Analysis of epigenetic landscape in a recombinant inbred line population developed by hybridizing natural and re-synthesized Brassica juncea (L.) with stable C-genome introgressions

Abstract

Epigenetic variation is one of the many consequences of wide hybridization and polyploidy. We have investigated changes in the epigenetic landscapes following re-synthesis of Brassica juncea lines. The intergenerational transfer of epigenetic changes and their association with trait phenotypes were also studied. Inferences were drawn from DNA methylation analysis of 137 recombinant inbred lines (RILs) that were developed through hybridization between a natural B. juncea cultivar and a re-synthesized B. juncea genotype. The re-synthesized B. juncea genotype (AnAnBcBc; 2n = 36) was extracted following hybridization between two related allotetraploids, B. napus (AnAnCnCn; 2n = 38) and B. carinata (BcBcCcCc; 2n = 34), and it also carried random C-genome introgressions. The RILs and the parents were genotyped with methylation-sensitive amplification polymorphism primers to investigate DNA methylation patterns. The re-synthesized B. juncea genotype was found to have a higher internal methylation (40.4%) level than the natural B. juncea cultivar (17.1%), but external methylation was almost the same (23.9 and 26.0%, respectively). The re-synthesized B. juncea genotype was significantly less non-methylated (35.7%) than the natural cultivar (49.5%). The RILs varied significantly in terms of their methylation levels, with many RILs exceeding both parents with respect to internal (up to 52%) or external methylation (up to 79%). Possible causes of this increased methylation may include induced hypermethylation or stochastic generation of more epialleles or trans-generational segregation distortions of differentially methylated trait loci during the development of the RIL population. Epialleles AAG-14, ACC-2,4,12, ACG-3,11, AGT-1,5,16, ATG-2,3,6,8, CAA-4, CCG-2,4,14, CGA-3 and CTG-6 appeared to be associated with flowering time, plant height and oil content.