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George L, Alex R, Gowane G, Vohra V, Joshi P, Kumar R, Verma A. Weighted single step GWAS reveals genomic regions associated with economic traits in Murrah buffaloes. Anim Biotechnol 2024; 35:2319622. [PMID: 38437001 DOI: 10.1080/10495398.2024.2319622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2024]
Abstract
The objective of the present study was to identify genomic regions influencing economic traits in Murrah buffaloes using weighted single step Genome Wide Association Analysis (WssGWAS). Data on 2000 animals, out of which 120 were genotyped using a double digest Restriction site Associated DNA (ddRAD) sequencing approach. The phenotypic data were collected from NDRI, India, on growth traits, viz., body weight at 6M (month), 12M, 18M and 24M, production traits like 305D (day) milk yield, lactation length (LL) and dry period (DP) and reproduction traits like age at first calving (AFC), calving interval (CI) and first service period (FSP). The biallelic genotypic data consisted of 49353 markers post-quality check. The heritability estimates were moderate to high, low to moderate, low for growth, production, reproduction traits, respectively. Important genomic regions explaining more than 0.5% of the total additive genetic variance explained by 30 adjacent SNPs were selected for further analysis of candidate genes. In this study, 105 genomic regions were associated with growth, 35 genomic regions with production and 42 window regions with reproduction traits. Different candidate genes were identified in these genomic regions, of which important are OSBPL8, NAP1L1 for growth, CNTNAP2 for production and ILDR2, TADA1 and POGK for reproduction traits.
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Affiliation(s)
- Linda George
- National Dairy Research Institute, Karnal, India
| | - Rani Alex
- National Dairy Research Institute, Karnal, India
| | - Gopal Gowane
- National Dairy Research Institute, Karnal, India
| | - Vikas Vohra
- National Dairy Research Institute, Karnal, India
| | - Pooja Joshi
- National Dairy Research Institute, Karnal, India
| | - Ravi Kumar
- National Dairy Research Institute, Karnal, India
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Li S, Liu L, Ahmed Z, Wang F, Lei C, Sun F. Identification of Heilongjiang crossbred beef cattle pedigrees and reveals functional genes related to economic traits based on whole-genome SNP data. Front Genet 2024; 15:1435793. [PMID: 39119576 PMCID: PMC11306169 DOI: 10.3389/fgene.2024.1435793] [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: 05/21/2024] [Accepted: 07/08/2024] [Indexed: 08/10/2024] Open
Abstract
Introduction: To enhance the beef cattle industry, Heilongjiang Province has developed a new Crossbred beef cattle variety through crossbreeding with exotic commercial breeds. This new variety exhibits relatively excellent meat quality, and efficient reproductive performance, catering to market demands. Method: This study employed whole genome resequencing technology to analyze the genetic pedigree and diversity of 19 Heilongjiang Crossbred beef cattle, alongside 59 published genomes from East Asian, Eurasian, and European taurine cattle as controls. In addition, genes related to production traits were also searched by identifying Runs of Homozygosity (ROH) islands and important fragments from ancestors. Results: A total of 14,427,729 biallelic SNPs were discovered, with the majority located in intergenic and intron regions and a small percentage in exon regions, impacting protein function. Population genetic analyses including Principal Component Analysis (PCA), Neighbor-Joining (NJ) tree, and ADMIXTURE identified Angus, Holstein, and Mishima as the main ancestors of Crossbred beef cattle. In genetic diversity analysis, nucleotide diversity, linkage disequilibrium, and inbreeding coefficient analysis reveal that the genetic diversity of Crossbred beef cattle is at a moderate level, and a higher inbreeding coefficient indicates the need for careful breeding management. In addition, some genes related to economic traits are identified through the identification of Runs of Homozygosity (ROH) islands and important fragments from ancestors. Conclusion: This comprehensive genomic characterization supports the targeted improvement of economically important traits in Crossbred beef cattle, facilitating advanced breeding strategies.
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Affiliation(s)
- Shuang Li
- Key Laboratory of Combining Farming and Animal Husbandry of Ministry of Agriculture, Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Harbin, China
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Li Liu
- Key Laboratory of Combining Farming and Animal Husbandry of Ministry of Agriculture, Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Zulfiqar Ahmed
- Department of Livestock and Poultry Production, Faculty of Veterinary and Animal Sciences, University of Poonch Rawalakot, Azad Kashmir, Pakistan
| | - Fuwen Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Chuzhao Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Fang Sun
- Key Laboratory of Combining Farming and Animal Husbandry of Ministry of Agriculture, Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Harbin, China
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Kolpakov V, Ruchay A, Kosyan D, Bukareva E. Analysis of Runs of Homozygosity in Aberdeen Angus Cattle. Animals (Basel) 2024; 14:2153. [PMID: 39123679 PMCID: PMC11311081 DOI: 10.3390/ani14152153] [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: 05/23/2024] [Revised: 07/20/2024] [Accepted: 07/23/2024] [Indexed: 08/12/2024] Open
Abstract
A large number of cattle breeds have marked phenotypic differences. They are valuable models for studying genome evolution. ROH analysis can facilitate the discovery of genomic regions that may explain phenotypic differences between breeds affecting traits of economic importance. This paper investigates genome-wide ROH of 189 Aberdeen Angus bulls using the Illumina Bovine GGP HD Beadchip150K to structurally and functionally annotate genes located within or in close ROH of the Aberdeen Angus cattle genome. The method of sequential SNP detection was used to determine the ROH. Based on this parameter, two ROH classes were allocated. The total length of all ROH islands was 11,493 Mb. As a result of studying the genomic architecture of the experimental population of Aberdeen Angus bulls, nine ROH islands and 255 SNPs were identified. Thirteen of these overlapped with regions bearing 'selection imprints' previously identified in other breeds of cattle, and five of these regions were identified in other Aberdeen Angus populations. The total length of the ROH islands was 11,493 Mb. The size of individual islands ranged from 0.038 to 1.812 Mb. Structural annotation showed the presence of 87 genes within the identified ROH islets.
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Affiliation(s)
- Vladimir Kolpakov
- Federal Research Centre of Biological Systems and Agro-Technologies of the Russian Academy of Sciences, 460000 Orenburg, Russia; (V.K.); (D.K.); (E.B.)
- Department of Biotechnology of Animal Raw Materials and Aquaculture, Orenburg State University, 460000 Orenburg, Russia
| | - Alexey Ruchay
- Federal Research Centre of Biological Systems and Agro-Technologies of the Russian Academy of Sciences, 460000 Orenburg, Russia; (V.K.); (D.K.); (E.B.)
- Department of Information Security, South Ural State University, 454080 Chelyabinsk, Russia
- Department of Mathematics, Chelyabinsk State University, 454001 Chelyabinsk, Russia
| | - Dianna Kosyan
- Federal Research Centre of Biological Systems and Agro-Technologies of the Russian Academy of Sciences, 460000 Orenburg, Russia; (V.K.); (D.K.); (E.B.)
| | - Elena Bukareva
- Federal Research Centre of Biological Systems and Agro-Technologies of the Russian Academy of Sciences, 460000 Orenburg, Russia; (V.K.); (D.K.); (E.B.)
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Atashi H, Chen Y, Vanderick S, Hubin X, Gengler N. Single-step genome-wide association analyses for milk urea concentration in Walloon Holstein cows. J Dairy Sci 2024; 107:3020-3031. [PMID: 38056570 DOI: 10.3168/jds.2023-23902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 11/07/2023] [Indexed: 12/08/2023]
Abstract
The aims of this study were to conduct a single-step genome-wide association to identify genomic regions associated with milk urea (MU) and to estimate genetic correlations between MU and milk yield (MY), milk composition (calcium content [CC], fat percentage [FP], protein percentage [PP], and casein percentage [CNP]), and cheese-making properties (CMP; coagulation time [CT], curd firmness after 30 min from rennet addition [a30], and titratable acidity [TA]). The used data have been collected from 2015 to 2020 on 78,073 first-parity (485,218 test-day records) and 48,766 second-parity (284,942 test-day records) Holstein cows distributed in 671 herds in the Walloon Region of Belgium. Data of 565,533 SNP located on 29 BTA of 6,617 animals (1,712 males) were used. Random regression test-day models were used to estimate genetic parameters through the Bayesian Gibbs sampling method. The SNP solutions were estimated using a single-step genomic BLUP approach. The proportion of the total additive genetic variance explained by windows of 50 consecutive SNPs (with an average size of ∼216 kb) was calculated, and the top-3 genomic regions explaining the largest rate of the genetic variance were considered promising regions and used to identify potential candidate genes. Mean (SD) MU was 25.38 (8.02) mg/dL and 25.03 (8.06) mg/dL in the first and second lactation, respectively. Mean heritability estimates for daily MU were 0.21 and 0.23 for the first and second lactation, respectively. The genetic correlations estimated between MU and MY, milk composition, and CMP were quite low (ranged from -0.10 [CC] to 0.10 [TA] and -0.05 [CT] to 0.13 [TA] for the first and second lactations, respectively). The top-3 regions associated with MU were located from 80.61 to 80.74 Mb on BTA6, 103.26 to 103.41 Mb on BTA11, and 1.59 to 2.15 Mb on BTA14. Genes including KCNT1, MROH1, SHARPIN, TSSK5, CPSF1, HSF1, TONSL, DGAT1, SCX, and MAF1 were identified as positional candidate genes for MU. The findings of this study can be used for a better understanding of the genomic architecture underlying MU in Holstein cattle.
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Affiliation(s)
- H Atashi
- TERRA Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium; Department of Animal Science, Shiraz University, 71441-13131 Shiraz, Iran.
| | - Y Chen
- TERRA Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium
| | - S Vanderick
- TERRA Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium
| | - X Hubin
- Elevéo asbl Awé Group, 5590 Ciney, Belgium
| | - N Gengler
- TERRA Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium
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Atashi H, Chen Y, Wilmot H, Bastin C, Vanderick S, Hubin X, Gengler N. Single-step genome-wide association analyses for selected infrared-predicted cheese-making traits in Walloon Holstein cows. J Dairy Sci 2023; 106:7816-7831. [PMID: 37567464 DOI: 10.3168/jds.2022-23206] [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: 12/28/2022] [Accepted: 05/01/2023] [Indexed: 08/13/2023]
Abstract
This study aimed to perform genome-wide association study to identify genomic regions associated with milk production and cheese-making properties (CMP) in Walloon Holstein cows. The studied traits were milk yield, fat percentage, protein percentage, casein percentage (CNP), calcium content, somatic cell score (SCS), coagulation time, curd firmness after 30 min from rennet addition, and titratable acidity. The used data have been collected from 2014 to 2020 on 78,073 first-parity (485,218 test-day records), 48,766 second-parity (284,942 test-day records), and 21,948 third-parity (105,112 test-day records) Holstein cows distributed in 671 herds in the Walloon Region of Belgium. Data of 565,533 single nucleotide polymorphisms (SNP), located on 29 Bos taurus autosomes (BTA) of 6,617 animals (1,712 males), were used. Random regression test-day models were used to estimate genetic parameters through the Bayesian Gibbs sampling method. The SNP solutions were estimated using a single-step genomic BLUP approach. The proportion of the total additive genetic variance explained by windows of 50 consecutive SNPs (with an average size of ∼216 KB) was calculated, and regions accounting for at least 1.0% of the total additive genetic variance were used to search for positional candidate genes. Heritability estimates for the studied traits ranged from 0.10 (SCS) to 0.53 (CNP), 0.10 (SCS) to 0.50 (CNP), and 0.12 (SCS) to 0.49 (CNP) in the first, second, and third parity, respectively. Genome-wide association analyses identified 6 genomic regions (BTA1, BTA14 [4 regions], and BTA20) associated with the considered traits. Genes including the SLC37A1 (BTA1), SHARPIN, MROH1, DGAT1, FAM83H, TIGD5, MROH6, NAPRT, ADGRB1, GML, LYPD2, JRK (BTA14), and TRIO (BTA20) were identified as positional candidate genes for the studied CMP. The findings of this study help to unravel the genomic background of a cow's ability for cheese production and can be used for the future implementation and use of genomic evaluation to improve the cheese-making traits in Walloon Holstein cows.
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Affiliation(s)
- H Atashi
- TERRA Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium; Department of Animal Science, Shiraz University, 71441-13131 Shiraz, Iran.
| | - Y Chen
- TERRA Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium
| | - H Wilmot
- TERRA Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium; National Fund for Scientific Research (FRS-FNRS), 1000 Brussels, Belgium
| | - C Bastin
- National Fund for Scientific Research (FRS-FNRS), 1000 Brussels, Belgium
| | - S Vanderick
- TERRA Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium
| | - X Hubin
- Elevéo asbl Awé Group, 5590 Ciney, Belgium
| | - N Gengler
- TERRA Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium
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Alam MZ, Haque MA, Iqbal A, Lee YM, Ha JJ, Jin S, Park B, Kim NY, Won JI, Kim JJ. Genome-Wide Association Study to Identify QTL for Carcass Traits in Korean Hanwoo Cattle. Animals (Basel) 2023; 13:2737. [PMID: 37685003 PMCID: PMC10486602 DOI: 10.3390/ani13172737] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 08/24/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023] Open
Abstract
This study aimed to identify genetic associations with carcass traits in Hanwoo cattle using a genome-wide association study. A total of 9302 phenotypes were analyzed, and all animals were genotyped using the Illumina Bovine 50K v.3 SNP chip. Heritabilities for carcass weight (CWT), eye muscle area (EMA), backfat thickness (BF), and marbling score (MS) were estimated as 0.42, 0.36, 0.36, and 0.47, respectively, using the GBLUP model, and 0.47, 0.37, 0.36, and 0.42, respectively, using the Bayes B model. We identified 129 common SNPs using DGEBV and 118 common SNPs using GEBV on BTA6, BTA13, and BTA14, suggesting their potential association with the traits of interest. No common SNPs were found between the GBLUP and Bayes B methods when using residuals as a response variable in GWAS. The most promising candidate genes for CWT included SLIT2, PACRGL, KCNIP4, RP1, XKR4, LYN, RPS20, MOS, FAM110B, UBXN2B, CYP7A1, SDCBP, NSMAF, TOX, CA8, LAP3, FAM184B, and NCAPG. For EMA, the genes IBSP, LAP3, FAM184B, LCORL, NCAPG, SLC30A9, and BEND4 demonstrated significance. Similarly, CYP7B1, ARMC1, PDE7A, and CRH were associated with BF, while CTSZ, GNAS, VAPB, and RAB22A were associated with MS. This finding offers valuable insights into genomic regions and molecular mechanisms influencing Hanwoo carcass traits, aiding efficient breeding strategies.
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Affiliation(s)
- Mohammad Zahangir Alam
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea; (M.Z.A.); (M.A.H.); (A.I.); (Y.-M.L.)
| | - Md Azizul Haque
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea; (M.Z.A.); (M.A.H.); (A.I.); (Y.-M.L.)
| | - Asif Iqbal
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea; (M.Z.A.); (M.A.H.); (A.I.); (Y.-M.L.)
| | - Yun-Mi Lee
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea; (M.Z.A.); (M.A.H.); (A.I.); (Y.-M.L.)
| | - Jae-Jung Ha
- Gyeongbuk Livestock Research Institute, Yeongju 36052, Republic of Korea;
| | - Shil Jin
- Hanwoo Research Institute, National Institute of Animal Science, Pyeongchang 25340, Republic of Korea; (S.J.); (B.P.); (N.-Y.K.)
| | - Byoungho Park
- Hanwoo Research Institute, National Institute of Animal Science, Pyeongchang 25340, Republic of Korea; (S.J.); (B.P.); (N.-Y.K.)
| | - Nam-Young Kim
- Hanwoo Research Institute, National Institute of Animal Science, Pyeongchang 25340, Republic of Korea; (S.J.); (B.P.); (N.-Y.K.)
| | - Jeong Il Won
- Hanwoo Research Institute, National Institute of Animal Science, Pyeongchang 25340, Republic of Korea; (S.J.); (B.P.); (N.-Y.K.)
| | - Jong-Joo Kim
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea; (M.Z.A.); (M.A.H.); (A.I.); (Y.-M.L.)
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Oster N, Szewczuk MA, Zych S, Stankiewicz T, Błaszczyk B, Wieczorek-Dąbrowska M. Association between Polymorphism in the Janus Kinase 2 ( JAK2) Gene and Selected Performance Traits in Cattle and Sheep. Animals (Basel) 2023; 13:2470. [PMID: 37570280 PMCID: PMC10416845 DOI: 10.3390/ani13152470] [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: 05/31/2023] [Revised: 07/17/2023] [Accepted: 07/29/2023] [Indexed: 08/13/2023] Open
Abstract
The Janus Kinase 2 (JAK2) tyrosine kinase is an essential component of signal transduction of the class II cytokine receptors, including the growth hormone receptor. Therefore, it may play a crucial role in the signaling pathway of the somatotropic axis, which influences growth, development, and reproductive traits in ruminants. For this purpose, for three breeds of cattle (Hereford, Angus, and Limousin; a total of 781 individuals), two polymorphic sites located in exon 16 (rs210148032; p.Ile704Val, within pseudokinase (JH2)) and exon 23 (silent mutation rs211067160, within JH1 kinase domain) were analyzed. For two breeds of sheep (Pomeranian and Suffolk; 333 individuals in total), two polymorphic sites in exon 6 (rs160146162 and rs160146160; encoding the FERM domain) and one polymorphic site in exon 24 of the JAK2 gene (rs160146116; JH1 kinase domain) were genotyped. In our study, the associations examined for cattle were inconclusive. However, Hereford and Limousin cattle with genotypes AA (e16/RsaI) and AA (e23/HaeIII) tended to have the highest body weight and better daily gains (p ≤ 0.05). No clear tendency was observed in the selected reproductive traits. In the case of sheep, regardless of breed, individuals with the AA (e6/EarI), GG (e6/seq), and AA (e24/Hpy188III) genotypes had the highest body weights and daily gains in the study periods (p ≤ 0.01). The same individuals in the Pomeranian breed also had better fertility and lamb survival (p ≤ 0.01). To the best of our knowledge, these are the first association studies for all these polymorphic sites. Single-nucleotide polymorphisms in the JAK2 gene can serve as genetic markers for growth and selected reproductive traits in ruminants given that they are further investigated in subsequent populations and analyzed using haplotype and/or combined genotype systems.
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Affiliation(s)
- Nicola Oster
- Department of Monogastric Animal Science, Faculty of Biotechnology and Animal Husbandry, West Pommeranian University of Technology in Szczecin, 29 Klemensa Janickiego, 71-270 Szczecin, Poland;
| | - Małgorzata Anna Szewczuk
- Department of Monogastric Animal Science, Faculty of Biotechnology and Animal Husbandry, West Pommeranian University of Technology in Szczecin, 29 Klemensa Janickiego, 71-270 Szczecin, Poland;
| | - Sławomir Zych
- Laboratory of Chromatography and Mass Spectroscopy, Faculty of Biotechnology and Animal Husbandry, West Pomeranian University of Technology in Szczecin, 29 Klemensa Janickiego, 71-270 Szczecin, Poland
| | - Tomasz Stankiewicz
- Department of Animal Reproduction Biotechnology and Environmental Hygiene, Faculty of Biotechnology and Animal Husbandry, West Pomeranian University of Technology in Szczecin, 29 Klemensa Janickiego, 71-270 Szczecin, Poland; (T.S.); (B.B.)
| | - Barbara Błaszczyk
- Department of Animal Reproduction Biotechnology and Environmental Hygiene, Faculty of Biotechnology and Animal Husbandry, West Pomeranian University of Technology in Szczecin, 29 Klemensa Janickiego, 71-270 Szczecin, Poland; (T.S.); (B.B.)
| | - Marta Wieczorek-Dąbrowska
- National Research Institute of Animal Production, Kraków, Experimental Department, Kołbacz, 1 Warcisława Street, 74-106 Stare Czarnowo, Poland
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George L, Alex R, Sukhija N, Jaglan K, Vohra V, Kumar R, Verma A. Genetic improvement of economic traits in Murrah buffalo using significant SNPs from genome-wide association study. Trop Anim Health Prod 2023; 55:199. [PMID: 37184817 DOI: 10.1007/s11250-023-03606-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 04/27/2023] [Indexed: 05/16/2023]
Abstract
GWAS helps to identify QTL and candidate genes of specific traits. Buffalo breeding has primarily focused on milk production, but its negative correlation with reproduction traits resulted in unfavorable decline of reproductive performance among buffaloes. A genome wide scan was performed on a total of 120 Murrah buffaloes genotyped by ddRAD sequencing for 13 traits related to female fertility, production, and growth. The identified 25 significant single nucleotide polymorphisms (SNPs) (P <1×106) are associated with age at first calving (AFC), age at first service (AFS), period from calving to 1st Artifical Insemination (AI), service period (SP) and 6 month body weight (6M). Fifteen genetic variants overlapped with different QTL regions of reported studies. Among the associated loci, outstanding candidate genes for fertility, including AQP1, TRNAE-CUC, NRIP1, CPNE4, and VOPP1, have effect in different fertility traits. AQP1 gene is expressed in ovulatory phase and various stages of pregnancy. TRNAE-CUC gene is associated with AFC and number . of calvings after 4 years of age. Glycogen content-associated gene CPNE4 regulates muscle glycogen and is upregulated during early pregnancy. NRIP1 generegulates ovulation, corpus luteum at pregnancy, and mammary gland development. The objective is to identify potential genomic regions and genetic variants associated with economic traits and to select the most significant SNP which have positive effect on all the traits.
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Affiliation(s)
- Linda George
- Division of Animal Genetics and Breeding, ICAR- National Dairy Research Institute, Karnal, Haryana, 132001, India.
| | - Rani Alex
- Division of Animal Genetics and Breeding, ICAR- National Dairy Research Institute, Karnal, Haryana, 132001, India
| | - Nidhi Sukhija
- Division of Animal Genetics and Breeding, ICAR- National Dairy Research Institute, Karnal, Haryana, 132001, India
| | - Komal Jaglan
- Division of Animal Genetics and Breeding, ICAR- National Dairy Research Institute, Karnal, Haryana, 132001, India
| | - Vikas Vohra
- Division of Animal Genetics and Breeding, ICAR- National Dairy Research Institute, Karnal, Haryana, 132001, India
| | - Ravi Kumar
- Division of Animal Genetics and Breeding, ICAR- National Dairy Research Institute, Karnal, Haryana, 132001, India
| | - Archana Verma
- Division of Animal Genetics and Breeding, ICAR- National Dairy Research Institute, Karnal, Haryana, 132001, India
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Adhikari M, Kantar MB, Longman RJ, Lee CN, Oshiro M, Caires K, He Y. Genome-wide association study for carcass weight in pasture-finished beef cattle in Hawai'i. Front Genet 2023; 14:1168150. [PMID: 37229195 PMCID: PMC10203587 DOI: 10.3389/fgene.2023.1168150] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 04/11/2023] [Indexed: 05/27/2023] Open
Abstract
Introduction: Genome-wide association studies (GWAS) have identified genetic markers for cattle production and reproduction traits. Several publications have reported Single Nucleotide Polymorphisms (SNPs) for carcass-related traits in cattle, but these studies were rarely conducted in pasture-finished beef cattle. Hawai'i, however, has a diverse climate, and 100% of its beef cattle are pasture-fed. Methods: Blood samples were collected from 400 cattle raised in Hawai'i islands at the commercial harvest facility. Genomic DNA was isolated, and 352 high-quality samples were genotyped using the Neogen GGP Bovine 100 K BeadChip. SNPs that did not meet the quality control standards were removed using PLINK 1.9, and 85 k high-quality SNPs from 351 cattle were used for association mapping with carcass weight using GAPIT (Version 3.0) in R 4.2. Four models were used for the GWAS analysis: General Linear Model (GLM), the Mixed Linear Model (MLM), the Fixed and Random Model Circulating Probability Unification (FarmCPU), the Bayesian-Information and Linkage-Disequilibrium Iteratively Nested Keyway (BLINK). Results and Discussion: Our results indicated that the two multi-locus models, FarmCPU and BLINK, outperformed single-locus models, GLM and MLM, in beef herds in this study. Specifically, five significant SNPs were identified using FarmCPU, while BLINK and GLM each identified the other three. Also, three of these eleven SNPs ("BTA-40510-no-rs", "BovineHD1400006853", and "BovineHD2100020346") were shared by multiple models. The significant SNPs were mapped to genes such as EIF5, RGS20, TCEA1, LYPLA1, and MRPL15, which were previously reported to be associated with carcass-related traits, growth, and feed intake in several tropical cattle breeds. This confirms that the genes identified in this study could be candidate genes for carcass weight in pasture-fed beef cattle and can be selected for further breeding programs to improve the carcass yield and productivity of pasture-finished beef cattle in Hawai'i and beyond.
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Affiliation(s)
- Mandeep Adhikari
- Department of Molecular Biosciences and Bioengineering, University of Hawai’i at Mānoa, Honolulu, HI, United States
| | - Michael B. Kantar
- Department of Tropical Plant and Soil Sciences, University of Hawai’i at Mānoa, Honolulu, HI, United States
| | - Ryan J. Longman
- East West Center, Honolulu, HI, United States
- Department of Geography and Environment, University of Hawai’i at Mānoa, Honolulu, HI, United States
| | - C. N. Lee
- Department of Human Nutrition, Food, and Animal Sciences, University of Hawai’i at Mānoa, Honolulu, HI, United States
| | - Melelani Oshiro
- Department of Human Nutrition, Food, and Animal Sciences, University of Hawai’i at Mānoa, Honolulu, HI, United States
| | - Kyle Caires
- Department of Human Nutrition, Food, and Animal Sciences, University of Hawai’i at Mānoa, Honolulu, HI, United States
| | - Yanghua He
- Department of Molecular Biosciences and Bioengineering, University of Hawai’i at Mānoa, Honolulu, HI, United States
- Department of Human Nutrition, Food, and Animal Sciences, University of Hawai’i at Mānoa, Honolulu, HI, United States
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Identification of Candidate Genes and Functional Pathways Associated with Body Size Traits in Chinese Holstein Cattle Based on GWAS Analysis. Animals (Basel) 2023; 13:ani13060992. [PMID: 36978532 PMCID: PMC10044097 DOI: 10.3390/ani13060992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 03/01/2023] [Accepted: 03/07/2023] [Indexed: 03/12/2023] Open
Abstract
Body size is one of the most economically important traits of dairy cattle, as it is significantly associated with cow longevity, production, health, fertility, and environmental adaptation. The identification and application of genetic variants using a novel genetic approach, such as genome-wide association studies (GWASs), may give more insights into the genetic architecture of complex traits. The identification of genes, single nucleotide polymorphisms (SNPs), and pathways associated with the body size traits may offer a contribution to genomic selection and long-term planning for selection in dairy cows. In this study, we performed GWAS analysis to identify the genetic markers and genes associated with four body size traits (body height, body depth, chest width, and angularity) in 1000 Chinese Holstein cows. We performed SNPs genotyping in 1000 individuals, based on the GeneSeek Genomic Profiler Bovine 100 K. In total, we identified 11 significant SNPs in association with body size traits at the threshold of Bonferroni correction (5.90 × 10−7) using the fixed and random model circulating probability unification (FarmCPU) model. Several genes within 200 kb distances (upstream or downstream) of the significant SNPs were identified as candidate genes, including MYH15, KHDRBS3, AIP, DCC, SQOR, and UBAP1L. Moreover, genes within 200 kb of the identified SNPs were significantly enriched (p ≤ 0.05) in 25 Gene Ontology terms and five Kyoto Encyclopedia of Genes and Genomes pathways. We anticipate that these results provide a foundation for understanding the genetic architecture of body size traits. They will also contribute to breeding programs and genomic selection work on Chinese Holstein cattle.
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11
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Zhang H, Mi S, Brito LF, Hu L, Wang L, Ma L, Xu Q, Guo G, Yu Y, Wang Y. Genomic and transcriptomic analyses enable the identification of important genes associated with subcutaneous fat deposition in Holstein cows. J Genet Genomics 2023:S1673-8527(23)00026-7. [PMID: 36738887 DOI: 10.1016/j.jgg.2023.01.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 01/18/2023] [Accepted: 01/20/2023] [Indexed: 02/05/2023]
Abstract
Subcutaneous fat deposition has many important roles in dairy cattle, including immunological defense and mechanical protection. The main objectives of this study are to identify key candidate genes regulating subcutaneous fat deposition in high-producing dairy cows by integrating genomic and transcriptomic datasets. A total of 1,654 genotyped Holstein cows are used to perform a genome-wide association study (GWAS) aiming to identify genes associated with subcutaneous fat deposition. Subsequently, weighted gene co-expression network analyses (WGCNA) are conducted based on RNA-sequencing data of 34 cows and de-regressed estimated breeding values of subcutaneous fat deposition. Lastly, differentially expressed (DE) mRNA, lncRNA, and differentially alternative splicing genes are obtained for 12 Holstein cows with extreme and divergent phenotypes for subcutaneous fat deposition. Forty-six protein-coding genes are identified as candidate genes regulating subcutaneous fat deposition in Holstein cattle based on the GWAS. Eleven overlapping genes are identified based on the analyses of DE genes and WGCNA. Furthermore, the candidate genes identified based on the GWAS, WGCNA, and analyses of DE genes are significantly enriched for pathways involved in metabolism, oxidative phosphorylation, thermogenesis, fatty acid degradation, and glycolysis/gluconeogenesis pathways. Integrating all findings, the NID2, STARD3, UFC1, DEDD, PPP1R1B, and USP21 genes are considered to be the most important candidate genes influencing subcutaneous fat deposition traits in Holstein cows. This study provides novel insights into the regulation mechanism underlying fat deposition in high-producing dairy cows, which will be useful when designing management and breeding strategies.
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Affiliation(s)
- Hailiang Zhang
- Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Siyuan Mi
- Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Luiz F Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Lirong Hu
- Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Lei Wang
- Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Longgang Ma
- Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Qing Xu
- Institute of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, China
| | - Gang Guo
- Beijing Sunlon Livestock Development Co. Ltd, Beijing, 100176, China
| | - Ying Yu
- Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
| | - Yachun Wang
- Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
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12
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Lopes FB, Baldi F, Brunes LC, Oliveira E Costa MF, da Costa Eifert E, Rosa GJM, Lobo RB, Magnabosco CU. Genomic prediction for meat and carcass traits in Nellore cattle using a Markov blanket algorithm. J Anim Breed Genet 2023; 140:1-12. [PMID: 36239216 DOI: 10.1111/jbg.12740] [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: 03/31/2022] [Accepted: 09/22/2022] [Indexed: 12/13/2022]
Abstract
This study was carried out to evaluate the advantage of preselecting SNP markers using Markov blanket algorithm regarding the accuracy of genomic prediction for carcass and meat quality traits in Nellore cattle. This study considered 3675, 3680, 3660 and 524 records of rib eye area (REA), back fat thickness (BF), rump fat (RF), and Warner-Bratzler shear force (WBSF), respectively, from the Nellore Brazil Breeding Program. The animals have been genotyped using low-density SNP panel (30 k), and subsequently imputed for arrays with 777 k SNPs. Four Bayesian specifications of genomic regression models, namely Bayes A, Bayes B, Bayes Cπ and Bayesian Ridge Regression methods were compared in terms of prediction accuracy using a five folds cross-validation. Prediction accuracy for REA, BF and RF was all similar using the Bayesian Alphabet models, ranging from 0.75 to 0.95. For WBSF, the predictive ability was higher using Bayes B (0.47) than other methods (0.39 to 0.42). Although the prediction accuracies using Markov blanket of SNP markers were lower than those using all SNPs, for WBSF the relative gain was lower than 13%. With a subset of informative SNPs markers, identified using Markov blanket, probably, is possible to capture a large proportion of the genetic variance for WBSF. The development of low-density and customized arrays using Markov blanket might be cost-effective to perform a genomic selection for this trait, increasing the number of evaluated animals, improving the management decisions based on genomic information and applying genomic selection on a large scale.
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Affiliation(s)
- Fernando Brito Lopes
- São Paulo State University - Júlio de Mesquita Filho (UNESP), Department of Animal Science, Prof. Paulo Donato Castelane, Jaboticabal, Brazil.,Embrapa Cerrados, Brasilia, Brazil
| | - Fernando Baldi
- São Paulo State University - Júlio de Mesquita Filho (UNESP), Department of Animal Science, Prof. Paulo Donato Castelane, Jaboticabal, Brazil
| | | | | | | | - Guilherme Jordão Magalhães Rosa
- Department of Animal Sciences, University of Wisconsin-Madison, Madison, Wisconsin, USA.,Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin, USA
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13
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Exploring and Identifying Candidate Genes and Genomic Regions Related to Economically Important Traits in Hanwoo Cattle. Curr Issues Mol Biol 2022; 44:6075-6092. [PMID: 36547075 PMCID: PMC9777506 DOI: 10.3390/cimb44120414] [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: 09/19/2022] [Revised: 11/28/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022] Open
Abstract
The purpose of the current review was to explore and summarize different studies concerning the detection and characterization of candidate genes and genomic regions associated with economically important traits in Hanwoo beef cattle. Hanwoo cattle, the indigenous premium beef cattle of Korea, were introduced for their marbled fat, tenderness, characteristic flavor, and juiciness. To date, there has been a strong emphasis on the genetic improvement of meat quality and yields, such as backfat thickness (BFT), marbling score (MS), carcass weight (CW), eye muscle area (EMA), and yearling weight (YW), as major selection criteria in Hanwoo breeding programs. Hence, an understanding of the genetics controlling these traits along with precise knowledge of the biological mechanisms underlying the traits would increase the ability of the industry to improve cattle to better meet consumer demands. With the development of high-throughput genotyping, genomewide association studies (GWAS) have allowed the detection of chromosomal regions and candidate genes linked to phenotypes of interest. This is an effective and useful tool for accelerating the efficiency of animal breeding and selection. The GWAS results obtained from the literature review showed that most positional genes associated with carcass and growth traits in Hanwoo are located on chromosomes 6 and 14, among which LCORL, NCAPG, PPARGC1A, ABCG2, FAM110B, FABP4, DGAT1, PLAG1, and TOX are well known. In conclusion, this review study attempted to provide comprehensive information on the identified candidate genes associated with the studied traits and genes enriched in the functional terms and pathways that could serve as a valuable resource for future research in Hanwoo breeding programs.
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14
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Carracelas B, Navajas EA, Vera B, Ciappesoni G. Genome-Wide Association Study of Parasite Resistance to Gastrointestinal Nematodes in Corriedale Sheep. Genes (Basel) 2022; 13:genes13091548. [PMID: 36140716 PMCID: PMC9498675 DOI: 10.3390/genes13091548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 08/19/2022] [Accepted: 08/23/2022] [Indexed: 11/16/2022] Open
Abstract
Selection of genetically resistant animals is one alternative to reduce the negative impact of gastrointestinal nematodes (GIN) on sheep production. The aim of this study was to identify genomic regions associated with GIN resistance in Corriedale sheep by single-step genome-wide association studies (ssGWAS) using 170, 507 and 50K single nucleotide polymorphisms (SNPs). Analysis included 19,547 lambs with faecal egg counts (FEC) records, a pedigree file of 40,056 animals and 454, 711 and 383 genotypes from 170, 507 and 50K SNPs, respectively. Genomic estimated breeding values (GEBV) were obtained with single-step genomic BLUP methodology (ssGBLUP), using a univariate animal model, which included contemporary group, type of birth and age of dam as class fixed effects and age at FEC recording as covariate. The SNP effects as wells as p-values were estimated with POSTGSF90 program. Significance level was defined by a chromosome-wise False Discovery Rate of 5%. Significant genomic regions were identified in chromosomes 1, 3, 12 and 19 with the 170 SNP set, in chromosomes 7, 12 and 24 using the 507 SNP chip and only in chromosome 7 with the 50K SNP chip. Candidate genes located in these regions, using Oar_v4.0 as reference genome, were TIMP3, TLR5, LEPR and TLR9 (170 SNPs), SYNDIG1L and MGRN1 (507 SNP chip) and INO80, TLN2, TSHR and EIF2AK4 (50K SNP chip). These results validate genomic regions associated with FEC previously identified in Corriedale and other breeds and report new candidate regions for further investigation.
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Affiliation(s)
- Beatriz Carracelas
- Department of Animal Breeding, Instituto Nacional de Investigación Agropecuaria, INIA Las Brujas, Ruta 48 Km 10, Canelones 90100, Uruguay
- National Research Program on Meat and Wool Production, Instituto Nacional de Investigación Agropecuaria, INIA Las Brujas, Ruta 48 Km 10, Canelones 90100, Uruguay
| | - Elly A. Navajas
- Department of Animal Breeding, Instituto Nacional de Investigación Agropecuaria, INIA Las Brujas, Ruta 48 Km 10, Canelones 90100, Uruguay
- National Research Program on Meat and Wool Production, Instituto Nacional de Investigación Agropecuaria, INIA Las Brujas, Ruta 48 Km 10, Canelones 90100, Uruguay
| | - Brenda Vera
- National Research Program on Meat and Wool Production, Instituto Nacional de Investigación Agropecuaria, INIA Las Brujas, Ruta 48 Km 10, Canelones 90100, Uruguay
| | - Gabriel Ciappesoni
- National Research Program on Meat and Wool Production, Instituto Nacional de Investigación Agropecuaria, INIA Las Brujas, Ruta 48 Km 10, Canelones 90100, Uruguay
- Correspondence: ; Tel.: +598-98-816-004
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15
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Du L, Li K, Chang T, An B, Liang M, Deng T, Cao S, Du Y, Cai W, Gao X, Xu L, Zhang L, Li J, Gao H. Integrating genomics and transcriptomics to identify candidate genes for subcutaneous fat deposition in beef cattle. Genomics 2022; 114:110406. [PMID: 35709924 DOI: 10.1016/j.ygeno.2022.110406] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 05/31/2022] [Accepted: 06/09/2022] [Indexed: 02/07/2023]
Abstract
Fat deposition is a complex economic trait regulated by polygenic genetic basis and environmental factors. Therefore, integrating multi-omics data to uncover its internal regulatory mechanism has attracted extensive attention. Here, we performed genomics and transcriptomics analysis to detect candidates affecting subcutaneous fat (SCF) deposition in beef cattle. The association of 770K SNPs with the backfat thickness captured nine significant SNPs within or near 11 genes. Additionally, 13 overlapping genes regarding fat deposition were determined via the analysis of differentially expressed genes and weighted gene co-expression network analysis (WGCNA). We then calculated the correlations of these genes with BFT and constructed their interaction network. Finally, seven biomarkers including ACACA, SCD, FASN, ACOX1, ELOVL5, HACD2, and HSD17B12 were screened. Notably, ACACA, identified by the integration of genomics and transcriptomics, was more likely to exert profound effects on SCF deposition. These findings provided novel insights into the regulation mechanism underlying bovine fat accumulation.
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Affiliation(s)
- Lili Du
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Keanning Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Tianpeng Chang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Bingxing An
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Mang Liang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Tianyu Deng
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Sheng Cao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Tianjin Agricultural University, Tianjin 300000, China
| | - Yueying Du
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Qingdao Agricultural University, Shandong 266000, China
| | - Wentao Cai
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xue Gao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Lingyang Xu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Lupei Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Junya Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Huijiang Gao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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16
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Li J, Wang Y, Mukiibi R, Karisa B, Plastow GS, Li C. Integrative analyses of genomic and metabolomic data reveal genetic mechanisms associated with carcass merit traits in beef cattle. Sci Rep 2022; 12:3389. [PMID: 35232965 PMCID: PMC8888742 DOI: 10.1038/s41598-022-06567-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 02/01/2022] [Indexed: 11/09/2022] Open
Abstract
Improvement of carcass merit traits is a priority for the beef industry. Discovering DNA variants and genes associated with variation in these traits and understanding biological functions/processes underlying their associations are of paramount importance for more effective genetic improvement of carcass merit traits in beef cattle. This study integrates 10,488,742 imputed whole genome DNA variants, 31 plasma metabolites, and animal phenotypes to identify genes and biological functions/processes that are associated with carcass merit traits including hot carcass weight (HCW), rib eye area (REA), average backfat thickness (AFAT), lean meat yield (LMY), and carcass marbling score (CMAR) in a population of 493 crossbred beef cattle. Regression analyses were performed to identify plasma metabolites associated with the carcass merit traits, and the results showed that 4 (3-hydroxybutyric acid, acetic acid, citric acid, and choline), 6 (creatinine, L-glutamine, succinic acid, pyruvic acid, L-lactic acid, and 3-hydroxybutyric acid), 4 (fumaric acid, methanol, D-glucose, and glycerol), 2 (L-lactic acid and creatinine), and 5 (succinic acid, fumaric acid, lysine, glycine, and choline) plasma metabolites were significantly associated with HCW, REA, AFAT, LMY, and CMAR (P-value < 0.1), respectively. Combining the results of metabolome-genome wide association studies using the 10,488,742 imputed SNPs, 103, 160, 83, 43, and 109 candidate genes were identified as significantly associated with HCW, REA, AFAT, LMY, and CMAR (P-value < 1 × 10-5), respectively. By applying functional enrichment analyses for candidate genes of each trait, 26, 24, 26, 24, and 28 significant cellular and molecular functions were predicted for HCW, REA, AFAT, LMY, and CMAR, respectively. Among the five topmost significantly enriched biological functions for carcass merit traits, molecular transport and small molecule biochemistry were two top biological functions associated with all carcass merit traits. Lipid metabolism was the most significant biological function for LMY and CMAR and it was also the second and fourth highest biological function for REA and HCW, respectively. Candidate genes and enriched biological functions identified by the integrative analyses of metabolites with phenotypic traits and DNA variants could help interpret the results of previous genome-wide association studies for carcass merit traits. Our integrative study also revealed additional potential novel genes associated with these economically important traits. Therefore, our study improves understanding of the molecular and biological functions/processes that influence carcass merit traits, which could help develop strategies to enhance genomic prediction of carcass merit traits with incorporation of metabolomic data. Similarly, this information could guide management practices, such as nutritional interventions, with the purpose of boosting specific carcass merit traits.
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Affiliation(s)
- Jiyuan Li
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Yining Wang
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada.,Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB, Canada
| | - Robert Mukiibi
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, Scotland, UK
| | - Brian Karisa
- Results Driven Agriculture Research, Edmonton, AB, Canada
| | - Graham S Plastow
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada.
| | - Changxi Li
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada. .,Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB, Canada.
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17
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Juengel J, Mosaad E, Mitchell M, Phyn C, French M, Meenken E, Burke C, Meier S. Relationships between prostaglandin concentrations, SNP in HSD17B12, and reproductive performance in dairy cows. J Dairy Sci 2022; 105:4643-4652. [DOI: 10.3168/jds.2021-21298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 01/06/2022] [Indexed: 11/19/2022]
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18
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Sustainable Intensification of Beef Production in the Tropics: The Role of Genetically Improving Sexual Precocity of Heifers. Animals (Basel) 2022; 12:ani12020174. [PMID: 35049797 PMCID: PMC8772995 DOI: 10.3390/ani12020174] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 01/07/2022] [Accepted: 01/08/2022] [Indexed: 12/16/2022] Open
Abstract
Simple Summary Tropical pasture-based beef production systems play a vital role in global food security. The importance of promoting sustainable intensification of such systems has been debated worldwide. Demand for beef is growing together with concerns over the impact of its production on the environment. Implementing sustainable livestock intensification programs relies on animal genetic improvement. In tropical areas, the lack of sexual precocity is a bottleneck for cattle efficiency, directly impacting the sustainability of production systems. In the present review we present and discuss the state of the art of genetic evaluation for sexual precocity in Bos indicus beef cattle, covering the definition of measurable traits, genetic parameter estimates, genomic analyses, and a case study of selection for sexual precocity in Nellore breeding programs. Abstract Increasing productivity through continued animal genetic improvement is a crucial part of implementing sustainable livestock intensification programs. In Zebu cattle, the lack of sexual precocity is one of the main obstacles to improving beef production efficiency. Puberty-related traits are complex, but large-scale data sets from different “omics” have provided information on specific genes and biological processes with major effects on the expression of such traits, which can greatly increase animal genetic evaluation. In addition, genetic parameter estimates and genomic predictions involving sexual precocity indicator traits and productive, reproductive, and feed-efficiency related traits highlighted the feasibility and importance of direct selection for anticipating heifer reproductive life. Indeed, the case study of selection for sexual precocity in Nellore breeding programs presented here show that, in 12 years of selection for female early precocity and improved management practices, the phenotypic means of age at first calving showed a strong decreasing trend, changing from nearly 34 to less than 28 months, with a genetic trend of almost −2 days/year. In this period, the percentage of early pregnancy in the herds changed from around 10% to more than 60%, showing that the genetic improvement of heifer’s sexual precocity allows optimizing the productive cycle by reducing the number of unproductive animals in the herd. It has a direct impact on sustainability by better use of resources. Genomic selection breeding programs accounting for genotype by environment interaction represent promising tools for accelerating genetic progress for sexual precocity in tropical beef cattle.
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Mancin E, Tuliozi B, Pegolo S, Sartori C, Mantovani R. Genome Wide Association Study of Beef Traits in Local Alpine Breed Reveals the Diversity of the Pathways Involved and the Role of Time Stratification. Front Genet 2022; 12:746665. [PMID: 35058966 PMCID: PMC8764395 DOI: 10.3389/fgene.2021.746665] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 12/02/2021] [Indexed: 12/12/2022] Open
Abstract
Knowledge of the genetic architecture of key growth and beef traits in livestock species has greatly improved worldwide thanks to genome-wide association studies (GWAS), which allow to link target phenotypes to Single Nucleotide Polymorphisms (SNPs) across the genome. Local dual-purpose breeds have rarely been the focus of such studies; recently, however, their value as a possible alternative to intensively farmed breeds has become clear, especially for their greater adaptability to environmental change and potential for survival in less productive areas. We performed single-step GWAS and post-GWAS analysis for body weight (BW), average daily gain (ADG), carcass fleshiness (CF) and dressing percentage (DP) in 1,690 individuals of local alpine cattle breed, Rendena. This breed is typical of alpine pastures, with a marked dual-purpose attitude and good genetic diversity. Moreover, we considered two of the target phenotypes (BW and ADG) at different times in the individuals' life, a potentially important aspect in the study of the traits' genetic architecture. We identified 8 significant and 47 suggestively associated SNPs, located in 14 autosomal chromosomes (BTA). Among the strongest signals, 3 significant and 16 suggestive SNPs were associated with ADG and were located on BTA10 (50-60 Mb), while the hotspot associated with CF and DP was on BTA18 (55-62 MB). Among the significant SNPs some were mapped within genes, such as SLC12A1, CGNL1, PRTG (ADG), LOC513941 (CF), NLRP2 (CF and DP), CDC155 (DP). Pathway analysis showed great diversity in the biological pathways linked to the different traits; several were associated with neurogenesis and synaptic transmission, but actin-related and transmembrane transport pathways were also represented. Time-stratification highlighted how the genetic architectures of the same traits were markedly different between different ages. The results from our GWAS of beef traits in Rendena led to the detection of a variety of genes both well-known and novel. We argue that our results show that expanding genomic research to local breeds can reveal hitherto undetected genetic architectures in livestock worldwide. This could greatly help efforts to map genomic complexity of the traits of interest and to make appropriate breeding decisions.
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20
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Rafter P, Gormley IC, Parnell AC, Naderi S, Berry DP. The Contribution of Copy Number Variants and Single Nucleotide Polymorphisms to the Additive Genetic Variance of Carcass Traits in Cattle. Front Genet 2021; 12:761503. [PMID: 34795696 PMCID: PMC8593468 DOI: 10.3389/fgene.2021.761503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 10/04/2021] [Indexed: 11/13/2022] Open
Abstract
The relative contributions of both copy number variants (CNVs) and single nucleotide polymorphisms (SNPs) to the additive genetic variance of carcass traits in cattle is not well understood. A detailed understanding of the relative importance of CNVs in cattle may have implications for study design of both genomic predictions and genome-wide association studies. The first objective of the present study was to quantify the relative contributions of CNV data and SNP genotype data to the additive genetic variance of carcass weight, fat, and conformation for 945 Charolais, 923 Holstein-Friesian, and 974 Limousin sires. The second objective was to jointly consider SNP and CNV data in a least absolute selection and shrinkage operator (LASSO) regression model to identify genomic regions associated with carcass weight, fat, and conformation within each of the three breeds separately. A genomic relationship matrix (GRM) based on just CNV data did not capture any variance in the three carcass traits when jointly evaluated with a SNP-derived GRM. In the LASSO regression analysis, a total of 987 SNPs and 18 CNVs were associated with at least one of the three carcass traits in at least one of the three breeds. The quantitative trait loci (QTLs) corresponding to the associated SNPs and CNVs overlapped with several candidate genes including previously reported candidate genes such as MSTN and RSAD2, and several potential novel candidate genes such as ACTN2 and THOC1. The results of the LASSO regression analysis demonstrated that CNVs can be used to detect associations with carcass traits which were not detected using the set of SNPs available in the present study. Therefore, the CNVs and SNPs available in the present study were not redundant forms of genomic data.
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Affiliation(s)
- Pierce Rafter
- Animal & Grassland Research and Innovation Centre, Fermoy, Ireland.,School of Mathematics and Statistics, University College Dublin, Dublin, Ireland
| | | | | | - Saeid Naderi
- Irish Cattle Breeding Federation, Bandon, Ireland
| | - Donagh P Berry
- Animal & Grassland Research and Innovation Centre, Fermoy, Ireland
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21
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Tyagi SK, Mehrotra A, Singh A, Kumar A, Dutt T, Mishra BP, Pandey AK. Comparative Signatures of Selection Analyses Identify Loci Under Positive Selection in the Murrah Buffalo of India. Front Genet 2021; 12:673697. [PMID: 34737760 PMCID: PMC8560740 DOI: 10.3389/fgene.2021.673697] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 09/17/2021] [Indexed: 12/18/2022] Open
Abstract
India is home to a large and diverse buffalo population. The Murrah breed of North India is known for its milk production, and it has been used in breeding programs in several countries. Selection signature analysis yield valuable information about how the natural and artificial selective pressures have shaped the genomic landscape of modern-day livestock species. Genotype information was generated on six buffalo breeds of India, namely, Murrah, Bhadawari, Mehsana, Pandharpuri, Surti, and Toda using ddRAD sequencing protocol. Initially, the genotypes were used to carry out population diversity and structure analysis among the six breeds, followed by pair-wise comparisons of Murrah with the other five breeds through XP-EHH and F ST methodologies to identify regions under selection in Murrah. Admixture results showed significant levels of Murrah inheritance in all the breeds except Pandharpuri. The selection signature analysis revealed six regions in Murrah, which were identified in more than one pair-wise comparison through both XP-EHH and F ST analyses. The significant regions overlapped with QTLs for milk production, immunity, and body development traits. Genes present in these regions included SLC37A1, PDE9A, PPBP, CXCL6, RASSF6, AFM, AFP, ALB, ANKRD17, CNTNAP2, GPC5, MYLK3, and GPT2. These genes emerged as candidates for future polymorphism studies of adaptability and performance traits in buffaloes. The results also suggested ddRAD sequencing as a useful cost-effective alternative for whole-genome sequencing to carry out diversity analysis and discover selection signatures in Indian buffalo breeds.
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Affiliation(s)
- Shiv K Tyagi
- Animal Genetics Division, ICAR-Indian Veterinary Research Institute, Izatnangar, Bareilly, India
| | - Arnav Mehrotra
- Animal Genetics Division, ICAR-Indian Veterinary Research Institute, Izatnangar, Bareilly, India
| | - Akansha Singh
- Animal Genetics Division, ICAR-Indian Veterinary Research Institute, Izatnangar, Bareilly, India
| | - Amit Kumar
- Animal Genetics Division, ICAR-Indian Veterinary Research Institute, Izatnangar, Bareilly, India
| | - Triveni Dutt
- Livestock Production and Management, Indian Council of Agricultural Research (ICAR)-Indian Veterinary Research Institute, Bareilly, India
| | - Bishnu P Mishra
- Animal Biotechnology, Indian Council of Agricultural Research (ICAR)-Indian Veterinary Research Institute, Bareilly, India
| | - Ashwni K Pandey
- Animal Genetics Division, ICAR-Indian Veterinary Research Institute, Izatnangar, Bareilly, India
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Tarekegn G, Strandberg E, Andonov S, Båge R, Ask-Gullstrand P, Rius-Vilarrasa E, Christensen J, Berglund B. Single-step genome-wide association study uncovers known and novel candidate genomic regions for endocrine and classical fertility traits in Swedish Red and Holstein dairy cows. Livest Sci 2021. [DOI: 10.1016/j.livsci.2021.104731] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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da Silveira DD, Schmidt PI, Campos GS, de Vargas L, de Souza FRP, Roso VM, Boligon AA. Genetic analysis of growth, visual scores, height, and carcass traits in Nelore cattle. Anim Sci J 2021; 92:e13611. [PMID: 34431165 DOI: 10.1111/asj.13611] [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: 04/02/2021] [Revised: 06/09/2021] [Accepted: 07/01/2021] [Indexed: 11/29/2022]
Abstract
Covariance components were estimated for growth traits (BW, birth weight; WW, weaning weight; YW, yearling weight), visual scores (BQ, breed quality; CS, conformation; MS, muscling; NS, navel; PS, finishing precocity), hip height (HH), and carcass traits (BF, backfat thickness; LMA, longissimus muscle area) measured at yearling. Genetic gains were obtained and validation models on direct and maternal effects for BW and WW were fitted. Genetic correlations of growth traits with CS, PS, MS, and HH ranged from 0.20 ± 0.01 to 0.94 ± 0.01 and were positive and low with NS (0.11 ± 0.01 to 0.20 ± 0.01) and favorable with BQ (0.14 ± 0.02 to 0.37 ± 0.02). Null to moderate genetic correlations were obtained between growth and carcass traits. Genetic gains were positive and significant, except for BW. An increase of 0.76 and 0.72 kg is expected for BW and WW, respectively, per unit increase in estimated breeding value (EBV) for direct effect and an additional 0.74 and 1.43, respectively, kg per unit increase in EBV for the maternal effect. Monitoring genetic gains for HH and NS is relevant to maintain an adequate body size and a navel morphological correction, if necessary. Simultaneous selection for growth, morphological, and carcass traits in line with improve maternal performance is a feasible strategy to increase herd productivity.
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Affiliation(s)
| | | | | | - Lucas de Vargas
- Department of Animal Science, Federal University of Pelotas, Pelotas, Brazil
| | | | | | - Arione Augusti Boligon
- Department of Animal Science, Federal University of Pelotas, Pelotas, Brazil.,National Council for Science and Technological Development, Brasília, Brazil
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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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Genome-Wide Association Study Provides Insights into Important Genes for Reproductive Traits in Nelore Cattle. Animals (Basel) 2021; 11:ani11051386. [PMID: 34068162 PMCID: PMC8152989 DOI: 10.3390/ani11051386] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 05/05/2021] [Accepted: 05/07/2021] [Indexed: 12/03/2022] Open
Abstract
Simple Summary In this study, we investigated the association between single nucleotide polymorphisms (SNPs) and reproductive traits in order to identify candidate genes and biological pathways associated with these traits in Nelore beef cattle. The genome-wide association analysis revealed genomic regions that could explain part of the genetic variance of the studied traits. The results revealed genes with important functions for reproductive traits, such as fertility and precocity. Some genes were associated with more than one trait, being important for reproductive efficiency. The identification of candidate genes that were associated with the studied traits as well as genes enriched in the functional terms and pathways may be useful for exploring the genetic architecture underlying reproductive traits and may be used in Nelore breeding programs. Abstract The identification of genomic regions associated with reproductive traits as well as their biological processes allows a better understanding of the phenotypic variability of these traits. This information could be applied to animal breeding programs to accelerate genetic gain. The aim of this study was to evaluate the association between single nucleotide polymorphisms (SNP) with a scrotal circumference at 365 days of age (SC365) and at 450 days of age (SC450), gestation length (GL) as a calf trait, age at first calving (AFC), accumulated productivity (ACP), heifer early calving until 30 months (HC30), and stayability (STAY) traits, in order to identify candidate genes and biological pathways associated with reproductive traits in Nelore cattle. The data set consisted of pedigree, phenotypes, and genotypes of Nelore cattle from the “Associação Nacional de Criadores e Pesquisadores” (ANCP). The association analyses were performed using the Weighted Single-Step Genome-Wide Association method; the regions, consisting of 10 consecutive SNP, which explained more than 0.5% of additive genetic variance, were considered as a significant association. A total of 3, 6, 7, 5, 10, 25, and 12 windows were associated with SC355, SC450, GL, AFC, ACP, HC30, and STAY, respectively. The results revealed genes with important functions for reproductive traits, such as fertility and precocity. Some genes were associated with more than one trait, among them CAMK1D, TASP1, ACOXL, RAB11FIP5, and SFXN5. Moreover, the genes were enriched in functional terms, like negative regulation of fat cell differentiation, fatty acid alpha-oxidation, and sphingolipids signaling pathway. The identification of the genes associated with the traits, as well as genes enriched in the terms and pathway mentioned above, should contribute to future biological validation studies and may be used as candidate genes in Nelore breeding programs.
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Allelic and genotypic frequencies for loci associated with meat quality in Mexican Braunvieh cattle. Trop Anim Health Prod 2021; 53:307. [PMID: 33956226 DOI: 10.1007/s11250-021-02757-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 05/02/2021] [Indexed: 10/21/2022]
Abstract
The objective was to estimate allelic and genotypic frequencies for loci associated with meat quality in a Mexican population of Braunvieh cattle. Information was obtained from 300 animals genotyped with the Genomic Profile Bovine LD chip of 30K and 50K SNPs. After the final edition, including quality control, the data contained information for 12 loci of the CAPN1, CAPN3, CAPN5, CAPN14, DGAT1, DGAT2, TG, ANK1, and MADH3 genes. Allelic and genotypic frequencies and Hardy-Weinberg equilibrium were estimated with the Cervus 3.0.7 software. The studied population markers were in Hardy-Weinberg equilibrium, except for those associated with CAPN1, DGAT1, and MADH3. Frequencies higher than those reported for other breeds were found for genotypes associated with meat softness, higher marbling score, lower quantity of saturated fatty acids, and lower shear force (CAPN1 and DGAT2). There were similarities with frequencies reported for Bos taurus breeds for the CAPN3 and TG genes. For the DGAT1 and ANK1 genes, the frequencies of the desired genotypes were low. A marker for DGAT1 and another for MADH3 were monomorphic. The results of this study are encouraging in terms of the potential of the Braunvieh population studied for breeding programs aiming to increase meat quality. The breed has strengths that could be used either by crossbreeding to generate heterozygous animals or by selection to increase frequencies of valuable alleles.
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Mancin E, Lourenco D, Bermann M, Mantovani R, Misztal I. Accounting for Population Structure and Phenotypes From Relatives in Association Mapping for Farm Animals: A Simulation Study. Front Genet 2021; 12:642065. [PMID: 33995481 PMCID: PMC8117227 DOI: 10.3389/fgene.2021.642065] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 04/07/2021] [Indexed: 11/16/2022] Open
Abstract
Population structure or genetic relatedness should be considered in genome association studies to avoid spurious association. The most used methods for genome-wide association studies (GWAS) account for population structure but are limited to genotyped individuals with phenotypes. Single-step GWAS (ssGWAS) can use phenotypes from non-genotyped relatives; however, its ability to account for population structure has not been explored. Here we investigate the equivalence among ssGWAS, efficient mixed-model association expedited (EMMAX), and genomic best linear unbiased prediction GWAS (GBLUP-GWAS), and how they differ from the single-SNP analysis without correction for population structure (SSA-NoCor). We used simulated, structured populations that mimicked fish, beef cattle, and dairy cattle populations with 1040, 5525, and 1,400 genotyped individuals, respectively. Larger populations were also simulated that had up to 10-fold more genotyped animals. The genomes were composed by 29 chromosomes, each harboring one QTN, and the number of simulated SNPs was 35,000 for the fish and 65,000 for the beef and dairy cattle populations. Males and females were genotyped in the fish and beef cattle populations, whereas only males had genotypes in the dairy population. Phenotypes for a trait with heritability varying from 0.25 to 0.35 were available in both sexes for the fish population, but only for females in the beef and dairy cattle populations. In the latter, phenotypes of daughters were projected into genotyped sires (i.e., deregressed proofs) before applying EMMAX and SSA-NoCor. Although SSA-NoCor had the largest number of true positive SNPs among the four methods, the number of false negatives was two–fivefold that of true positives. GBLUP-GWAS and EMMAX had a similar number of true positives, which was slightly smaller than in ssGWAS, although the difference was not significant. Additionally, no significant differences were observed when deregressed proofs were used as pseudo-phenotypes in EMMAX compared to daughter phenotypes in ssGWAS for the dairy cattle population. Single-step GWAS accounts for population structure and is a straightforward method for association analysis when only a fraction of the population is genotyped and/or when phenotypes are available on non-genotyped relatives.
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Affiliation(s)
- Enrico Mancin
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Padua, Italy.,Department of Animal and Dairy Science, University of Georgia, Athens, GA, United States
| | - Daniela Lourenco
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, United States
| | - Matias Bermann
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, United States
| | - Roberto Mantovani
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Padua, Italy
| | - Ignacy Misztal
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, United States
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Freitas PHF, Wang Y, Yan P, Oliveira HR, Schenkel FS, Zhang Y, Xu Q, Brito LF. Genetic Diversity and Signatures of Selection for Thermal Stress in Cattle and Other Two Bos Species Adapted to Divergent Climatic Conditions. Front Genet 2021; 12:604823. [PMID: 33613634 PMCID: PMC7887320 DOI: 10.3389/fgene.2021.604823] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 01/15/2021] [Indexed: 12/21/2022] Open
Abstract
Understanding the biological mechanisms of climatic adaptation is of paramount importance for the optimization of breeding programs and conservation of genetic resources. The aim of this study was to investigate genetic diversity and unravel genomic regions potentially under selection for heat and/or cold tolerance in thirty-two worldwide cattle breeds, with a focus on Chinese local cattle breeds adapted to divergent climatic conditions, Datong yak (Bos grunniens; YAK), and Bali (Bos javanicus) based on dense SNP data. In general, moderate genetic diversity levels were observed in most cattle populations. The proportion of polymorphic SNP ranged from 0.197 (YAK) to 0.992 (Mongolian cattle). Observed and expected heterozygosity ranged from 0.023 (YAK) to 0.366 (Sanhe cattle; SH), and from 0.021 (YAK) to 0.358 (SH), respectively. The overall average inbreeding (±SD) was: 0.118 ± 0.028, 0.228 ± 0.059, 0.194 ± 0.041, and 0.021 ± 0.004 based on the observed versus expected number of homozygous genotypes, excess of homozygosity, correlation between uniting gametes, and runs of homozygosity (ROH), respectively. Signatures of selection based on multiple scenarios and methods (F ST, HapFLK, and ROH) revealed important genomic regions and candidate genes. The candidate genes identified are related to various biological processes and pathways such as heat-shock proteins, oxygen transport, anatomical traits, mitochondrial DNA maintenance, metabolic activity, feed intake, carcass conformation, fertility, and reproduction. This highlights the large number of biological processes involved in thermal tolerance and thus, the polygenic nature of climatic resilience. A comprehensive description of genetic diversity measures in Chinese cattle and YAK was carried out and compared to 24 worldwide cattle breeds to avoid potential biases. Numerous genomic regions under positive selection were detected using three signature of selection methods and candidate genes potentially under positive selection were identified. Enriched function analyses pinpointed important biological pathways, molecular function and cellular components, which contribute to a better understanding of the biological mechanisms underlying thermal tolerance in cattle. Based on the large number of genomic regions identified, thermal tolerance has a complex polygenic inheritance nature, which was expected considering the various mechanisms involved in thermal stress response.
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Affiliation(s)
- Pedro H. F. Freitas
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
| | - Yachun Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA – National Engineering Laboratory for Animal Breeding – College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ping Yan
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Hinayah R. Oliveira
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - Flavio S. Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - Yi Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA – National Engineering Laboratory for Animal Breeding – College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Qing Xu
- College of Life Sciences and Bioengineering, School of Science, Beijing Jiaotong University, Beijing, China
| | - Luiz F. Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
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Ruan D, Zhuang Z, Ding R, Qiu Y, Zhou S, Wu J, Xu C, Hong L, Huang S, Zheng E, Cai G, Wu Z, Yang J. Weighted Single-Step GWAS Identified Candidate Genes Associated with Growth Traits in a Duroc Pig Population. Genes (Basel) 2021; 12:genes12010117. [PMID: 33477978 PMCID: PMC7835741 DOI: 10.3390/genes12010117] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 01/07/2021] [Accepted: 01/11/2021] [Indexed: 12/17/2022] Open
Abstract
Growth traits are important economic traits of pigs that are controlled by several major genes and multiple minor genes. To better understand the genetic architecture of growth traits, we performed a weighted single-step genome-wide association study (wssGWAS) to identify genomic regions and candidate genes that are associated with days to 100 kg (AGE), average daily gain (ADG), backfat thickness (BF) and lean meat percentage (LMP) in a Duroc pig population. In this study, 3945 individuals with phenotypic and genealogical information, of which 2084 pigs were genotyped with a 50 K single-nucleotide polymorphism (SNP) array, were used for association analyses. We found that the most significant regions explained 2.56–3.07% of genetic variance for four traits, and the detected significant regions (>1%) explained 17.07%, 18.59%, 23.87% and 21.94% for four traits. Finally, 21 genes that have been reported to be associated with metabolism, bone growth, and fat deposition were treated as candidate genes for growth traits in pigs. Moreover, gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses implied that the identified genes took part in bone formation, the immune system, and digestion. In conclusion, such full use of phenotypic, genotypic, and genealogical information will accelerate the genetic improvement of growth traits in pigs.
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Affiliation(s)
- Donglin Ruan
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (D.R.); (Z.Z.); (R.D.); (Y.Q.); (S.Z.); (J.W.); (C.X.); (L.H.); (S.H.); (E.Z.); (G.C.)
- Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou 510642, China
| | - Zhanwei Zhuang
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (D.R.); (Z.Z.); (R.D.); (Y.Q.); (S.Z.); (J.W.); (C.X.); (L.H.); (S.H.); (E.Z.); (G.C.)
- Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou 510642, China
| | - Rongrong Ding
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (D.R.); (Z.Z.); (R.D.); (Y.Q.); (S.Z.); (J.W.); (C.X.); (L.H.); (S.H.); (E.Z.); (G.C.)
- Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou 510642, China
| | - Yibin Qiu
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (D.R.); (Z.Z.); (R.D.); (Y.Q.); (S.Z.); (J.W.); (C.X.); (L.H.); (S.H.); (E.Z.); (G.C.)
- Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou 510642, China
| | - Shenping Zhou
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (D.R.); (Z.Z.); (R.D.); (Y.Q.); (S.Z.); (J.W.); (C.X.); (L.H.); (S.H.); (E.Z.); (G.C.)
- Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou 510642, China
| | - Jie Wu
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (D.R.); (Z.Z.); (R.D.); (Y.Q.); (S.Z.); (J.W.); (C.X.); (L.H.); (S.H.); (E.Z.); (G.C.)
- Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou 510642, China
| | - Cineng Xu
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (D.R.); (Z.Z.); (R.D.); (Y.Q.); (S.Z.); (J.W.); (C.X.); (L.H.); (S.H.); (E.Z.); (G.C.)
- Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou 510642, China
| | - Linjun Hong
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (D.R.); (Z.Z.); (R.D.); (Y.Q.); (S.Z.); (J.W.); (C.X.); (L.H.); (S.H.); (E.Z.); (G.C.)
- Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou 510642, China
| | - Sixiu Huang
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (D.R.); (Z.Z.); (R.D.); (Y.Q.); (S.Z.); (J.W.); (C.X.); (L.H.); (S.H.); (E.Z.); (G.C.)
- Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou 510642, China
| | - Enqin Zheng
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (D.R.); (Z.Z.); (R.D.); (Y.Q.); (S.Z.); (J.W.); (C.X.); (L.H.); (S.H.); (E.Z.); (G.C.)
- Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou 510642, China
| | - Gengyuan Cai
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (D.R.); (Z.Z.); (R.D.); (Y.Q.); (S.Z.); (J.W.); (C.X.); (L.H.); (S.H.); (E.Z.); (G.C.)
| | - Zhenfang Wu
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (D.R.); (Z.Z.); (R.D.); (Y.Q.); (S.Z.); (J.W.); (C.X.); (L.H.); (S.H.); (E.Z.); (G.C.)
- Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou 510642, China
- Correspondence: (Z.W.); (J.Y.)
| | - Jie Yang
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (D.R.); (Z.Z.); (R.D.); (Y.Q.); (S.Z.); (J.W.); (C.X.); (L.H.); (S.H.); (E.Z.); (G.C.)
- Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou 510642, China
- Correspondence: (Z.W.); (J.Y.)
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Raschia M, Nani J, Carignano H, Amadio A, Maizon D, Poli M. Weighted single-step genome-wide association analyses for milk traits in Holstein and Holstein x Jersey crossbred dairy cattle. Livest Sci 2020. [DOI: 10.1016/j.livsci.2020.104294] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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31
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de Las Heras-Saldana S, Lopez BI, Moghaddar N, Park W, Park JE, Chung KY, Lim D, Lee SH, Shin D, van der Werf JHJ. Use of gene expression and whole-genome sequence information to improve the accuracy of genomic prediction for carcass traits in Hanwoo cattle. Genet Sel Evol 2020; 52:54. [PMID: 32993481 PMCID: PMC7525992 DOI: 10.1186/s12711-020-00574-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 09/18/2020] [Indexed: 12/21/2022] Open
Abstract
Background In this study, we assessed the accuracy of genomic prediction for carcass weight (CWT), marbling score (MS), eye muscle area (EMA) and back fat thickness (BFT) in Hanwoo cattle when using genomic best linear unbiased prediction (GBLUP), weighted GBLUP (wGBLUP), and a BayesR model. For these models, we investigated the potential gain from using pre-selected single nucleotide polymorphisms (SNPs) from a genome-wide association study (GWAS) on imputed sequence data and from gene expression information. We used data on 13,717 animals with carcass phenotypes and imputed sequence genotypes that were split in an independent GWAS discovery set of varying size and a remaining set for validation of prediction. Expression data were used from a Hanwoo gene expression experiment based on 45 animals. Results Using a larger number of animals in the reference set increased the accuracy of genomic prediction whereas a larger independent GWAS discovery dataset improved identification of predictive SNPs. Using pre-selected SNPs from GWAS in GBLUP improved accuracy of prediction by 0.02 for EMA and up to 0.05 for BFT, CWT, and MS, compared to a 50 k standard SNP array that gave accuracies of 0.50, 0.47, 0.58, and 0.47, respectively. Accuracy of prediction of BFT and CWT increased when BayesR was applied with the 50 k SNP array (0.02 and 0.03, respectively) and was further improved by combining the 50 k array with the top-SNPs (0.06 and 0.04, respectively). By contrast, using BayesR resulted in limited improvement for EMA and MS. wGBLUP did not improve accuracy but increased prediction bias. Based on the RNA-seq experiment, we identified informative expression quantitative trait loci, which, when used in GBLUP, improved the accuracy of prediction slightly, i.e. between 0.01 and 0.02. SNPs that were located in genes, the expression of which was associated with differences in trait phenotype, did not contribute to a higher prediction accuracy. Conclusions Our results show that, in Hanwoo beef cattle, when SNPs are pre-selected from GWAS on imputed sequence data, the accuracy of prediction improves only slightly whereas the contribution of SNPs that are selected based on gene expression is not significant. The benefit of statistical models to prioritize selected SNPs for estimating genomic breeding values is trait-specific and depends on the genetic architecture of each trait.
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Affiliation(s)
| | - Bryan Irvine Lopez
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Nasir Moghaddar
- School of Environmental and Rural Science, University of New England, Armidale, NSW 2351, Australia
| | - Woncheoul Park
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Jong-Eun Park
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Ki Y Chung
- Department of Beef Science, Korea National College of Agriculture and Fisheries, Jeonju, Republic of Korea
| | - Dajeong Lim
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 55365, Republic of Korea.
| | - Seung H Lee
- Division of Animal and Dairy Science, Chungnam National University, Deajeon, 34148, Republic of Korea
| | - Donghyun Shin
- The Animal Molecular Genetics and Breeding Centre, Jeonbuk National University, Jeonju, 54896, Republic of Korea
| | - Julius H J van der Werf
- School of Environmental and Rural Science, University of New England, Armidale, NSW 2351, Australia.
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Lozada-Soto EA, Maltecca C, Wackel H, Flowers W, Gray K, He Y, Huang Y, Jiang J, Tiezzi F. Evidence for recombination variability in purebred swine populations. J Anim Breed Genet 2020; 138:259-273. [PMID: 32975329 DOI: 10.1111/jbg.12510] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 08/27/2020] [Accepted: 09/05/2020] [Indexed: 01/04/2023]
Abstract
This study aimed to investigate interpopulation variation due to sex, breed and age, and the intrapopulation variation in the form of genetic variance for recombination in swine. Genome-wide recombination rate and recombination occurrences (RO) were traits studied in Landrace (LR) and Large White (LW) male and female populations. Differences were found for sex, breed, sex-breed interaction, and age effects for genome-wide recombination rate and RO at one or more chromosomes. Dams were found to have a higher genome-wide recombination rate and RO at all chromosomes than sires. LW animals had higher genome-wide recombination rate and RO at seven chromosomes but lower at two chromosomes than LR individuals. The sex-breed interaction effect did not show any pattern not already observable by sex. Recombination increased with increasing parity in females, while in males no effect of age was observed. We estimated heritabilities and repeatabilities for both investigated traits and obtained the genetic correlation between male and female genome-wide recombination rate within each of the two breeds studied. Estimates of heritability and repeatability were low (h2 = 0.01-0.26; r = 0.18-0.42) for both traits in all populations. Genetic correlations were high and positive, with estimates of 0.98 and 0.94 for the LR and LW breeds, respectively. We performed a GWAS for genome-wide recombination rate independently in the four sex/breed populations. The results of the GWAS were inconsistent across the four populations with different significant genomic regions identified. The results of this study provide evidence of variability for recombination in purebred swine populations.
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Affiliation(s)
| | - Christian Maltecca
- Department of Animal Science, North Carolina State University, Raleigh, NC, USA
| | - Hanna Wackel
- Department of Animal Science, North Carolina State University, Raleigh, NC, USA
| | - William Flowers
- Department of Animal Science, North Carolina State University, Raleigh, NC, USA
| | - Kent Gray
- Smithfield Premium Genetics, Rose Hill, NC, USA
| | - Yuqing He
- Department of Animal Science, North Carolina State University, Raleigh, NC, USA
| | | | - Jicai Jiang
- Department of Animal Science, North Carolina State University, Raleigh, NC, USA
| | - Francesco Tiezzi
- Department of Animal Science, North Carolina State University, Raleigh, NC, USA
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Hong JK, Lee JB, Ramayo-Caldas Y, Kim SD, Cho ES, Kim YS, Cho KH, Lee DH, Park HB. Single-step genome-wide association study for social genetic effects and direct genetic effects on growth in Landrace pigs. Sci Rep 2020; 10:14958. [PMID: 32917921 PMCID: PMC7486944 DOI: 10.1038/s41598-020-71647-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 08/03/2020] [Indexed: 02/08/2023] Open
Abstract
In livestock social interactions, social genetic effects (SGE) represent associations between phenotype of one individual and genotype of another. Such associations occur when the trait of interest is affected by transmissible phenotypes of social partners. The aim of this study was to estimate SGE and direct genetic effects (DGE, genetic effects of an individual on its own phenotype) on average daily gain (ADG) in Landrace pigs, and to conduct single-step genome-wide association study using SGE and DGE as dependent variables to identify quantitative trait loci (QTLs) and their positional candidate genes. A total of 1,041 Landrace pigs were genotyped using the Porcine SNP 60K BeadChip. Estimates of the two effects were obtained using an extended animal model. The SGE contributed 16% of the total heritable variation of ADG. The total heritability estimated by the extended animal model including both SGE and DGE was 0.52. The single-step genome-wide association study identified a total of 23 QTL windows for the SGE on ADG distributed across three chromosomes (i.e., SSC1, SSC2, and SSC6). Positional candidate genes within these QTL regions included PRDM13, MAP3K7, CNR1, HTR1E, IL4, IL5, IL13, KIF3A, EFHD2, SLC38A7, mTOR, CNOT1, PLCB2, GABRR1, and GABRR2, which have biological roles in neuropsychiatric processes. The results of biological pathway and gene network analyses also support the association of the neuropsychiatric processes with SGE on ADG in pigs. Additionally, a total of 11 QTL windows for DGE on ADG in SSC2, 3, 6, 9, 10, 12, 14, 16, and 17 were detected with positional candidate genes such as ARL15. We found a putative pleotropic QTL for both SGE and DGE on ADG on SSC6. Our results in this study provide important insights that can help facilitate a better understanding of the molecular basis of SGE for socially affected traits.
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Affiliation(s)
- Joon-Ki Hong
- National Institute of Animal Science, Rural Development Administration, Cheonan, 31000, Republic of Korea
| | - Jae-Bong Lee
- Korea Zoonosis Research Institute, Chonbuk National University, 54531, Iksan, Republic of Korea
| | - Yuliaxis Ramayo-Caldas
- Animal Breeding and Genetics Program, Institute for Research and Technology in Food and Agriculture (IRTA), Torre Marimon, 08140, Caldes de Montbui, Spain
| | - Si-Dong Kim
- National Institute of Animal Science, Rural Development Administration, Cheonan, 31000, Republic of Korea
| | - Eun-Seok Cho
- National Institute of Animal Science, Rural Development Administration, Cheonan, 31000, Republic of Korea
| | - Young-Sin Kim
- National Institute of Animal Science, Rural Development Administration, Cheonan, 31000, Republic of Korea
| | - Kyu-Ho Cho
- National Institute of Animal Science, Rural Development Administration, Cheonan, 31000, Republic of Korea
| | - Deuk-Hwan Lee
- Department of Animal Life Resources, Hankyong National University, Anseong, 17579, Republic of Korea
| | - Hee-Bok Park
- Department of Animal Resources Science, Kongju National University, Yesan, 32439, Republic of Korea.
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Raza SHA, Khan S, Amjadi M, Abdelnour SA, Ohran H, Alanazi KM, Abd El-Hack ME, Taha AE, Khan R, Gong C, Schreurs NM, Zhao C, Wei D, Zan L. Genome-wide association studies reveal novel loci associated with carcass and body measures in beef cattle. Arch Biochem Biophys 2020; 694:108543. [PMID: 32798459 DOI: 10.1016/j.abb.2020.108543] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 07/26/2020] [Accepted: 08/08/2020] [Indexed: 12/18/2022]
Abstract
Genomic selection has an essential role in the livestock economy by increasing selection productivity. Genomics provides a mechanism to increase the rate of genetic gain using marker-assisted selection. Various quantitative trait loci (QTL) associated with body, carcass and meat quality traits in beef cattle have been found. It is widely accepted that QTL traits in livestock species are regulated by several genes and factors from the environment. Genome-wide association studies (GWAS) are a powerful approach in identifying QTL and to establish genomic regions harboring the genes and polymorphisms associated with specific characteristics in beef cattle. Due to their impact on economic returns, growth, carcass and meat quality traits of cattle are frequently used as essential criteria in selection in breeding programs., GWAS has been used in beef cattle breeding and genetic program and some progress has been made. Furthermore, numerous genes and markers related to productivity traits in beef cattle have been found. This review summarizes the advances in the use of GWAS in beef cattle production and outlines the associations with growth, carcass, and meat quality.
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Affiliation(s)
- Sayed Haidar Abbas Raza
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
| | - Samiullah Khan
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Motahareh Amjadi
- Department of Genetics, Eötvös Loránd University, Budapest, Hungary
| | - Sameh A Abdelnour
- Department of Animal Production, Faculty of Agriculture, Zagazig University, Zagazig, 44511, Egypt
| | - Hussien Ohran
- Department of Physiology, University of Sarajevo, Veterinary Faculty, Zmajaod Bosne 90, 71000, Sarajevo, Bosnia and Herzegovina
| | - Khalid M Alanazi
- Zoology Department, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Mohamed E Abd El-Hack
- Department of Poultry, Faculty of Agriculture, Zagazig University, Zagazig, 44511, Egypt
| | - Ayman E Taha
- Department of Animal Husbandry and Animal Wealth Development, Faculty of Veterinary Medicine, Alexandria University, Edfina, 22578, Egypt
| | - Rajwali Khan
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Cheng Gong
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Nicola M Schreurs
- Animal Science, School of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | - Chunping Zhao
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Dawei Wei
- School of Agriculture, Ningxia University, Yinchuan, China
| | - Linsen Zan
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China; National Beef Cattle Improvement Center, Northwest A&F University, Yangling, 712100, China.
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35
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Brunes LC, Baldi F, Lopes FB, Lôbo RB, Espigolan R, Costa MFO, Stafuzza NB, Magnabosco CU. Weighted single-step genome-wide association study and pathway analyses for feed efficiency traits in Nellore cattle. J Anim Breed Genet 2020; 138:23-44. [PMID: 32654373 DOI: 10.1111/jbg.12496] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 06/11/2020] [Accepted: 06/13/2020] [Indexed: 02/06/2023]
Abstract
The aim was to conduct a weighted single-step genome-wide association study to detect genomic regions and putative candidate genes related to residual feed intake, dry matter intake, feed efficiency (FE), feed conversion ratio, residual body weight gain, residual intake and weight gain in Nellore cattle. Several protein-coding genes were identified within the genomic regions that explain more than 0.5% of the additive genetic variance for these traits. These genes were associated with insulin, leptin, glucose, protein and lipid metabolisms; energy balance; heat and oxidative stress; bile secretion; satiety; feed behaviour; salivation; digestion; and nutrient absorption. Enrichment analysis revealed functional pathways (p-value < .05) such as neuropeptide signalling (GO:0007218), negative regulation of canonical Wingless/Int-1 (Wnt) signalling (GO:0090090), bitter taste receptor activity (GO:0033038), neuropeptide hormone activity (GO:0005184), bile secretion (bta04976), taste transduction (bta0742) and glucagon signalling pathway (bta04922). The identification of these genes, pathways and their respective functions should contribute to a better understanding of the genetic and physiological mechanisms regulating Nellore FE-related traits.
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Affiliation(s)
- Ludmilla C Brunes
- Department of Animal Science, Federal University of Goiás (UFG), Goiânia, Brazil.,Embrapa Rice and Beans, Santo Antônio de Goiás, Brazil
| | - Fernando Baldi
- Department of Animal Science, São Paulo State University (UNESP), Jaboticabal, Brazil
| | | | - Raysildo B Lôbo
- National Association of Breeders and Researchers (ANCP), Ribeirão Preto, Brazil
| | - Rafael Espigolan
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, Brazil
| | | | - Nedenia B Stafuzza
- Beef Cattle Research Center, Animal Science Institute, Sertãozinho, Brazil
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36
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Rodríguez-Vázquez R, Mato A, López-Pedrouso M, Franco D, Sentandreu MA, Zapata C. Measuring quantitative proteomic distance between Spanish beef breeds. Food Chem 2020; 315:126293. [PMID: 32028200 DOI: 10.1016/j.foodchem.2020.126293] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 01/21/2020] [Accepted: 01/23/2020] [Indexed: 01/11/2023]
Abstract
Estimates of quantitative proteomic distance between populations have not been reported to date. Here, quantitative proteomic distances between three Spanish bovine breeds (Asturiana de los Valles, AV; Retinta, RE; and Rubia Gallega, RG) were estimated from two-dimensional electrophoresis profiles of meat samples of longissimus thoracis muscle at 2 h post-mortem. Statistically significant distances were detected between AV/RG and the most genetically different RE breed, using the novel QD measure of quantitative proteomic distance. In total, 18 differentially abundant myofibrillar and sarcoplasmic proteins/isoforms contributing to proteomic distances between breeds were confidently identified by tandem mass spectrometry. The fast skeletal myosin regulatory light chain 2 followed by other five interacting proteins exhibited the most pronounced relative change between breeds. In addition, most differentially represented proteins could be associated with variations in meat tenderness. Therefore, they could be candidate biomarkers for molecular breeding programs and authentication of the three Spanish beef breeds.
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Affiliation(s)
- R Rodríguez-Vázquez
- Department of Zoology, Genetics and Physical Anthropology, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - A Mato
- Department of Zoology, Genetics and Physical Anthropology, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - M López-Pedrouso
- Department of Zoology, Genetics and Physical Anthropology, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - D Franco
- Meat Technology Center of Galicia, 32900 San Cibrao das Viñas, Ourense, Spain
| | - M A Sentandreu
- Instituto de Agroquímica y Tecnología de Alimentos (CSIC), 46980 Paterna, Valencia, Spain
| | - C Zapata
- Department of Zoology, Genetics and Physical Anthropology, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain.
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37
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Edea Z, Jung KS, Shin SS, Yoo SW, Choi JW, Kim KS. Signatures of positive selection underlying beef production traits in Korean cattle breeds. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2020; 62:293-305. [PMID: 32568261 PMCID: PMC7288235 DOI: 10.5187/jast.2020.62.3.293] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 03/04/2020] [Accepted: 03/15/2020] [Indexed: 01/01/2023]
Abstract
The difference in the breeding programs and population history may have diversely
shaped the genomes of Korean native cattle breeds. In the absence of phenotypic
data, comparisons of breeds that have been subjected to different selective
pressures can aid to identify genomic regions and genes controlling qualitative
and complex traits. In this study to decipher genetic variation and identify
evidence of divergent selection, 3 Korean cattle breeds were genotyped using the
recently developed high-density GeneSeek Genomic Profiler F250 (GGP-F250) array.
The three Korean cattle breeds clustered according to their coat color
phenotypes and breeding programs. The Heugu breed reliably showed smaller
effective population size at all generations considered. Across the autosomal
chromosomes, 113 and 83 annotated genes were identified from Hanwoo-Chikso and
Hanwoo-Heugu comparisons, respectively of which 16 genes were shared between the
two pairwise comparisons. The most important signals of selection were detected
on bovine chromosomes 14 (24.39–25.13 Mb) and 18 (13.34–15.07 Mb),
containing genes related to body size, and coat color (XKR4,
LYN, PLAG1, SDR16C5,
TMEM68, CDH15, MC1R, and
GALNS). Some of the candidate genes are also associated
with meat quality traits (ACSF3, EIF2B1,
BANP, APCDD1, and GALM)
and harbor quantitative trait locus (QTL) for beef production traits. Further
functional analysis revealed that the candidate genes (DBI,
ACSF3, HINT2, GBA2,
AGPAT5, SCAP, ELP6,
APOB, and RBL1) were involved in gene
ontology (GO) terms relevant to meat quality including fatty acid oxidation,
biosynthesis, and lipid storage. Candidate genes previously known to affect beef
production and quality traits could be used in the beef cattle selection
strategies.
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Affiliation(s)
- Zewdu Edea
- Department of Animal Science, Chungbuk National University, Cheongju 28644, Korea
| | - Kyoung Sub Jung
- Institute of Livestock and Veterinary Research, Cheongju 28153, Korea
| | - Sung-Sub Shin
- Korea Institute for Animal Products Quality Evaluation, Sejong 30100, Korea
| | - Song-Won Yoo
- Korea Institute for Animal Products Quality Evaluation, Sejong 30100, Korea
| | - Jae Won Choi
- Institute of Livestock and Veterinary Research, Cheongju 28153, Korea
| | - Kwan-Suk Kim
- Department of Animal Science, Chungbuk National University, Cheongju 28644, Korea
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Atashi H, Salavati M, De Koster J, Crowe MA, Opsomer G, Hostens M. Genome-wide association for metabolic clusters in early-lactation Holstein dairy cows. J Dairy Sci 2020; 103:6392-6406. [PMID: 32331880 DOI: 10.3168/jds.2019-17369] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 01/22/2020] [Indexed: 11/19/2022]
Abstract
The aim of this study was to detect the genomic region or regions associated with metabolic clusters in early-lactation Holstein cows. This study was carried out in 2 experiments. In experiment I, which was carried out on 105 multiparous Holstein cows, animals were classified through k-means clustering on log-transformed and standardized concentrations of blood glucose, insulin-like growth factor I, free fatty acids, and β-hydroxybutyrate at 14 and 35 d in milk (DIM), into metabolic clusters, either balanced (BAL) or other (OTR). Forty percent of the animals were categorized in the BAL group, and the remainder were categorized as OTR. The cows were genotyped for a total of 777,962 SNP. A genome-wide association study was performed, using a case-control approach through the GEMMA software, accounting for population structure. We found 8 SNP (BTA11, BTA23, and BTAX) associated with the predicted metabolic clusters. In experiment II, carried out on 4,267 second-parity Holstein cows, milk samples collected starting from the first week until 50 DIM were used to determine Fourier-transform mid-infrared (FT-MIR) spectra and subsequently to classify the animals into the same metabolic clusters (BAL vs. OTR). Twenty-eight percent of the animals were categorized in the BAL group, and the remainder were classified in the OTR category. Although daily milk yield was lower in BAL cows, we found no difference in daily fat- and protein-corrected milk yield in cows from the BAL metabolic cluster compared with those in the OTR metabolic cluster. In the next step, a single-step genomic BLUP was used to identify the genomic region(s) associated with the predicted metabolic clusters. The results revealed that prediction of metabolic clusters is a highly polygenic trait regulated by many small-sized effects. The region of 36,258 to 36,295 kb on BTA27 was the highly associated region for the predicted metabolic clusters, with the closest genes to this region (ANK1 and miR-486) being related to hematopoiesis, erythropoiesis, and mammary gland development. The heritability for metabolic clustering was 0.17 (SD 0.03), indicating that the use of FT-MIR spectra in milk to predict metabolic clusters in early-lactation across a large number of cows has satisfactory potential to be included in genetic selection programs for modern dairy cows.
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Affiliation(s)
- H Atashi
- Department of Reproduction, Obstetrics and Herd Health, Ghent University, Merelbeke 9820, Belgium; Department of Animal Science, Shiraz University, Shiraz 71441-65186, Iran
| | - M Salavati
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - J De Koster
- Department of Reproduction, Obstetrics and Herd Health, Ghent University, Merelbeke 9820, Belgium
| | - M A Crowe
- University College Dublin, 4 Dublin, Ireland
| | - G Opsomer
- Department of Reproduction, Obstetrics and Herd Health, Ghent University, Merelbeke 9820, Belgium
| | | | - M Hostens
- Department of Reproduction, Obstetrics and Herd Health, Ghent University, Merelbeke 9820, Belgium.
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Lukić B, Ferenčaković M, Šalamon D, Čačić M, Orehovački V, Iacolina L, Curik I, Cubric-Curik V. Conservation Genomic Analysis of the Croatian Indigenous Black Slavonian and Turopolje Pig Breeds. Front Genet 2020; 11:261. [PMID: 32296459 PMCID: PMC7136467 DOI: 10.3389/fgene.2020.00261] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 03/05/2020] [Indexed: 12/19/2022] Open
Abstract
The majority of the nearly 400 existing local pig breeds are adapted to specific environments and human needs. The demand for large production quantities and the industrialized pig production have caused a rapid decline of many local pig breeds in recent decades. Black Slavonian pig and Turopolje pig, the latter highly threatened, are the two Croatian local indigenous breeds typically grown in extensive or semi-intensive systems. In order to guide a long-term breeding program to prevent the disappearance of these breeds, we analyzed their genetic diversity, inbreeding level and relationship with other local breeds across the world, as well as modern breeds and several wild populations, using high throughput genomic data obtained using the Illumina Infinium PorcineSNP60 v2 BeadChip. Multidimensional scaling analysis positioned Black Slavonian pigs close to the UK/North American breeds, while the Turopolje pig clustered within the Mediterranean breeds. Turopolje pig showed a very high inbreeding level (FROH>4Mb = 0.400 and FROH>8Mb = 0.332) that considerably exceeded the level of full-sib mating, while Black Slavonian pig showed much lower inbreeding (FROH>4Mb = 0.098 and FROH>8Mb = 0.074), indicating a planned mating strategy. In Croatian local breeds we identified several genome regions showing adaptive selection signals that were not present in commercial breeds. The results obtained in this study reflect the current genetic status and breeding management of the two Croatian indigenous local breeds. Given the small populations of both breeds, a controlled management activity has been implemented in Black Slavonian pigs since their commercial value has been recognized. In contrast, the extremely high inbreeding level observed in Turopolje pig argues for an urgent conservation plan with a long-term, diversity-oriented breeding program.
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Affiliation(s)
- Boris Lukić
- Department for Animal Production and Biotechnology, Faculty of Agrobiotechnical Sciences Osijek, J.J. Strossmayer University of Osijek, Osijek, Croatia
| | - Maja Ferenčaković
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
| | - Dragica Šalamon
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
| | - Mato Čačić
- Ministry of Agriculture, Zagreb, Croatia
| | | | - Laura Iacolina
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.,Department for Apiculture, Wildlife Management and Special Zoology, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
| | - Ino Curik
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
| | - Vlatka Cubric-Curik
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
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A Genome-Wide Association Study for Calving Interval in Holstein Dairy Cows Using Weighted Single-Step Genomic BLUP Approach. Animals (Basel) 2020; 10:ani10030500. [PMID: 32192064 PMCID: PMC7143202 DOI: 10.3390/ani10030500] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 03/13/2020] [Accepted: 03/14/2020] [Indexed: 12/15/2022] Open
Abstract
The aim of the present study was to identify genomic region(s) associated with the length of the calving interval in primiparous (n = 6866) and multiparous (n = 5071) Holstein cows. The single nucleotide polymorphism (SNP) solutions were estimated using a weighted single-step genomic best linear unbiased prediction (WssGBLUP) approach and imputed high-density panel (777 k) genotypes. The effects of markers and the genomic estimated breeding values (GEBV) of the animals were obtained by five iterations of WssGBLUP. The results showed that the accuracies of GEBVs with WssGBLUP improved by +5.4 to +5.7, (primiparous cows) and +9.4 to +9.7 (multiparous cows) percent points over accuracies from the pedigree-based BLUP. The most accurate genomic evaluation was provided at the second iteration of WssGBLUP, which was used to identify associated genomic regions using a windows-based GWAS procedure. The proportion of additive genetic variance explained by windows of 50 consecutive SNPs (with an average of 165 Kb) was calculated and the region(s) that accounted for equal to or more than 0.20% of the total additive genetic variance were used to search for candidate genes. Three windows of 50 consecutive SNPs (BTA3, BTA6, and BTA7) were identified to be associated with the length of the calving interval in primi- and multiparous cows, while the window with the highest percentage of explained genetic variance was located on BTA3 position 49.42 to 49.52 Mb. There were five genes including ARHGAP29, SEC24D, METTL14, SLC36A2, and SLC36A3 inside the windows associated with the length of the calving interval. The biological process terms including alanine transport, L-alanine transport, proline transport, and glycine transport were identified as the most important terms enriched by the genes inside the identified windows.
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Grigoletto L, Ferraz JBS, Oliveira HR, Eler JP, Bussiman FO, Abreu Silva BC, Baldi F, Brito LF. Genetic Architecture of Carcass and Meat Quality Traits in Montana Tropical ® Composite Beef Cattle. Front Genet 2020; 11:123. [PMID: 32180796 PMCID: PMC7057717 DOI: 10.3389/fgene.2020.00123] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 02/03/2020] [Indexed: 12/16/2022] Open
Abstract
The Montana Tropical® Composite is a recently developed beef cattle population that is rapidly expanding in Brazil and other tropical countries. This is mainly due to its improved meat quality and adaptation to tropical climate conditions compared to Zebu and Taurine cattle breeds, respectively. This study aimed to investigate the genetic architecture of ultrasound-based carcass and meat quality traits in Montana Tropical® Composite beef cattle. Therefore, we estimated variance components and genetic parameters and performed genome-wide association studies using the weighted single-step Genomic Best Linear Unbiased Prediction (GBLUP) approach. A pedigree dataset containing 28,480 animals was used, in which 1,436 were genotyped using a moderate-density Single Nucleotide Polymorphism panel (30K; 30,105 SNPs). A total of 9,358, 5,768, 7,996, and 1,972 phenotypic records for the traits Longissimus muscle area (LMA), backfat thickness (BFT), rump fat thickness (RFT), and for marbling score (MARB), respectively, were used for the analyses. Moderate to high heritability estimates were obtained and ranged from 0.16 ± 0.03 (RFT) to 0.33 ± 0.05 (MARB). A high genetic correlation was observed between BFT and RFT (0.97 ± 0.02), suggesting that a similar set of genes affects both traits. The most relevant genomic regions associated with LMA, BFT, RFT, and MARB were found on BTA10 (5.4–5.8 Mb), BTA27 (25.2–25.5 Mb), BTA18 (60.6–61.0 Mb), and BTA21 (14.8–15.4 Mb). Two overlapping genomic regions were identified for RFT and MARB (BTA13:47.9–48.1 Mb) and for BFT and RFT (BTA13:61.5–62.3 Mb). Candidate genes identified in this study, including PLAG1, LYN, WWOX, and PLAGL2, were previously reported to be associated with growth, stature, skeletal muscle growth, fat thickness, and fatty acid composition. Our results indicate that ultrasound-based carcass and meat quality traits in the Montana Tropical® Composite beef cattle are heritable, and therefore, can be improved through selective breeding. In addition, various novel and already known genomic regions related to these traits were identified, which contribute to a better understanding of the underlying genetic background of LMA, BFT, RFT, and MARB in the Montana Tropical Composite population.
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Affiliation(s)
- Laís Grigoletto
- Department of Animal Sciences, College of Animal Sciences and Food Engineering, University of São Paulo, Pirassununga, Brazil.,Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
| | - José B S Ferraz
- Department of Animal Sciences, College of Animal Sciences and Food Engineering, University of São Paulo, Pirassununga, Brazil
| | - Hinayah R Oliveira
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
| | - Joanir P Eler
- Department of Animal Sciences, College of Animal Sciences and Food Engineering, University of São Paulo, Pirassununga, Brazil
| | - Fernando O Bussiman
- Department of Animal Sciences, College of Animal Sciences and Food Engineering, University of São Paulo, Pirassununga, Brazil
| | - Barbara C Abreu Silva
- Department of Animal Sciences, College of Animal Sciences and Food Engineering, University of São Paulo, Pirassununga, Brazil
| | - Fernando Baldi
- Department of Animal Sciences, College of Agricultural and Veterinary Sciences, São Paulo State University, Jaboticabal, Brazil
| | - Luiz F Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
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de las Heras-Saldana S, Clark SA, Duijvesteijn N, Gondro C, van der Werf JHJ, Chen Y. Combining information from genome-wide association and multi-tissue gene expression studies to elucidate factors underlying genetic variation for residual feed intake in Australian Angus cattle. BMC Genomics 2019; 20:939. [PMID: 31810463 PMCID: PMC6898931 DOI: 10.1186/s12864-019-6270-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 11/07/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genome-wide association studies (GWAS) are extensively used to identify single nucleotide polymorphisms (SNP) underlying the genetic variation of complex traits. However, much uncertainly often still exists about the causal variants and genes at quantitative trait loci (QTL). The aim of this study was to identify QTL associated with residual feed intake (RFI) and genes in these regions whose expression is also associated with this trait. Angus cattle (2190 steers) with RFI records were genotyped and imputed to high density arrays (770 K) and used for a GWAS approach to identify QTL associated with RFI. RNA sequences from 126 Angus divergently selected for RFI were analyzed to identify the genes whose expression was significantly associated this trait with special attention to those genes residing in the QTL regions. RESULTS The heritability for RFI estimated for this Angus population was 0.3. In a GWAS, we identified 78 SNPs associated with RFI on six QTL (on BTA1, BTA6, BTA14, BTA17, BTA20 and BTA26). The most significant SNP was found on chromosome BTA20 (rs42662073) and explained 4% of the genetic variance. The minor allele frequencies of significant SNPs ranged from 0.05 to 0.49. All regions, except on BTA17, showed a significant dominance effect. In 1 Mb windows surrounding the six significant QTL, we found 149 genes from which OAS2, STC2, SHOX, XKR4, and SGMS1 were the closest to the most significant QTL on BTA17, BTA20, BTA1, BTA14, and BTA26, respectively. In a 2 Mb windows around the six significant QTL, we identified 15 genes whose expression was significantly associated with RFI: BTA20) NEURL1B and CPEB4; BTA17) RITA1, CCDC42B, OAS2, RPL6, and ERP29; BTA26) A1CF, SGMS1, PAPSS2, and PTEN; BTA1) MFSD1 and RARRES1; BTA14) ATP6V1H and MRPL15. CONCLUSIONS Our results showed six QTL regions associated with RFI in a beef Angus population where five of these QTL contained genes that have expression associated with this trait. Therefore, here we show that integrating information from gene expression and GWAS studies can help to better understand the genetic mechanisms that determine variation in complex traits.
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Affiliation(s)
| | - Samuel A. Clark
- School of Environmental and Rural Science, University of New England, Armidale, NSW Australia
| | - Naomi Duijvesteijn
- School of Environmental and Rural Science, University of New England, Armidale, NSW Australia
| | - Cedric Gondro
- School of Environmental and Rural Science, University of New England, Armidale, NSW Australia
- Department of Animal Science, Michigan State University, East Lansing, MI USA
| | | | - Yizhou Chen
- Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, NSW Australia
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Nolte W, Weikard R, Brunner RM, Albrecht E, Hammon HM, Reverter A, Kühn C. Biological Network Approach for the Identification of Regulatory Long Non-Coding RNAs Associated With Metabolic Efficiency in Cattle. Front Genet 2019; 10:1130. [PMID: 31824560 PMCID: PMC6883949 DOI: 10.3389/fgene.2019.01130] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 10/17/2019] [Indexed: 12/17/2022] Open
Abstract
Background: Genomic regions associated with divergent livestock feed efficiency have been found predominantly outside protein coding sequences. Long non-coding RNAs (lncRNA) can modulate chromatin accessibility, gene expression and act as important metabolic regulators in mammals. By integrating phenotypic, transcriptomic, and metabolomic data with quantitative trait locus data in prioritizing co-expression network analyses, we aimed to identify and functionally characterize lncRNAs with a potential key regulatory role in metabolic efficiency in cattle. Materials and Methods: Crossbred animals (n = 48) of a Charolais x Holstein F2-population were allocated to groups of high or low metabolic efficiency based on residual feed intake in bulls, energy corrected milk in cows and intramuscular fat content in both genders. Tissue samples from jejunum, liver, skeletal muscle and rumen were subjected to global transcriptomic analysis via stranded total RNA sequencing (RNAseq) and blood plasma samples were used for profiling of 640 metabolites. To identify lncRNAs within the indicated tissues, a project-specific transcriptome annotation was established. Subsequently, novel transcripts were categorized for potential lncRNA status, yielding a total of 7,646 predicted lncRNA transcripts belonging to 3,287 loci. A regulatory impact factor approach highlighted 92, 55, 35, and 73 lncRNAs in jejunum, liver, muscle, and rumen, respectively. Their ensuing high regulatory impact factor scores indicated a potential regulatory key function in a gene set comprising loci displaying differential expression, tissue specificity and loci overlapping with quantitative trait locus regions for residual feed intake or milk production. These were subjected to a partial correlation and information theory analysis with the prioritized gene set. Results and Conclusions: Independent, significant and group-specific correlations (|r| > 0.8) were used to build a network for the high and the low metabolic efficiency group resulting in 1,522 and 1,732 nodes, respectively. Eight lncRNAs displayed a particularly high connectivity (>100 nodes). Metabolites and genes from the partial correlation and information theory networks, which each correlated significantly with the respective lncRNA, were included in an enrichment analysis indicating distinct affected pathways for the eight lncRNAs. LncRNAs associated with metabolic efficiency were classified to be functionally involved in hepatic amino acid metabolism and protein synthesis and in calcium signaling and neuronal nitric oxide synthase signaling in skeletal muscle cells.
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Affiliation(s)
- Wietje Nolte
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Rosemarie Weikard
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Ronald M Brunner
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Elke Albrecht
- Institute of Muscle Biology and Growth, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Harald M Hammon
- Institute of Nutritional Physiology "Oskar Kellner," Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Antonio Reverter
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture and Food, Queensland Bioscience Precinct, St Lucia, QLD, Australia
| | - Christa Kühn
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany.,Faculty of Agricultural and Environmental Sciences, University Rostock, Rostock, Germany
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Peripolli E, Stafuzza NB, Amorim ST, Lemos MVA, Grigoletto L, Kluska S, Ferraz JBS, Eler JP, Mattos EC, Baldi F. Genome‐wide scan for runs of homozygosity in the composite Montana Tropical
®
beef cattle. J Anim Breed Genet 2019; 137:155-165. [DOI: 10.1111/jbg.12428] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 07/09/2019] [Accepted: 07/11/2019] [Indexed: 12/17/2022]
Affiliation(s)
- Elisa Peripolli
- Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia UNESP Univ Estadual Paulista Júlio de Mesquita Filho Jaboticabal Brazil
| | | | - Sabrina Thaise Amorim
- Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia UNESP Univ Estadual Paulista Júlio de Mesquita Filho Jaboticabal Brazil
| | - Marcos Vinícius Antunes Lemos
- Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia UNESP Univ Estadual Paulista Júlio de Mesquita Filho Jaboticabal Brazil
| | - Laís Grigoletto
- Faculdade de Zootecnia e Engenharia de Alimentos, Departamento de Medicina Veterinária Universidade de São Paulo Pirassununga Brazil
| | - Sabrina Kluska
- Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia UNESP Univ Estadual Paulista Júlio de Mesquita Filho Jaboticabal Brazil
| | - José Bento Sterman Ferraz
- Faculdade de Zootecnia e Engenharia de Alimentos, Departamento de Medicina Veterinária Universidade de São Paulo Pirassununga Brazil
| | - Joanir Pereira Eler
- Faculdade de Zootecnia e Engenharia de Alimentos, Departamento de Medicina Veterinária Universidade de São Paulo Pirassununga Brazil
| | - Elisângela Chicaroni Mattos
- Faculdade de Zootecnia e Engenharia de Alimentos, Departamento de Medicina Veterinária Universidade de São Paulo Pirassununga Brazil
| | - Fernando Baldi
- Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia UNESP Univ Estadual Paulista Júlio de Mesquita Filho Jaboticabal Brazil
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Li Y, Lee YM, Kim YS, Park SP, Kim JJ. Identifying Loci Under Positive Selection in Yellow Korean Cattle (Hanwoo). Evol Bioinform Online 2019; 15:1176934319859001. [PMID: 35210744 PMCID: PMC8862131 DOI: 10.1177/1176934319859001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 05/23/2019] [Indexed: 11/21/2022] Open
Abstract
Jeju Black cattle is one of the aboriginal Korean cattle breeds that has been isolated in Jeju island for a long time, while Yellow Hanwoo cattle has been extensively selected for beef production traits for the last several decades. Aiming to investigate broader patterns of selection, we genotyped 352 Yellow Hanwoo and 169 Jeju Black cattle using a customized 150 K bovine chip. Our composite selection signals’ analysis to identify selection signatures (cross-population extended haplotype homozygosity [XP-EHH], ΔSAF, and FST) identified recent and strong signature of selection near many loci with mutations affecting the traits under strong selection as outlier in Yellow Hanwoo, including SCP2 (P = 8.41 × 10−10) that may be involved in the meat quality. We found nine candidate regions with significant clusters of selection signals, and further bioinformatics analyses of the genes located within these regions revealed mainly genes involved in G-protein coupled receptor signaling pathway (GO:0007186) or olfactory transduction (bta04740), which may be due to adaptation to natural environments in Jeju island. Based on the stronger correlation of Ne10/Ne100 ratio between Yellow Hanwoo (0.61) and Jeju Black (0.66) cattle, our results suggest that the difference of chromosomal regions of selection signature between the 2 cattle breeds was due to a consequence of selection processes to adapt to environmental differences between Jeju island and the main inland, Korean peninsula.
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Affiliation(s)
- Yi Li
- School of Statistics, Shanxi University of Finance and Economics, Taiyuan, China
| | - Yun-Mi Lee
- Department of Biotechnology, Yeungnam University, Gyeongsan, Republic of Korea
| | - You-Sam Kim
- Department of Biotechnology, Yeungnam University, Gyeongsan, Republic of Korea
| | - Se-Pil Park
- Faculty of Biotechnology, Jeju National University, Jeju, Republic of Korea
| | - Jong-Joo Kim
- Department of Biotechnology, Yeungnam University, Gyeongsan, Republic of Korea
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46
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Zhou C, Li C, Cai W, Liu S, Yin H, Shi S, Zhang Q, Zhang S. Genome-Wide Association Study for Milk Protein Composition Traits in a Chinese Holstein Population Using a Single-Step Approach. Front Genet 2019; 10:72. [PMID: 30838020 PMCID: PMC6389681 DOI: 10.3389/fgene.2019.00072] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 01/28/2019] [Indexed: 12/13/2022] Open
Abstract
Genome-wide association studies (GWASs) have been widely used to determine the genetic architecture of quantitative traits in dairy cattle. In this study, with the aim of identifying candidate genes that affect milk protein composition traits, we conducted a GWAS for nine such traits (αs1-casein, αs2-casein, β-casein, κ-casein, α-lactalbumin, β-lactoglobulin, casein index, protein percentage, and protein yield) in 614 Chinese Holstein cows using a single-step strategy. We used the Illumina BovineSNP50 Bead chip and imputed genotypes from high-density single-nucleotide polymorphisms (SNPs) ranging from 50 to 777 K, and subsequent to genotype imputation and quality control, we screened a total of 586,304 informative high-quality SNPs. Phenotypic observations for six major milk proteins (αs1-casein, αs2-casein, β-casein, κ-casein, α-lactalbumin, and β-lactoglobulin) were evaluated as weight proportions of the total protein fraction (wt/wt%) using a commercial enzyme-linked immunosorbent assay kit. Informative windows comprising five adjacent SNPs explaining no < 0.5% of the genomic variance per window were selected for gene annotation and gene network and pathway analyses. Gene network analysis performed using the STRING Genomics 10.0 database revealed a co-expression network comprising 46 interactions among 62 of the most plausible candidate genes. A total of 178 genomic windows and 194 SNPs on 24 bovine autosomes were significantly associated with milk protein composition or protein percentage. Regions affecting milk protein composition traits were mainly observed on chromosomes BTA 1, 6, 11, 13, 14, and 18. Of these, several windows were close to or within the CSN1S1, CSN1S2, CSN2, CSN3, LAP3, DGAT1, RPL8, and HSF1 genes, which have well-known effects on milk protein composition traits of dairy cattle. Taken together with previously reported quantitative trait loci and the biological functions of the identified genes, we propose 19 novel candidate genes affecting milk protein composition traits: ARL6, SST, EHHADH, PCDHB4, PCDHB6, PCDHB7, PCDHB16, SLC36A2, GALNT14, FPGS, LARP4B, IDI1, COG4, FUK, WDR62, CLIP3, SLC25A21, IL5RA, and ACADSB. Our findings provide important insights into milk protein synthesis and indicate potential targets for improving milk quality.
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Affiliation(s)
- Chenghao Zhou
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Cong Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Wentao Cai
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Shuli Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Hongwei Yin
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Shaolei Shi
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Qin Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Shengli Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
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Morton MJL, Awlia M, Al‐Tamimi N, Saade S, Pailles Y, Negrão S, Tester M. Salt stress under the scalpel - dissecting the genetics of salt tolerance. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:148-163. [PMID: 30548719 PMCID: PMC6850516 DOI: 10.1111/tpj.14189] [Citation(s) in RCA: 123] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 11/28/2018] [Accepted: 11/30/2018] [Indexed: 05/08/2023]
Abstract
Salt stress limits the productivity of crops grown under saline conditions, leading to substantial losses of yield in saline soils and under brackish and saline irrigation. Salt tolerant crops could alleviate these losses while both increasing irrigation opportunities and reducing agricultural demands on dwindling freshwater resources. However, despite significant efforts, progress towards this goal has been limited, largely because of the genetic complexity of salt tolerance for agronomically important yield-related traits. Consequently, the focus is shifting to the study of traits that contribute to overall tolerance, thus breaking down salt tolerance into components that are more genetically tractable. Greater consideration of the plasticity of salt tolerance mechanisms throughout development and across environmental conditions furthers this dissection. The demand for more sophisticated and comprehensive methodologies is being met by parallel advances in high-throughput phenotyping and sequencing technologies that are enabling the multivariate characterisation of vast germplasm resources. Alongside steady improvements in statistical genetics models, forward genetics approaches for elucidating salt tolerance mechanisms are gaining momentum. Subsequent quantitative trait locus and gene validation has also become more accessible, most recently through advanced techniques in molecular biology and genomic analysis, facilitating the translation of findings to the field. Besides fuelling the improvement of established crop species, this progress also facilitates the domestication of naturally salt tolerant orphan crops. Taken together, these advances herald a promising era of discovery for research into the genetics of salt tolerance in plants.
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Affiliation(s)
- Mitchell J. L. Morton
- Division of Biological and Environmental Sciences and EngineeringKing Abdullah University of Science and Technology (KAUST)Thuwal23955‐6900Kingdom of Saudi Arabia
| | - Mariam Awlia
- Division of Biological and Environmental Sciences and EngineeringKing Abdullah University of Science and Technology (KAUST)Thuwal23955‐6900Kingdom of Saudi Arabia
| | - Nadia Al‐Tamimi
- Division of Biological and Environmental Sciences and EngineeringKing Abdullah University of Science and Technology (KAUST)Thuwal23955‐6900Kingdom of Saudi Arabia
| | - Stephanie Saade
- Division of Biological and Environmental Sciences and EngineeringKing Abdullah University of Science and Technology (KAUST)Thuwal23955‐6900Kingdom of Saudi Arabia
| | - Yveline Pailles
- Division of Biological and Environmental Sciences and EngineeringKing Abdullah University of Science and Technology (KAUST)Thuwal23955‐6900Kingdom of Saudi Arabia
| | - Sónia Negrão
- Division of Biological and Environmental Sciences and EngineeringKing Abdullah University of Science and Technology (KAUST)Thuwal23955‐6900Kingdom of Saudi Arabia
| | - Mark Tester
- Division of Biological and Environmental Sciences and EngineeringKing Abdullah University of Science and Technology (KAUST)Thuwal23955‐6900Kingdom of Saudi Arabia
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Silva RP, Berton MP, Grigoletto L, Carvalho FE, Silva RMO, Peripolli E, Castro LM, Ferraz JBS, Eler JP, Lôbo RB, Baldi F. Genomic regions and enrichment analyses associated with carcass composition indicator traits in Nellore cattle. J Anim Breed Genet 2018; 136:118-133. [PMID: 30592105 DOI: 10.1111/jbg.12373] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 10/29/2018] [Accepted: 11/17/2018] [Indexed: 12/30/2022]
Abstract
The aim of this study was to estimate genetic parameters and identify genomic regions associated with carcass traits obtained by ultrasound and visual scores in Nellore cattle. Data from ~66,000 animals from the National Association of Breeders and Researchers (ANCP) were used. The variance components for backfat thickness, rump fat thickness and Longissimus muscle area (LMA) were estimated considering a linear model whereas a threshold model for body structure (BS), finishing precocity (FP) and musculature (MS) traits. The SNP solutions were estimated using the ssGBLUP approach by considering windows of 10 consecutive SNPs. Regions that accounted for more than 1.0% of the additive genetic variance were used. Genes identified within the significant windows, such as FOXA3, AP2S1, FKRP, NPASI and ATP6V1G1, were found to be related with MS, while OMA1 and FFGY with BS and FP traits. The PLTP, TNNC2 and GPAT2 genes were found in the regions associated with LMA, as well as TKT, FNDC5 and CHRND can strongly be related with fat deposition. Gene enrichment analysis revealed processes that might be directly influenced the organism growth and development. These results should help to better understand the genetic and physiological mechanisms regulating growth and body composition, muscle tissue development and subcutaneous fat expression, and this information might be useful for future genomic studies in Nellore cattle.
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Affiliation(s)
- Rosiane P Silva
- Departament of Veterinary Medicine, College of Animal Science and Food Engineer, University of São Paulo (USP), Pirassununga, SP, Brazil
| | - Mariana P Berton
- Departament of Animal Science, College of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, SP, Brazil
| | - Laís Grigoletto
- Departament of Veterinary Medicine, College of Animal Science and Food Engineer, University of São Paulo (USP), Pirassununga, SP, Brazil
| | - Felipe E Carvalho
- Departament of Veterinary Medicine, College of Animal Science and Food Engineer, University of São Paulo (USP), Pirassununga, SP, Brazil
| | - Rafael M O Silva
- Zoetis, Edifício Morumbi Corporate, Diamond Tower, São Paulo, SP, Brazil
| | - Elisa Peripolli
- Departament of Animal Science, College of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, SP, Brazil
| | - Letícia M Castro
- Nacional Association of Breeders and Researchers (ANCP), Ribeirão Preto, SP, Brazil
| | - José Bento S Ferraz
- Departament of Veterinary Medicine, College of Animal Science and Food Engineer, University of São Paulo (USP), Pirassununga, SP, Brazil
| | - Joanir P Eler
- Departament of Veterinary Medicine, College of Animal Science and Food Engineer, University of São Paulo (USP), Pirassununga, SP, Brazil
| | - Raysildo B Lôbo
- Nacional Association of Breeders and Researchers (ANCP), Ribeirão Preto, SP, Brazil
| | - Fernando Baldi
- Departament of Veterinary Medicine, College of Animal Science and Food Engineer, University of São Paulo (USP), Pirassununga, SP, Brazil
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Guarini AR, Lourenco DAL, Brito LF, Sargolzaei M, Baes CF, Miglior F, Misztal I, Schenkel FS. Genetics and genomics of reproductive disorders in Canadian Holstein cattle. J Dairy Sci 2018; 102:1341-1353. [PMID: 30471913 DOI: 10.3168/jds.2018-15038] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 09/29/2018] [Indexed: 01/25/2023]
Abstract
In Canada, reproductive disorders known to affect the profitability of dairy cattle herds have been recorded by producers on a voluntary basis since 2007. Previous studies have shown the feasibility of using producer-recorded health data for genetic evaluations. Despite low heritability estimates and limited availability of phenotypic information, sufficient genetic variation has been observed for those traits to indicate that genetic progress, although slow, can be achieved. Pedigree- and genomic-based analyses were performed on producer-recorded health data of reproductive disorders, including retained placenta (RETP), metritis (METR), and cystic ovaries (CYST) using traditional BLUP and single-step genomic BLUP. Genome-wide association studies and functional analyses were carried out to unravel significant genomic regions and biological pathways, and to better understand the genetic mechanisms underlying RETP, METR, and CYST. Heritability estimates (posterior standard deviation in parentheses) were 0.02 (0.003), 0.01 (0.004), and 0.02 (0.003) for CYST, METR, and RETP, respectively. A moderate to strong genetic correlation of 0.69 (0.102) was found between METR and RETP. Averaged over all traits, sire proof reliabilities increased by approximately 11 percentage points with the incorporation of genomic data using a multiple-trait linear model. Biological pathways and associated genes underlying the studied traits were identified and will contribute to a better understanding of the biology of these 3 health disorders in dairy cattle.
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Affiliation(s)
- A R Guarini
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada N1G 2W1
| | - D A L Lourenco
- Department of Animal and Dairy Science, University of Georgia, Athens 30602
| | - L F Brito
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada N1G 2W1
| | - M Sargolzaei
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada N1G 2W1; The Semex Alliance, Guelph, ON, Canada N1H 6J2
| | - C F Baes
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada N1G 2W1
| | - F Miglior
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada N1G 2W1; Canadian Dairy Network, Guelph, ON, Canada N1K 1E5
| | - I Misztal
- Department of Animal and Dairy Science, University of Georgia, Athens 30602
| | - F S Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada N1G 2W1.
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Iung LHDS, Mulder HA, Neves HHDR, Carvalheiro R. Genomic regions underlying uniformity of yearling weight in Nellore cattle evaluated under different response variables. BMC Genomics 2018; 19:619. [PMID: 30115034 PMCID: PMC6097312 DOI: 10.1186/s12864-018-5003-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 08/08/2018] [Indexed: 02/22/2023] Open
Abstract
BACKGROUND In livestock, residual variance has been studied because of the interest to improve uniformity of production. Several studies have provided evidence that residual variance is partially under genetic control; however, few investigations have elucidated genes that control it. The aim of this study was to identify genomic regions associated with within-family residual variance of yearling weight (YW; N = 423) in Nellore bulls with high density SNP data, using different response variables. For this, solutions from double hierarchical generalized linear models (DHGLM) were used to provide the response variables, as follows: a DGHLM assuming non-null genetic correlation between mean and residual variance (rmv ≠ 0) to obtain deregressed EBV for mean (dEBVm) and residual variance (dEBVv); and a DHGLM assuming rmv = 0 to obtain two alternative response variables for residual variance, dEBVv_r0 and log-transformed variance of estimated residuals (ln_[Formula: see text]). RESULTS The dEBVm and dEBVv were highly correlated, resulting in common regions associated with mean and residual variance of YW. However, higher effects on variance than the mean showed that these regions had effects on the variance beyond scale effects. More independent association results between mean and residual variance were obtained when null rmv was assumed. While 13 and 4 single nucleotide polymorphisms (SNPs) showed a strong association (Bayes Factor > 20) with dEBVv and ln_[Formula: see text], respectively, only suggestive signals were found for dEBVv_r0. All overlapping 1-Mb windows among top 20 between dEBVm and dEBVv were previously associated with growth traits. The potential candidate genes for uniformity are involved in metabolism, stress, inflammatory and immune responses, mineralization, neuronal activity and bone formation. CONCLUSIONS It is necessary to use a strategy like assuming null rmv to obtain genomic regions associated with uniformity that are not associated with the mean. Genes involved not only in metabolism, but also stress, inflammatory and immune responses, mineralization, neuronal activity and bone formation were the most promising biological candidates for uniformity of YW. Although no clear evidence of using a specific response variable was found, we recommend consider different response variables to study uniformity to increase evidence on candidate regions and biological mechanisms behind it.
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Affiliation(s)
- Laiza Helena de Souza Iung
- School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp), Via de Acesso Prof. Paulo Donato Castelane, S/N, Vila Industrial, FCAV/UNESP, Jaboticabal, São Paulo, 14884-900 Brazil
| | - Herman Arend Mulder
- Wageningen University & Research Animal Breeding and Genomics, P.O. Box 338, 6700 AH Wageningen, The Netherlands
| | | | - Roberto Carvalheiro
- School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp), Via de Acesso Prof. Paulo Donato Castelane, S/N, Vila Industrial, FCAV/UNESP, Jaboticabal, São Paulo, 14884-900 Brazil
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