Exploration of SNORKEL1 ( SK1 ) and SNORKEL2 ( SK2 ) QTLs in Deep Water Rice Germplasm Through Genotyping and In-silico Approach

Abstract

The molecular screening of deep water rice landraces showed that out of 21 landraces, 15 landraces possess the SNORKEL1 (SK1) and SNORKEL2 (SK2) genes conferring stem elongation of paddy plant survive in increased water level of deep water ecosystem. Both genes/Quantitative trait loci (QTLs) were subjected to study through in-silico approaches. The fasta sequences, secondary structure and 3D structure of those proteins were identified and verified using bioinformatics tools. The physico-chemical properties and functions were also predicted. The in-silico study of SNORKEL1 (SK1) and SNORKEL2 (SK2) QTL have also revealed the capacity and way of survival of deep water rice germplasm noticeably. This study illustrates the many deep water rice varieties having SNORKEL1 (SK1) and SNORKEL2 (SK2) QTL and others do not possess the these QTLs though they are cultivated in deep water ecosystem. The molecular screening and in-silico study output of deep water rice landraces can be applied for establishing morphological correlation that 15 landraces are more elongating type than others and more adapted in natural deep water condition.