Bulked segregant analysis reveals candidate genes responsible for dwarf formation in woody oilseed crop castor bean

AbstractPlant dwarfism is a desirable agronomic trait in non-timber trees, but little is known about the physiological and molecular mechanism underlying dwarfism in woody plants. Castor bean (Ricinus communis) is a typical woody oilseed crop. We performed cytological observations within xylem, phloem and cambia tissues, revealing that divergent cell growth in all tissues might play a role in the dwarf phenotype in cultivated castor bean. Based on bulked segregant analyses for a F2 population generated from the crossing of a tall and a dwarf accession, we identified two QTLs associated with plant height, covering 325 candidate genes. One of these, Rc5NG4-1 encoding a putative IAA transport protein localized in the tonoplast was functionally characterized. A non-synonymous SNP (altering the amino acid sequence from Y to C at position 218) differentiated the tall and dwarf plants and we confirmed, through heterologous yeast transformation, that the IAA uptake capacities of Rc5NG4-1Y and Rc5NG4-1C were significantly different. This study provides insights into the physiological and molecular mechanisms of dwarfing in woody non-timber economically important plants, with potential to aid in the genetic breeding of castor bean and other related crops.

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High light exposure on seed coat increases lipid accumulation in seeds of castor bean (Ricinus communis L.), a nongreen oilseed crop

Photosynthesis Research ◽

10.1007/s11120-015-0206-x ◽

2015 ◽

Vol 128 (2) ◽

pp. 125-140 ◽

Cited By ~ 8

Author(s):

Yang Zhang ◽

Sujatha Mulpuri ◽

Aizhong Liu

Keyword(s):

Seed Coat ◽

Lipid Accumulation ◽

Castor Bean ◽

Light Exposure ◽

Ricinus Communis ◽

High Light ◽

Oilseed Crop ◽

Ricinus Communis L

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

Genome Biology ◽

10.1186/s13059-021-02333-y ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Wei Xu ◽

Di Wu ◽

Tianquan Yang ◽

Chao Sun ◽

Zaiqing Wang ◽

...

Keyword(s):

Castor Bean ◽

Genetic Basis ◽

Genome Wide Association Study ◽

De Novo ◽

Agronomic Traits ◽

Ricinus Communis ◽

Oilseed Crop ◽

A Genome ◽

Trait Locus ◽

Wild Progenitors

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.

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Salt-Tolerance in Castor Bean (Ricinus communis L.) Is Associated with Thicker Roots and Better Tissue K+/Na+ Distribution

Agriculture ◽

10.3390/agriculture11090821 ◽

2021 ◽

Vol 11 (9) ◽

pp. 821

Author(s):

Junlin Zheng ◽

Gilang B. F. Suhono ◽

Yinghao Li ◽

Maggie Ying Jiang ◽

Yinglong Chen ◽

...

Keyword(s):

Salt Stress ◽

Salt Tolerance ◽

Castor Bean ◽

Ricinus Communis ◽

Dry Weight ◽

Root Diameter ◽

Oilseed Crop ◽

Salt Tolerant ◽

Ricinus Communis L ◽

Young Leaves

Soil salinity is a serious threat to agriculture worldwide. Castor bean (Ricinus communis L.) is an in-demand oilseed crop containing 40–60% highly valued oil in its seeds. It is moderately sensitive to salinity. Two glasshouse experiments were conducted to assess plant growth and ion tissue distribution in different castor bean genotypes under various salt stress conditions to explore their potential for cultivation on saline land. Experiment 1 evaluated the response of five castor bean genotypes to four salt treatments (0, 50, 100, or 150 mM NaCl) up to 91 days after sowing (DAS). Experiment 2 further evaluated two genotypes selected from Experiment 1 in 1 m deep PVC tubes exposed to 0, 100, or 200 mM NaCl treatment for 112 DAS (Experiment 2). Experiment 1 showed that salt addition (particularly 150 mM NaCl) reduced plant height, stem diameter, shoot and root dry weights, photosynthetic traits, and leaf K+/Na+ ratio while increasing the leaf Na+ concentration of castor bean plants. Two genotypes, Zibo (Chinese variety) and Freo (Australian wild type), were more salt-tolerant than the other tested genotypes. In Experiment 2, salt-stressed Zibo flowered earlier than the control, while flowering time of Freo was not influenced by salt stress. The 200 mM NaCl treatment reduced the total root length and increased the average root diameter of both Zibo and Freo compared to the control. In addition, the 200 mM NaCl treatment significantly decreased total leaf area, chlorophyll content, and shoot and root dry weight of both castor bean genotypes by 50%, 10.6%, 53.1%, and 59.4%, respectively, relative to the control. In contrast, the 100 mM NaCl treatment did not significantly affect these traits, indicating that both genotypes tolerated salt stress up to 100 mM NaCl. In general, Freo had greater salt tolerance than Zibo, due to its higher average root diameter, lower Na+ concentration, and higher K+/Na+ ratio in young leaves under salt conditions. In conclusion, genotype Freo is recommended for cultivation in saline soils and could be used to breed high-yielding and salt-tolerant castor bean genotypes.

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Metabolic alterations and X-ray chlorophyll fluorescence for the early detection of lead stress in castor bean (Ricinus communis) plants

Acta Scientiarum Agronomy ◽

10.4025/actasciagron.v40i1.39392 ◽

2018 ◽

Vol 40 (1) ◽

pp. 39392 ◽

Cited By ~ 3

Author(s):

Clístenes Williams Araújo do Nascimento ◽

Marise Conceição Marques

Keyword(s):

Chlorophyll Fluorescence ◽

Early Detection ◽

Photosynthetic Pigments ◽

Enzyme Activities ◽

Castor Bean ◽

Ricinus Communis ◽

Soluble Proteins ◽

Oilseed Crop ◽

Pb Toxicity ◽

X Ray

The remediation of lead-contaminated areas poses a serious challenge to soil chemists because Pb has low solubility in soil. Thus, Pb phytostabilization is considered to be an attractive remediation technique. Castor bean (Ricinus communis) is an oilseed crop known for its tolerance to heavy metals, and our aim was to assess the early detection of Pb toxicity and the effects of Pb on the biomass, photosynthetic pigments, antioxidative enzyme activities, and total soluble proteins of this plant. Specimens were grown in a nutrient solution spiked with Pb concentrations of 25, 50, 100, 150, or 200 µmol L-1. A control without Pb was also grown. The results show that X-ray chlorophyll fluorescence is an efficient technique for the early detection of photosystem II alterations driven by Pb toxicity. Castor bean was tolerant to the Pb doses tested; plants presented no changes in photosynthetic pigments, defense enzyme activities, or total soluble proteins in leaves. Given its ability to tolerate and accumulate Pb in its roots, castor bean is a viable alternative for phytostabilization and phytoattenuation of lead-contaminated areas. It is also economically attractive for industrial and biofuel oil production while being used for remediation.

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Genetic Diversity of Castor Bean (Ricinus communis L.) Revealed by ISSR and RAPD Markers

Agronomy ◽

10.3390/agronomy11030457 ◽

2021 ◽

Vol 11 (3) ◽

pp. 457

Author(s):

HyokChol Kim ◽

Pei Lei ◽

Aizhi Wang ◽

Shuo Liu ◽

Yong Zhao ◽

...

Keyword(s):

Genetic Diversity ◽

Castor Bean ◽

Genetic Similarity ◽

Rapd Markers ◽

Ricinus Communis ◽

Similarity Coefficient ◽

Morphological Data ◽

Oilseed Crop ◽

Ricinus Communis L ◽

Polymorphic Bands

Castor (Ricinus communis L.), known as castor oil plant or castor bean, is a non-edible oilseed crop. In the present study, the genetic diversity among 54 samples (3 wild and 51 cultivated) collected worldwide was evaluated using inter-simple sequence repeats (ISSRs) and random amplified polymorphic DNA (RAPD) markers. A total of 9 ISSR primers produced 83 high-resolution bands with 61 (74.53%) as polymorphic. The percentage of polymorphic bands per primer and the genetic similarity coefficient ranged from 54.55% (UBC-836) to 100% (UBC-808) and from 0.74 to 0.96, respectively. A total of 11 out of 20 RAPD primers amplified unique polymorphic products with an average percentage of polymorphic bands of 60.98% (56 polymorphic bands out of a total of 90 bands obtained). The percentage of polymorphic bands per primer ranged from 25% (OPA-02 and B7) to 90.91% (B21) with the genetic similarity coefficient ranging from 0.73 to 0.98. The unweighted pair group method with arithmetic averages (UPGMA) dendrogram using two molecular markers divided 54 castor genotypes into three groups. Furthermore, based on morphological data, all 54 castor varieties were grouped into three main clusters. The genetic diversity analysis based on two molecular makers showed that most varieties from China were closely related to each other with three varieties (GUANGDONGwild, ZHEJIANGWild, and HANNANWild) belonging to a wild group separated from most of the cultivated castor samples from China, India, France, and Jordan. These results suggested that the cultivated castor contains a narrow genetic base. Accordingly, we recommend that wild castor genetic resources be introduced for breeding novel castor varieties. Furthermore, the Vietnam, Malaysia, Indonesia, and Nigeria accessions were clustered into the same group. The results of principal coordinate analysis (PCoA) and UPGMA cluster analysis were consistent with each other. The findings of this study are important for future breeding studies of castor.

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Genomics analysis of genes encoding respiratory burst oxidase homologs (RBOHs) in jatropha and the comparison with castor bean

PeerJ ◽

10.7717/peerj.7263 ◽

2019 ◽

Vol 7 ◽

pp. e7263 ◽

Cited By ~ 1

Author(s):

Yongguo Zhao ◽

Zhi Zou

Keyword(s):

Stress Responses ◽

Respiratory Burst ◽

Castor Bean ◽

Ricinus Communis ◽

Expression Patterns ◽

Global Gene Expression ◽

Oilseed Crop ◽

A Genome ◽

Global Gene Expression Profiling ◽

Respiratory Burst Oxidase

Respiratory burst oxidase homologs (RBOHs), which catalyze the production of superoxide from oxygen and NADPH, play key roles in plant growth and development, hormone signaling, and stress responses. Compared with extensive studies in model plants arabidopsis and rice, little is known about RBOHs in other species. This study presents a genome-wide analysis of Rboh family genes in jatropha (Jatropha curcas) as well as the comparison with castor bean (Ricinus communis), another economically important non-food oilseed crop of the Euphorbiaceae family. The family number of seven members identified from the jatropha genome is equal to that present in castor bean, and further phylogenetic analysis assigned these genes into seven groups named RBOHD, -C, -B, -E, -F, -N, and -H. In contrast to a high number of paralogs present in arabidopsis and rice that experienced several rounds of recent whole-genome duplications, no duplicate was identified in both jatropha and castor bean. Conserved synteny and one-to-one orthologous relationship were observed between jatropha and castor bean Rboh genes. Although exon-intron structures are usually highly conserved between orthologs, loss of certain introns was observed for JcRbohB, JcRbohD, and RcRbohN, supporting their divergence. Global gene expression profiling revealed diverse patterns of JcRbohs over various tissues. Moreover, expression patterns of JcRbohs during flower development as well as various stresses were also investigated. These findings will not only improve our knowledge on species-specific evolution of the Rboh gene family, but also provide valuable information for further functional analysis of Rboh genes in jatropha.

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Genome-wide Association Study Reveals Novel Quantitative Trait Loci and Candidate Genes of Lint Percentage in Upland Cotton Based on the CottonSNP80K Array

10.21203/rs.3.rs-648403/v1 ◽

2021 ◽

Author(s):

Yu Chen ◽

Yang Gao ◽

Pengyun Chen ◽

Juan Zhou ◽

Chuanyun Zhang ◽

...

Keyword(s):

Association Study ◽

Candidate Genes ◽

Upland Cotton ◽

Molecular Mechanisms ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Oilseed Crop ◽

Cotton Production ◽

Lint Percentage ◽

Genome Wide

Abstract Cotton (Gossypium spp.) is an important natural textile fiber and oilseed crop widely cultivated in the world. Lint percentage (LP, %) is one of the important yield factor, thus increasing lint percentage is a core goal of cotton breeding improvement. However, the underlying genetic and molecular mechanisms that control lint percentage in upland cotton remain largely unknown. Here, we performed a Genome-wide association study (GWAS) for LP based on phenotypic tests of 254 upland cotton accessions in four environments and BLUPs using the high-density CottonSNP80K array. A total of 41,413 high-quality single-nucleotide polymorphisms (SNPs) were screened and 34 SNPs within 22 QTLs were identified as significantly associated with lint percentage trait in different environments. In total, 175 candidate genes were identified from two major genomic loci (GR1 and GR2) of upland cotton and 50 hub genes were identified through GO enrichment and WGCNA analysis. Furthermore, two candidate/causal genes, Gh_D01G0162 and Gh_D07G0463, which pleiotropically increased lint percentage were identified and further verified its function through LD blocks, haplotypes and qRT-PCR analysis. Co-expression network analysis showed that the candidate/causal and hub gene, Gh_D07G0463, was significantly related to another candidate gene, Gh_D01G0162, and the simultaneous pyramid of the two genes lays the foundation for a more efficient increase in cotton production. Our study provides crucial insights into the genetic and molecular mechanisms underlying variations of yield traits and serves as an important foundation for lint percentage improvement via marker-assisted breeding.

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Genomic Characterization and Expressional Profiles of Autophagy-Related Genes (ATGs) in Oilseed Crop Castor Bean (Ricinus communis L.)

International Journal of Molecular Sciences ◽

10.3390/ijms21020562 ◽

2020 ◽

Vol 21 (2) ◽

pp. 562 ◽

Cited By ~ 2

Author(s):

Bing Han ◽

Hui Xu ◽

Yingting Feng ◽

Wei Xu ◽

Qinghua Cui ◽

...

Keyword(s):

Potential Function ◽

Seed Development ◽

Seed Coat ◽

Castor Bean ◽

Lipid Droplets ◽

Ricinus Communis ◽

Expression Patterns ◽

Oilseed Crop ◽

Seed Biology ◽

Cellular Autophagy

Cellular autophagy is a widely-occurring conserved process for turning over damaged organelles or recycling cytoplasmic contents in cells. Although autophagy-related genes (ATGs) have been broadly identified from many plants, little is known about the potential function of autophagy in mediating plant growth and development, particularly in recycling cytoplasmic contents during seed development and germination. Castor bean (Ricinus communis) is one of the most important inedible oilseed crops. Its mature seed has a persistent and large endosperm with a hard and lignified seed coat, and is considered a model system for studying seed biology. Here, a total of 34 RcATG genes were identified in the castor bean genome and their sequence structures were characterized. The expressional profiles of these RcATGs were examined using RNA-seq and real-time PCR in a variety of tissues. In particular, we found that most RcATGs were significantly up-regulated in the later stage of seed coat development, tightly associated with the lignification of cell wall tissues. During seed germination, the expression patterns of most RcATGs were associated with the decomposition of storage oils. Furthermore, we observed by electron microscopy that the lipid droplets were directly swallowed by the vacuoles, suggesting that autophagy directly participates in mediating the decomposition of lipid droplets via the microlipophagy pathway in germinating castor bean seeds. This study provides novel insights into understanding the potential function of autophagy in mediating seed development and germination.

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