Characterization of Sucrose transporter alleles and their association with seed yield-related traits in Brassica napus L

<p>Abstract</p> <p>Background</p> <p>Sucrose is the primary photosynthesis product and the principal translocating form within higher plants. <it>Sucrose transporters </it>(<it>SUC/SUT</it>) play a critical role in phloem loading and unloading. Photoassimilate transport is a major limiting factor for seed yield. Our previous research demonstrated that <it>SUT </it>co-localizes with yield-related quantitative trait loci. This paper reports the isolation of <it>BnA7.SUT1 </it>alleles and their promoters and their association with yield-related traits.</p> <p>Results</p> <p>Two novel <it>BnA7.SUT1 </it>genes were isolated from <it>B. napus </it>lines 'Eagle' and 'S-1300' and designated as <it>BnA7.SUT1.a </it>and <it>BnA7.SUT1.b</it>, respectively. The BnA7.SUT1 protein exhibited typical SUT features and showed high amino acid homology with related species. Promoters of <it>BnA7.SUT1.a </it>and <it>BnA7.SUT1.b </it>were also isolated and classified as <it>pBnA7.SUT1.a </it>and <it>pBnA7.SUT1.b</it>, respectively. Four dominant sequence-characterized amplified region markers were developed to distinguish <it>BnA7.SUT1.a </it>and <it>BnA7.SUT1.b</it>. The two genes were estimated as alleles with two segregating populations (F₂and BC₁) obtained by crossing '3715'×'3769'. <it>BnA7.SUT1 </it>was mapped to the A7 linkage group of the TN doubled haploid population. <it>In silico </it>analysis of 55 segmental <it>BnA7.SUT1 </it>alleles resulted three <it>BnA7.SUT1 </it>clusters: <it>pBnA7.SUT1.a- BnA7.SUT1.a </it>(type I), <it>pBnA7.SUT1.b- BnA7.SUT1.a </it>(type II), and <it>pBnA7.SUT1.b- BnA7.SUT1.b </it>(type III). Association analysis with a diverse panel of 55 rapeseed lines identified single nucleotide polymorphisms (SNPs) in promoter and coding domain sequences of <it>BnA7.SUT1 </it>that were significantly associated with one of three yield-related traits: number of effective first branches (EFB), siliques per plant (SP), and seed weight (n = 1000) (TSW) across all four environments examined. SNPs at other <it>BnA7.SUT1 </it>sites were also significantly associated with at least one of six yield-related traits: EFB, SP, number of seeds per silique, seed yield per plant, block yield, and TSW. Expression levels varied over various tissue/organs at the seed-filling stage, and <it>BnA7.SUT1 </it>expression positively correlated with EFB and TSW.</p> <p>Conclusions</p> <p>Sequence, mapping, association, and expression analyses collectively showed significant diversity between the two <it>BnA7.SUT1 </it>alleles, which control some of the phenotypic variation for branch number and seed weight in <it>B. napus </it>consistent with expression levels. The associations between allelic variation and yield-related traits may facilitate selection of better genotypes in breeding.</p

Genome-wide analysis of transcriptome and histone modifications in Brassica napus hybrid

Although utilization of heterosis has largely improved the yield of many crops worldwide, the underlying molecular mechanism of heterosis, particularly for allopolyploids, remains unclear. Here, we compared epigenome and transcriptome data of an elite hybrid and its parental lines in three assessed tissues (seedling, flower bud, and silique) to explore their contribution to heterosis in allopolyploid B. napus. Transcriptome analysis illustrated that a small proportion of non-additive genes in the hybrid compared with its parents, as well as parental expression level dominance, might have a significant effect on heterosis. We identified histone modification (H3K4me3 and H3K27me3) variation between the parents and hybrid, most of which resulted from the differences between parents. H3K4me3 variations were positively correlated with gene expression differences among the hybrid and its parents. Furthermore, H3K4me3 and H3K27me3 were rather stable in hybridization and were mainly inherited additively in the B. napus hybrid. Together, our data revealed that transcriptome reprogramming and histone modification remodeling in the hybrid could serve as valuable resources for better understanding heterosis in allopolyploid crops

A male sterility-associated cytotoxic protein ORF288 in Brassica juncea causes aborted pollen development

Cytoplasmic male sterility (CMS) is a widespread phenomenon in higher plants, and several studies have established that this maternally inherited defect is often associated with a mitochondrial mutant. Approximately 10 chimeric genes have been identified as being associated with corresponding CMS systems in the family Brassicaceae, but there is little direct evidence that these genes cause male sterility. In this study, a novel chimeric gene (named orf288) was found to be located downstream of the atp6 gene and co-transcribed with this gene in the hau CMS sterile line. Western blotting analysis showed that this predicted open reading frame (ORF) was translated in the mitochondria of male-sterile plants. Furthermore, the growth of Escherichia coli was significantly repressed in the presence of ORF288, which indicated that this protein is toxic to the E. coli host cells. To confirm further the function of orf288 in male sterility, the gene was fused to a mitochondrial-targeting pre-sequence under the control of the Arabidopsis APETALA3 promoter and introduced into Arabidopsis thaliana. Almost 80% of transgenic plants with orf288 failed to develop anthers. It was also found that the independent expression of orf288 caused male sterility in transgenic plants, even without the transit pre-sequence. Furthermore, transient expression of orf288 and green fluorescent protein (GFP) as a fused protein in A. thaliana protoplasts showed that ORF288 was able to anchor to mitochondria even without the external mitochondrial-targeting peptide. These observations provide important evidence that orf288 is responsible for the male sterility of hau CMS in Brassica juncea

BnMs3 is required for tapetal differentiation and degradation, microspore separation, and pollen-wall biosynthesis in Brassica napus

7365AB, a recessive genetic male sterility system, is controlled by BnMs3 in Brassica napus, which encodes a Tic40 protein required for tapetum development. However, the role of BnMs3 in rapeseed anther development is still largely unclear. In this research, cytological analysis revealed that anther development of a Bnms3 mutant has defects in the transition of the tapetum to the secretory type, callose degradation, and pollen-wall formation. A total of 76 down-regulated unigenes in the Bnms3 mutant, several of which are associated with tapetum development, callose degeneration, and pollen development, were isolated by suppression subtractive hybridization combined with a macroarray analysis. Reverse genetics was applied by means of Arabidopsis insertional mutant lines to characterize the function of these unigenes and revealed that MSR02 is only required for transport of sporopollenin precursors through the plasma membrane of the tapetum. The real-time PCR data have further verified that BnMs3 plays a primary role in tapetal differentiation by affecting the expression of a few key transcription factors, participates in tapetal degradation by modulating the expression of cysteine protease genes, and influences microspore separation by manipulating the expression of BnA6 and BnMSR66 related to callose degradation and of BnQRT1 and BnQRT3 required for the primary cell-wall degradation of the pollen mother cell. Moreover, BnMs3 takes part in pollen-wall formation by affecting the expression of a series of genes involved in biosynthesis and transport of sporopollenin precursors. All of the above results suggest that BnMs3 participates in tapetum development, microspore release, and pollen-wall formation in B. napus

The principal characteristics of the lithosphere of China

The lithospheric structure of China and its adjacent area is very complex and is marked by several prominent characteristics. Firstly, China’s continental crust is thick in the west but thins to the east, and thick in the south but thins to the north. Secondly, the continental crust of the Qinghai–Tibet Plateau has an average thickness of 60–65 km with a maximum thickness of 80 km, whereas in eastern China the average thickness is 30–35 km, with a minimum thickness of only 5 km in the center of the South China Sea. The average thickness of continental crust in China is 47.6 km, which greatly exceeds the global average thickness of 39.2 km. Thirdly, as with the crust, the lithosphere of China and its adjacent areas shows a general pattern of thicker in the west and south, and thinner in the east and north. The lithosphere of the Qinghai–Tibet Plateau and northwestern China has an average thickness of 165 km, with a maximum thickness of 180–200 km in the central and eastern parts of the Tarim Basin, Pamir, and Changdu areas. In contrast, the vast areas to the east of the Da Hinggan Ling–Taihang–Wuling Mountains, including the marginal seas, are characterized by lithospheric thicknesses of only 50–85 km. Fourthly, in western China the lithosphere and asthenosphere behave as a “layered structure”, reflecting their dynamic background of plate collision and convergence. The lithosphere and asthenosphere in eastern China display a “block mosaic structure”, where the lithosphere is thin and the asthenosphere is very thick, a pattern reflecting the consequences of crustal extension and an upsurge of asthenospheric materials. The latter is responsible for a huge low velocity anomaly at a depth of 85–250 km beneath East Asia and the western Pacific Ocean. Finally, in China there is an age structure of “older in the upper layers and younger in the lower layers” between both the upper and lower crusts and between the crust and the lithospheric mantle

Bacterial-Artificial-Chromosome-Based Genome Editing Methods and the Applications in Herpesvirus Research

Herpesviruses are major pathogens that infect humans and animals. Manipulating the large genome is critical for exploring the function of specific genes and studying the pathogenesis of herpesviruses and developing novel anti-viral vaccines and therapeutics. Bacterial artificial chromosome (BAC) technology significantly advanced the capacity of herpesviruses researchers to manipulate the virus genomes. In the past years, advancements in BAC-based genome manipulating and screening strategies of recombinant BACs have been achieved, which has promoted the study of the herpes virus. This review summarizes the advances in BAC-based gene editing technology and selection strategies. The merits and drawbacks of BAC-based herpesvirus genome editing methods and the application of BAC-based genome manipulation in viral research are also discussed. This review provides references relevant for researchers in selecting gene editing methods in herpes virus research. Despite the achievements in the genome manipulation of the herpes viruses, the efficiency of BAC-based genome manipulation is still not satisfactory. This review also highlights the need for developing more efficient genome-manipulating methods for herpes viruses

Geochronology, geochemistry, Sr–Nd–Hf isotopic composition of the late Permian adakite in West Ujimqin, Inner Mongolia: petrogenesis and tectonic implications

We report new zircon U–Pb ages, whole-rock major and trace elements, and the Sr–Nd–Hf isotope composition for adakitic intrusives collected from the West Ujimqin district in the Southeast region of the Central Asian Orogenic Belt (CAOB). These data provide important constraints on the petrogenetic evolution and geodynamic setting of late Permian magmatism in the Southeast CAOB. The U–Pb dating of zircon shows that the ages of Seerbeng pluton and Nuhetingshala pluton in West Ujimqin are 255.3 0.71 Ma and 254.4 1.2 Ma, respectively, which signifies that these are products of magmatic activity in the late Permian. The adakitic intrusives are characterized by high Sr (Sr ≥ 741 ppm), low Y, low Yb, as well as high Sr/Y ratios, and strongly fractionated rare earth elements (10.3The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

Unsupervised Learning for Enhanced Computed Photoacoustic Microscopy

Photoacoustic microscopy (PAM) is a medical-imaging technique with the merits of high contrast and resolution. Nevertheless, conventional PAM scans specimens in a diameter-by-diameter fashion, resulting in a time-consuming process. Furthermore, deep-learning-based PAM image enhancement necessitates acquiring ground-truth data for training purposes. In this paper, we built an optical-resolution photoacoustic microscopy system and introduced an innovative unsupervised-learning algorithm. First, we enhanced the rotational-scanning method, transitioning from a diameter-by-diameter approach to a sector-by-sector one, significantly reducing imaging time (from 280 s to 109 s). Second, by establishing a metric for unsupervised learning, we eliminated the need for collecting reliable and high-quality ground truth, which is a challenging task in photoacoustic microscopy. A total of 324 pairs of datasets (mouse ears) were collected for unsupervised learning, with 274 for training and 50 for testing. Additionally, carbon-fiber data were sampled for lateral resolution and contrast evaluation, as well as the effective rate evaluation of the algorithm. The enhanced images demonstrated superior performance compared with that of maximum projection, both subjectively and objectively. A 76% improvement in the lateral resolution was observed. The effective rate of the algorithm was measured to be 100%, which was tested on 50 random samples. The technique presented in this paper holds substantial potential for image postprocessing and opens new avenues for unsupervised learning in photoacoustic microscopy