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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.
Keywords: tGBS, SNP identification, functional annotation, background genome recovery
Umer Maqsood, Jauhar Al, Ma. Anna Lynn Sevilla, Muhammad Arif. (2022) Basmati genome recovery and functional annotation using tunable-genotyping by sequencing, Pakistan Journal of Agricultural Sciences, Volume 59, Issue 3.
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