Adapting Genotyping-by-Sequencing for Rice F2 Populations

• DOI: 10.1534/g3.116.038190
• Publication Date: 2017-03-10T17:25:12Z
• Authors: Tomoyuki Furuta; Motoyuki Ashikari; Kshirod K Jena; Kazuyuki Doi; Stefan Reuscher
• Keywords: Introgression; SNP genotyping

Abstract Rapid and cost-effective genotyping of large mapping populations can be achieved by sequencing a reduced representation the genome every individual in given population, using that information to generate genetic markers. A customized genotyping-by-sequencing (GBS) pipeline was developed genotype rice F2 population from cross Oryza sativa ssp. japonica cv. Nipponbare African wild species O. longistaminata. While most GBS pipelines aim analyze mainly homozygous populations, we attempted highly heterozygous population. We show how species- population-specific improvements established protocols drastically increase sample throughput quality. Using as few 50,000 reads for some individuals (134,000 on average), were able up 8154 informative SNP markers 1081 individuals. Additionally, effects enzyme choice, read coverage, data postprocessing are evaluated. GBS-derived markers, assemble map 1536 cM. To demonstrate usefulness our pipeline, determined quantitative trait loci (QTL) number tillers. four QTL chromosomes 1, 3, 4, 8, partially confirm their introgression lines. provide an example successfully use with populations. By comparatively low-cost MiSeq platform, method is flexible cost-effective, even smaller laboratories.