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Montes DE, Braz CU, Ribeiro AMF, Cavani L, Barbero MMD, Albuquerque LG, Curi RA, Oliveira HN. Selection signatures in candidate genes and QTL for reproductive traits in Nellore heifers. Anim Reprod Sci 2019; 207:1-8. [PMID: 31266598 DOI: 10.1016/j.anireprosci.2019.06.004] [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] [Received: 11/06/2018] [Revised: 03/18/2019] [Accepted: 06/04/2019] [Indexed: 12/19/2022]
Abstract
The identification of selection signature genes may help to detect genomic regions that underwent artificial selection and contributed to phenotypic diversity. The aim of this study, therefore, was to detect selection signatures in candidate genes and quantitative trait locus (QTL) for reproductive traits in a Nellore population being selected for sexual precocity. A total of 2035 Nellore heifers, sourced from breeding programs focused on sexual precocity, were used. Candidate genes and some specific QTL related to reproductive traits were chosen based on published literature and Animal QTL databases, respectively, for investigation whether these regions were affected by selection. Selection signature DNA sequences were detected in the selected regions using the extended haplotype homozygosity (EHH) and relative extended haplotype homozygosity (REHH) methods. From 22,241 single nucleotide polymorphisms (SNPs) located in the candidate genes and QTL, 17,312 SNPs generated 2756 haplotype blocks. A total of 7518 EHH tests were analyzed using haplotypes with a frequency of more than 25%, for which there were 39 tests that were significant for REHH (P<0.01). Selection signature DNA sequences were detected that contained several QTLs for important reproductive traits in cattle, suggesting that reproductive traits may have been affected by selection for sexual precocity in this population. Forty-six genes were located in the selection signature regions, whereas 24 genes participated in important biological processes or pathways that may underlie sexual precocity. These results indicate there are possible molecular mechanisms related to sexual precocity in the Nellore breed.
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Affiliation(s)
- Donicer E Montes
- São Paulo State University (Unesp), School of Agricultural and Veterinarian Sciences, Campus (Jaboticabal), Department of Animal Science, Brazil; Universidad de Sucre, Facultad de Ciencias Agropecuarias, Departamento de Zootecnia, Sincelejo, Colombia
| | - Camila U Braz
- São Paulo State University (Unesp), School of Agricultural and Veterinarian Sciences, Campus (Jaboticabal), Department of Animal Science, Brazil
| | - André M F Ribeiro
- São Paulo State University (Unesp), School of Agricultural and Veterinarian Sciences, Campus (Jaboticabal), Department of Animal Science, Brazil
| | - Lígia Cavani
- São Paulo State University (Unesp), School of Agricultural and Veterinarian Sciences, Campus (Jaboticabal), Department of Animal Science, Brazil
| | - Marina M D Barbero
- São Paulo State University (Unesp), School of Agricultural and Veterinarian Sciences, Campus (Jaboticabal), Department of Animal Science, Brazil
| | - Lucia G Albuquerque
- São Paulo State University (Unesp), School of Agricultural and Veterinarian Sciences, Campus (Jaboticabal), Department of Animal Science, Brazil
| | - Rogério A Curi
- São Paulo State University (UNESP), School of Veterinary Medicine and Animal Science, Campus (Botucatu), Department of Animal Improvement and Nutrition, Brazil
| | - Henrique N Oliveira
- São Paulo State University (Unesp), School of Agricultural and Veterinarian Sciences, Campus (Jaboticabal), Department of Animal Science, Brazil.
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Kumar C, Song S, Dewani P, Kumar M, Parkash O, Ma Y, Malhi KK, Yang N, Mwacharo JM, He X, Jiang L. Population structure, genetic diversity and selection signatures within seven indigenous Pakistani goat populations. Anim Genet 2018; 49:592-604. [PMID: 30229969 DOI: 10.1111/age.12722] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/25/2018] [Indexed: 12/20/2022]
Abstract
Goat farming in Pakistan depends on indigenous breeds that have adapted to specific agro-ecological conditions. Pakistan has a rich resource of goat breeds, and the genetic diversity of these goat breeds is largely unknown. In this study, genetic diversity and population structure were characterized from seven indigenous goat breeds using the goat 50K SNP chip. The genetic diversity analysis showed that Bugi toori goats have the highest inbreeding level, consistent with the highest linkage disequilibrium, lowest diversity and long run of heterozygosity segments. This indicates that this breed should be prioritized in future conservation activities. The population structure analysis revealed four fairly distinct clusters (including Bugi toori, Bari, Black Tapri and some Kamori) and three other breeds that are seemingly the results of admixture between these or related groups (some Kamori, Pateri, Tapri and White Tapri). The selection signatures were evaluated in each breed. A total of 2508 putative selection signals were reported. The 26 significant windows were identified in more than four breeds, and selection signatures spanned several genes that directly or indirectly influence traits included coat colour variation (KIT), reproduction (BMPR1B, GNRHR, INSL6, JAK2 and EGR4), body size (SOCS2), ear size (MSRB3) and milk composition (ABCG2, SPP1, CSN1S2, CSN2, CSN3 and PROLACTIN).
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Affiliation(s)
- C Kumar
- Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China.,Directorate of Veterinary Research and Diagnostic Central Veterinary Diagnostic Laboratory, Tando Jam, 70050, Sindh, Pakistan.,Department of Animal Breeding and Genetics, Faculty of Animal Husbandry and Veterinary Sciences, Sindh Agricultural University, Tando Jam, 70060, Sindh, Pakistan
| | - S Song
- Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China.,Department of Animal Genetics and Breeding, China Agricultural University, Beijing, 100094, China
| | - P Dewani
- Directorate of Veterinary Research and Diagnostic Central Veterinary Diagnostic Laboratory, Tando Jam, 70050, Sindh, Pakistan
| | - M Kumar
- Department of Animal Breeding and Genetics, Faculty of Animal Husbandry and Veterinary Sciences, Sindh Agricultural University, Tando Jam, 70060, Sindh, Pakistan
| | - O Parkash
- Directorate of Veterinary Research and Diagnostic Central Veterinary Diagnostic Laboratory, Tando Jam, 70050, Sindh, Pakistan
| | - Y Ma
- Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - K K Malhi
- Department of Animal Breeding and Genetics, Faculty of Animal Husbandry and Veterinary Sciences, Sindh Agricultural University, Tando Jam, 70060, Sindh, Pakistan
| | - N Yang
- Department of Animal Genetics and Breeding, China Agricultural University, Beijing, 100094, China
| | - J M Mwacharo
- Small Ruminant Genomics Group, International Center for Agricultural Research in the Dry Areas (ICARDA), P.O. Box 5689, Addis Ababa, Ethiopia
| | - X He
- Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - L Jiang
- Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
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Gorlov IF, Kolosov YA, Shirokova NV, Getmantseva LV, Slozhenkina MI, Mosolova NI, Bakoev NF, Leonova MA, Kolosov AY, Zlobina EY. GDF9 gene polymorphism and its association with litter size in two Russian sheep breeds. RENDICONTI LINCEI-SCIENZE FISICHE E NATURALI 2017. [DOI: 10.1007/s12210-017-0659-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Abstract
Growth differentiation factor 9 (GDF9) has been shown to be involved in regulating follicular development and reproduction in many mammalian species. However, related information about the effect of the GDF9 gene on reproductive traits of New Zealand white rabbits was rarely reported. In this study, rabbits were distributed into two groups (poor and prolific offspring productions) and cloning and quantitative real-time PCR (qPCR) were employed to characterize the rabbit GDF9 gene. By cloning, 2515-bp genomic DNA and 1359-bp cDNA sequences were obtained. Comparing the two cDNA sequences, three potential mutation sites (C.539C>T,C.562G>C and C.718C>G) in exon 2 of the GDF9 gene were found, and the corresponding amino acids changed (P.183T>M, P.188E>Q and P.240L>V). The qPCR results revealed that GDF9 was not tissue-specific, but rather expressed in all collected tissues. The expression level of the GDF9 gene was highest in the ovary, and was significantly increased (P< 0.05) compared with the other tissues. The liver had the second highest expression, and the heart and spleen had the least expression in New Zealand white rabbits. In the prolific group, the expression quantity of the GDF9 gene significantly increased (P < 0.05) in the heart, spleen, ovary, liver and uterus (P < 0.01) than the other groups. The amino acid sequence identities of human, sheep, goat, mouse, cattle, pig, cat, donkey, Nancy Ma's night monkey and olive baboon were 72, 68, 69, 66, 69, 71, 67, 73, 75 and 73%, respectively. Bioinformatics analysis was executed, and a random coil was determined to be the primary secondary structure.
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