Dynamic QTL mapping revealed primarily the genetic structure of photosynthetic traits in castor (Ricinus communis L.).

High photosynthetic efficiency is the basis of high biomass and high harvest index in castor (Ricinus communis L.). Understanding the genetic law of photosynthetic traits will facilitate the breeding for high photosynthetic efficiency. In this study, the dynamic QTL mapping was performed with the populations F2 and BC1 derived from 2 parents with significant difference in net photosynthetic rate (Pn) at 3 stages, in order to reveal the genetic structure of photosynthetic traits. In F2 population, 26 single-locus QTLs were identified, including 3/3/1 (the QTL number at stage I/II/III, the same below), 1/2/0, 1/2/2, 1/3/1, 0/1/1, and 1/1/2 QTLs conferring Pn, water use efficiency (Wue), transpiration rate (Tr), stomatal conductance (Gs), intercellular CO2 concentration (Ci) and chlorophyll content (Cc), with a phenotypic variation explained (PVE) of 8.40%/8.91%/6.17%, 5.36%/31.74%/0, 7.31%/12.80%/15.15%, 1.60%/6.44%/0.02%, 0/1.10%/0.70% and 2.77%/3.96%/6.50% respectively. And 53 epistatic QTLs (31 pairs) were identified, including 2/2/5, 5/6/3, 4/4/2, 6/3/2, 3/2/0 and 4/0/0 ones conferring the above 6 traits, with a PVE of 6.52%/6.47%/19.04%, 16.72%/15.67%/14.12%, 18.57%/15.58%/7.34%, 21.72%/8.52%/7.13%, 13.33%/4.94%/0 and 7.84%/0/0 respectively. The QTL mapping results in BC1 population were consistent with those in F2 population, except fewer QTLs detected. Most QTLs identified were minor-effect ones, only a few were main-effect ones (PVE > 10%), focused on 2 traits, Wue and Tr, such as qWue1.1, qWue1.2, FqTr1.1, FqTr6, BqWue1.1 and BqTr3; The epistatic effects, especially those related to the dominance effects were the main genetic component of photosynthetic traits, and all the epistatic QTLs had no single-locus effects except qPn1.2, FqGs1.2, FqCi1.2 and qCc3.2; The detected QTLs underlying each trait varied at different stages except stable QTLs qGs1.1, detected at 3 stages, qWue2, qTr1.2 and qCc3.2, detected at 2 stages; 6 co-located QTLs were identified, each of which conferring 2-5 different traits, demonstrated the gene pleiotropy between photosynthetic traits; 2 QTL clusters, located within the marker intervals RCM1842-RCM1335 and RCM523-RCM83, contained 15/5 (F2/BC1) and 4/4 (F2/BC1) QTLs conferring multiple traits, including co-located QTLs and main-effect QTLs. The above results provided new insights into the genetic structure of photosynthetic traits and important references for the high photosynthetic efficiency breeding in castor plant.

Evaluation of two wild castor (Ricinus communis L.) accessions for cadmium tolerance in relation to antioxidant systems and lipid peroxidation.

The present study was conducted to assess the effect of toxicity of cadmium (Cd) on growth, tolerance index (TI), antioxidant activities, and malondialdehyde (MDA) content in two contrasting wild castor accessions (16-024 and S2-4) via hydroponic experiment (0 and 100 mg/L Cd). The results showed that Cd significantly reduced the growth rate, seedling height, root length, and shoot length of the castor accessions compared to the control, with the Cd effect being more severe in S2-4 than in 16-024. In addition, biomass response including the root and shoot fresh weight and root dry weight decreased in both accessions compared to the control. Compared to the control group, the shoot dry weight of accession S2-4 declined by 21.7%, whereas there was no change in 16-024, suggesting a level of tolerance in 16-024. Analysis of TI on all the growth parameters and biomass content revealed that accession 16-024 was highly tolerant to Cd stress than S2-4. The results further revealed that the expression of the antioxidant enzymes, viz., superoxide dismutase (SOD), catalase (CAT), non-enzymatic antioxidant, glutathione, and MDA content, was influenced by genotype. S2-4 exhibited a higher antioxidant activity (SOD, CAT) and lipid peroxidation activity than 16-024, indicative of oxidative damage from Cd stress.

SRAP analysis of the genetic diversity of wild castor (Ricinus communis L.) in South China.

Castor bean is an important seed oil crop. Castor oil is a highly demanded oil for several industrial uses. Currently, castor bean varieties suffer from low productivity and high risk of insect pests and diseases. It is in urgent need to mine elite genes from wild materials for castor breeding. 29 pairs of polymorphic SRAP primers out of 361 pairs were used to analyse the genetic diversity of 473 wild castor materials from South China. 203 bands were amplified by the 29 pairs of primers, of which 169 bands were polymorphic, with a polymorphic percentage of 83.25%. With an average number of alleles per locus (Ap) of 1.801, average number of effective alleles per locus (Ae) of 1.713 and average percentage of polymorphic loci (P) of 90.04%, these primers were proven to be useful and effective. Nei' genetic distance between the materials ranged from 1.04 to 25.02, with an average of 13.03. At the genetic distance of 25.02, the materials clustered into two major groups, consistent with the result of population structure analysis. However, more subgroups existed between 5.21 and 13.32. Although not all the materials from the same region were clustered in the same group, an obvious trend existed where the groups were related to regions to a great extent. Based on multiple indices, the genetic diversity of materials from Hainan was the lowest. However, there was not much difference between West Guangdong and Guangxi, although the former was slightly higher. Moderate genetic differentiation was observed in wild materials in South China. The genetic differentiation mainly occurred within population, with maximum differentiation in Guangxi, followed by West Guangdong and the minimum in Hainan. Nonetheless, there was an extensive geneflow between populations. The above results provided a direction for the conservation and breeding application of these materials.

RcPAL, a key gene in lignin biosynthesis in Ricinus communis L.

BACKGROUND: Castor (Ricinus communis L.) is an important seed oil crop. Castor oil is a highly demanded oil for several industrial uses. Current castor bean varieties suffer from low productivity and high risk of insect pests and diseases. High productive and pest/disease resistance varieties are needed. Lignin has been associated to the resistance for pest, disease and lodging. Lignin is produced from several metabolites of the phenylpropanoid pathway. PAL is the key enzyme of the phenylpropanoid pathway. The gene PAL may assist in the improvement of resistance of castor bean. RESULTS: The RcPAL CDs was amplified and its function was examined by transgenic overexpression and antisense expression, lignin histochemical staining, real-time PCR, lignin content measurement and morphological investigation. Its full length was 2145 bp, encoding 714 amino acids. The overexpression of RcPAL (7.2 times) increased significantly the PAL activity, dyeing depth of xylem cells and lignin content (14.44%), resulting in a significantly lower plant height, deeper and thicker blade, more green leaves, shorter internode, thicker stem diameter, and opposite in antisense expression plants (lignin content lowered by 27.1%), demonstrated that the gene RcPAL was a key gene in castor lignin biosynthesis. CONCLUSIONS: The gene RcPAL is a key gene in castor lignin biosynthesis and can be induced to express under mechanical damage stress. When up-regulated, it increased the lignin content significantly and dwarfed the plant height, and opposite when down-regulated. The gene RcPAL may assist in the improvement of resistance and plant type of castor bean.

Divergent Evolutionary Patterns of NAC Transcription Factors Are Associated with Diversification and Gene Duplications in Angiosperm.

NAC (NAM/ATAF/CUC) proteins constitute one of the biggest plant-specific transcription factor (TF) families and have crucial roles in diverse developmental programs during plant growth. Phylogenetic analyses have revealed both conserved and lineage-specific NAC subfamilies, among which various origins and distinct features were observed. It is reasonable to hypothesize that there should be divergent evolutionary patterns of NAC TFs both between dicots and monocots, and among NAC subfamilies. In this study, we compared the gene duplication and loss, evolutionary rate, and selective pattern among non-lineage specific NAC subfamilies, as well as those between dicots and monocots, through genome-wide analyses of sequence and functional data in six dicot and five grass lineages. The number of genes gained in the dicot lineages was much larger than that in the grass lineages, while fewer gene losses were observed in the grass than that in the dicots. We revealed (1) uneven constitution of Clusters of Orthologous Groups (COGs) and contrasting birth/death rates among subfamilies, and (2) two distinct evolutionary scenarios of NAC TFs between dicots and grasses. Our results demonstrated that relaxed selection, resulting from concerted gene duplications, may have permitted substitutions responsible for functional divergence of NAC genes into new lineages. The underlying mechanism of distinct evolutionary fates of NAC TFs shed lights on how evolutionary divergence contributes to differences in establishing NAC gene subfamilies and thus impacts the distinct features between dicots and grasses.

Solar Radiation-Associated Adaptive SNP Genetic Differentiation in Wild Emmer Wheat, Triticum dicoccoides.

Whole-genome scans with large number of genetic markers provide the opportunity to investigate local adaptation in natural populations and identify candidate genes under positive selection. In the present study, adaptation genetic differentiation associated with solar radiation was investigated using 695 polymorphic SNP markers in wild emmer wheat originated in a micro-site at Yehudiyya, Israel. The test involved two solar radiation niches: (1) sun, in-between trees; and (2) shade, under tree canopy, separated apart by a distance of 2-4 m. Analysis of molecular variance showed a small (0.53%) but significant portion of overall variation between the sun and shade micro-niches, indicating a non-ignorable genetic differentiation between sun and shade habitats. Fifty SNP markers showed a medium (0.05 ≤ FST ≤ 0.15) or high genetic differentiation (FST > 0.15). A total of 21 outlier loci under positive selection were identified by using four different FST -outlier testing algorithms. The markers and genome locations under positive selection are consistent with the known patterns of selection. These results suggested that genetic differentiation between sun and shade habitats is substantial, radiation-associated, and therefore ecologically determined. Hence, the results of this study reflected effects of natural selection through solar radiation on EST-related SNP genetic diversity, resulting presumably in different adaptive complexes at a micro-scale divergence. The present work highlights the evolutionary theory and application significance of solar radiation-driven natural selection in wheat improvement.

Adaptive Genetic Differentiation and Solar Radiation in Wild Emmer Wheat, Triticum dicoccoides.

BACKGROUND: Microgeographic studies of molecular markers could reveal the nature and dynamics of genetic diversity and the evolutionary driving forces shaping evolution. METHODS: The microclimatic genetic divergence of wild emmer wheat associated with solar radiation was investigated, in the present study, using multiple types of molecular markers including allozyme, amplified polymorphic DNA (RAPD), simple sequence repeat (SSR), and single nucleotide polymorphisms (SNP). The studies included two climatic microniches: (1) sunny between oak trees; and (2) shady under the canopies of oak trees. RESULTS: All four types of markers showed a similar microniche tendency of genetic variance, i.e., lower in the shady than in the sunny niche. Significant genetic divergence at some loci including allozyme, RAPD, SSR, and SNP was detected between the two climatic microniches, and also, the observed genetic differentiation is mainly due to natural selection. Based on different FST outlier detection algorithms, there were 21 candidate loci subjected to positive selection. Importantly, most of the identified candidate loci were mapped in the selection "hot spots" of wheat genome. CONCLUSION: The present work implies that microclimatic selection appears to play an important role either in the protein-coding region or in the non-coding region of wheat genomes, and hence, highlights the evolutionary theory of natural selection.