Genomic insights into the origin, domestication and genetic basis of agronomic traits of castor bean

Abstract

Background Castor bean (Ricinus communis L.) is an important oil crop, which belongs to the Euphorbiaceae family. The seed oil of castor bean is currently the only commercial source of ricinoleic acid that can be used for producing about 2000 industrial products. However, it remains largely unknown regarding the origin, domestication, and the genetic basis of key traits of castor bean. Results Here we perform a de novo chromosome-level genome assembly of the wild progenitor of castor bean. By resequencing and analyzing 505 worldwide accessions, we reveal that the accessions from East Africa are the extant wild progenitors of castor bean, and the domestication occurs ~ 3200 years ago. We demonstrate that significant genetic differentiation between wild populations in Kenya and Ethiopia is associated with past climate fluctuation in the Turkana depression ~ 7000 years ago. This dramatic change in climate may have caused the genetic bottleneck in wild castor bean populations. By a genome-wide association study, combined with quantitative trait locus analysis, we identify important candidate genes associated with plant architecture and seed size. Conclusions This study provides novel insights of domestication and genome evolution of castor bean, which facilitates genomics-based breeding of this important oilseed crop and potentially other tree-like crops in future.

High-quality genome assembly of an important biodiesel plant, Euphorbia lathyris L

“…First, a de novo prediction was performed using Augustus v3.2.3 38 with default Arabidopsis thaliana parameters. Second, a homology-based prediction was conducted by aligning the protein sequences of R. communis , 39 M. esculenta , 40 H. brasiliensis , 41 Populus trichocarpa , 42 and Arabidopsis thaliana 43 to the caper spurge genome with TBLASTN v2.2.31+ 44 and GeneWise v2.4.1. 45 Third, a comprehensive transcriptome database was built using de novo and genome-guided RNA-seq assembly, and gene structures were further predicted using PASA v2.2.0.…”

Large-scale whole-genome resequencing unravels the domestication history of Cannabis sativa

“…It should be noted that the groups we defined in our study are not actual panmictic populations, but (with the possible exception of feral plants) evolved independently due to separate breeding at presumably small N e , in particular the hemp-and drug-type cultivars. Nucleotide diversity () and population divergence (F ST ) are the two most commonly used parameters when measuring selective signatures in similarly inbred populations, such as crops and domesticated animals [e.g., (75)(76)(77)]. However, to reliably identify signatures of selection and to discern selective sweeps from potential background divergence caused by bottleneck effects, we combined F ST ,  ratio (e.g., -Hemp-type/-Drug-type), and a third approach [the cross-population composite likelihood ratio test (XP-CLR), which uses allele frequency differentiation at linked loci to detect selective sweeps; https://github.com/hardingnj/xpclr (78)] for each comparison to represent the selective signatures, taking the highest 5% value as the cutoff.…”

Beyond a reference genome: pangenomes and population genomics of underutilized and orphan crops for future food and nutrition security

“…GWAS of 368 cowpea accessions found candidate genes involved in endosperm development, embryo development and cell elongation associated with seed size, some of which also play a role in common bean (Lo et al ., 2019). Similar analyses in castor bean identified candidate genes for seed traits that differentiate the wild and cultivated types (Xu et al ., 2021). Recently, GWAS of Tartary buckwheat identified a mutation in the GCC cis ‐element of an AP2 transcription factor associated with grain weight (Zhang et al ., 2021).…”