Candidate genes associated with economically important traits in dairy goats

Getaneh, Mezgebu; Alemayehu, Kefyalew

doi:10.1080/23311932.2022.2149131

Cited by 5 publications

(5 citation statements)

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“…Additionally, we identified specifically expressed genes in the transcriptional profiles, some of which have been reported to be associated with growth traits, milk traits, reproductive performance, and mammary gland diseases in livestock [ 20 , 21 ]. The expression of genes encoding production traits ( WSCD1 , NR6A1 , ITGB8 ) was significantly absent during the pregnancy stage, as lactation does not occur during this period [ 72 , 73 ]. Similarly, the MTNR1A gene is specifically expressed in the blood of high-yielding camels, and it encodes the receptor responsible for transducing melatonin signaling [ 74 ].…”

Section: Discussionmentioning

confidence: 99%

Transcriptome analysis of the Bactrian camel (Camelus bactrianus) reveals candidate genes affecting milk production traits

Yao,

Dou,

Zhao

et al. 2023

BMC Genomics

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Background Milk production traits are complex traits with vital economic importance in the camel industry. However, the genetic mechanisms regulating milk production traits in camels remain poorly understood. Therefore, we aimed to identify candidate genes and metabolic pathways that affect milk production traits in Bactrian camels. Methods We classified camels (fourth parity) as low- or high-yield, examined pregnant camels using B-mode ultrasonography, observed the microscopic changes in the mammary gland using hematoxylin and eosin (HE) staining, and used RNA sequencing to identify differentially expressed genes (DEGs) and pathways. Results The average standard milk yield over the 300 days during parity was recorded as 470.18 ± 9.75 and 978.34 ± 3.80 kg in low- and high-performance camels, respectively. Nine female Junggar Bactrian camels were subjected to transcriptome sequencing, and 609 and 393 DEGs were identified in the low-yield vs. high-yield (WDL vs. WGH) and pregnancy versus colostrum period (RSQ vs. CRQ) comparison groups, respectively. The DEGs were compared with genes associated with milk production traits in the Animal Quantitative Trait Loci database and in Alashan Bactrian camels, and 65 and 46 overlapping candidate genes were obtained, respectively. Functional enrichment and protein–protein interaction network analyses of the DEGs and candidate genes were conducted. After comparing our results with those of other livestock studies, we identified 16 signaling pathways and 27 core candidate genes associated with maternal parturition, estrogen regulation, initiation of lactation, and milk production traits. The pathways suggest that emerged milk production involves the regulation of multiple complex metabolic and cellular developmental processes in camels. Finally, the RNA sequencing results were validated using quantitative real-time PCR; the 15 selected genes exhibited consistent expression changes. Conclusions This study identified DEGs and metabolic pathways affecting maternal parturition and milk production traits. The results provides a theoretical foundation for further research on the molecular mechanism of genes related to milk production traits in camels. Furthermore, these findings will help improve breeding strategies to achieve the desired milk yield in camels. Graphical Abstract

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Section: Discussionmentioning

confidence: 99%

Transcriptome analysis of the Bactrian camel (Camelus bactrianus) reveals candidate genes affecting milk production traits

Yao,

Dou,

Zhao

et al. 2023

BMC Genomics

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“…Interrogation of the regions harbouring the significant SNPs of the present study revealed that the markers were located either within or directly upstream of annotated genes (Table 4). A significant SNP associated with breast muscle percentage was located within the NIN gene, which has been reportedly implicated in developmental delay (Dauber et al, 2012) and short stature and skeletal deformities (Grosch et al, 2013) in humans, as well as embryonic development in goats (Berihulay et al, 2022;Getaneh and Alemayehu, 2022). This suggests a potential role of the NIN gene in growth traits of other species, too.…”

Section: Genomic Characterisation Of Chicken Performancementioning

confidence: 97%

Phenotypic and genomic characterisation of performance of tropically adapted chickens raised in smallholder farm conditions in Ethiopia

Morris,

Sutton,

Girma

et al. 2024

Front. Genet.

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Background:In sub-Saharan Africa, 80% of poultry production is on smallholder village farms, where chickens are typically reared outdoors in free-ranging conditions. There is limited knowledge on chickens’ phenotypic characteristics and genetics under these conditions.Objective:The present is a large-scale study set out to phenotypically characterise the performance of tropically adapted commercial chickens in typical smallholder farm conditions, and to examine the genetic profile of chicken phenotypes associated with growth, meat production, immunity, and survival.Methods:A total of 2,573 T451A dual-purpose Sasso chickens kept outdoors in emulated free-ranging conditions at the poultry facility of the International Livestock Research Institute in Addis Ababa, Ethiopia, were included in the study. The chickens were raised in five equally sized batches and were individually monitored and phenotyped from the age of 56 days for 8 weeks. Individual chicken data collected included weekly body weight, growth rate, body and breast meat weight at slaughter, Newcastle Disease Virus (NDV) titres and intestinal Immunoglobulin A (IgA) levels recorded at the beginning and the end of the period of study, and survival rate during the same period. Genotyping by sequencing was performed on all chickens using a low-coverage and imputation approach. Chicken phenotypes and genotypes were combined in genomic association analyses.Results:We discovered that the chickens were phenotypically diverse, with extensive variance levels observed in all traits. Batch number and sex of the chicken significantly affected the studied phenotypes. Following quality assurance, genotypes consisted of 2.9 million Single Nucleotide Polymorphism markers that were used in the genomic analyses. Results revealed a largely polygenic mode of genetic control of all phenotypic traits. Nevertheless, 15 distinct markers were identified that were significantly associated with growth, carcass traits, NDV titres, IgA levels, and chicken survival. These markers were located in regions harbouring relevant annotated genes.Conclusion:Results suggest that performance of chickens raised under smallholder farm conditions is amenable to genetic improvement and may inform selective breeding programmes for enhanced chicken productivity in sub-Saharan Africa.

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“…For goats in general, and dairy goats in particular, there have been significantly fewer studies compared to dairy cattle [6][7][8]. Nevertheless, there are certain results from research conducted on different breeds of dairy goats in various countries [9][10][11]. For instance, a GWAS has been conducted and candidate genes for milk production traits in Saanen and Alpine goats have been identified in France (Martin et al, , 2017(Martin et al, , 2018; Talouarn et al, 2020 [15]), the United Kingdom (Mucha et al, 2018 [16]), New Zealand (Scholtens et al, 2020 [17]), Canada (Massender et al, 2023 [18]), and America (Tilahun et al, 2020 [19]).…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Association Study of Milk Composition in Karachai Goats

Selionova,

Trukhachev,

Aibazov

et al. 2024

Animals

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This study is first to perform a genome-wide association study (GWAS) to investigate the milk quality traits in Karachai goats. The objective of the study was to identify candidate genes associated with milk composition traits based on the identification and subsequent analysis of all possible SNPs, both genome-wide (high-confidence) and suggestive (subthreshold significance). To estimate the milk components, 22 traits were determined, including several types of fatty acids. DNA was extracted from ear tissue or blood samples. A total of 167 Karachai goats were genotyped using an Illumina GoatSNP53K BeadChip panel (Illumina Inc., San Diego, CA, USA). Overall, we identified 167 highly significant and subthreshold SNPs associated with the milk components of Karachai goats. A total of 10 SNPs were located within protein-coding genes and 33 SNPs in close proximity to them (±0.2 Mb). The largest number of genome-wide significant SNPs was found on chromosomes 2 and 8 and some of them were associated with several traits. The greatest number of genome-wide significant SNPs was identified for crude protein and lactose (6), and the smallest number—only 1 SNP—for freezing point depression. No SNPs were identified for monounsaturated and polyunsaturated fatty acids. Functional annotation of all 43 SNPs allowed us to identify 66 significant candidate genes on chromosomes 1, 2, 3, 4, 5, 8, 10, 13, 16, 18, 21, 23, 25, 26, and 27. We considered these genes potential DNA markers of the fatty acid composition of Karachai goat milk. Also, we found 12 genes that had a polygenic effect: most of them were simultaneously associated with the dry matter content and fatty acids (METTL, SLC1A 8, PHACTR1, FMO2, ECI1, PGP, ABCA3, AMDHD2). Our results suggest that the genes identified in our study affecting the milk components in Karachai goats differed from those identified in other breeds of dairy goats.

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Candidate genes associated with economically important traits in dairy goats

Cited by 5 publications

References 110 publications

Transcriptome analysis of the Bactrian camel (Camelus bactrianus) reveals candidate genes affecting milk production traits

Transcriptome analysis of the Bactrian camel (Camelus bactrianus) reveals candidate genes affecting milk production traits

Phenotypic and genomic characterisation of performance of tropically adapted chickens raised in smallholder farm conditions in Ethiopia

Genome-Wide Association Study of Milk Composition in Karachai Goats

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