biostudies-otherUnknownRavindra Reddy GundalaGerman Research FoundationGerman Federal Ministry of Food and AgricultureTriticum aestivum (wheat)https://www.ebi.ac.uk/biostudies/studies/S-BSST2136biostudies-otherPRJEB89343501899475FKZ2818408B18Jianting ChuJochen Christoph ReifYusheng ZhaoAnne FiebigRavindra Reddy GundalafalseWhole-genome shotgun resequencing of 160 wheat elite linesIn this study, we present data whole-genome shotgun resequencing of a set of 160 wheat elite lines (Table 1). The sequence data was generated at the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) using Illumina NovaSeq 6000. DNA was extracted from a single leaf that was harvested from each line from 10-day-old seedlings using the NucleoSpin 96 Plant II kit (Macherey-Nagel) following the manufacturer's protocol. The extracted DNA was then used as input for whole-genome sequencing library preparation with the Nextera DNA Flex Library Prep (Illumina) and paired-end sequencing was conducted on the NovaSeq 6000 platform with a threefold coverage. Reads with a minimum quality score (Q) of 20 were aligned to the Chinese Spring reference genome (RefSeq v2.1; Zhu et al., 2021) using the MEM algorithm of BWA with default parameters (Li 2013). The resulting alignment was converted to BAM format using SAMtools (v1.9; Li et al. 2009), followed by sorting with NovoSort (v3.06.05). Variant calling was performed using the Chinese Spring reference genome (RefSeq v2.1) through the mpileup and call functions of SAMtools with the ‘-DV’ parameter (Li 2011). Bi-allelic SNPs were called with a minimum mapping quality score of 40. Homozygous variants required a minimum read depth of 1, while heterozygous genotypes were called with a minimum total read depth of 2. This resulted in 417,254,504 single nucleotide polymorphisms for 160 genotypes2025-08-12T00:00:00Z2026-06-16T19:00:29.762Z2025-08-12T07:42:08.687ZS-BSST2136PRJEB92007PRJEB89343