Scientific Reports 5

Single-copy gene based 50 K SNP chip for genetic studies and molecular breeding in rice

Nisha Singh, Pawan Kumar Jayaswal, Kabita Panda, Paritra Mandal, Vinod Kumar, Balwant Singh, Shefali Mishra, Yashi Singh, Renu Singh, Vandna Rai, Anita Gupta, Tilak Raj Sharma, Nagendra Kumar Singh.
Single nucleotide polymorphism (SNP) is the most abundant DNA sequence variation present in plant genomes. Here, we report the design and validation of a unique genic-SNP genotyping chip for genetic and evolutionary studies as well as molecular breeding applications in rice. The chip incorporates 50,051 SNPs from 18,980 different genes spanning 12 rice chromosomes, including 3,710 single-copy (SC) genes conserved between wheat and rice, 14,959 SC genes unique to rice, 194 agronomically important cloned rice genes and 117 multi-copy rice genes. Assays with this chip showed high success rate and reproducibility because of the SC gene based array with no sequence redundancy and cross-hybridisation problems. The usefulness of the chip in genetic diversity and phylogenetic studies of cultivated and wild rice germplasm was demonstrated. Furthermore, its efficacy was validated for analysing background recovery in improved mega rice varieties with submergence tolerance developed through marker-assisted backcross breeding.