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Priyo TW, Edo A, Taura Y, Yamato O, Ono T, Taniguchi M, Widodo OS, Islam MS, Maki S, Takagi M. Novel Approach for Evaluating Pregnancy-Associated Glycoprotein and Inflammation Markers during the Postpartum Period in Holstein Friesian Cows. Animals (Basel) 2024; 14:1459. [PMID: 38791678 PMCID: PMC11117242 DOI: 10.3390/ani14101459] [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: 04/08/2024] [Revised: 05/08/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024] Open
Abstract
We evaluated the relationship between decreased pregnancy-associated glycoprotein (PAG) levels, inflammatory parameters (serum amyloid A [SAA] and milk amyloid A [MAA]), postpartum inflammatory conditions (mastitis, ketosis, and follicular cysts), and the FOXP3 gene. Nineteen Holstein-Friesian cows were included in this study. Up to approximately eight weeks after delivery, weekly health examinations were performed for mastitis and ketosis, and reproductive organ ultrasonography was performed. The decreasing PAG rate was negatively correlated with SAA concentration (r = -0.493, p = 0.032). Cows with mastitis exhibited a slower trend of PAG decrease (p = 0.095), and a greater percentage of these cows had MAA concentrations above 12 µg/mL (p = 0.074) compared with those without mastitis. A negative correlation, although nonsignificant (r = -0.263, p = 0.385), was observed between the day-open period and decreased PAG rate. The day-open period was correlated with the presence or absence of follicular cysts (p = 0.046). Four cows that developed follicular cysts were homozygous for the G allele of the FOXP3 gene related to repeat breeders. These results indicate a relationship between a decreased PAG rate and inflammatory status during the postpartum period. Thus, suppressing inflammation during the perinatal period may improve reproductive efficiency in the dairy industry.
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Affiliation(s)
- Topas Wicaksono Priyo
- Joint Graduate School of Veterinary Science, Yamaguchi University, Yamaguchi 753-8515, Japan; (T.W.P.J.); (M.T.); (O.S.W.)
- Department of Reproduction and Obstetrics, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia
| | - Ayane Edo
- Joint Faculty of Veterinary Science, Yamaguchi University, Yamaguchi 753-8515, Japan; (A.E.); (Y.T.); (T.O.)
| | - Yasuho Taura
- Joint Faculty of Veterinary Science, Yamaguchi University, Yamaguchi 753-8515, Japan; (A.E.); (Y.T.); (T.O.)
| | - Osamu Yamato
- Joint Faculty of Veterinary Science, Kagoshima University, Kagoshima 890-0065, Japan; (O.Y.); (M.S.I.); (S.M.)
- Division of Animal Husbandry, Faculty of Veterinary Medicine, Universitas Airlangga, Surabaya 60115, Indonesia
| | - Tetsushi Ono
- Joint Faculty of Veterinary Science, Yamaguchi University, Yamaguchi 753-8515, Japan; (A.E.); (Y.T.); (T.O.)
| | - Masayasu Taniguchi
- Joint Graduate School of Veterinary Science, Yamaguchi University, Yamaguchi 753-8515, Japan; (T.W.P.J.); (M.T.); (O.S.W.)
- Joint Faculty of Veterinary Science, Yamaguchi University, Yamaguchi 753-8515, Japan; (A.E.); (Y.T.); (T.O.)
| | - Oky Setyo Widodo
- Joint Graduate School of Veterinary Science, Yamaguchi University, Yamaguchi 753-8515, Japan; (T.W.P.J.); (M.T.); (O.S.W.)
- Division of Animal Husbandry, Faculty of Veterinary Medicine, Universitas Airlangga, Surabaya 60115, Indonesia
| | - Md Shafiqul Islam
- Joint Faculty of Veterinary Science, Kagoshima University, Kagoshima 890-0065, Japan; (O.Y.); (M.S.I.); (S.M.)
| | - Shinichiro Maki
- Joint Faculty of Veterinary Science, Kagoshima University, Kagoshima 890-0065, Japan; (O.Y.); (M.S.I.); (S.M.)
| | - Mitsuhiro Takagi
- Joint Graduate School of Veterinary Science, Yamaguchi University, Yamaguchi 753-8515, Japan; (T.W.P.J.); (M.T.); (O.S.W.)
- Joint Faculty of Veterinary Science, Yamaguchi University, Yamaguchi 753-8515, Japan; (A.E.); (Y.T.); (T.O.)
- Division of Animal Husbandry, Faculty of Veterinary Medicine, Universitas Airlangga, Surabaya 60115, Indonesia
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Trebes H, Wang Y, Reynolds E, Tiplady K, Harland C, Lopdell T, Johnson T, Davis S, Harris B, Spelman R, Couldrey C. Identification of candidate novel production variants on the Bos taurus chromosome X. J Dairy Sci 2023; 106:7799-7815. [PMID: 37562645 DOI: 10.3168/jds.2022-23095] [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: 12/01/2022] [Accepted: 04/26/2023] [Indexed: 08/12/2023]
Abstract
Chromosome X is often excluded from bovine genetic studies due to complications caused by the sex specific nature of the chromosome. As chromosome X is the second largest cattle chromosome and makes up approximately 6% of the female genome, finding ways to include chromosome X in dairy genetic studies is important. Using female animals and treating chromosome X as an autosome, we performed X chromosome inclusive genome-wide association studies in the selective breeding environment of the New Zealand dairy industry, aiming to identify chromosome X variants associated with milk production traits. We report on the findings of these genome-wide association studies and their potential effect within the dairy industry. We identify missense mutations in the MOSPD1 and CCDC160 genes that are associated with decreased milk volume and protein production and increased fat production. Both of these mutations are exonic SNP that are more prevalent in the Jersey breed than in Holstein-Friesians. Of the 2 candidates proposed it is likely that only one is causal, though we have not been able to identify which is more likely.
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Affiliation(s)
- H Trebes
- Research and Development, Livestock Improvement Corporation, Hamilton 3240, New Zealand.
| | - Y Wang
- Research and Development, Livestock Improvement Corporation, Hamilton 3240, New Zealand
| | - E Reynolds
- Research and Development, Livestock Improvement Corporation, Hamilton 3240, New Zealand
| | - K Tiplady
- Research and Development, Livestock Improvement Corporation, Hamilton 3240, New Zealand
| | - C Harland
- Research and Development, Livestock Improvement Corporation, Hamilton 3240, New Zealand
| | - T Lopdell
- Research and Development, Livestock Improvement Corporation, Hamilton 3240, New Zealand
| | - T Johnson
- Research and Development, Livestock Improvement Corporation, Hamilton 3240, New Zealand
| | - S Davis
- Research and Development, Livestock Improvement Corporation, Hamilton 3240, New Zealand
| | - B Harris
- Research and Development, Livestock Improvement Corporation, Hamilton 3240, New Zealand
| | - R Spelman
- Research and Development, Livestock Improvement Corporation, Hamilton 3240, New Zealand
| | - C Couldrey
- Research and Development, Livestock Improvement Corporation, Hamilton 3240, New Zealand
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3
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Kinukawa M, Ito M, Uemoto Y, Ogino A, Haruta S, Kurogi K, Watanabe T, Sasaki S, Naniwa Y, Uchiyama K, Togashi K. A potent allele marker related to low bull conception rate in Japanese Black bulls. Animal 2023; 17:100804. [PMID: 37141635 DOI: 10.1016/j.animal.2023.100804] [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: 11/28/2022] [Revised: 03/24/2023] [Accepted: 03/31/2023] [Indexed: 05/06/2023] Open
Abstract
Over the years, there has been considerable variation in the bull conception rate (BCR) of Japanese Black cattle; moreover, several Japanese Black bulls with a low BCR of ≤10% have been identified. However, the alleles responsible for the low BCR are not determined yet. Therefore, in this study, we aimed to identify single-nucleotide polymorphisms (SNPs) for predicting low BCR. To this end, the genome of Japanese Black bulls was comprehensively examined by a genome-wide association study with whole-exome sequencing (WES), and the effect of the identified marker regions on BCR was determined. The WES analysis of six sub-fertile bulls with a BCR of ≤10% and 73 normal bulls with a BCR of ≥40% identified a homozygous genotype for low BCR in Bos taurus autosome 5 in the region between 116.2 and 117.9 Mb. The g.116408653G > A SNP in this region had the most significant effect on the BCR (P-value = 1.0 × 10-23), and the GG (55.4 ± 11.2%) and AG (54.4 ± 9.4%) genotypes in the SNP had a higher phenotype than the AA (9.5 ± 6.1%) genotype for the BCR. The mixed model analysis revealed that g.116408653G > A was related to approximately 43% of the total genetic variance. In conclusion, the AA genotype of g.116408653G > A is a useful index for identifying sub-fertile Japanese Black bulls. Some positive and negative effects of SNP on the BCR were presumed to identify the causative mutations, which can help evaluate bull fertility.
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Affiliation(s)
- M Kinukawa
- Livestock Improvement Association of Japan, Inc., 316 Kanamaru, Maebashi, Gunma 371-0121, Japan.
| | - M Ito
- Department of Virology and Parasitology, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka 431-3192, Japan
| | - Y Uemoto
- Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi 980-8572, Japan
| | - A Ogino
- Livestock Improvement Association of Japan, Inc., 316 Kanamaru, Maebashi, Gunma 371-0121, Japan
| | - S Haruta
- Livestock Improvement Association of Japan, Inc., 316 Kanamaru, Maebashi, Gunma 371-0121, Japan
| | - K Kurogi
- Livestock Improvement Association of Japan, Inc., 316 Kanamaru, Maebashi, Gunma 371-0121, Japan
| | - T Watanabe
- Livestock Improvement Association of Japan, Inc., 316 Kanamaru, Maebashi, Gunma 371-0121, Japan
| | - S Sasaki
- Faculty of Agriculture, University of the Ryukyus, Nishihara, Okinawa 903-0213, Japan
| | - Y Naniwa
- Livestock Improvement Association of Japan, Inc., 316 Kanamaru, Maebashi, Gunma 371-0121, Japan
| | - K Uchiyama
- Livestock Improvement Association of Japan, Inc., 316 Kanamaru, Maebashi, Gunma 371-0121, Japan
| | - K Togashi
- Livestock Improvement Association of Japan, Inc., 316 Kanamaru, Maebashi, Gunma 371-0121, Japan
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Chaikol W, Yadmak C, Yama P, Jitjumnong J, Sangkate M, U-Krit W, Promsao N, Suriard A, Mektrirat R, Panatuk J, Van Doan H, Wang CK, Tang PC, Moonmanee T. Ovarian luteal category at the time of exogenous progesterone treatment alters pre-ovulatory follicle size and pregnancy outcome but not initial GnRH treatment in repeat-breeder crossbred dairy heifers submitted to the 7-day fixed-time AI protocol. Vet Anim Sci 2022; 17:100257. [PMID: 35812775 PMCID: PMC9256640 DOI: 10.1016/j.vas.2022.100257] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 06/04/2022] [Accepted: 06/17/2022] [Indexed: 11/25/2022] Open
Abstract
Ovarian and fertility outcomes were similar for repeat-breeder crossbred dairy heifers with or without initial GnRH treatment. Presence of luteal tissue at the time of progesterone (P4) treatment in infertile heifers resulted in a 68.6% pregnancy rate (PR). The likelihood of PR was higher in infertile heifers bearing luteal tissue on the day of exogenous P4 trigger.
Repeat breeding is a substantial problem in heifer and cow breeding leading to greater infertility for female dairy herds. The aim of present study was to investigate the impact of corpus luteum (CL) presence and category and the first gonadotropin-releasing hormone (GnRH) administration concurrent with exogenous progesterone (P4) treatment on the largest follicle (LF) size and pregnancy rate (PR) in repeat-breeder crossbred dairy heifers submitted to the fixed-time artificial insemination (AI) protocol. Heifers (n= 243) were synchronised with (+GnRH) or without (–GnRH) first GnRH in the 7-day P4-GnRH-prostaglandin F2α-based programme. Each GnRH group was divided on presence of CL into two groups (+CL and –CL) in a 2 × 2 factorial arrangement. The PR was similar among –GnRH–CL (20.7%), –GnRH+CL (68.8%), +GnRH–CL (30.4%), and +GnRH+CL (68.3%) groups. However, presence of CL in heifers produced a 43.6% increase in PR compared to PR of heifers without CL (odds ratio = 6.550). Heifers bearing large-sized CL had greater large-sized LF on the day of fixed-time AI and PR. Plasma P4 concentration was positively related with CL diameter (r= 0.845; p < 0.001). The diameter of ovarian LF on the day of fixed-time AI was positively associated with P4 concentrations (r= 0.512; p < 0.001). We highlight that ovarian CL presence and category at the time of exogenous P4 treatment alters pre-ovulatory follicle size and PR but not initial GnRH treatment in repeat-breeder crossbred dairy heifers submitted to service with the 7-day fixed-time AI programme.
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Affiliation(s)
- Warunya Chaikol
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Thailand
| | | | - Punnawut Yama
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Thailand
| | - Jakree Jitjumnong
- Department of Animal Science, National Chung Hsing University, Taiwan
| | - Molarat Sangkate
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Thailand
| | - Warittha U-Krit
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Thailand.,Sing Buri College of Agriculture and Technology, Thailand
| | - Nalinthip Promsao
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Thailand
| | - Assawadet Suriard
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Thailand
| | - Raktham Mektrirat
- Department of Veterinary Biosciences and Public Health, Faculty of Veterinary Medicine, Chiang Mai University, Thailand
| | - Julakorn Panatuk
- Faculty of Animal Science and Technology, Maejo University, Thailand
| | - Hien Van Doan
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Thailand.,Innovative Agriculture Research Center, Faculty of Agriculture, Chiang Mai University, Thailand
| | - Chien-Kai Wang
- Department of Animal Science, National Chung Hsing University, Taiwan.,The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taiwan
| | - Pin-Chi Tang
- Department of Animal Science, National Chung Hsing University, Taiwan.,The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taiwan
| | - Tossapol Moonmanee
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Thailand.,Innovative Agriculture Research Center, Faculty of Agriculture, Chiang Mai University, Thailand
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5
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Islam MS, Takagi M, Lee KW, Chang HS, Okawa H, Yunus M, Lestari TD, Tacharina MR, Pervin S, Rakib TM, Yabuki A, Yamato O. Frequency of an X-Linked Maternal Variant of the Bovine FOXP3 Gene Associated with Infertility in Different Cattle Breeds: A Pilot Study. Animals (Basel) 2022; 12:1044. [PMID: 35454290 PMCID: PMC9030747 DOI: 10.3390/ani12081044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/11/2022] [Accepted: 04/14/2022] [Indexed: 11/16/2022] Open
Abstract
Immune adaptation plays an essential role in determining pregnancy, which has been shown to be dependent on sufficient immunological tolerance mediated by FOXP3+ regulatory T cells. Recently, an X-linked maternal single-nucleotide polymorphism (SNP), located 2175 base pairs upstream of the start codon in the bovine FOXP3 gene (NC_037357.1: g.87298881A>G, rs135720414), was identified in Japanese Black (JB: Bos taurus) cows in association with recurrent infertility. However, with the exception of JB cows, the frequency of this SNP has yet to be studied in other cow populations. In this study, we thus aimed to evaluate the frequency of this SNP in different cow breeds. Between 2018 and 2021, a total of 809 DNA samples were obtained from 581 JB, 73 Holstein Friesian (HF: B. taurus), 125 Korean Hanwoo (KH: B. taurus coreanae), and 30 Indonesian Madura (IM: a crossbreed between B. indicus and B. javanicus) cows, which were genotyped using a TaqMan probe-based real-time polymerase chain reaction assay designed in this study. The frequency of the G allele was found to be relatively high in local IM (0.700), moderate in dairy HF (0.466), and low in beef JB (0.250) and KH (0.112) cows, with differences in the frequencies between each group being shown to be statistically significant (p < 0.005) using Fisher’s exact test. The results obtained in this study indicate that the G allele frequencies of the identified the SNP differ markedly in different breeds of taurine and indicine cattle. Given these findings, it would thus be important to evaluate the relationships between high frequencies of the G allele and infertility in different breeds.
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Affiliation(s)
- Md Shafiqul Islam
- Laboratory of Clinical Pathology, Joint Faculty of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan; (M.S.I.); (H.-S.C.); (S.P.); (T.M.R.); (A.Y.)
- Department of Pathology and Parasitology, Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University, Khulshi, Chattogram 4225, Bangladesh
| | - Mitsuhiro Takagi
- Laboratory of Theriogenology, Joint Faculty of Veterinary Medicine, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8511, Japan;
| | - Keun-Woo Lee
- Department of Veterinary Internal Medicine, College of Veterinary Medicine, Kyungpook National University, 80, Daehak-ro, Buk-gu, Daegu 41566, North Gyeongsang, Korea;
| | - Hye-Sook Chang
- Laboratory of Clinical Pathology, Joint Faculty of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan; (M.S.I.); (H.-S.C.); (S.P.); (T.M.R.); (A.Y.)
- Animal and Plant Quarantine Agency, 177, Hyeoksin 8-ro, Gimcheon-si 39660, Gyeongsangbuk-do, Korea
| | - Hiroaki Okawa
- Guardian Co., Ltd., 2794-127 Nishi-Beppu-cho, Kagoshima 890-0033, Japan;
| | - Muchammad Yunus
- Faculty of Veterinary Medicine, Airlangga University, Campus C, Mulyorejo, Surabaya 60115, Indonesia; (M.Y.); (T.D.L.); (M.R.T.)
| | - Tita Damayanti Lestari
- Faculty of Veterinary Medicine, Airlangga University, Campus C, Mulyorejo, Surabaya 60115, Indonesia; (M.Y.); (T.D.L.); (M.R.T.)
| | - Martia Rani Tacharina
- Faculty of Veterinary Medicine, Airlangga University, Campus C, Mulyorejo, Surabaya 60115, Indonesia; (M.Y.); (T.D.L.); (M.R.T.)
| | - Shahnaj Pervin
- Laboratory of Clinical Pathology, Joint Faculty of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan; (M.S.I.); (H.-S.C.); (S.P.); (T.M.R.); (A.Y.)
| | - Tofazzal Md Rakib
- Laboratory of Clinical Pathology, Joint Faculty of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan; (M.S.I.); (H.-S.C.); (S.P.); (T.M.R.); (A.Y.)
- Department of Pathology and Parasitology, Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University, Khulshi, Chattogram 4225, Bangladesh
| | - Akira Yabuki
- Laboratory of Clinical Pathology, Joint Faculty of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan; (M.S.I.); (H.-S.C.); (S.P.); (T.M.R.); (A.Y.)
| | - Osamu Yamato
- Laboratory of Clinical Pathology, Joint Faculty of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan; (M.S.I.); (H.-S.C.); (S.P.); (T.M.R.); (A.Y.)
- Faculty of Veterinary Medicine, Airlangga University, Campus C, Mulyorejo, Surabaya 60115, Indonesia; (M.Y.); (T.D.L.); (M.R.T.)
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Ibrahim AHM, Megaley AFM, Sallam AMA. Variation in the ovine FOXP3 gene and its effect on growth traits in Egyptian Barki sheep. Anim Biotechnol 2021:1-7. [PMID: 34727013 DOI: 10.1080/10495398.2021.1996387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The aim of the present study was to detect the FOXP3 gene polymorphisms in Barki sheep at a variable region covering exon 13, intron 13 and the coding sequence in exon 14 and to test the association of these polymorphisms with growth traits. 122 Barki lambs were phenotyped for various growth traits, viz., birth weight (BW), weaning weight (WW), pre-weaning daily gain in weight (ADG1), post-weaning daily gain in weight (ADG2) and marketing bodyweight (MW). The polymerase chain reaction - single-strand conformational polymorphisms (PCR-SSCP) and DNA sequencing methods were used to identify the genetic variants in the FOXP3 gene. The associations between the variation in FOXP3 gene and growth traits were tested using a general linear model. Two variants (F1 and F2 with gene frequencies of 0.64 and 0.36, respectively), and three genotypes (F1F1, F1F2 and F2F2 with frequencies of 0.37, 0.53 and 0.10, respectively) were detected. The association of FOXP3 genotype was significant (p < 0.05) with ADG2 and MW. It is concluded that FOXP3 genotype might be helpful for sheep breeders to produce fast-growing lambs. However, further studies are needed in a large population to confirm the association we found.
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Affiliation(s)
- Adel H M Ibrahim
- Department of Animal Breeding, Desert Research Center, Cairo, Egypt
| | | | - Ahmed M A Sallam
- Department of Animal Breeding, Desert Research Center, Cairo, Egypt
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7
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Druet T, Legarra A. Theoretical and empirical comparisons of expected and realized relationships for the X-chromosome. Genet Sel Evol 2020; 52:50. [PMID: 32819272 PMCID: PMC7441635 DOI: 10.1186/s12711-020-00570-6] [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: 04/10/2020] [Accepted: 08/12/2020] [Indexed: 01/08/2023] Open
Abstract
Background X-chromosomal loci present different inheritance patterns compared to autosomal loci and must be modeled accordingly. Sexual chromosomes are not systematically considered in whole-genome relationship matrices although rules based on genealogical or marker information have been derived. Loci on the X-chromosome could have a significant contribution to the additive genetic variance, in particular for some traits such as those related to reproduction. Thus, accounting for the X-chromosome relationship matrix might be informative to better understand the architecture of complex traits (e.g., by estimating the variance associated to this chromosome) and to improve their genomic prediction. For such applications, previous studies have shown the benefits of combining information from genotyped and ungenotyped individuals. Results In this paper, we start by presenting rules to compute a genomic relationship matrix (GRM) for the X-chromosome (GX) without making any assumption on dosage compensation, and based on coding of gene content with 0/1 for males and 0/1/2 for females. This coding adjusts naturally to previously derived pedigree-based relationships (S) for the X-chromosome. When needed, we propose to accommodate and estimate dosage compensation and genetic heterogeneity across sexes via multiple trait models. Using a Holstein dairy cattle dataset, including males and females, we then empirically illustrate that realized relationships (GX) matches expectations (S). However, GX presents high deviations from S. GX has also a lower dimensionality compared to the autosomal GRM. In particular, individuals are frequently identical along the entire chromosome. Finally, we confirm that the heritability of gene content for markers on the X-chromosome that are estimated by using S is 1, further demonstrating that S and GX can be combined. For the pseudo-autosomal region, we demonstrate that the expected relationships vary according to position because of the sex-gradient. We end by presenting the rules to construct the 'H matrix’ by combining both relationship matrices. Conclusions This work shows theoretically and empirically that a pedigree-based relationship matrix built with rules specifically developed for the X-chromosome (S) matches the realized GRM for the X-chromosome. Therefore, applications that combine expected relationships and genotypes for markers on the X-chromosome should use S and GX.
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Affiliation(s)
- Tom Druet
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège, Liège, Belgium.
| | - Andres Legarra
- GenPhySE, INPT, INRAE, ENVT, 31326, Castanet Tolosan, France.
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8
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Zhang J, Kadri NK, Mullaart E, Spelman R, Fritz S, Boichard D, Charlier C, Georges M, Druet T. Genetic architecture of individual variation in recombination rate on the X chromosome in cattle. Heredity (Edinb) 2020; 125:304-316. [PMID: 32651548 DOI: 10.1038/s41437-020-0341-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 07/01/2020] [Accepted: 07/01/2020] [Indexed: 12/26/2022] Open
Abstract
Meiotic recombination is an essential biological process that ensures proper chromosome segregation and creates genetic diversity. Individual variation in global recombination rates has been shown to be heritable in several species, and variants significantly associated with this trait have been identified. Recombination on the sex chromosome has often been ignored in these studies although this trait may be particularly interesting as it may correspond to a biological process distinct from that on autosomes. For instance, recombination in males is restricted to the pseudo-autosomal region (PAR). We herein used a large cattle pedigree with more than 100,000 genotyped animals to improve the genetic map of the X chromosome and to study the genetic architecture of individual variation in recombination rate on the sex chromosome (XRR). The length of the genetic map was 46.4 and 121.2 cM in males and females, respectively, but the recombination rate in the PAR was six times higher in males. The heritability of CO counts on the X chromosome was comparable to that of autosomes in males (0.011) but larger than that of autosomes in females (0.024). XRR was highly correlated (0.76) with global recombination rate (GRR) in females, suggesting that both traits might be governed by shared variants. In agreement, a set of eleven previously identified variants associated with GRR had correlated effects on female XRR (0.86). In males, XRR and GRR appeared to be distinct traits, although more accurate CO counts on the PAR would be valuable to confirm these results.
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Affiliation(s)
- Junjie Zhang
- Unit of Animal Genomics, GIGA-R and Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Naveen Kumar Kadri
- Unit of Animal Genomics, GIGA-R and Faculty of Veterinary Medicine, University of Liège, Liège, Belgium.,Animal Genomics, Institute of Agricultural Science, ETH Zürich, Zürich, Switzerland
| | | | | | - Sébastien Fritz
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France.,Allice, Paris, France
| | | | - Carole Charlier
- Unit of Animal Genomics, GIGA-R and Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Michel Georges
- Unit of Animal Genomics, GIGA-R and Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Tom Druet
- Unit of Animal Genomics, GIGA-R and Faculty of Veterinary Medicine, University of Liège, Liège, Belgium.
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9
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Zhang Y, Zhang J, Liu H, He F, Chen A, Yang H, Pi B. Meta-analysis of FOXP3 gene rs3761548 and rs2232365 polymorphism and multiple sclerosis susceptibility. Medicine (Baltimore) 2019; 98:e17224. [PMID: 31567981 PMCID: PMC6756718 DOI: 10.1097/md.0000000000017224] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND Multiple sclerosis (MS) is a common autoimmune disease of the central nervous system (CNS), and is associated with genetic factors. FOXP3 gene polymorphism has been reported as the risk factor for MS, however, previous studies have showed conflicting results. The purpose of this study is to investigate the association between FOXP3 gene polymorphism and the susceptibility to MS. METHODS Pubmed, Embase, library of Cochrane, and Web of Science were used to search the eligible articles from January 1980 up to October 2018. The odds ratio (ORs) and its 95% confidence intervals (CI) were used to evaluate the strength of association. Allele model, homozygote model, heterozygote model, dominant model, and recessive model were used to evaluate the association between FOXP3 gene polymorphism and MS. RESULTS A total of 5 studies contained 1276 MS patients and 1447 controls (for rs3761548) and 600 MS patients and 640 controls (for rs2232365) were enrolled in this meta-analysis. The association showed significant differences in allele and dominant model for rs3761548 polymorphism. In addition, a clear tendency to significance was detected in homozygote and recessive model for rs3761548 (P = .052). Subgroup analysis indicated a significant risk of MS in all genotype models but heterozygotes in Asians. CONCLUSION FOXP3 gene polymorphism rs3761548 was associated with a higher MS risk, especially in Asians. This conclusion needs to be validated in more large samples and multiracial studies. LEVEL OF EVIDENCE Level III diagnostic study.
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Affiliation(s)
- Yijian Zhang
- Department of Orthopedics, The First Affiliated Hospital of Soochow University
- Orthopedic Institute, Soochow University, Suzhou, China
| | - Junxin Zhang
- Department of Orthopedics, The First Affiliated Hospital of Soochow University
- Orthopedic Institute, Soochow University, Suzhou, China
| | - Hao Liu
- Department of Orthopedics, The First Affiliated Hospital of Soochow University
- Orthopedic Institute, Soochow University, Suzhou, China
| | - Fan He
- Department of Orthopedics, The First Affiliated Hospital of Soochow University
- Orthopedic Institute, Soochow University, Suzhou, China
| | | | - Huilin Yang
- Department of Orthopedics, The First Affiliated Hospital of Soochow University
- Orthopedic Institute, Soochow University, Suzhou, China
| | - Bin Pi
- Department of Orthopedics, The First Affiliated Hospital of Soochow University
- Orthopedic Institute, Soochow University, Suzhou, China
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Carvalho CVD, Hermisdorff IDC, Souza IS, Junqueira GSB, Magalhães AFB, Fonseca LFS, de Albuquerque LG, Tonhati H, Carvalheiro R, de Camargo GMF, Costa RB. Influence of X-chromosome markers on reproductive traits of beef cattle. Livest Sci 2019. [DOI: 10.1016/j.livsci.2018.12.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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