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Long-term impact of conventional and optimal contribution conservation methods on genetic diversity and genetic gain in local pig breeds

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Long-term impact of conventional and optimal contribution conservation methods on genetic diversity and genetic gain in local pig breeds. / Zhao, Qingbo; Liu, Huiming; Qadri, Qamar Raza et al.

In: Heredity, Vol. 127, No. 6, 12.2021, p. 546-553.

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@article{a00a368a88524958a745061e51ffc1cb,
title = "Long-term impact of conventional and optimal contribution conservation methods on genetic diversity and genetic gain in local pig breeds",
abstract = "There are rich and vast genetic resources of indigenous pig breeds in the world. Currently, great attention is paid to either crossbreeding or conservation of these indigenous pig breeds, and insufficient attention is paid to the combination of conservation and breeding along with their long-term effects on genetic diversity. Therefore, the objective of this study is to compare the long-term effects of using conventional conservation and optimal contribution selection methods on genetic diversity and genetic gain. A total of 11 different methods including conventional conservation and optimal contribution selection methods were investigated using stochastic simulations. The long-term effects of using these methods were evaluated in terms of genetic diversity metrices such as expected heterozygosity (He) and the rate of genetic gain. The results indicated that the rates of true inbreeding in these conventional conservation methods were maintained at around 0.01. The optimal contribution selection methods based either on the pedigree (POCS) or genome (GOCS) information showed more genetic gain than conventional methods, and POCS achieved the largest genetic gain. Furthermore, the effect of using GOCS methods on most of the genetic diversity metrics was slightly better than the conventional conservation methods when the rate of true inbreeding was the same, but this also required more sires used in OCS methods. According to the rate of true inbreeding, there was no significant difference among these conventional methods. In conclusion, there is no significant difference in different ways of selecting sows on inbreeding when we use different conventional conservation methods. Compared with conventional methods, POCS method could achieve the most genetic gain. However, GOCS methods can not only achieve higher genetic gain, but also maintain a relatively high level of genetic diversity. Therefore, GOCS is a better choice if we want to combine conservation and breeding in actual production in the conservation farms.",
keywords = "CONTRIBUTION SELECTION, GENOMIC SELECTION, POPULATIONS, PREDICTION, RATES, SCHEMES, TRAITS",
author = "Qingbo Zhao and Huiming Liu and Qadri, {Qamar Raza} and Qishan Wang and Yuchun Pan and Guosheng Su",
year = "2021",
month = dec,
doi = "10.1038/s41437-021-00484-z",
language = "English",
volume = "127",
pages = "546--553",
journal = "Heredity",
issn = "0018-067X",
publisher = "Nature Publishing Group",
number = "6",

}

RIS

TY - JOUR

T1 - Long-term impact of conventional and optimal contribution conservation methods on genetic diversity and genetic gain in local pig breeds

AU - Zhao, Qingbo

AU - Liu, Huiming

AU - Qadri, Qamar Raza

AU - Wang, Qishan

AU - Pan, Yuchun

AU - Su, Guosheng

PY - 2021/12

Y1 - 2021/12

N2 - There are rich and vast genetic resources of indigenous pig breeds in the world. Currently, great attention is paid to either crossbreeding or conservation of these indigenous pig breeds, and insufficient attention is paid to the combination of conservation and breeding along with their long-term effects on genetic diversity. Therefore, the objective of this study is to compare the long-term effects of using conventional conservation and optimal contribution selection methods on genetic diversity and genetic gain. A total of 11 different methods including conventional conservation and optimal contribution selection methods were investigated using stochastic simulations. The long-term effects of using these methods were evaluated in terms of genetic diversity metrices such as expected heterozygosity (He) and the rate of genetic gain. The results indicated that the rates of true inbreeding in these conventional conservation methods were maintained at around 0.01. The optimal contribution selection methods based either on the pedigree (POCS) or genome (GOCS) information showed more genetic gain than conventional methods, and POCS achieved the largest genetic gain. Furthermore, the effect of using GOCS methods on most of the genetic diversity metrics was slightly better than the conventional conservation methods when the rate of true inbreeding was the same, but this also required more sires used in OCS methods. According to the rate of true inbreeding, there was no significant difference among these conventional methods. In conclusion, there is no significant difference in different ways of selecting sows on inbreeding when we use different conventional conservation methods. Compared with conventional methods, POCS method could achieve the most genetic gain. However, GOCS methods can not only achieve higher genetic gain, but also maintain a relatively high level of genetic diversity. Therefore, GOCS is a better choice if we want to combine conservation and breeding in actual production in the conservation farms.

AB - There are rich and vast genetic resources of indigenous pig breeds in the world. Currently, great attention is paid to either crossbreeding or conservation of these indigenous pig breeds, and insufficient attention is paid to the combination of conservation and breeding along with their long-term effects on genetic diversity. Therefore, the objective of this study is to compare the long-term effects of using conventional conservation and optimal contribution selection methods on genetic diversity and genetic gain. A total of 11 different methods including conventional conservation and optimal contribution selection methods were investigated using stochastic simulations. The long-term effects of using these methods were evaluated in terms of genetic diversity metrices such as expected heterozygosity (He) and the rate of genetic gain. The results indicated that the rates of true inbreeding in these conventional conservation methods were maintained at around 0.01. The optimal contribution selection methods based either on the pedigree (POCS) or genome (GOCS) information showed more genetic gain than conventional methods, and POCS achieved the largest genetic gain. Furthermore, the effect of using GOCS methods on most of the genetic diversity metrics was slightly better than the conventional conservation methods when the rate of true inbreeding was the same, but this also required more sires used in OCS methods. According to the rate of true inbreeding, there was no significant difference among these conventional methods. In conclusion, there is no significant difference in different ways of selecting sows on inbreeding when we use different conventional conservation methods. Compared with conventional methods, POCS method could achieve the most genetic gain. However, GOCS methods can not only achieve higher genetic gain, but also maintain a relatively high level of genetic diversity. Therefore, GOCS is a better choice if we want to combine conservation and breeding in actual production in the conservation farms.

KW - CONTRIBUTION SELECTION

KW - GENOMIC SELECTION

KW - POPULATIONS

KW - PREDICTION

KW - RATES

KW - SCHEMES

KW - TRAITS

UR - http://www.scopus.com/inward/record.url?scp=85118664371&partnerID=8YFLogxK

U2 - 10.1038/s41437-021-00484-z

DO - 10.1038/s41437-021-00484-z

M3 - Journal article

C2 - 34750534

VL - 127

SP - 546

EP - 553

JO - Heredity

JF - Heredity

SN - 0018-067X

IS - 6

ER -