A copia-like retrotransposon insertion in the upstream region of the SHATTERPROOF1 gene, BnSHP1.A9, is associated with quantitative variation in pod shattering resistance in oilseed rape

Abstract

Seed loss resulting from pod shattering is a major constraint in production of oilseed rape (Brassica napus L.). 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 one of the B. napus SHATTERPROOF1 homologs, BnSHP1.A9, in a doubled haploid population generated from parents designated R1 and R2 as well as in a diverse panel of oilseed rape. The R1 maternal parental line of the doubled haploid population carried the allele for shattering at qSRI.A9.1, while the R2 parental line carried the allele for shattering resistance. Quantitative RT-PCR showed that BnSHP1.A9 was expressed specifically in flower buds, flowers, and developing siliques in R1, while it was not expressed in any tissue of R2. Transgenic plants constitutively expressing either of the BnSHP1.A9 alleles from the R1 and R2 parental lines showed that both alleles are responsible for pod shattering, via a mechanism that promotes lignification of the enb layer. These findings indicated that the allelic differences in the BnSHP1.A9 gene per se are not the causal factor for quantitative variation in shattering resistance at qSRI.A9.1. Instead, a highly methylated copia-like long terminal repeat retrotransposon insertion (4803 bp) in the promotor region of the R2 allele of BnSHP1.A9 repressed the expression of BnSHP1.A9, and thus contributed to pod shatter resistance. Finally, we showed a copia-like retrotransposon-based marker, BnSHP1.A9R2, can be used for marker-assisted breeding targeting the pod shatter resistance trait in oilseed rape.

On the Role of Transposable Elements in the Regulation of Gene Expression and Subgenomic Interactions in Crop Genomes

“…Results showed that a copia LTR-RT insertion (4.8 kb) was found in the promoter of BnSHPA9.1 and was involved in repressing the expression of the BnSHP.A9.1 gene. This association analysis suggested that the above TE insertion can be used as a breeding marker for pod resistance (Liu, Zhou, et al, 2020). In another example, a CACTA-like transposable element inserted in the upstream region of CYP78A9, a gene encoding a P450 monooxygenase, acts as a positive regulator of silique length in rapeseed.…”

Pangenomics in crop improvement—from coding structural variations to finding regulatory variants with pangenome graphs

“…These SVs were used in a pangenome graph‐based PAV GWAS, which lead to the identification of a 10‐kb PAV. The deleted gene located in this region encodes a hydrophobic protein from soybean (HPS) and is associated with seed luster (Liu et al., 2020).…”

“…A total of 79 genes absent from the reference genome were confirmed as differentially expressed during drought stress, including two resistance specific genes, Sobic.005G069800 and Sobic.006G127800 , which were found to co‐map with plant height and leaf pigment traits. Analysis of structural variations in a soybean pangenome identified a gene encoding a Fe 2+ /Zn 2+ regulated transporter associated with iron deficiency chlorosis (Liu et al., 2020).…”

Formation Mechanism and Occurrence Law of Pod Shattering in Soybean: A Review

“…Relevant studies have shown that seed shattering is more common in wild-type and small-grain soybeans [9]. Soybean mechanized harvesting reduces labor costs and can increase seed shattering, but seed shattering is a key factor affecting soybean mechanical harvesting.…”