A single-step genomic evaluation for milk production in Egyptian buffalo

Abdel-Shafy, Hamdy; Awad, Mohamed Attia Ahmed; El-Regalaty, Hussein; Ismael, Ahmed; El-Assal, Salah El-Din; Abou-Bakr, S.

doi:10.1016/j.livsci.2020.103977

Cited by 16 publications

(11 citation statements)

References 37 publications

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“…The differences between the Egyptian buffalo types depend only on the environment. This breed is very important in the dairy industry in Egypt, as it produces 45% of the milk consumed in the country (50). These animals are blackish gray in color, with long and narrow heads, and horns varying in format (from lyre to sword-shaped) (7).…”

Section: Water Buffalo Breedsmentioning

confidence: 99%

Bubalus bubalis: A Short Story

Zava²,

et al. 2020

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The domestic buffalo (Bubalus bubalis), also known as water buffalo or Asian buffalo to prevent confusion with the American bison (Bison bison), wrongly named buffalo in North America, comprises two subspecies: the river buffalo (B. bubalis bubalis) and the swamp buffalo (B. bubalis kerebau). The swamp buffalo has a consistent phenotype and is considered as one type, even if many breeds are recognized within it; conversely, the river buffalo subspecies has many breeds. We found limited information available regarding the worldwide distribution of buffaloes. The best estimate is that 208,098,759 buffalo head are distributed in 77 countries in five continents. In this review, we presented the basic aspects of the water buffalo and unraveled the buffalo path followed from the origin of the species to its current global distribution. We reviewed several data sources to provide a better estimate of the world buffalo count and distribution.

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Section: Water Buffalo Breedsmentioning

confidence: 99%

Bubalus bubalis: A Short Story

Zava²,

et al. 2020

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“…For buffalo, development of Axiom Buffalo Genotyping Array (90k SNPs) opens new opportunities to identify candidate genes associated with buffalo milk production traits and provides the possibility of predicting genomic breeding values for buffalo breeds in different countries. So far, 87 significant and 354 suggestive genomic regions were reported for milk production traits in Brazilian, Chinese, Egyptian, Iranian, Italian and Philippino buffalo (de Camargo et al ., 2015; El-Halawany et al ., 2017; Iamartino et al ., 2017; Mokhber, 2017; da Costa Barros et al ., 2018; Herrera et al ., 2018; Liu et al ., 2018; Abdel-Shafy et al ., 2020; Awad et al ., 2020; Lu et al ., 2020). Despite the fact that these loci were distributed on almost all chromosomes, none of these SNPs were overlapped between studies indicating the complexity of milk production traits and the modest effect of such SNPs (Abdel-Shafy et al ., 2020).…”

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confidence: 99%

Prospecting genomic regions associated with milk production traits in Egyptian buffalo

Abdel-Shafy

Awad

El-Regalaty

et al. 2020

Journal of Dairy Research

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The objectives of the current study were to detect putative genomic loci and to identify candidate genes associated with milk production traits in Egyptian buffalo. A total number of 161 479 daily milk yield (DMY) records and 60 318 monthly measures for fat and protein percentages (FP and PP, respectively), along with fat and protein yields (FY and PY, respectively) from 1670 animals were used. Genotyping was performed using Axiom® Buffalo Genotyping 90 K array. Genome-wide association study (GWAS) for each trait was performed using PLINK. After Bonferroni correction, 47 SNPs were associated with one or more milk production traits. These SNPs were distributed over 36 quantitative trait loci (QTL) and located on 20 buffalo chromosomes (BBU). For the 47 SNPs, one was overlapped for three traits (DMY, FY, and PY), six were associated with two traits (one for PP and PY and five for FY and PY) while the rest were associated with only one trait. Out of 36 identified QTL, eleven were overlapped with previously reported loci in buffalo and/or cattle populations. Some of these SNPs are placed within or close to potential candidate genes, for example: TPD52, ZBTB10, RALYL and SNX16 on BBU15, ADGRD1 on BBU17, ESRRG on BBU5 and GRIP1 on BBU4. This is the first reported study between genome-wide markers and milk components in Egyptian buffalo. Our findings provide useful information to explore the genetic mechanisms and relevant genes contributing to the variation in milk production traits. Further confirmation studies with larger population size are necessary to validate the findings and detect the causal genetic variants.

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“…The implementation of genetic evaluations in the Water Buffalo based on a BLUP animal model has been increasing over the last decade across several countries ( Agudelo-Gómez et al, 2015 ; Safari et al, 2018 ; Abdel-Shafy et al, 2020 ). The prediction of breeding values (EBVs) constitutes an integral part of most breeding programs which are based on two fundamental pillars: phenotypic data (e.g., milk production%, fat%, protein, or morphological trait) and genealogical information (i.e., a pedigree).…”

Section: Introductionmentioning

confidence: 99%

“…BLUP methodology allows for the simultaneous estimation of fixed and random effects but gaps in the relationship matrix may jeopardize its unbiasedness due to the inability of correctly estimating and disentangling genetic and environmental components ( Postma, 2006 ; Gómez et al, 2016 ; Wolak and Reid, 2017 ). Indeed, incomplete pedigree information can lead to inaccurate prediction of animal genetic potential, overestimating or underestimating animal breeding value and hampering decisions based on the selection eventually causing economic losses ( Raoul et al, 2016 ; Carneiro et al, 2017 ; Abdel-Shafy et al, 2020 ).…”

Section: Introductionmentioning

confidence: 99%

Accounting for Genetic Differences Among Unknown Parents in Bubalus bubalis: A Case Study From the Italian Mediterranean Buffalo

Gómez¹,

Rossi²,

Cimmino³

et al. 2021

Front. Genet.

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The use of genetic evaluations in the Water Buffalo by means of a Best Linear Unbiased Prediction (BLUP) animal model has been increased over the last two-decades across several countries. However, natural mating is still a common reproductive strategy that can increase the proportion of missing pedigree information. The inclusion of genetic groups in variance component (VC) and breeding value (EBV) estimation is a possible solution. The aim of this study was to evaluate two different genetic grouping strategies and their effects on VC and EBV for composite (n = 5) and linear (n = 10) type traits in the Italian Mediterranean Buffalo (IMB) population. Type traits data from 7,714 buffalo cows plus a pedigree file including 18,831 individuals were provided by the Italian National Association of Buffalo Breeders. VCs and EBVs were estimated for each trait fitting a single-trait animal model and using the official DNA-verified pedigree. Successively, EBVs were re-estimated using modified pedigrees with two different proportion of missing genealogies (30 or 60% of buffalo with records), and two different grouping strategies, year of birth (Y30/Y60) or genetic clustering (GC30, GC60). The different set of VCs, estimated EBVs and their standard errors were compared with the results obtained using the original pedigree. Results were also compared in terms of efficiency of selection. Differences among VCs varied according to the trait and the scenario considered. The largest effect was observed for two traits, udder teat and body depth in the GC60 genetic cluster, whose heritability decreased by −0.07 and increased by +0.04, respectively. Considering buffalo cows with record, the average correlation across traits between official EBVs and EBVs from different scenarios was 0.91, 0.88, 0.84, and 0.79 for Y30, CG30, Y60, and CG60, respectively. In bulls the correlations between EBVs ranged from 0.90 for fore udder attachment and udder depth to 0.96 for stature and body length in the GC30 scenario and from 0.75 for udder depth to 0.90 for stature in the GC60 scenario. When a variable proportion of missing pedigree is present using the appropriate strategy to define genetic groups and including them in VC and EBV is a worth-while and low-demanding solution.

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A single-step genomic evaluation for milk production in Egyptian buffalo

Cited by 16 publications

References 37 publications

Bubalus bubalis: A Short Story

Bubalus bubalis: A Short Story

Prospecting genomic regions associated with milk production traits in Egyptian buffalo

Accounting for Genetic Differences Among Unknown Parents in Bubalus bubalis: A Case Study From the Italian Mediterranean Buffalo

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