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(Reference retrieved automatically from Web of Science through information on FAPESP grant and its corresponding number as mentioned in the publication by the authors.)

Optimizing imputation of marker data from genotyping-by-sequencing (GBS) for genomic selection in non-model species: Rubber tree (Hevea brasiliensis) as a case study

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Munyengwa, Norman [1, 2] ; Guen, Vincent Le [3, 4] ; Bille, Hermine Ngalle [2] ; Souza, Livia M. [5] ; Clement-Demange, Andre [3, 4] ; Mournet, Pierre [3, 4] ; Masson, Aurelien [6] ; Soumahoro, Mouman [7] ; Kouassi, Daouda [6] ; Cros, David [3, 4, 8]
Total Authors: 10
[1] Univ Zimbabwe, Fac Agr, Crop Sci Dept, POB MP167, Harare - Zimbabwe
[2] Univ Yaounde I, Fac Sci, Dept Plant Biol, Yaounde - Cameroon
[3] CIRAD, UMR AGAP, F-34398 Montpellier - France
[4] Univ Montpellier, INRAE, CIRAD, AGAP, Inst Agro, Montpellier - France
[5] Univ Campinas UNICAMP, Mol Biol & Genet Engn Ctr CBMEG, Campinas - Brazil
[6] SOCFIN SOGB Soc Caoutchoucs Grand Bereby, Abidjan - Cote Ivoire
[7] SAPH Soc Africaine Plantat Heveas, Abidjan - Cote Ivoire
[8] Univ Yaounde I, CETIC African Ctr Excellence Informat & Commun Te, Yaounde - Cameroon
Total Affiliations: 8
Document type: Journal article
Source: Genomics; v. 113, n. 2, p. 655-668, MAR 2021.
Web of Science Citations: 0

Genotyping-by-sequencing (GBS) provides the marker density required for genomic predictions (GP). However, GBS gives a high proportion of missing SNP data which, for species without a chromosome-level genome assembly, must be imputed without knowing the SNP physical positions. Here, we compared GP accuracy with seven map-independent and two map-dependent imputation approaches, and when using all SNPs against the subset of genetically mapped SNPs. We used two rubber tree (Hevea brasiliensis) datasets with three traits. The results showed that the best imputation approaches were LinkImputeR, Beagle and FImpute. Using the genetically mapped SNPs increased GP accuracy by 4.3%. Using LinkImputeR on all the markers allowed avoiding genetic mapping, with a slight decrease in GP accuracy. LinkImputeR gave the highest level of correctly imputed genotypes and its performances were further improved by its ability to define a subset of SNPs imputed optimally. These results will contribute to the efficient implementation of genomic selection with GBS. For Hevea, GBS is promising for rubber yield improvement, with GP accuracies reaching 0.52. (AU)

FAPESP's process: 12/05473-1 - Evaluation of the linkage desequilibrium and population structure in rubber tree ex situ germplasm (Hevea brasiliensis) using SNPs (Single Nucleotide Polymorphism)
Grantee:Livia Moura de Souza
Support Opportunities: Scholarships in Brazil - Post-Doctoral
FAPESP's process: 12/50491-8 - Evaluation of allelic variability, population structure and linkage desequilibrium in the rubber tree ex situ germoplasm (Hevea brasiliensis)
Grantee:Anete Pereira de Souza
Support Opportunities: Regular Research Grants