De novo transcriptome of a bast fibre crop Crotalaria juncea reveals T2 ribonuclease genes to investigate late-acting self-rejection of pollens

Abstract

The biology of gametophytic late-acting self-rejection of pollen in pre-zygotic ovules is relatively unknown in the Fabaceae family of plants. Our understanding of the genetic basis of late-acting self-incompatibility (LSI) is limited due to a lack of sequence data and candidate genes. Crotalaria juncea, a Fabaceae family member that produces commercially important phloem fiber, possesses LSI. Due to a lack of selfed seeds, it is difficult to maintain genetic purity in germplasm and develop breeding lines for improved fiber quality and yield. To investigate candidate genes for LSI in C. juncea, a high-quality de novo transcriptome was generated. It facilitated the identification of genes from the self-incompatibility-related ribonuclease (RNase) family, specifically a Class III T2/RNase gene with sequence properties similar to S-RNase proteins. Based on conserved amino acid motifs, histidine residues, and a high isoelectric point (pI ≥9.0), Cjun_RNS3.1 was identified as an S-RNase homologue (non-S-RNase) or relic S-RNase gene. Unlike typical S-RNases found in known SI plant systems, evolutionary analysis of the Cjun_RNS3.1 protein revealed its ancestral origin. The expression of Cjun_RNS3.1 and other T2/RNase genes revealed differential expression patterns in the pistils of LSI and self-compatible Crotalaria species. The upregulation of the Cjun_RNS3.1 gene during the different stages of pollen tube development indicates that it may be involved in the LSI. In summary, the sunn hemp transcriptome is the first genomic resource reported from a Fabaceae family plant with the LSI trait. A non-S-RNase gene with an ancestral evolutionary origin and a diverse function was found, which could be related to gametophytic LSI. This could be used as a model system to investigate the molecular basis of LSI in the Fabaceae family and help develop C. juncea breeding lines for fibre improvement.