Basmati genome recovery and functional annotation using tunable-genotyping by sequencing

Basmati rice is famous for its aroma and cooking quality around the world. Many biotic and abiotic factors have role in Basmati yield reduction. The development of high-yielding, stress-resilient varieties, using molecular breeding tools is the aim of different breeding programs. Among available genotyping techniques, Tunable Genotyping By Sequencing (tGBS) has an advantage by giving a fewer missing positions and more accurate SNPs. In the current study, we used tGBS for Basmati genome recovery and functional SNP annotation among Super Basmati (recurrent parent), IRBB57 and IR55419-04 (donor parents), with four progeny lines. Among these lines NIBGE-BR1 and NIBGE-BR18 are BLB resistant lines developed by the cross of Super Basmati (recurrent parent) and IRBB57 as donor parent. Similarly, NIBGE-DT11 and NIBGE-DT12 are drought resistant lines developed through cross of Super Basmati (recurrent parent) with drought resistant IRRI bred IR55419-04. The Ion Proton run yielded 2050620 raw reads with 84.3% of reads aligning to the reference genome. 61% reads were retained as uniquely aligned reads with average read depth of 15.4. SNPs were filtered maintaining minimum call rate of 50% and a final set of 4206 MCR50 SNPs was obtained. Phylogenetic analysis showed that selected progeny lines were genetically closer to recurrent parent. Background genome recovery analysis also confirmed that progeny lines carrying 88% to 90% of Super Basmati genome. Functional annotation showed 20 non-synonymous SNPs having a deleterious effect. Out of these seven highly deleterious SNPs were further probed for their functional importance and the status of these SNPs in rice lines currently being used has been discussed. Further studies of these SNPs may be helpful in the development of new stress related genomic markers.