation(s)
- Miri Cohen-Zinder
- Beef cattle section, Newe-Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel;
| | - Aviv Asher
- Beef cattle section, Newe-Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel; Israeli Center for Interdisciplinary Research in Chronobiology, University of Haifa, Haifa, Israel
| | - Ehud Lipkin
- Department of Genetics, The Hebrew University of Jerusalem, Jerusalem, Israel; and
| | - Roi Feingersch
- Faculty of Medicine in the Galilee, Bar-Ilan University, Safed, Israel
| | - Rotem Agmon
- Beef cattle section, Newe-Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel
| | - David Karasik
- Faculty of Medicine in the Galilee, Bar-Ilan University, Safed, Israel
| | - Arieh Brosh
- Beef cattle section, Newe-Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel
| | - Ariel Shabtay
- Beef cattle section, Newe-Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel
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9
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Wang SH, You ZY, Ye LP, Che J, Qian Q, Nanjo Y, Komatsu S, Zhong BX. Quantitative Proteomic and Transcriptomic Analyses of Molecular Mechanisms Associated with Low Silk Production in Silkworm Bombyx mori. J Proteome Res 2014; 13:735-51. [DOI: 10.1021/pr4008333] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Shao-hua Wang
- College
of Animal Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, P.R. China
| | - Zheng-ying You
- College
of Animal Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, P.R. China
| | - Lu-peng Ye
- College
of Animal Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, P.R. China
| | - Jiaqian Che
- College
of Animal Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, P.R. China
| | - Qiujie Qian
- College
of Animal Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, P.R. China
| | - Yohei Nanjo
- National
Institute of Crop Science, NARO, Kannondai 2-1-18, Tsukuba 305-8518, Japan
| | - Setsuko Komatsu
- National
Institute of Crop Science, NARO, Kannondai 2-1-18, Tsukuba 305-8518, Japan
| | - Bo-xiong Zhong
- College
of Animal Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, P.R. China
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10
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Osteoporosis genetics: year 2011 in review. BONEKEY REPORTS 2012; 1:114. [PMID: 23951496 DOI: 10.1038/bonekey.2012.114] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Accepted: 05/09/2012] [Indexed: 02/08/2023]
Abstract
Increased rates of osteoporotic fractures represent a worldwide phenomenon, which result from a progressing aging in the population around the world and creating socioeconomic problems. This review will focus mostly on human genetic studies identifying genomic regions, genes and mutations associated with osteoporosis (bone mineral density (BMD) and bone loss) and related fractures, which were published during 2011. Although multiple genome-wide association studies (GWAS) were performed to date, the genetic cause of osteoporosis and fractures has not yet been found, and only a small fraction of high heritability of bone mass was successfully explained. GWAS is a successful tool to initially define and prioritize specific chromosomal regions showing associations with the desired traits or diseases. Following the initial discovery and replication, targeted sequencing is needed in order to detect those rare variants which GWAS does not reveal by design. Recent GWAS findings for BMD included WNT16 and MEF2C. The role of bone morphogenetic proteins in fracture healing has been explored by several groups, and new single-nucleotide polymorphisms present in genes such as NOGGIN and SMAD6 were found to be associated with a greater risk of fracture non-union. Finding new candidate genes, and mutations associated with BMD and fractures, also provided new biological connections. Thus, candidates for molecular link between bone metabolism and lactation (for example, RAP1A gene), as well as possible pleiotropic effects for bone and muscle (ACTN3 gene) were suggested. The focus of contemporary studies seems to move toward whole-genome sequencing, epigenetic and functional genomics strategies to find causal variants for osteoporosis.
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