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Wang D, Teng J, Ning C, Wang W, Liu S, Zhang Q, Tang H. Mitogenome-wide association study on body measurement traits of Wenshang Barred chickens. Anim Biotechnol 2023; 34:3154-3161. [PMID: 36282276 DOI: 10.1080/10495398.2022.2137035] [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: 11/01/2022]
Abstract
Mitochondria are best known for synthesizing ATP through the tricarboxylic acid cycle and oxidative phosphorylation. The cytoplasmic mitochondrial DNA (mtDNA) is important for maintaining the function. This study was designed to reveal the effect of mtDNA on chicken body measurement traits (BMTs). A population of 605 Wenshang Barred chickens were recorded BMTs, including body slope length, keel length, chest width, etc. The single-nucleotide polymorphisms (SNPs) of their mitogenomes were detected by PCR amplification and DNA sequencing. Totally 69 mutations in mitogenome were discovered, including 18 in noncoding region and 51 in coding region. By multi-sequence alignment and haplotype construction, the chickens were clustered into eight haplotypes and further three haplogroups. The association between BMTs and mtDNA SNPs, haplotypes and haplogroups were analyzed in the linear model by ASReml, respectively. Among them, the SNP mt11086 T/C in ND3 was found to significantly affect chest dept (p < .05) and was highly conservative by phylogenetic conservation analyses, which reflected the genetic effect on body size and growth of chickens. No significant association between the mitochondrial haplotypes or haplogroups and BMTs was found. The polymorphic site reflecting body size could be put into chicken breeding programs as the genetic marker.
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Affiliation(s)
- Dan Wang
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an, China
| | - Jun Teng
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an, China
| | - Chao Ning
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an, China
| | - Wenwen Wang
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an, China
| | - Shuai Liu
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an, China
| | - Qin Zhang
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an, China
| | - Hui Tang
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an, China
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2
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Chen ZH, Xu YX, Xie XL, Wang DF, Aguilar-Gómez D, Liu GJ, Li X, Esmailizadeh A, Rezaei V, Kantanen J, Ammosov I, Nosrati M, Periasamy K, Coltman DW, Lenstra JA, Nielsen R, Li MH. Whole-genome sequence analysis unveils different origins of European and Asiatic mouflon and domestication-related genes in sheep. Commun Biol 2021; 4:1307. [PMID: 34795381 PMCID: PMC8602413 DOI: 10.1038/s42003-021-02817-4] [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: 04/27/2021] [Accepted: 10/27/2021] [Indexed: 02/06/2023] Open
Abstract
The domestication and subsequent development of sheep are crucial events in the history of human civilization and the agricultural revolution. However, the impact of interspecific introgression on the genomic regions under domestication and subsequent selection remains unclear. Here, we analyze the whole genomes of domestic sheep and their wild relative species. We found introgression from wild sheep such as the snow sheep and its American relatives (bighorn and thinhorn sheep) into urial, Asiatic and European mouflons. We observed independent events of adaptive introgression from wild sheep into the Asiatic and European mouflons, as well as shared introgressed regions from both snow sheep and argali into Asiatic mouflon before or during the domestication process. We revealed European mouflons might arise through hybridization events between a now extinct sheep in Europe and feral domesticated sheep around 6000-5000 years BP. We also unveiled later introgressions from wild sheep to their sympatric domestic sheep after domestication. Several of the introgression events contain loci with candidate domestication genes (e.g., PAPPA2, NR6A1, SH3GL3, RFX3 and CAMK4), associated with morphological, immune, reproduction or production traits (wool/meat/milk). We also detected introgression events that introduced genes related to nervous response (NEURL1), neurogenesis (PRUNE2), hearing ability (USH2A), and placental viability (PAG11 and PAG3) into domestic sheep and their ancestral wild species from other wild species.
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Affiliation(s)
- Ze-Hui Chen
- grid.9227.e0000000119573309CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences (UCAS), Beijing, China ,grid.22935.3f0000 0004 0530 8290College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ya-Xi Xu
- grid.22935.3f0000 0004 0530 8290College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xing-Long Xie
- grid.9227.e0000000119573309CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Dong-Feng Wang
- grid.9227.e0000000119573309CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Diana Aguilar-Gómez
- grid.47840.3f0000 0001 2181 7878Center for Computational Biology, University of California at Berkeley, Berkeley, CA 94720 USA
| | | | - Xin Li
- grid.9227.e0000000119573309CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Ali Esmailizadeh
- grid.412503.10000 0000 9826 9569Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Vahideh Rezaei
- grid.412503.10000 0000 9826 9569Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Juha Kantanen
- grid.22642.300000 0004 4668 6757Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | - Innokentyi Ammosov
- grid.495192.2Laboratory of Reindeer Husbandry and Traditional Industries, Yakut Scientific Research Institute of Agriculture, The Sakha Republic (Yakutia), Yakutsk, Russia
| | - Maryam Nosrati
- grid.412462.70000 0000 8810 3346Department of Agriculture, Payame Noor University, Tehran, Iran
| | - Kathiravan Periasamy
- grid.420221.70000 0004 0403 8399Animal Production and Health Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, International Atomic Energy Agency, Vienna, Austria
| | - David W. Coltman
- grid.17089.37Department of Biological Sciences, University of Alberta, Edmonton, AB T6G2E9 Canada
| | - Johannes A. Lenstra
- grid.5477.10000000120346234Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Rasmus Nielsen
- Department of Integrative Biology, University of California at Berkeley, Berkeley, CA, 94720, USA. .,Department of Statistics, UC Berkeley, Berkeley, CA, 94707, USA. .,Globe Institute, University of Copenhagen, 1350, København K, Denmark.
| | - Meng-Hua Li
- College of Animal Science and Technology, China Agricultural University, Beijing, China.
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Gui LS, Raza SHA, Zhou L, Garcia M, Abd El-Aziz AH, Wei D, Hou S, Jia J, Wang Z. Association between Single Nucleotide Polymorphisms in SIRT1 and SIRT2 Loci and Growth in Tibetan Sheep. Animals (Basel) 2020; 10:ani10081362. [PMID: 32781630 PMCID: PMC7459998 DOI: 10.3390/ani10081362] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 08/05/2020] [Indexed: 12/19/2022] Open
Abstract
Simple Summary In summary, three single nucleotide polymorphisms (SNPs) were observed including two SNPs (g.3148 C > T and g.3570 G > A) in SIRT1, and one SNP (g.8074 T > A) in SIRT2 through sequence analysis. Association analyses suggested that all three SNPs were associated growth-related traits in Tibetan sheep. These findings imply that both SIRT1 and SIRT2 may play an important role in growth traits and are potential biomarkers for Marker-assisted selection (MAS). Abstract Silent information regulator 1 and 2 (SIRT1, 2) were NAD+-dependent histone or non-histone deacetylase, which emerged as key metabolic sensors in several tissues of mammals. In the present study, the search for polymorphisms within the ovine SIRT1 and SIRT2 loci as well as association analyses between SNPs and growth-related traits were performed in Tibetan sheep. To determine the expression pattern of SIRT1 and SIRT2 genes in Tibetan sheep, the quantitative real-time polymerase chain reaction (qPCR) analysis revealed that those two genes were widely expressed in diverse tissues. Expression of SIRT1 was less in abomasum of lamb, whereas it was greater in duodenum within adult stage. In the case of SIRT2, the greatest expression was observed in reticulum (lamb) and in muscle (adult), whereas the least expression was in liver for lamb and in kidney for adult animals. The association analysis demonstrated that g.3148 C > T polymorphism of SIRT1 affected heart girth (p = 0.002). The g.8074 T > A SNP of SIRT2 had a significant correlation with body weight (p = 0.011) and body length (p = 0.008). These findings suggested that the SIRT1 and SIRT2 polymorphism was involved in growth-related traits in Tibetan sheep, which may be considered to be genetic markers for improving the growth traits of Tibetan sheep.
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Affiliation(s)
- Lin-sheng Gui
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, Qinghai, China; (L.-s.G.); (L.Z.); (S.H.); (J.J.)
| | - Sayed Haidar Abbas Raza
- National Beef Cattle Improvement Center, Northwest A&F University, Yangling 712100, Shaanxi, China;
| | - Li Zhou
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, Qinghai, China; (L.-s.G.); (L.Z.); (S.H.); (J.J.)
| | - Matthew Garcia
- School of Animal Dairy and Veterinary Sciences, Utah State University, Logan, UT 84322, USA;
| | - Ayman Hassan Abd El-Aziz
- Animal Husbandry and Animal Wealth Development Department, Faculty of Veterinary Medicine, Damanhour University, Damanhour 22511, Egypt;
| | - Dawei Wei
- School of Agriculture, Ningxia University, Yinchuan 750021, China;
| | - Shengzhen Hou
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, Qinghai, China; (L.-s.G.); (L.Z.); (S.H.); (J.J.)
| | - Jianlei Jia
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, Qinghai, China; (L.-s.G.); (L.Z.); (S.H.); (J.J.)
| | - Zhiyou Wang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, Qinghai, China; (L.-s.G.); (L.Z.); (S.H.); (J.J.)
- Correspondence:
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4
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MALDI-TOF-MS-based high throughput genotyping of mutations associated with body measurement traits in cattle. Mamm Genome 2020; 31:228-239. [PMID: 32385542 DOI: 10.1007/s00335-020-09840-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 04/22/2020] [Indexed: 10/24/2022]
Abstract
Exploration of genes in relation to body measurement traits through large-scaled mutation identification is highly conductive for the genomics-assisted breeding of superior productivity cattle. In this investigation, 31 objective mutations were genotyped synchronously in 384 yellow cattle of 8 breeds through the application of optimized MALDI-TOF-MS and multiplex PCR techniques. High genotyping rate was obtained as well as greatly decreased cost which was below one thirtieth of the routine analysis. Results from genotyping revealed 23 mutations as valid mutations in the studied cattle population with gene heterozygosity and effective allele number varying from 0.0052 to 0.4998 and 1.0052 to 1.9991, respectively. Among the 23 effective mutations, 12 was classified as moderate polymorphism (0.25 < PIC < 0.5) while the other 11 belonged to low polymorphism (PIC < 0.25), 7 mutations did not obey the HW equilibrium (p < 0.05) and linkage mainly appeared between mutations of UCP2 and PTHR1 genes. Furthermore, 8 body measurement traits in the 384 cattle were recorded to validate their association with tag mutations, and significant correlations were found in 12 mutations of 9 genes including PTHR1, CDK6, IHH, HHIP, GHRL, COL1A1, INS, GDF5 and UCP2, of which, PTHR1 was proved to be the most potential contributor to bone modeling in cattle. Results highlight the potential application value of 12 novel mutations in enhancing cattle production traits as well as the high genotyping rate achieved by MALDI-TOF-MS coupled with multiplex PCR technique.
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5
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Wang S, Zhao H, Wu M, Yi X, Chen P, Liu S, Pan Y, Li Q, Tang X, Sun X. Exploring of InDel in bovine PSAP gene and their association with growth traits in different development stages. Anim Biotechnol 2020; 33:1-12. [PMID: 32367774 DOI: 10.1080/10495398.2020.1758122] [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] [Indexed: 12/12/2022]
Abstract
PSAP (prosaposin) is widely expressed in different organs, and plays an important role in fat deposit. Insertion/Deletion (InDel) is a relatively simple and effective DNA marker. However, the association of molecular marker at different stages of animal development has not received enough attention, especially fat deposition related traits. Therefore, eight cattle breeds were used to explore novel InDels variants within bovine PSAP gene, and to evaluate their effects on growth traits in different development stages. Herein, two novel InDels (P5:NC037355.1g.27974439-27974440 ins AGTGTGGTTAATGTCAAC and P8:NC037355.1g.27980734-27980752 del GTCAAAAAATCAGGGGAAAC) within the bovine PSAP gene were found, and their association with growth traits in different development stages were analyzed. Interestingly, the dominant genotype was different in different development stages both in NY cattle and JX cattle for daily gain and body weight. PSAP Gene expression patterns were analyzed in this study, high expression in the middle stage of adipocytes differentiation suggests that it plays a certain role in fat development. It reveals that InDels could affect phenotype in different development stages, which depend on the expression pattern of the host gene and their function in different tissues. These findings could provide a new way for molecular marker studies in bovine breeding and genetics.
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Affiliation(s)
- Shuhui Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Haidong Zhao
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Mingli Wu
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xiaohua Yi
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Pingbo Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Shirong Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yun Pan
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Qi Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xiaoqin Tang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xiuzhu Sun
- College of Animal Science and Technology, Northwest A&F University, Yangling, China.,College of Grassland Agriculture, Northwest A&F University, Yangling, China
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6
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Gao J, Song X, Wu H, Tang Q, Wei Z, Wang X, Lan X, Zhang B. Detection of rs665862918 (15-bp Indel) of the HIAT1 Gene and its Strong Genetic Effects on Growth Traits in Goats. Animals (Basel) 2020; 10:ani10020358. [PMID: 32102183 PMCID: PMC7070599 DOI: 10.3390/ani10020358] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 02/15/2020] [Accepted: 02/17/2020] [Indexed: 12/14/2022] Open
Abstract
Simple Summary Growth traits are important in goats and can affect their body size and meat production. In this study, the hippocampus abundant transcript 1 (HIAT1) gene, which has been reported as a meat-associated trait in elite goat breeds and a dairy-associated trait in water buffalo, was chosen to detect its correlation with growth traits in goats. The results show that the rs665862918 polymorphism (a 15 bp insertion) in HIAT1 is associated with body length, chest width, chest depth, height at hip cross and heart girth in Shaanbei white cashmere goats (SBWC, n = 1013). Our results reveal that rs665862918 in HIAT1 is relevant to the growth traits of goats and could be used for marker-assisted selection (MAS) as a molecular marker in goat populations. Abstract The hippocampus abundant transcript 1 (HIAT1) gene, which was detected by the genome-wide identification of selective sweeps among elite goat breeds and water buffalo, is proposed to play an important role in meat characteristics. Four indels of the HIAT1 gene selected from the NCBI and Ensembl databases were detected via a pooling and sequencing strategy. A 15 bp insertion (rs665862918) in the first intron of HIAT1 was selected and classified on an electrophoresis platform in the Shaanbei white cashmere goat (SBWC) population. The correlation analysis revealed that rs665862918 is significantly highly associated with chest width (p = 1.57 × 10−5), chest depth (p = 8.85 × 10−5), heart girth (p = 1.05 × 10−7), body length (p = 0.022), and height at hip cross (p = 0.023) in the SBWC population (n = 1013). Further analysis revealed that individuals with a genotype insertion/insertion (II) of the rs665862918 locus exhibited better growth trait performance than individuals with an insertion/deletion (ID) or deletion/deletion (DD). These findings verify that HIAT1 affects the body size of goats and that rs665862918 could be a potential molecular marker for growth traits in goat breeding.
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Affiliation(s)
- Jiayang Gao
- College of Medicine & Forensic, Health Science Center, Xi’an Jiaotong University, Xi’an 710061, Shaanxi, China;
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science, Northwest A&F University, Yangling 712100, Shaanxi, China; (H.W.); (Q.T.); (Z.W.); (X.W.)
| | - Xiaoyue Song
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin 719000, Shaanxi, China;
- Life Science Research Center, Yulin University, Yulin 719000, Shaanxi, China
| | - Hui Wu
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science, Northwest A&F University, Yangling 712100, Shaanxi, China; (H.W.); (Q.T.); (Z.W.); (X.W.)
| | - Qi Tang
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science, Northwest A&F University, Yangling 712100, Shaanxi, China; (H.W.); (Q.T.); (Z.W.); (X.W.)
| | - Zhenyu Wei
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science, Northwest A&F University, Yangling 712100, Shaanxi, China; (H.W.); (Q.T.); (Z.W.); (X.W.)
| | - Xinyu Wang
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science, Northwest A&F University, Yangling 712100, Shaanxi, China; (H.W.); (Q.T.); (Z.W.); (X.W.)
| | - Xianyong Lan
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science, Northwest A&F University, Yangling 712100, Shaanxi, China; (H.W.); (Q.T.); (Z.W.); (X.W.)
- Correspondence: (X.L.); (B.Z.)
| | - Bao Zhang
- College of Medicine & Forensic, Health Science Center, Xi’an Jiaotong University, Xi’an 710061, Shaanxi, China;
- Correspondence: (X.L.); (B.Z.)
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7
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Association of a new 99-bp indel of the CEL gene promoter region with phenotypic traits in chickens. Sci Rep 2020; 10:3215. [PMID: 32081917 PMCID: PMC7035288 DOI: 10.1038/s41598-020-60168-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 02/04/2020] [Indexed: 02/08/2023] Open
Abstract
Carboxyl ester lipase (CEL) encodes a cholesterol ester hydrolase that is secreted into the duodenum as a component of pancreatic juice. The objective of this study was to characterize the CEL gene, investigate the association between the CEL promoter variants and chicken phenotypic traits, and explore the CEL gene regulatory mechanism. An insertion/deletion (indel) caused by a 99-bp insertion fragment was shown for the first time in the chicken CEL promoter, and large differences in allelic frequency were found among commercial breeds, indigenous and feral birds. Association analysis demonstrated that this indel site had significant effects on shank length, shank girth, chest breadth at 8 weeks (p < 0.01), evisceration weight, sebum weight, breast muscle weight, and leg weight (p < 0.05). Tissue expression profiles showed extremely high levels of the CEL gene in pancreatic tissue. Moreover, the expression levels of the genes APOB, MTTP, APOV1 and SREBF1, which are involved in lipid transport, were significantly reduced by adding a 4% oxidized soybean oil diet treatment at the individual level and transfecting the embryonic primary hepatocytes with a CEL-overexpression vector. Interestingly, the results showed that the expression level of the II homozygous genotype was significantly higher than that of the ID and DD genotypes, while individuals with DD genotypes had higher phenotypic values. Therefore, these data suggested that the CEL gene might affect body growth by participating in hepatic lipoprotein metabolism and that the 99-bp indel polymorphism could be a potentially useful genetic marker for improving the economically important traits of chickens.
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8
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Tang Q, Zhang X, Wang X, Wang K, Yan H, Zhu H, Lan X, Lei Q, Pan C. Detection of two insertion/deletions (indels) within the ADAMTS9 gene and their associations with growth traits in goat. Small Rumin Res 2019. [DOI: 10.1016/j.smallrumres.2019.09.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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9
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Peng K, Zhang GL, Yu T, Cao Y, Yu YS, Chen H, Lei CZ, Lan XY, Zhao YM. Detection of InDel variations within seven candidate genes and their associations with phenotypic traits in three cattle breeds. Anim Biotechnol 2019; 31:463-471. [PMID: 31159648 DOI: 10.1080/10495398.2019.1620258] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The Xinjiang brown cattle, Red steppe cattle, and Yunling cattle are indigenous cultivated cattle breeds in Chinese frontier provinces, and they produce high-grade beef and milk products, however, their genetic diversity in many important genes related to excellent meat and milk production is still unknown. Our previous studies have found that several candidate genes (e.g., SREBP1c and PAX7) were associated with bovine economically important phenotypic traits, but none has been reported in the above-mentioned three cattle breeds. Since the InDel (insertion/deletion) marker becomes a useful tool applied in the animal molecular breeding, herein, we firstly found that the InDel variations of seven candidate genes in these cattle. Results showed that the genotypic and allelic distributions of these seven genes were remarkably different among these three cattle (p < 0.05 or p < 0.01). Furthermore, the InDel variations of SREBP1c and PAX7 genes were significantly associated with eight phenotypic traits in Xinjiang brown cattle (p < 0.05 or p < 0.01), respectively, suggesting that they can become the useful DNA markers.
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Affiliation(s)
- Kun Peng
- Branch of Animal Husbandry, Jilin Academy of Agricultural Sciences, Changchun, Jilin, P.R. China.,Key Laboratory of Beef Cattle Genetics and Breeding in Ministry of Agriculture and Rural Agriculture, Changchun, Jilin, P.R. China.,College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, P.R. China
| | - Guo-Liang Zhang
- Branch of Animal Husbandry, Jilin Academy of Agricultural Sciences, Changchun, Jilin, P.R. China.,Key Laboratory of Beef Cattle Genetics and Breeding in Ministry of Agriculture and Rural Agriculture, Changchun, Jilin, P.R. China
| | - Ting Yu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, P.R. China
| | - Yang Cao
- Branch of Animal Husbandry, Jilin Academy of Agricultural Sciences, Changchun, Jilin, P.R. China.,Key Laboratory of Beef Cattle Genetics and Breeding in Ministry of Agriculture and Rural Agriculture, Changchun, Jilin, P.R. China
| | - Yong-Sheng Yu
- Branch of Animal Husbandry, Jilin Academy of Agricultural Sciences, Changchun, Jilin, P.R. China.,Key Laboratory of Beef Cattle Genetics and Breeding in Ministry of Agriculture and Rural Agriculture, Changchun, Jilin, P.R. China
| | - Hong Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, P.R. China
| | - Chu-Zhao Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, P.R. China
| | - Xian-Yong Lan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, P.R. China
| | - Yu-Min Zhao
- Branch of Animal Husbandry, Jilin Academy of Agricultural Sciences, Changchun, Jilin, P.R. China.,Key Laboratory of Beef Cattle Genetics and Breeding in Ministry of Agriculture and Rural Agriculture, Changchun, Jilin, P.R. China
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10
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Liu X, Ma L, Wang M, Wang K, Li J, Yan H, Zhu H, Lan X. Two indel variants of prolactin receptor ( PRLR) gene are associated with growth traits in goat. Anim Biotechnol 2019; 31:314-323. [PMID: 30987502 DOI: 10.1080/10495398.2019.1594863] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Prolactin receptor (PRLR) gene plays a crucial role in the milk production, reproduction and the growth of mammals. To fully characterize the structure of the mutation and to further study the function of the goat PRLR gene, two insertion/deletion (indel) loci (12 bp; 16-bp; 5-bp) were detected in 1038 Shaanbei white cashmere (SBWC) goats. Associated analysis revealed that the 16-bp indel mutation was significantly associated the body length, body height, chest depth (CD), body length index (BLI), heart girth index and cannon circumference index (CCI) (p < 0.05). The polymorphism of 5-bp indel was significantly associated with CD, heart girth, CCI and BLI (p < 0.05). Overall, individuals with genotype DD showed better phenotypic traits than individuals with other genotypes at the two loci of PRLR gene in SBWC goat. These findings suggested that the two novel indels within the caprine PRLR gene could be considered as effective DNA molecular markers and could provide a valuable theoretical basis for the application of marker-assisted selection in the goat industry.
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Affiliation(s)
- Xinfeng Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Lin Ma
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Min Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Ke Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Jie Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Hailong Yan
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin, Shaanxi, People's Republic of China.,Life Science Research Center, Yulin University, Yulin, Shaanxi, People's Republic of China
| | - Haijing Zhu
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin, Shaanxi, People's Republic of China.,Life Science Research Center, Yulin University, Yulin, Shaanxi, People's Republic of China
| | - Xianyong Lan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
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Zhang Q, Jin Y, Jiang F, Cheng H, Wang Y, Lan X, Song E. Relationship between an indel mutation within the SIRT4 gene and growth traits in Chinese cattle. Anim Biotechnol 2019; 30:352-357. [DOI: 10.1080/10495398.2018.1520716] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Qingfeng Zhang
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, Shandong, China
- Shandong Key Laboratory of Animal Disease control and Breeding, Jinan, Shandong, China
| | - Yunyun Jin
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Fugui Jiang
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, Shandong, China
- Shandong Key Laboratory of Animal Disease control and Breeding, Jinan, Shandong, China
| | - Haijian Cheng
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, Shandong, China
- Shandong Key Laboratory of Animal Disease control and Breeding, Jinan, Shandong, China
| | - Yafang Wang
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, Shandong, China
- College of Life Sciences, Shandong Normal University, Jinan, Shandong, China
| | - Xianyong Lan
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Enliang Song
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, Shandong, China
- Shandong Key Laboratory of Animal Disease control and Breeding, Jinan, Shandong, China
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12
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Wang K, Cui Y, Wang Z, Yan H, Meng Z, Zhu H, Qu L, Lan X, Pan C. One 16 bp insertion/deletion (indel) within the KDM6A gene revealing strong associations with growth traits in goat. Gene 2018; 686:16-20. [PMID: 30408547 DOI: 10.1016/j.gene.2018.11.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 10/31/2018] [Accepted: 11/03/2018] [Indexed: 01/02/2023]
Abstract
Lysine demethylase 6A (KDM6A), as a candidate gene associated with skeletal dysplasia and the differentiation of osteogenesis, might affect the growth traits in animals. In the previous study (Cui et al., 2018), one 16 bp intronic insertion/deletion (NW_017189516.1: g.138, 431_138,446delAATGTATAGCTTAAAA) within the KDM6A gene significantly influenced KDM6A gene expression. The objective of this work was to investigate the association between this 16 bp indel and growth-related traits in Shaanbei White Cashmere goat (SWCG). Association analyses showed the 16 bp indel was related to growth traits strongly (body height, chest depth, height across the hip, body length and chest circumference) in SWCG population (n = 1953, P < 0.05). Insertion/insertion (II) genotype individuals (n = 1502) had the best growth traits, by comparison of those of insertion/deletion (ID) (n = 410) and the deletion/deletion (DD) genotypes (n = 41). Particularly, the body weight of II genotype individuals were significantly higher than ID and DD genotypes (P < 0.01). Besides, the remarkable influence of this indel on traits might cause by the change of MEF2 binding site. These findings hinted that the 16 bp deletion mutation in KDM6A gene, which was significantly associated with growth-related traits, could be assigned to an effective molecular marker for growth traits in goat breeding.
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Affiliation(s)
- Ke Wang
- College of Animal Science and Technology, Northwest A&F University, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Yangling, Shaanxi, China
| | - Yang Cui
- College of Animal Science and Technology, Northwest A&F University, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Yangling, Shaanxi, China
| | - Zhen Wang
- College of Animal Science and Technology, Northwest A&F University, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Yangling, Shaanxi, China
| | - Hailong Yan
- College of Animal Science and Technology, Northwest A&F University, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Yangling, Shaanxi, China; Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin, China; Life Science Research Center, Yulin University, Yulin, China
| | - Zhe Meng
- College of Animal Science and Technology, Northwest A&F University, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Yangling, Shaanxi, China
| | - Haijing Zhu
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin, China; Life Science Research Center, Yulin University, Yulin, China
| | - Lei Qu
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin, China; Life Science Research Center, Yulin University, Yulin, China
| | - Xianyong Lan
- College of Animal Science and Technology, Northwest A&F University, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Yangling, Shaanxi, China
| | - Chuanying Pan
- College of Animal Science and Technology, Northwest A&F University, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Yangling, Shaanxi, China.
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