1
|
Zhou A, Ding Y, Zhang X, Zhou Y, Liu Y, Li T, Xiao L. Whole-genome resequencing reveals new mutations in candidate genes for Beichuan-white goat prolificacya. Anim Biotechnol 2024; 35:2258166. [PMID: 37729465 DOI: 10.1080/10495398.2023.2258166] [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: 09/22/2023]
Abstract
In this study, we evaluated the copy number variation in the genomes of two groups of Beichuan-white goat populations with large differences in litter size by FST method, and identified 1739 genes and 485 missense mutations in the genes subject to positive selection. Through functional enrichment, ITGAV, LRP4, CDH23, TPRN, RYR2 and CELSR1 genes, involved in embryonic morphogenesis, were essential for litter size trait, which received intensive attention. In addition, some mutation sites of these genes have been proposed (ITGAV: c.38C > T; TPRN: c.133A > T, c.1192A > G, c.1250A > C; CELSR1: c.7640T > C), whose allele frequencies were significantly changed in the high fecundity goat group. Besides, we found that new mutations at these sites altered the hydrophilicity and 3D structure of the protein. Candidate genes related to litter size in this study and their missense mutation sites were identified. These candidate genes are helpful to understand the genetic mechanism of fecundity in Beichuan white goat, and have important significance for future goat breeding.
Collapse
Affiliation(s)
- Aimin Zhou
- Animal Husbandry Research Institute, Mianyang Academy of Agricultural Sciences, Mianyang, P. R. China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, P. R. China
| | - Yi Ding
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, P. R. China
| | - Xiaohui Zhang
- Animal Husbandry Research Institute, Mianyang Academy of Agricultural Sciences, Mianyang, P. R. China
| | - Yugang Zhou
- Animal Husbandry Research Institute, Mianyang Academy of Agricultural Sciences, Mianyang, P. R. China
| | - Yadong Liu
- Animal Husbandry Research Institute, Mianyang Academy of Agricultural Sciences, Mianyang, P. R. China
| | - Tingjian Li
- Animal Husbandry Research Institute, Mianyang Academy of Agricultural Sciences, Mianyang, P. R. China
| | - Long Xiao
- Animal Husbandry Research Institute, Mianyang Academy of Agricultural Sciences, Mianyang, P. R. China
| |
Collapse
|
2
|
Habib HN, Saleh WMM, Gheni QJ. Genetic profiling of HSP70 gene in local Iraqi goats. BRAZILIAN JOURNAL OF VETERINARY MEDICINE 2022; 44:e004121. [PMID: 36212990 PMCID: PMC9536216 DOI: 10.29374/2527-2179.bjvm004121] [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: 10/12/2021] [Accepted: 09/18/2022] [Indexed: 11/10/2022] Open
Abstract
Animals display numerous physiological and behavioral responses that reduce the effects of heat stress. Moreover, genetic variance is strongly associated with responses to heat stress, including variants of heat shock proteins (HSPs) that are necessary for thermoregulation and stress resistance. Herein, we performed the molecular profiling of the HSP70 gene, and its polymorphism was demonstrated as a possible factor in the stress tolerance of local Iraqi goats. A number of different mutations were found owing to seven main polymorphisms. Results indicated the occurrence of silent and missense mutations in sequences obtained for Iraqi local goats. Genetic diversity was observed in the HSP70 gene of Iraqi local goats on the basis of phylogenetic-tree analysis as some mutations occurred once whereas others occurred multiple times. The polymorphisms LC616787, LC616788, and LC616791 were combined with the reference gene in the same branch, whereas polymorphisms (LC616785 and LC616786) and (LC616789 and LC616790) met in different branches, respectively. Moreover, all studied proteins had mismatches in their three-dimensional structures. Therefore, the presence of specific genetic differences within the HSP70 gene in Iraqi goats can increase the possibility of selecting animals more suitable to various levels of stress.
Collapse
Affiliation(s)
- Hassan Nima Habib
- Biotechnology and Molecular Genetics, PhD, Department of Animal Production, College of Agriculture, University of Basrah, Basrah, Iraq
| | - Wessam Monther Mohammed Saleh
- Veterinarian, PhD, Department of Internal and Preventive Medicine, College of Veterinary, Medicine, University of Basrah, Basrah, Iraq,Correspondence Wessam Monther Mohammed Saleh Department of Internal and Preventive Medicine, College of Veterinary Medicine, University of Basrah 57 Baghdad Street Basrah, Iraq E-mail: ;
| | - Qutaiba Jassim Gheni
- Veternarian, PhD, Department of Animal Production, College of Agriculture, University of Basrah, Basrah, Iraq
| |
Collapse
|
3
|
Liao CM, Tan GH, You MF, Li JZ, Wu L, Qin YY, Zhang YY. Genetic variants in SCNN1B and AHCYL1 are associated with eggshell quality in Chinese domestic laying ducks ( Anas platyrhynchos). Br Poult Sci 2021; 63:454-465. [PMID: 34923880 DOI: 10.1080/00071668.2021.2019678] [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: 11/02/2022]
Abstract
1. The objective of this study was to investigate the evolution of SCNN1B and AHCYL1 proteins among 10 domestic and mammalian animals, to uncover the expression patterns of SCNN1B and AHCYL1 genes in ducks, identify the genetic variants of the SCNN1B and AHCYL1 genes and analyse their effects on eggshell quality.2. Expression profiles of the SCNN1B and AHCYL1 genes in Sansui female ducks were determined using real-time fluorescence quantitative PCR to identify SNPs. The duck SCNN1B and AHCYL1 genes were amplified to identify SNPs. A total of 502 Sansui female ducks were genotyped by sequencing, and the associations between the mRNA expression/SNP genotypes and six eggshell quality indices were analysed using PASW Statistics 18.0.3. The results showed that the SCNN1B and AHCYL1 proteins are highly conserved in different mammalian or domestic animals, especially the AHCYL1 protein. The SCNN1B and AHCYL1 genes were widely expressed in different tissues of male and female ducks, and expression level in the uterus was greater than in other tissues. The expression of SCNN1B and AHCYL1 during oviposition cycle indicated that expression levels were related to the eggshell mineralisation stage.4. The mRNA expression levels of uterine SCNN1B and AHCYL1 genes were positively correlated with eggshell strength (ESS), percentage (ESP) and weight (ESW) (P<0.05), respectively. Ten novel SNPs in SCNN1B and AHCYL1 genes from Chinese domestic laying ducks were identified through PCR amplicon sequencing.5. Genetic association analysis indicated g.797509 C > T, g.797573 C > T and g.797834 C > T in SCNN1B gene and g.169244 T > A, g.169265 T > C and g.175311T > C in AHCYL1 gene had a significant effect on eggshell quality. Correlation analysis between the SNP genotype and SCNN1B and AHCYL1 genes expression in the uterus showed that the genotypes of g.797509 C>T, g.797573 C>T, g.797834 C>T, g.169244 T>A and g.175311T>C sites affected the expression of SCNN1B and AHCYL1 genes in utero (P<0.05).6. The study indicated SCNN1B and AHCYL1 as candidate genes to improve eggshell traits in ducks.
Collapse
Affiliation(s)
- Chao-Mei Liao
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Animal Science, Guizhou University, People's Republic of China
| | - Guang-Hui Tan
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Animal Science, Guizhou University, People's Republic of China
| | - Ming-Fang You
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Animal Science, Guizhou University, People's Republic of China
| | - Jie-Zhang Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Animal Science, Guizhou University, People's Republic of China
| | - Lei Wu
- China Guizhou Anshun Lihua Animal Husbandry Co., Ltd
| | - Yuan-Yu Qin
- Agriculture and Rural Bureau of zhijin county, Guizhou Province, China
| | - Yi-Yu Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Animal Science, Guizhou University, People's Republic of China
| |
Collapse
|
4
|
Abousoliman I, Reyer H, Oster M, Murani E, Mohamed I, Wimmers K. Genome-Wide Analysis for Early Growth-Related Traits of the Locally Adapted Egyptian Barki Sheep. Genes (Basel) 2021; 12:genes12081243. [PMID: 34440417 PMCID: PMC8394750 DOI: 10.3390/genes12081243] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 08/09/2021] [Accepted: 08/11/2021] [Indexed: 12/28/2022] Open
Abstract
Sheep play a critical role in the agricultural and livestock sector in Egypt. For sheep meat production, growth traits such as birth and weaning weights are very important and determine the supply and income of local farmers. The Barki sheep originates from the northeastern coastal zone of Africa, and due to its good adaptation to the harsh environmental conditions, it contributes significantly to the meat production in these semi-arid regions. This study aimed to use a genome-wide SNP panel to identify genomic regions that are diversified between groups of individuals of Egyptian Barki sheep with high and low growth performance traits. In this context, from a phenotyped population of 140 lambs of Barki sheep, 69 lambs were considered for a genome-wide scan with the Illumina OvineSNP50 V2 BeadChip. The selected lambs were grouped into divergent subsets with significantly different performance for birth weight and weaning weight. After quality control, 63 animals and 40,383 SNPs were used for analysis. The fixation index (FST) for each SNP was calculated between the groups. The results verified genomic regions harboring some previously proposed candidate genes for traits related to body growth, i.e., EYA2, GDF2, GDF10, MEF2B, SLC16A7, TBX15, TFAP2B, and TNNC2. Moreover, novel candidate genes were proposed with known functional implications on growth processes such as CPXM2 and LRIG3. Subsequent association analysis showed significant effects of the considered SNPs on birth and weaning weights. Results highlight the genetic diversity associated with performance traits and thus the potential to improve growth traits in the Barki sheep breed.
Collapse
Affiliation(s)
- Ibrahim Abousoliman
- Leibniz Institute for Farm Animal Biology, Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany; (I.A.); (H.R.); (M.O.); (E.M.)
- Desert Research Center, Department of Animal and Poultry Breeding, 1 Mathaf El-Matareya St., El-Matareya, Cairo 11753, Egypt;
| | - Henry Reyer
- Leibniz Institute for Farm Animal Biology, Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany; (I.A.); (H.R.); (M.O.); (E.M.)
| | - Michael Oster
- Leibniz Institute for Farm Animal Biology, Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany; (I.A.); (H.R.); (M.O.); (E.M.)
| | - Eduard Murani
- Leibniz Institute for Farm Animal Biology, Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany; (I.A.); (H.R.); (M.O.); (E.M.)
| | - Ismail Mohamed
- Desert Research Center, Department of Animal and Poultry Breeding, 1 Mathaf El-Matareya St., El-Matareya, Cairo 11753, Egypt;
| | - Klaus Wimmers
- Leibniz Institute for Farm Animal Biology, Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany; (I.A.); (H.R.); (M.O.); (E.M.)
- Faculty of Agricultural and Environmental Sciences, University of Rostock, Justus-von-Liebig-Weg 7, 18059 Rostock, Germany
- Correspondence: ; Tel.: +49-382-08-68-600
| |
Collapse
|
5
|
Genome-Wide SNP Analysis for Milk Performance Traits in Indigenous Sheep: A Case Study in the Egyptian Barki Sheep. Animals (Basel) 2021; 11:ani11061671. [PMID: 34205212 PMCID: PMC8228706 DOI: 10.3390/ani11061671] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 05/28/2021] [Accepted: 05/31/2021] [Indexed: 01/04/2023] Open
Abstract
Simple Summary The Barki sheep is one of the three main breeds in Egypt, which is spread mainly throughout the northwestern coastal zone, which has harsh conditions. Considering the harsh, semi-arid habitat of this breed, milk performance traits such as milk yield and milk composition have a very important role in the feeding of newborn lambs and affect their growth during the early stage of life. In this study, rare milk performance data and genomic information of Barki sheep were used to uncover diversified genomic regions that could explain the variability of milk yield and milk quality traits in the studied population of Barki ewes. Genome-wide analysis identified genomic regions harboring interesting candidate genes such as SLC5A8, NUB1, TBC1D1, KLF3 and ABHD5 for milk yield and PPARA and FBLN1 genes for milk quality traits. The findings offer valuable information for obtaining a better understanding of the genetics of milk performance traits and contribute to the genetic improvement of these traits in Barki sheep. Abstract Sheep milk yield and milk composition traits play an important role in supplying newborn lambs with essential components such as amino acids, energy, vitamins and immune antibodies and are also of interest in terms of the nutritional value of the milk for human consumption. The aim of this study was to identify genomic regions and candidate genes for milk yield and milk composition traits through genome-wide SNP analyses between high and low performing ewes of the Egyptian Barki sheep breed, which is well adapted to the harsh conditions of North-East Africa. Therefore, out of a herd of 111 ewes of the Egyptian Barki sheep breed (IBD = 0.08), ewes representing extremes in milk yield and milk quality traits (n = 25 for each group of animals) were genotyped using the Illumina OvineSNP50 V2 BeadChip. The fixation index (FST) for each SNP was calculated between the diversified groups. FST values were Z-transformed and used to identify putative SNPs for further analysis (Z(FST) > 10). Genome-wide SNP analysis revealed genomic regions covering promising candidate genes related to milk performance traits such as SLC5A8, NUB1, TBC1D1, KLF3 and ABHD5 for milk yield and PPARA and FBLN1 genes for milk quality trait. The results of this study may contribute to the genetic improvement of milk performance traits in Barki sheep breed and to the general understanding of the genetic contribution to variability in milk yield and quality traits.
Collapse
|