A combined coalescence gene-dropping tool for evaluating genomic selection in complex scenarios (ms2gs)
2016
Pérez-Enciso, Miguel | Legarra, Andres | Consejo Superior de Investigaciones Cientificas [España] = Spanish National Research Council [Spain] (CSIC) | Institució Catalana de Recerca i Estudis Avançats = Catalan Institution for Research and Advanced Studies (ICREA) | Génétique Physiologie et Systèmes d'Elevage (GenPhySE) ; Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT) ; Institut National Polytechnique (Toulouse) (Toulouse INP) ; Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP) ; Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT) ; Institut National Polytechnique (Toulouse) (Toulouse INP) ; Université de Toulouse (UT)-Université de Toulouse (UT)
International audience
اظهر المزيد [+] اقل [-]إنجليزي. We present ms2gs, a combined coalescence – gene dropping (i.e. backward–forward) simulator for complex traits. It therefore aims at combining the advantages of both approaches. It is primarily conceived for very short term, recent scenarios such as those that are of interest in animal and plant breeding. It is very flexible in terms of defining QTL architecture and SNP ascertainment bias, and it allows for easy modelling of alternative markers such as RADs. It can use real sequence or chip data or generate molecular polymorphisms via the coalescence. It can generate QTL conditional on extant molecular information, such as low-density genotyping. It models (simplistically) sequence, imputation or genotyping errors. It requires as input both genotypic data in plink or ms formats, and a pedigree that is used to perform the gene dropping. By default, it compares accuracy for BLUP, SNP ascertained data, sequence, and causal SNPs. It employs VanRaden's linear (GBLUP) and nonlinear method for incorporating molecular information. To illustrate the program, we present a small application in a half-sib population and a multiparental (MAGIC) cross. The program, manual and examples are available at https://github.com/mperezenciso/ms2gs.
اظهر المزيد [+] اقل [-]الكلمات المفتاحية الخاصة بالمكنز الزراعي (أجروفوك)
المعلومات البيبليوغرافية
تم تزويد هذا السجل من قبل Institut national de la recherche agronomique