Study on essential derivation in maize: III. Selection and evaluation of a panel of single nucleotide polymorphism loci for use in European and North American germplasm
Yves Rousselle
(1)
,
Elizabeth Jones
(2)
,
Alain Charcosset
(1)
,
Philippe Moreau
(3)
,
Kelly Robbins
(4)
,
Benjamin Stich
(5)
,
Carsten Knaak
(6)
,
Pascal Flament
(7, 8)
,
Zivian Karaman
(8)
,
Jean-Pierre Martinant
(8)
,
Michael Fourneau
(9)
,
Alain Taillardat
(9)
,
Michel Romestant
(10)
,
Claude Tabel
(10)
,
Javier Bertran
(11)
,
Nicolas Ranc
(11)
,
Denis Lespinasse
(11)
,
Philippe Blanchard
(3)
,
Alex Kahler
(12)
,
Jialiang Chen
(13)
,
Jonathan Kahler
(12)
,
Seth Dobrin
(14)
,
Todd Warner
(11)
,
Ron Ferris
(2)
,
Stephen Smith
(15)
1
GQE-Le Moulon -
Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale)
2 Syngenta Biotechnology inc
3 Laboratoire de Génétique Moléculaire
4 Dow AgroSciences
5 MPIPZ - Max Planck Institute for Plant Breeding Research
6 KWS SAAT SE & Co.KGaA
7 Limagrain Europe
8 Laboratoire de génotypage
9 Maïsadour Semences
10 Rouergue Auvergne Gévaudan Tarnais
11 Syngenta France
12 Biogenetics Services
13 AgReliant Genetics
14 Monsanto Company
15 DuPont Pioneer
2 Syngenta Biotechnology inc
3 Laboratoire de Génétique Moléculaire
4 Dow AgroSciences
5 MPIPZ - Max Planck Institute for Plant Breeding Research
6 KWS SAAT SE & Co.KGaA
7 Limagrain Europe
8 Laboratoire de génotypage
9 Maïsadour Semences
10 Rouergue Auvergne Gévaudan Tarnais
11 Syngenta France
12 Biogenetics Services
13 AgReliant Genetics
14 Monsanto Company
15 DuPont Pioneer
Yves Rousselle
- Fonction : Auteur
- PersonId : 737918
- IdHAL : yves-rousselle
- ORCID : 0000-0001-9520-0862
- IdRef : 145466302
Alain Charcosset
- Fonction : Auteur
- PersonId : 958141
- ORCID : 0000-0001-6125-503X
- IdRef : 120256932
Philippe Moreau
- Fonction : Auteur
- PersonId : 759214
- ORCID : 0000-0003-1780-8746
Philippe Blanchard
- Fonction : Auteur
- PersonId : 178310
- IdHAL : philippeblanchard-hal
- ORCID : 0000-0002-9408-8108
- IdRef : 090186532
Stephen Smith
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- Fonction : Auteur correspondant
- PersonId : 1010186
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Résumé
Pairwise distance data for maize (Zea mays L.) inbred lines generated using sets of single nucleotide polymorphisms (SNPs) selected from a 50k Infinium array were compared with pairwise distances generated using a set of 163 simple sequence repeat (SSR) loci previously identified to help determine essentially derived variety (EDV) status (UPOV, 1991). Final comparisons were made using 26,874 SNPs after discarding SNPs with insufficient data quality or vulnerability to ascertainment bias. Inbred lines developed in the United States or in western Europe that had been previously published to establish SSR-based thresholds provided the means to determine equivalent SNP-based protocols. Use of 3072 SNPs selected to provide even genomic coverage according to genetic and physical maps provided robust, precise, high discrimination among inbred lines with consistent zonal classification with up to 20% missing data. Comparisons of intercepts and slopes for SSR and SNP inbred pairwise distance data translated the 82% SSR green-orange similarity threshold to 91% using SNPs and the 90% SSR orange-red threshold to 95% using SNPs. Information required to conduct analyses using these 3072 SNPS is presented.