The prediction of genetic structure of East African smallholder dairy cattle

Shalanee Weerasinghe; Cedric Gondro; M Gilbert Jeyaruban; O Mwai; D F Mjuibi; John Gibson

The prediction of genetic structure of East African smallholder dairy cattle

Shalanee Weerasinghe
, Cedric Gondro
, M Gilbert Jeyaruban
, O Mwai
, D F Mjuibi
, John Gibson

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

Abstract

Identification of genetic structure and estimation of individual breed proportions in livestock species based on molecular data have become important tools in improvement of breeding programs in the developed world. In this study, we have applied high density SNP assays to understand genetic structure and breed composition of a developing world smallholder dairy system, which does not have pedigree records. Approximately 2000 East African smallholder crossbred dairy cattle were genotyped for 770k SNP. Principal component analysis (PCA) was used to identify the genetic structure and the ADMIXTURE program was used to estimate the proportional breed composition of individual animals. Genomic prediction and farmer prediction for breed proportions were compared. PCA revealed that the range of breed composition of smallholder dairy cattle is much larger than commonly believed. The correlation between breed proportion estimated using ADMIXTURE and the farmer's assessment of breed proportion was only 0.4, revealing that in this system farmers do not have a good understanding of the breed composition of their animals. This will be a problem to be overcome if farmers are to make optimum breeding choices to produce replacement heifers.

Original language	English
Title of host publication	Proceedings of the Association for the Advancement of Animal Breeding and Genetics
Editors	Nicolas Lopez Villalobos
Place of Publication	Armidale, Australia
Publisher	Association for the Advancement of Animal Breeding and Genetics (AAABG)
Pages	163-166
Volume	20
ISBN (Print)	9780473260569
Publication status	Published - 2013
Event	AAABG 2013: 20th Conference of the Association for the Advancement of Animal Breeding and Genetics: Translating Science into Action - Napier, New Zealand Duration: 20 Oct 2013 → 23 Oct 2013

Conference

Conference	AAABG 2013: 20th Conference of the Association for the Advancement of Animal Breeding and Genetics: Translating Science into Action
City	Napier, New Zealand
Period	20/10/13 → 23/10/13

Keywords

Population, Ecological and Evolutionary Genetics

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https://hdl.handle.net/1959.11/14141

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Weerasinghe, S., Gondro, C., Jeyaruban, M. G., Mwai, O., Mjuibi, D. F., & Gibson, J. (2013). The prediction of genetic structure of East African smallholder dairy cattle. In N. Lopez Villalobos (Ed.), Proceedings of the Association for the Advancement of Animal Breeding and Genetics (Vol. 20, pp. 163-166). Association for the Advancement of Animal Breeding and Genetics (AAABG). https://hdl.handle.net/1959.11/14141

Weerasinghe, Shalanee ; Gondro, Cedric ; Jeyaruban, M Gilbert et al. / The prediction of genetic structure of East African smallholder dairy cattle. Proceedings of the Association for the Advancement of Animal Breeding and Genetics. editor / Nicolas Lopez Villalobos. Vol. 20 Armidale, Australia : Association for the Advancement of Animal Breeding and Genetics (AAABG), 2013. pp. 163-166

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title = "The prediction of genetic structure of East African smallholder dairy cattle",

abstract = "Identification of genetic structure and estimation of individual breed proportions in livestock species based on molecular data have become important tools in improvement of breeding programs in the developed world. In this study, we have applied high density SNP assays to understand genetic structure and breed composition of a developing world smallholder dairy system, which does not have pedigree records. Approximately 2000 East African smallholder crossbred dairy cattle were genotyped for 770k SNP. Principal component analysis (PCA) was used to identify the genetic structure and the ADMIXTURE program was used to estimate the proportional breed composition of individual animals. Genomic prediction and farmer prediction for breed proportions were compared. PCA revealed that the range of breed composition of smallholder dairy cattle is much larger than commonly believed. The correlation between breed proportion estimated using ADMIXTURE and the farmer's assessment of breed proportion was only 0.4, revealing that in this system farmers do not have a good understanding of the breed composition of their animals. This will be a problem to be overcome if farmers are to make optimum breeding choices to produce replacement heifers.",

keywords = "Population, Ecological and Evolutionary Genetics",

author = "Shalanee Weerasinghe and Cedric Gondro and Jeyaruban, \{M Gilbert\} and O Mwai and Mjuibi, \{D F\} and John Gibson",

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publisher = "Association for the Advancement of Animal Breeding and Genetics (AAABG)",

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Weerasinghe, S, Gondro, C, Jeyaruban, MG, Mwai, O, Mjuibi, DF & Gibson, J 2013, The prediction of genetic structure of East African smallholder dairy cattle. in N Lopez Villalobos (ed.), Proceedings of the Association for the Advancement of Animal Breeding and Genetics. vol. 20, Association for the Advancement of Animal Breeding and Genetics (AAABG), Armidale, Australia, pp. 163-166, AAABG 2013: 20th Conference of the Association for the Advancement of Animal Breeding and Genetics: Translating Science into Action, Napier, New Zealand, 20/10/13. <https://hdl.handle.net/1959.11/14141>

The prediction of genetic structure of East African smallholder dairy cattle. / Weerasinghe, Shalanee; Gondro, Cedric; Jeyaruban, M Gilbert et al.
Proceedings of the Association for the Advancement of Animal Breeding and Genetics. ed. / Nicolas Lopez Villalobos. Vol. 20 Armidale, Australia: Association for the Advancement of Animal Breeding and Genetics (AAABG), 2013. p. 163-166.

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

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AB - Identification of genetic structure and estimation of individual breed proportions in livestock species based on molecular data have become important tools in improvement of breeding programs in the developed world. In this study, we have applied high density SNP assays to understand genetic structure and breed composition of a developing world smallholder dairy system, which does not have pedigree records. Approximately 2000 East African smallholder crossbred dairy cattle were genotyped for 770k SNP. Principal component analysis (PCA) was used to identify the genetic structure and the ADMIXTURE program was used to estimate the proportional breed composition of individual animals. Genomic prediction and farmer prediction for breed proportions were compared. PCA revealed that the range of breed composition of smallholder dairy cattle is much larger than commonly believed. The correlation between breed proportion estimated using ADMIXTURE and the farmer's assessment of breed proportion was only 0.4, revealing that in this system farmers do not have a good understanding of the breed composition of their animals. This will be a problem to be overcome if farmers are to make optimum breeding choices to produce replacement heifers.

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ER -

Weerasinghe S, Gondro C, Jeyaruban MG, Mwai O, Mjuibi DF, Gibson J. The prediction of genetic structure of East African smallholder dairy cattle. In Lopez Villalobos N, editor, Proceedings of the Association for the Advancement of Animal Breeding and Genetics. Vol. 20. Armidale, Australia: Association for the Advancement of Animal Breeding and Genetics (AAABG). 2013. p. 163-166

The prediction of genetic structure of East African smallholder dairy cattle

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Conference

Keywords

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