Genotyping more cows increases genetic gain and reduces rate of true inbreeding in a dairy cattle breeding scheme using female reproductive technologies

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Genotyping more cows increases genetic gain and reduces rate of true inbreeding in a dairy cattle breeding scheme using female reproductive technologies. / Thomasen, J. R.; Liu, Huiming; Sørensen, A. C.

I: Journal of Dairy Science, Bind 103, Nr. 1, 01.01.2020, s. 597-606.

Publikation: Bidrag til tidsskrift/Konferencebidrag i tidsskrift /Bidrag til avisTidsskriftartikelForskningpeer review

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@article{2dcf1878349b429fafcd498af4d6f363,
title = "Genotyping more cows increases genetic gain and reduces rate of true inbreeding in a dairy cattle breeding scheme using female reproductive technologies",
abstract = "Both small dairy cattle populations and dairy cattle populations with a low level of linkage disequilibrium (LD) suffer from low reliability of genomic prediction. In this study, we investigated whether adding more genotyped cows to the reference population influences the rate of genetic gain and rate of inbreeding by affecting the reliability. A standard breeding program with a large reference population and high LD, which mimicked a breeding program for Danish Holstein population, was simulated as a reference. A Danish Jersey population with a small reference population and high LD and a Red Dairy Cattle population with a large reference population and low LD were also simulated. Two additional breeding programs were simulated for Danish Jersey and Red Dairy Cattle populations, where 2,000 additional genotyped cows were included in the population for genomic selection. All 5 simulated breeding programs were initiated by a founder population to generate LD resembling the real LD pattern, followed by a 20-yr conventional progeny-testing scheme with 1,000 or 10,000 genotyped progeny-tested bulls and a 10-yr genomic selection scheme with or without 2,000 additional genotyped cows. Evaluation criteria were annual monetary genetic gain and rate of true inbreeding. Our results showed that adding more genotyped cows to the reference in dairy cattle populations has the potential to increase genetic gain and reduce the rate of inbreeding, regardless of reference population size and level of LD. However, it is still not possible to reach the same genetic gain as in the simulated Danish Holstein population with either a small reference population or low LD. Our results also showed that in a small reference population with high LD, it is difficult to manage inbreeding because of lower accuracy compared with the simulated Danish Holstein population and a smaller number of relevant families to select from. Therefore, breeding strategies need to be chosen to match population size and structure. The rate of true inbreeding is always underestimated by pedigree inbreeding and even more in genomic breeding programs, indicating that some forms of genome-wide inbreeding, instead of pedigree-based inbreeding, should be used to monitor inbreeding when genomic selection is implemented.",
keywords = "genomic selection, genotyped cow, inbreeding, reference population and linkage disequilibrium",
author = "Thomasen, {J. R.} and Huiming Liu and S{\o}rensen, {A. C.}",
year = "2020",
month = jan,
day = "1",
doi = "10.3168/jds.2019-16974",
language = "English",
volume = "103",
pages = "597--606",
journal = "Journal of Dairy Science",
issn = "0022-0302",
publisher = "Elsevier Inc.",
number = "1",

}

RIS

TY - JOUR

T1 - Genotyping more cows increases genetic gain and reduces rate of true inbreeding in a dairy cattle breeding scheme using female reproductive technologies

AU - Thomasen, J. R.

AU - Liu, Huiming

AU - Sørensen, A. C.

PY - 2020/1/1

Y1 - 2020/1/1

N2 - Both small dairy cattle populations and dairy cattle populations with a low level of linkage disequilibrium (LD) suffer from low reliability of genomic prediction. In this study, we investigated whether adding more genotyped cows to the reference population influences the rate of genetic gain and rate of inbreeding by affecting the reliability. A standard breeding program with a large reference population and high LD, which mimicked a breeding program for Danish Holstein population, was simulated as a reference. A Danish Jersey population with a small reference population and high LD and a Red Dairy Cattle population with a large reference population and low LD were also simulated. Two additional breeding programs were simulated for Danish Jersey and Red Dairy Cattle populations, where 2,000 additional genotyped cows were included in the population for genomic selection. All 5 simulated breeding programs were initiated by a founder population to generate LD resembling the real LD pattern, followed by a 20-yr conventional progeny-testing scheme with 1,000 or 10,000 genotyped progeny-tested bulls and a 10-yr genomic selection scheme with or without 2,000 additional genotyped cows. Evaluation criteria were annual monetary genetic gain and rate of true inbreeding. Our results showed that adding more genotyped cows to the reference in dairy cattle populations has the potential to increase genetic gain and reduce the rate of inbreeding, regardless of reference population size and level of LD. However, it is still not possible to reach the same genetic gain as in the simulated Danish Holstein population with either a small reference population or low LD. Our results also showed that in a small reference population with high LD, it is difficult to manage inbreeding because of lower accuracy compared with the simulated Danish Holstein population and a smaller number of relevant families to select from. Therefore, breeding strategies need to be chosen to match population size and structure. The rate of true inbreeding is always underestimated by pedigree inbreeding and even more in genomic breeding programs, indicating that some forms of genome-wide inbreeding, instead of pedigree-based inbreeding, should be used to monitor inbreeding when genomic selection is implemented.

AB - Both small dairy cattle populations and dairy cattle populations with a low level of linkage disequilibrium (LD) suffer from low reliability of genomic prediction. In this study, we investigated whether adding more genotyped cows to the reference population influences the rate of genetic gain and rate of inbreeding by affecting the reliability. A standard breeding program with a large reference population and high LD, which mimicked a breeding program for Danish Holstein population, was simulated as a reference. A Danish Jersey population with a small reference population and high LD and a Red Dairy Cattle population with a large reference population and low LD were also simulated. Two additional breeding programs were simulated for Danish Jersey and Red Dairy Cattle populations, where 2,000 additional genotyped cows were included in the population for genomic selection. All 5 simulated breeding programs were initiated by a founder population to generate LD resembling the real LD pattern, followed by a 20-yr conventional progeny-testing scheme with 1,000 or 10,000 genotyped progeny-tested bulls and a 10-yr genomic selection scheme with or without 2,000 additional genotyped cows. Evaluation criteria were annual monetary genetic gain and rate of true inbreeding. Our results showed that adding more genotyped cows to the reference in dairy cattle populations has the potential to increase genetic gain and reduce the rate of inbreeding, regardless of reference population size and level of LD. However, it is still not possible to reach the same genetic gain as in the simulated Danish Holstein population with either a small reference population or low LD. Our results also showed that in a small reference population with high LD, it is difficult to manage inbreeding because of lower accuracy compared with the simulated Danish Holstein population and a smaller number of relevant families to select from. Therefore, breeding strategies need to be chosen to match population size and structure. The rate of true inbreeding is always underestimated by pedigree inbreeding and even more in genomic breeding programs, indicating that some forms of genome-wide inbreeding, instead of pedigree-based inbreeding, should be used to monitor inbreeding when genomic selection is implemented.

KW - genomic selection

KW - genotyped cow

KW - inbreeding

KW - reference population and linkage disequilibrium

UR - http://www.scopus.com/inward/record.url?scp=85075437629&partnerID=8YFLogxK

U2 - 10.3168/jds.2019-16974

DO - 10.3168/jds.2019-16974

M3 - Journal article

C2 - 31733861

AN - SCOPUS:85075437629

VL - 103

SP - 597

EP - 606

JO - Journal of Dairy Science

JF - Journal of Dairy Science

SN - 0022-0302

IS - 1

ER -