Development of a genomic tool for breed assignment by comparison of different classification models : Application to three local cattle breeds
© 2021 Wiley-VCH GmbH..
Assignment of individual cattle to a specific breed can often not rely on pedigree information. This is especially the case for local breeds for which the development of genomic assignment tools is required to allow individuals of unknown origin to be included to their herd books. A breed assignment model can be based on two specific stages: (a) the selection of breed-informative markers and (b) the assignment of individuals to a breed with a classification method. However, the performance of combination of methods used in these two stages has been rarely studied until now. In this study, the combination of 16 different SNP panels with four classification methods was developed on 562 reference genotypes from 12 cattle breeds. Based on their performances, best models were validated on three local breeds of interest. In cross-validation, 14 models had a global cross-validation accuracy higher than 90%, with a maximum of 98.22%. In validation, best models used 7,153 or 2,005 SNPs, based on a partial least squares-discriminant analysis (PLS-DA) and assigned individuals to breeds based on nearest shrunken centroids. The average validation sensitivity of the first two best models for the three local breeds of interest were 98.33% and 97.5%. Moreover, results reported in this study suggest that further studies should consider the PLS-DA method when selecting breed-informative SNPs.
| Medienart: |
E-Artikel |
|---|
| Erscheinungsjahr: |
2022 |
|---|---|
| Erschienen: |
2022 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:139 |
|---|---|
| Enthalten in: |
Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie - 139(2022), 1 vom: 25. Jan., Seite 40-61 |
| Sprache: |
Englisch |
|---|
| Beteiligte Personen: |
Wilmot, Hélène [VerfasserIn] |
|---|
| Links: |
|---|
| Themen: |
Breed assignment |
|---|
| Anmerkungen: |
Date Completed 16.12.2021 Date Revised 16.12.2021 published: Print-Electronic Citation Status MEDLINE |
|---|
| doi: |
10.1111/jbg.12643 |
|---|
| funding: |
|
|---|---|
| Förderinstitution / Projekttitel: |
|
| PPN (Katalog-ID): |
NLM329706268 |
|---|
| LEADER | 01000naa a22002652 4500 | ||
|---|---|---|---|
| 001 | NLM329706268 | ||
| 003 | DE-627 | ||
| 005 | 20231225205708.0 | ||
| 007 | cr uuu---uuuuu | ||
| 008 | 231225s2022 xx |||||o 00| ||eng c | ||
| 024 | 7 | |a 10.1111/jbg.12643 |2 doi | |
| 028 | 5 | 2 | |a pubmed24n1098.xml |
| 035 | |a (DE-627)NLM329706268 | ||
| 035 | |a (NLM)34427366 | ||
| 040 | |a DE-627 |b ger |c DE-627 |e rakwb | ||
| 041 | |a eng | ||
| 100 | 1 | |a Wilmot, Hélène |e verfasserin |4 aut | |
| 245 | 1 | 0 | |a Development of a genomic tool for breed assignment by comparison of different classification models |b Application to three local cattle breeds |
| 264 | 1 | |c 2022 | |
| 336 | |a Text |b txt |2 rdacontent | ||
| 337 | |a ƒaComputermedien |b c |2 rdamedia | ||
| 338 | |a ƒa Online-Ressource |b cr |2 rdacarrier | ||
| 500 | |a Date Completed 16.12.2021 | ||
| 500 | |a Date Revised 16.12.2021 | ||
| 500 | |a published: Print-Electronic | ||
| 500 | |a Citation Status MEDLINE | ||
| 520 | |a © 2021 Wiley-VCH GmbH. | ||
| 520 | |a Assignment of individual cattle to a specific breed can often not rely on pedigree information. This is especially the case for local breeds for which the development of genomic assignment tools is required to allow individuals of unknown origin to be included to their herd books. A breed assignment model can be based on two specific stages: (a) the selection of breed-informative markers and (b) the assignment of individuals to a breed with a classification method. However, the performance of combination of methods used in these two stages has been rarely studied until now. In this study, the combination of 16 different SNP panels with four classification methods was developed on 562 reference genotypes from 12 cattle breeds. Based on their performances, best models were validated on three local breeds of interest. In cross-validation, 14 models had a global cross-validation accuracy higher than 90%, with a maximum of 98.22%. In validation, best models used 7,153 or 2,005 SNPs, based on a partial least squares-discriminant analysis (PLS-DA) and assigned individuals to breeds based on nearest shrunken centroids. The average validation sensitivity of the first two best models for the three local breeds of interest were 98.33% and 97.5%. Moreover, results reported in this study suggest that further studies should consider the PLS-DA method when selecting breed-informative SNPs | ||
| 650 | 4 | |a Journal Article | |
| 650 | 4 | |a SNP panel | |
| 650 | 4 | |a breed assignment | |
| 650 | 4 | |a classification | |
| 650 | 4 | |a informative SNPs | |
| 650 | 4 | |a local breeds | |
| 650 | 4 | |a partial least squares | |
| 700 | 1 | |a Bormann, Jeanne |e verfasserin |4 aut | |
| 700 | 1 | |a Soyeurt, Hélène |e verfasserin |4 aut | |
| 700 | 1 | |a Hubin, Xavier |e verfasserin |4 aut | |
| 700 | 1 | |a Glorieux, Géry |e verfasserin |4 aut | |
| 700 | 1 | |a Mayeres, Patrick |e verfasserin |4 aut | |
| 700 | 1 | |a Bertozzi, Carlo |e verfasserin |4 aut | |
| 700 | 1 | |a Gengler, Nicolas |e verfasserin |4 aut | |
| 773 | 0 | 8 | |i Enthalten in |t Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie |d 1993 |g 139(2022), 1 vom: 25. Jan., Seite 40-61 |w (DE-627)NLM156932512 |x 1439-0388 |7 nnns |
| 773 | 1 | 8 | |g volume:139 |g year:2022 |g number:1 |g day:25 |g month:01 |g pages:40-61 |
| 856 | 4 | 0 | |u http://dx.doi.org/10.1111/jbg.12643 |3 Volltext |
| 912 | |a GBV_USEFLAG_A | ||
| 912 | |a GBV_NLM | ||
| 951 | |a AR | ||
| 952 | |d 139 |j 2022 |e 1 |b 25 |c 01 |h 40-61 | ||