Targeted identification of novel stress responsive gene copies in Brassica arisen through gene duplication

Abstract

Abiotic stress severely affects agricultural crop productivity world-wide. Since our objective was to identify the effects of gene duplication in abiotic stress tolerance in Brassica, a reference tolerant Brassica genotype for assessment of stress tolerance mechanism was required . As Brassica. juncea is an economically important crop and is also know to contain various tolerant genotypes. Therefore, a cumulative study which included study in both laboratory and field settings was conducted on 104 Brassica juncea and their responses to salt stress was assessed using diverse morphological and biochemical parameters. The finding identifies the germplasms selected to show maximum tolerance for different parameters. For example B. junceaRH-781 showed highest tolerance for Sodium and potassium content of shoot tissues, B. junceaNC1-jhumka showed maximum tolerance for proline content in shoot tissues,B. juncea NPJ-200 for dry biomass of shoot tissues, B. junceaRW-46-6-3 for total number of seeds per plant ,B. junceaSitara- Srinagar showed best tolerance in case of number of siliques per plant. In the insilico experiments comparison of gene model of homologs of B. rapa, B.juncea and T.halophila to that of A. thaliana predicted out many major loss or gain of exon regions that may affect the overall functionality of the proteins. For example in case of TH.HKT1.3 and BJ.HKT1.4 exon loss had led to loss of three conserved domains- M1D, F2D and M2D . Study of the major cis-elements responsive to abiotic stress (ABRE, HSE,MYB, MBS) also provides major cues which helped in the identification of important gene copy responsible for providing stress tolerance. For example in TH.HKT1.2 total of 11 cis elements were found in comparison with 3 in AT.HKT1. This gain of cis elements possible could provide stress tolerance to T. halophila.