Genotypic data, phenotypic data and GWAS summary statistics for 1129 triploid banana hybrids evaluated for 24 agro-morphological traits in Guadeloupe (2011-2016) and genotyped-by-sequencing for 200K single-nucleotide-polymorphism markers

Version 1.0
Rio, Simon; Toniutti, Lucile; Salmon, Frédéric; Hervouet, Catherine; Cardi, Céline; Mournet, Pierre; Guiougou, Chantal; Marius, Franck; Mina, Claude; Delos, Jean-Marie; Lambert, Frédéric; Madec, Camille; Efile, Jean-Claude; Cruaud, Corinne; Aury, Jean-Marc; D'Hont Angélique; Hoarau, Jean-Yves; Martin, Guillaume, 2024, "Genotypic data, phenotypic data and GWAS summary statistics for 1129 triploid banana hybrids evaluated for 24 agro-morphological traits in Guadeloupe (2011-2016) and genotyped-by-sequencing for 200K single-nucleotide-polymorphism markers", https://doi.org/10.18167/DVN1/FTM7GC, CIRAD Dataverse, V1
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Description
Data include:
(i) variant call format (VCF) for 1129 triploid banana hybrids from biparental crosses implying 38 M. acuminata accessions genotyped for 200K bi-allelic single nucleotide polymorphisms obtained by genotyping-by-sequencing,
(ii) a table (TSV) presenting best linear unbiased prediction of genotypic effects for 24 agro-morphological traits evaluated between 2011 and 2020 at CIRAD Neufchateau station, Capesterre Belle-Eau, Guadeloupe, French West Indies (16°05’N, 61°35’W), along with pedigree information for 2727 triploid banana hybrids including the 1129 genotyped hybrids,
(iii) an archive (TAR.GZ) of genome-wide association study summary statistics obtained from the standard K model, and
(iv) an archive (TAR.GZ) of genome-wide association study summary statistics obtained from the Kc model with chromosome-specific kinships that aims at recovering statistical power at alleles carried by long non-recombined haplotypic segments
Subject Agricultural Sciences
Keyword Musa acuminata, genome-wide association studies, genetics
Related Publication Rio, S., Toniutti, L., Salmon, F., Hervouet, C., Cardi, C., Mournet, P., Guiougou, C., Marius, F., Mina, C., Delos, J.M., Lambert, F., Madec, C., Efile, J.C., Cruaud, C., Aury, J.M., D'Hont, A., Hoarau, J.Y., Martin, G. (2024) Genome-wide association for agro-morphological traits in a triploid banana population with large chromosome rearrangements. Horticulture Research: uhae307. https://doi.org/10.1093/hr/uhae307
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Genotyping_1129hybrids_200Ksnps.vcf.gz
Gzip Archive - 759,2 MB
Published 8 nov. 2024
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MD5: 846dfdb752f869fae1bf874e7e65dca4
Variant Call Format (VCF) for 1129 triploid banana hybrids genotyped for 200K bi-allelic single nucleotide polymorphisms obtained by genotyping-by-sequencing
GWAS_summary_stats_Kc_model.tar.gz
Gzip Archive - 897,4 MB
Published 8 nov. 2024
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MD5: ff576752f521995903dc6cbc31d9483c
Archive (TAR.GZ) of genome-wide association study summary statistics obtained from the Kc model for 24 agro-morphological traits: pseudostem height, pseudostem girth, robustness index, number of leaves at flowering, number of leaves at harvesting, leaf blade length, leaf blade width, leaf index, bunch angle, peduncle length, peduncle diameter, peduncle index, bunch length at maturity, bunch compactness index, fruit pedicel length, fruit pedicel diameter, fruit length, fruit grade, number of hands on a bunch, number of fruits on a bunch, number of fruits per hand, bunch weight, fruit weight, and days to fruit maturity
GWAS_summary_stats_K_model.tar.gz
Gzip Archive - 897,4 MB
Published 8 nov. 2024
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MD5: a98183f275761145bcfdf24a19ec79b5
Archive (TAR.GZ) of genome-wide association study summary statistics obtained from the standard K model for 24 agro-morphological traits: pseudostem height, pseudostem girth, robustness index, number of leaves at flowering, number of leaves at harvesting, leaf blade length, leaf blade width, leaf index, bunch angle, peduncle length, peduncle diameter, peduncle index, bunch length at maturity, bunch compactness index, fruit pedicel length, fruit pedicel diameter, fruit length, fruit grade, number of hands on a bunch, number of fruits on a bunch, number of fruits per hand, bunch weight, fruit weight, and days to fruit maturity
Phenotyping_2727hybrids_24traits.tsv
Tab-Separated Values - 1,3 MB
Published 8 nov. 2024
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MD5: 560e948cdcee4b8150247a6e832f5bcd
Table (TSV) presenting best linear unbiased prediction of genotypic effects for 24 agro-morphological traits along with pedigree information for 2727 triploid banana hybrids, including four checks and 1464 hybrids which were genotyped-by-sequencing. Among the 1464 hybrids genotyped, 1129 hybrids were conserved in the VCF for genome-wide association study after filtering steps. Columns include: "Hybrid" name in experimental design, "Genotyping ID" in the VCF, "Parent (2x)", "Parent (4x)", "Cross (female x male)", "Cross (2x x 4x)", and one column for each of the 24 traits
Preview "Phenotyping_2727hybrids_24traits.tsv"
README.md
Markdown Text - 5,4 KB
Published 8 nov. 2024
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MD5: ccb11091c22ba7bb7bd58d1c435d1168
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