Genome wide SNPs data generated using GBS on forage type hybrid parents in Pearl millet

This data set contains single nucleotide polymorphism (SNP) markers identified by genotyping by sequencing (GBS) approach, and was used to identify marker-trait association for forage quality traits crude protein (CP) and in vitro organic matter digestibility (IVOMD) among 105 forage type hybrid parents. The DNA of 105 hybrid parents was genotyped using GBS by digesting DNA with ApeKI endonuclease restriction enzyme. PCR (Polymerase chain reaction) amplification of pooled amplicons was carried out before sequencing on Illumina Hiseq2500 platform. Raw sequencing reads and barcode information were processed for SNP identification from the published pearl millet reference genome using TASSEL v4.0 software. Barcode containing reads were retained and used for SNP calling. These reads were trimmed to 64 bp from barcode side, aligned against each other and used for SNP identification. The identified SNPs were assigned to each hybrid parent based on the information of the barcode sequence. Further, the SNP data were filtered with minor allele frequency (MAF) cut off of 0.10 (10%) and SNP with ≥25% missing data. These were further filtered for site coverage (90%), minor allele frequency (0.05), and maximum heterozygosity (50%); 34, 691 SNPs were identified and used for the GWAS analysis. One SNP was identified on LG4 for CP, and nine SNPs for IVOMD distributed across all linkage groups except on LG2. Results generated from this study could help breeders to improve the forage productivity in their breeding programs. <br><br> <b><a href="https://www.google.com/maps/d/u/0/viewer?mid=13LximEQA9zGvjOcjE08tW_A97WwfRdPV&ll=11.024382169097601%2C76.92611855679762&z=17">Experiment location on Google Map</a> </b> <br> <br> <b><a href="https://www.google.com/maps/d/u/0/viewer?mid=19VptTaVZ0uWBc5boSTA-Z2B8_MF0fLA9&ll=17.506608054545282%2C78.27348445000003&z=16">Experiment location on Google Map</a> </b> <br> <br>