Genome-wide Association Analysis Of Important Agronomic Traits In Castor And Wild Castor Genome Assembly

Castor(Ricinus communis L.)belongs to Euphorbia family,which is one of the most important oil crops in the world.The castor bean seeds have high oil content,and the main component of fatty acid is ricinoleic acid,which contains more than80%.Because of its special physical and chemical properties,castor oil seeds are widely used in lubricants,cosmetics,paints,coatings,pharmaceuticals,inks and fuel oil,making it known as "natural petroleum".Castor are widely adapted,it can grow in highly saline soil and is also have drought tolerance,which are the best cash crop for marginal land use and soil improvement.These excellent qualities provide an advantageous basis for large-scale cultivation of castor.However,researches on castor is still in the beginning stage,the varieties shows great differences in agronomic traits and without accurate phenotypic data,which result in the genetic mechanism of agronomic traits has not yet been fully explored.All these factors seriously hinder the breeding process of castor bean.In addition,the African wild castor provided a good research material for revealing the adaptation of plants to high ultraviolet radiation,strong light and extreme dryness.During long-term adaptive evolution,some genes or alleles,existing in the genome of the wild castor bean to prevent extinction under extreme conditions,but are often lost during domestication due to the relaxation of natural selection.In order to explore the genetic mechanism of variation among castor bean germplasm resources and the internal mechanism of adaptation of wild castor to wild environment,we firstly conducted resource evaluation and genome-wide association analysis using 405 castor bean germplasm resources from China and African.Secondly,a chromosome level wild castor bean genome(WT05)was assembled by combining various sequencing and assembly methods,which not only improved the quality of the reference genome,but also provided accurate genetic information for castor bean research.The main results are as follows:(1)We evaluated 405 castor germplasm resources,including total 18 phenotypic data of yield and quality traits,namely,capsule dehiscence,endocarp thickness,hundred-grain weight,panicle height,panicle length,plant height,ratio of male to female flowers,seed length,seed volume,seed oil content as well as other seven kinds of fatty acid compositions in castor seed.We have constructed a castor phenotypic database base on these natural population with the phenotypic data.Analysis of phenotypic traits showed that castor varieties had large geographical characteristics vary in Africa,Southern,Middle and Northeastern of China.For example,the endocarp of southern varieties is thicker and the plant height is higher.The content of ricinoleic acid in African varieties is higher but the hundred-grain weight was lower.(2)Whole genome-wide association analysis were performed for 18 yield and quality traits based on the genomic resequencing results of 405 castor germplasm resources and accurate phenotypic data.We identified dozens of candidate genes related to important agronomic traits in castor beans,including potential regulatory genes related to plant height,panicle height,seed length,seed width,hundred-grain weight,and seed fatty acids.Our research provided a large number of targets for the improvement of agronomic traits and precision breeding of castor.(3)A chromosome-level genome of the wild castor bean was assembled,with significant improvements in completeness and accuracy compared to previous versions.The genome heterogenesis rate was 0.337% and the genome size of the assembly was 316.11 Mb,of which 312.39 Mb(98.8%)was anchored onto ten chromosomes.The genome scaffold and contig N50 were 31.93 Mb and 8.96 Mb respectively,and total 30,066 protein coding genes were annotated.(4)Using the newly assembled genome,we re-annotated two families of important genes in castor,namely,ricin-coding genes and genes involved in ricinoleic acid synthesis.Based on transcriptome data,we analyzed the tissue specific expression profiles of these two families of genes in castor bean,which providing new insights into the function of these genes.Besides,comparative genomic analysis revealed that 43 amino acid peptides unique to castor were obtained from the Ricin A chain,which may be potential factor for ricin toxicity.(5)Compared with cultivated castor and other Euphorbiaceae plants,wild castor exhibits positive selection and gene family expansion for genes involved in DNA repair,photosynthesis and abiotic stress responses.Notably,several key genes involved in nucleotide resection repair(NER)and base resection repair(BER)pathway,such as DNA ligase 1(LIG1),damaged DNA binding 2(DDB2)and DNA polymerase,are positively selected.In conclusion,the results of this study provide an important reference for the breeding of castor bean varieties and the evaluation of agronomic traits.Genome-wide association analysis revealed the potential regulatory mechanisms of important agronomic traits and also provided numerous targets for precision breeding.The genome assembly of wild castor bean at chromosome level provides reference genomic information for the study of wild resources.The reannotation of ricin and ricinoleic acid synthesis genes provided important information for the analysis of ricin and ricinoleic acid synthesis.Finally,the analysis of environmental adaptation evolution of wild castor beans in Africa provides new evidence for the mechanism of genomic evolution in response to environmental changes.