Sequencing of Chinese castor lines reveals genetic signatures of selection and yield-associated loci

Abstract

Oil produced by castor ( Ricinus communis ) has broad industrial applications. However, knowledge on the genetic diversity, especially genetic alterations that occurred during domestication and subsequent traits selection, of this oil crop is limited. Here, our population genomics analyses show that the Chinese castors have developed a geographic pattern, classified into the southern-, the middle-, and the northern-China groups. We detect a number of candidate genomic loci that are associated with the selection signals during the geographical differentiation and domestication. Using genome-wide association analysis, we identify candidate genes associated with nine agronomically important traits. One of the candidate genes encoding a glycosyltransferase related to cellulose and lignin biosynthesis is associated with both capsule dehiscence and endocarp thickness. We hypothesize that the abundance of cellulose or lignin in endocarp is an important factor for capsule dehiscence. Our results provide foundation for castor breeding and genetic study.

A comparative transcriptional landscape of two castor cultivars obtained by single-molecule sequencing comparative analysis

“…In recent years, comparative transcriptome analyses have successfully revealed specific genes responsible for C4 photosynthesis in many grasses, including maize and switch grass [1]. Furthermore, recent studies of the castor transcriptomes are mainly focused on gene expression from short-reads of RNA sequencing[12] [13] which cannot identify alternative gene splice forms [1]. Developing of full-length sequence technology provides a span-new approach to study full-length sequence, alterative splice, gene structure and APA of RNA[14,15].…”

“…Alternative splicing of eukaryotic transcripts is a mechanism that enables cells to generate vast protein diversity from a limited number of genes [17,18]. The mechanism and outcomes of alternative splicing of individual transcripts are well understood [1]. Some studies find that AS regulation is independent or partially independent of transcriptional regulation[19] and implement great function at the early stage of heat response[19,20], useful for future heat sensing and signaling studies [1].…”

“…The castor plant ( Ricinus communis L.), originated in Africa, is an annual or perennial dicotyledonous. High ricinoleic acid content (80-90%) and high fatty acid content (more than 45%) in seed oil make oit one of the most important non-edible oilseed crops, and has attracted much attention of chemists, biologists and medical scientists [1]. The inflorescence of common castor plants is gradient monoecious raceme, with staminate flowers on the lower portion and female flowers at the apex[2].…”

“…With the development of sequencing technology, next-generation sequencing (NGS) has become an essential method for studies of genomes, epigenomes, and transcriptomes [1]. The NGS method has been used in many model and non-model plant species, and large-scale genome sequences and transcriptome data have been produced for deep analysis [1]. However, the deficiency of NGS, for example short reads, result in incompletely assembled transcripts limiting to better understand the transcriptomic data [1].…”

“…The NGS method has been used in many model and non-model plant species, and large-scale genome sequences and transcriptome data have been produced for deep analysis [1]. However, the deficiency of NGS, for example short reads, result in incompletely assembled transcripts limiting to better understand the transcriptomic data [1]. PacBio platform, based on the single-molecule real-time (SMRT) sequencing technology and providing longer and full-length transcripts without assembly, can provide better information to understand the full-length transcriptome, such as alternative splicing, fusion transcripts, alternative polyadenylation, novel genes and non-coding RNAs [1].…”