Whole‐genome sequence analysis reveals candidate genomic footprints and genes associated with reproductive traits in Thoroughbred horse

Nanaei, Hojjat Asadollahpour; Mehrgardi, Ahmad Ayatollahi; Esmailizadeh, Ali

doi:10.1111/rda.13608

Cited by 3 publications

(3 citation statements)

References 69 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…A total of 35 regions were found to be associated to STAY in only one of the intermediate calvings (fifth or sixth). Identified for the fifth calving, the BTA9: 58.4–58.9 Mb harbors the 7SK gene that was associated to reproductive traits in horses [ 74 ], and beef cattle [ 75 ]. Moreover, the BTA12:60,7–61,4 Mb encloonses the HTATSF1 (HIV-1 Tat Specific Factor 1) gene that was related to estrogen receptor of precocious puberty women [ 76 ] and transcript in preimplantation of mouse embryos in 2-cell stage [ 77 ].…”

Section: Resultsmentioning

confidence: 99%

Genome-wide association study for stayability at different calvings in Nellore beef cattle

Silva,

Fernandes Júnior,

Fonseca

et al. 2024

BMC Genomics

View full text Add to dashboard Cite

Backgrounding Stayability, which may be defined as the probability of a cow remaining in the herd until a reference age or at a specific number of calvings, is usually measured late in the animal’s life. Thus, if used as selection criteria, it will increase the generation interval and consequently might decrease the annual genetic gain. Measuring stayability at an earlier age could be a reasonable strategy to avoid this problem. In this sense, a better understanding of the genetic architecture of this trait at different ages and/or at different calvings is important. This study was conducted to identify possible regions with major effects on stayability measured considering different numbers of calvings in Nellore cattle as well as pathways that can be involved in its expression throughout the female’s productive life. Results The top 10 most important SNP windows explained, on average, 17.60% of the genetic additive variance for stayability, varying between 13.70% (at the eighth calving) and 21% (at the fifth calving). These SNP windows were located on 17 chromosomes (1, 2, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 27, and 28), and they harbored a total of 176 annotated genes. The functional analyses of these genes, in general, indicate that the expression of stayability from the second to the sixth calving is mainly affected by genetic factors related to reproductive performance, and nervous and immune systems. At the seventh and eighth calvings, genes and pathways related to animal health, such as density bone and cancer, might be more relevant. Conclusion Our results indicate that part of the target genomic regions in selecting for stayability at earlier ages (from the 2th to the 6th calving) would be different than selecting for this trait at later ages (7th and 8th calvings). While the expression of stayability at earlier ages appeared to be more influenced by genetic factors linked to reproductive performance together with an overall health/immunity, at later ages genetic factors related to an overall animal health gain relevance. These results support that selecting for stayability at earlier ages (perhaps at the second calving) could be applied, having practical implications in breeding programs since it could drastically reduce the generation interval, accelerating the genetic progress.

show abstract

Section: Resultsmentioning

confidence: 99%

Genome-wide association study for stayability at different calvings in Nellore beef cattle

Silva,

Fernandes Júnior,

Fonseca

et al. 2024

BMC Genomics

View full text Add to dashboard Cite

show abstract

“…With the development of genotype imputation software, a low-cost method to increase the number of animals with WGS data has been proposed by imputing the lower-density microarray data to the WGS level. Recently, GWAS using imputed WGS data has been widely used in different livestock, such as pigs ( Li X. et al, 2020 ), chickens ( Ni et al, 2017 ; Visscher et al, 2017 ), cattle ( Van Binsbergen et al, 2015 ; Zhang et al, 2016 ), and horses ( Asadollahpour Nanaei et al, 2020 ). Especially for cattle, many studies have detected significant important candidate genes by using imputed WGS data in GWAS ( Chen N. et al, 2018 ).…”

Section: Discussionmentioning

confidence: 99%

Genetic parameters and genome-wide association for milk production traits and somatic cell score in different lactation stages of Shanghai Holstein population

Liu

Zhao

et al. 2022

Front. Genet.

View full text Add to dashboard Cite

The aim of this study was to investigate the genetic parameters and genetic architectures of six milk production traits in the Shanghai Holstein population. The data used to estimate the genetic parameters consisted of 1,968,589 test-day records for 305,031 primiparous cows. Among the cows with phenotypes, 3,016 cows were genotyped with Illumina Bovine SNP50K BeadChip, GeneSeek Bovine 50K BeadChip, GeneSeek Bovine LD BeadChip v4, GeneSeek Bovine 150K BeadChip, or low-depth whole-genome sequencing. A genome-wide association study was performed to identify quantitative trait loci and genes associated with milk production traits in the Shanghai Holstein population using genotypes imputed to whole-genome sequences and both fixed and random model circulating probability unification and a mixed linear model with rMVP software. Estimated heritabilities (h2) varied from 0.04 to 0.14 for somatic cell score (SCS), 0.07 to 0.22 for fat percentage (FP), 0.09 to 0.27 for milk yield (MY), 0.06 to 0.23 for fat yield (FY), 0.09 to 0.26 for protein yield (PY), and 0.07 to 0.35 for protein percentage (PP), respectively. Within lactation, genetic correlations for SCS, FP, MY, FY, PY, and PP at different stages of lactation estimated in random regression model were ranged from -0.02 to 0.99, 0.18 to 0.99, 0.04 to 0.99, 0.04 to 0.99, 0.01 to 0.99, and 0.33 to 0.99, respectively. The genetic correlations were highest between adjacent DIM but decreased as DIM got further apart. Candidate genes included those related to production traits (DGAT1, MGST1, PTK2, and SCRIB), disease-related (LY6K, COL22A1, TECPR2, and PLCB1), heat stress–related (ITGA9, NDST4, TECPR2, and HSF1), and reproduction-related (7SK and DOCK2) genes. This study has shown that there are differences in the genetic mechanisms of milk production traits at different stages of lactation. Therefore, it is necessary to conduct research on milk production traits at different stages of lactation as different traits. Our results can also provide a theoretical basis for subsequent molecular breeding, especially for the novel genetic loci.

show abstract

“…We identified a few more candidate genes associated with reproduction traits, including GSK3B on BTA 1 [126], ADAD1 on BTA 17 [127,128], and UBE3B on BTA 21 [129,130], in the Yaroslavl breed. These genes are associated mainly with female fertility traits, that can reflect the unique capacity of cows of Yaroslavl breed to produce healthy calves even with severe weight losses because of poor feeding in winter [4].…”

Section: Plos Onementioning

confidence: 99%

Selection signatures in two oldest Russian native cattle breeds revealed using high-density single nucleotide polymorphism analysis

et al. 2020

View full text Add to dashboard Cite

Native cattle breeds can carry specific signatures of selection reflecting their adaptation to the local environmental conditions and response to the breeding strategy used. In this study, we comprehensively analysed high-density single nucleotide polymorphism (SNP) genotypes to characterise the population structure and detect the selection signatures in Russian native Yaroslavl and Kholmogor dairy cattle breeds, which have been little influenced by introgression with transboundary breeds. Fifty-six samples of pedigree-recorded purebred animals, originating from different breeding farms and representing different sire lines, of the two studied breeds were genotyped using a genome-wide bovine genotyping array (Bovine HD BeadChip). Three statistical analyses—calculation of fixation index (FST) for each SNP for the comparison of the pairs of breeds, hapFLK analysis, and estimation of the runs of homozygosity (ROH) islands shared in more than 50% of animals—were combined for detecting the selection signatures in the genome of the studied cattle breeds. We confirmed nine and six known regions under putative selection in the genomes of Yaroslavl and Kholmogor cattle, respectively; the flanking positions of most of these regions were elucidated. Only two of the selected regions (localised on BTA 14 at 24.4–25.1 Mbp and on BTA 16 at 42.5–43.5 Mb) overlapped in Yaroslavl, Kholmogor and Holstein breeds. In addition, we detected three novel selection sweeps in the genome of Yaroslavl (BTA 4 at 4.74–5.36 Mbp, BTA 15 at 17.80–18.77 Mbp, and BTA 17 at 45.59–45.61 Mbp) and Kholmogor breeds (BTA 12 at 82.40–81.69 Mbp, BTA 15 at 16.04–16.62 Mbp, and BTA 18 at 0.19–1.46 Mbp) by using at least two of the above-mentioned methods. We expanded the list of candidate genes associated with the selected genomic regions and performed their functional annotation. We discussed the possible involvement of the identified candidate genes in artificial selection in connection with the origin and development of the breeds. Our findings on the Yaroslavl and Kholmogor breeds obtained using high-density SNP genotyping and three different statistical methods allowed the detection of novel putative genomic regions and candidate genes that might be under selection. These results might be useful for the sustainable development and conservation of these two oldest Russian native cattle breeds.

show abstract

Whole‐genome sequence analysis reveals candidate genomic footprints and genes associated with reproductive traits in Thoroughbred horse

Cited by 3 publications

References 69 publications

Genome-wide association study for stayability at different calvings in Nellore beef cattle

Genome-wide association study for stayability at different calvings in Nellore beef cattle

Genetic parameters and genome-wide association for milk production traits and somatic cell score in different lactation stages of Shanghai Holstein population

Selection signatures in two oldest Russian native cattle breeds revealed using high-density single nucleotide polymorphism analysis

Contact Info

Product

Resources

About