Divergence of gene regulation through chromosomal rearrangements

<p>Abstract</p> <p>Background</p> <p>The molecular mechanisms that modify genome structures to give birth and death to alleles are still not well understood. To investigate the causative chromosomal rearrangements, we took advantage of the allelic diversity of the duplicated <it>p1 </it>and <it>p2 </it>genes in maize. Both genes encode a transcription factor involved in maysin synthesis, which confers resistance to corn earworm. However, <it>p1 </it>also controls accumulation of reddish pigments in floral tissues and has therefore acquired a new function after gene duplication. <it>p1 </it>alleles vary in their tissue-specific expression, which is indicated in their allele designation: the first suffix refers to red or white pericarp pigmentation and the second to red or white glume pigmentation.</p> <p>Results</p> <p>Comparing chromosomal regions comprising <it>p1-ww[4Co63]</it>, <it>P1-rw1077 </it>and <it>P1-rr4B2 </it>alleles with that of the reference genome, <it>P1-wr[B73]</it>, enabled us to reconstruct additive events of transposition, chromosome breaks and repairs, and recombination that resulted in phenotypic variation and chimeric regulatory signals. The <it>p1-ww[4Co63] </it>null allele is probably derived from <it>P1-wr[B73] </it>by unequal crossover between large flanking sequences. A transposon insertion in a <it>P1-wr</it>-like allele and NHEJ (non-homologous end-joining) could have resulted in the formation of the <it>P1-rw1077 </it>allele. A second NHEJ event, followed by unequal crossover, probably led to the duplication of an enhancer region, creating the <it>P1-rr4B2 </it>allele. Moreover, a rather dynamic picture emerged in the use of polyadenylation signals by different <it>p1 </it>alleles. Interestingly, <it>p1 </it>alleles can be placed on both sides of a large retrotransposon cluster through recombination, while functional <it>p2 </it>alleles have only been found proximal to the cluster.</p> <p>Conclusions</p> <p>Allelic diversity of the <it>p </it>locus exemplifies how gene duplications promote phenotypic variability through composite regulatory signals. Transposition events increase the level of genomic complexity based not only on insertions but also on excisions that cause DNA double-strand breaks and trigger illegitimate recombination.</p

Genetic Architecture of Soybean Yield and Agronomic Traits

Soybean is the world’s leading source of vegetable protein and demand for its seed continues to grow. Breeders have successfully increased soybean yield, but the genetic architecture of yield and key agronomic traits is poorly understood. We developed a 40-mating soybean nested association mapping (NAM) population of 5,600 inbred lines that were characterized by single nucleotide polymorphism (SNP) markers and six agronomic traits in field trials in 22 environments. Analysis of the yield, agronomic, and SNP data revealed 23 significant marker-trait associations for yield, 19 for maturity, 15 for plant height, 17 for plant lodging, and 29 for seed mass. A higher frequency of estimated positive yield alleles was evident from elite founder parents than from exotic founders, although unique desirable alleles from the exotic group were identified, demonstrating the value of expanding the genetic base of US soybean breeding

Change of Gene Structure and Function by Non-Homologous End-Joining, Homologous Recombination, and Transposition of DNA

An important objective in genome research is to relate genome structure to gene function. Sequence comparisons among orthologous and paralogous genes and their allelic variants can reveal sequences of functional significance. Here, we describe a 379-kb region on chromosome 1 of maize that enables us to reconstruct chromosome breakage, transposition, non-homologous end-joining, and homologous recombination events. Such a high-density composition of various mechanisms in a small chromosomal interval exemplifies the evolution of gene regulation and allelic diversity in general. It also illustrates the evolutionary pace of changes in plants, where many of the above mechanisms are of somatic origin. In contrast to animals, somatic alterations can easily be transmitted through meiosis because the germline in plants is contiguous to somatic tissue, permitting the recovery of such chromosomal rearrangements. The analyzed region contains the P1-wr allele, a variant of the genetically well-defined p1 gene, which encodes a Myb-like transcriptional activator in maize. The P1-wr allele consists of eleven nearly perfect P1-wr 12-kb repeats that are arranged in a tandem head-to-tail array. Although a technical challenge to sequence such a structure by shotgun sequencing, we overcame this problem by subcloning each repeat and ordering them based on nucleotide variations. These polymorphisms were also critical for recombination and expression analysis in presence and absence of the trans-acting epigenetic factor Ufo1. Interestingly, chimeras of the p1 and p2 genes, p2/p1 and p1/p2, are framing the P1-wr cluster. Reconstruction of sequence amplification steps at the p locus showed the evolution from a single Myb-homolog to the multi-gene P1-wr cluster. It also demonstrates how non-homologous end-joining can create novel gene fusions. Comparisons to orthologous regions in sorghum and rice also indicate a greater instability of the maize genome, probably due to diploidization following allotetraploidization

Effect of PEF Treatment on Extraction of Valuable Compounds from Microalgae C. vulgaris

Recovery of intracellular components from microalgae requires a cell disruption step. In recent years, pulsed electric field (PEF) treatment has been discussed to be an efficient alternative to conventional cell disruption techniques, i.e. homogenization or bead milling. In this work the effect of the main processing parameters of the PEF treatment on the extraction of valuable compounds from microalgae Chlorella Vulgaris was investigated. Culture of C. vulgaris strain inoculated in TAP-medium, were cultivated in batch 26 L photo-bioreactor. The algae were harvested after 24 days and concentrated up to a final biomass concentration of 40.8 gdw/kg of suspension. PEF experiments at different field strength (E=27-35 kV/cm) and energy input (WT=50-100-150 kJ/kg) were carried out in a laboratory scale continuous flow unit. Determinations of time-conductivity profile as well as quantification of dry matter, carbohydrates, protein content, and total phenolics of the supernatant collected after 1 h extraction, were performed. Results showed a higher increase of the electrical conductivity of PEF treated suspension, when compared to the untreated samples, as a result of the irreversible electroporation induced by pulse treatment. Moreover, the PEF treatment increased the dry matter content as well as the amount of carbohydrates, proteins and phenolic compounds released into the supernatant from inside the algae cells. The results obtained from this study demonstrate the potential of PEF for improving extraction yield of valuable compounds from microalgae

PEF assisted extraction of valuable compounds from microalgae C. vulgaris

In recent years the cultivation and exploitation of Microalgae biomass has stimulated intensive research due both to its high productivity, when compared to agriculturally grown biomass, and the large relative content of more than 50% of valuable cell components, like lipids, proteins, polysaccharides, antioxidants, vitamins and pigments (Goettel et al., 2013; Luengo et al., 2014). However, the extraction of these compounds is limited by the mass transfer of these compounds through cell membranes. In this frame, thanks to the reduction of the resistances to mass transfer due to the induced permeabilization of plant cells, Pulsed Electric Field (PEF) technology can be used as a pre-treatment of concentrated microalgae suspension in order to enhance the extraction yield of valuable compounds (such as antioxidants and colorants) from the inner parts of the cells(Mahnič-Kalamiza et al., 2014). In this work the effect of different PEF treatment intensity on the extraction of valuable compound from microalgae Chlorella Vulgaris was investigated. Culture of C. vulgaris strain inoculated in TAP-medium, were cultivated in batch 26 L photo-bioreactor. Growth conditions were monitored by OD measurements at 750 nm. The algae were harvested after 18-24 days and concentrated up to a final biomass concentration of about 40-50 gdw/kgsus. PEF experiments of different intensities (E=27-35 kV/cm, and WT=50-100- 150 kJ/kg) were carried out in a laboratory scale continuous flow unit. Determinations of time-conductivity profile as well as quantification of dry matter, protein content, total polyphenolics (TP), and antioxidant activity (AA) of the supernatant were performed. Results showed a higher increase of the electrical conductivity of PEF treated suspension, when compared to the untreated sample. Moreover, the PEF treatment increased the dry matter content as well as the amount of proteins released into the supernatant from inside the algae cells. Additionally, increments of total phenolics and antioxidant activity were also detected. The results obtained from this study demonstrate the potential of PEF for improving extraction of compounds of interest from the microalgae C. vulgaris

Selection of GmSWEET39 for oil and protein improvement in soybean.

Soybean [Glycine max (L.) Merr.] was domesticated from wild soybean (G. soja Sieb. and Zucc.) and has been further improved as a dual-use seed crop to provide highly valuable oil and protein for food, feed, and industrial applications. However, the underlying genetic and molecular basis remains less understood. Having combined high-confidence bi-parental linkage mapping with high-resolution association analysis based on 631 whole sequenced genomes, we mapped major soybean protein and oil QTLs on chromosome15 to a sugar transporter gene (GmSWEET39). A two-nucleotide CC deletion truncating C-terminus of GmSWEET39 was strongly associated with high seed oil and low seed protein, suggesting its pleiotropic effect on protein and oil content. GmSWEET39 was predominantly expressed in parenchyma and integument of the seed coat, and likely regulates oil and protein accumulation by affecting sugar delivery from maternal seed coat to the filial embryo. We demonstrated that GmSWEET39 has a dual function for both oil and protein improvement and undergoes two different paths of artificial selection. A CC deletion (CC-) haplotype H1 has been intensively selected during domestication and extensively used in soybean improvement worldwide. H1 is fixed in North American soybean cultivars. The protein-favored (CC+) haplotype H3 still undergoes ongoing selection, reflecting its sustainable role for soybean protein improvement. The comprehensive knowledge on the molecular basis underlying the major QTL and GmSWEET39 haplotypes associated with soybean improvement would be valuable to design new strategies for soybean seed quality improvement using molecular breeding and biotechnological approaches