An Epigenetic LTR-retrotransposon insertion in the upstream region ofBnSHP1.A9controls quantitative pod shattering resistance inBrassica napus

Seed loss resulting from pod shattering is a major problem in oilseed rape ( Brassica napus L.) production worldwide. However, the molecular mechanisms underlying pod shatter resistance are not well understood. Here we show that the pod shatter resistance at quantitative trait locus, qSRI.A9.1 is controlled by a SHATTERPROOF1 ( SHP1 ) paralog in B. napus ( BnSHP1.A9 ). Expression analysis by quantitative RT-PCR showed that Bn SHP1.A9 was specifically expressed in flower buds, flowers and developing siliques in the oilseed rape line (R1) carrying the qSRI.A9.1 allele with negative effect, but not expressed in any tissue of the line (R2) carrying the positive effect qSRI.A9.1 allele. Transgenic plants constitutively expressing Bn SHP1.A9 alleles from pod resistant and pod shattering parental lines showed that both alleles are responsible for pod shattering via promoting lignification of en b layer, which indicated allelic difference of Bn SHP1.A9 gene per se is not the causal factor of the QTL. The upstream sequence of Bn SHP1.A9 in the promotor region harboring highly methylated long terminal repeat retrotransposon insertion (LTR, 4803bp) in R2 repressed the expression of Bn SHP.A9, and thus contributed to the positive effect on pod shatter resistance. Genetic and association analysis revealed that the copia LTR retrotransposon based marker BnSHP1.A9 - R2 can be used for breeding for pod shatter resistant varieties and reducing the loss of seed yield in oilseed rape.