A graph-based pan-genome of Brassica oleracea provides new insights into its domestication and morphotype diversification

The domestication of Brassica oleracea has resulted in diverse morphological types with distinct patterns of organ development. Here we report a graph-based pan-genome of B. oleracea constructed from high-quality genome assemblies of different morphotypes. The pan-genome harbors over 200 structural variant hotspot regions enriched in auxin- and flowering-related genes. Population genomic analyses revealed that early domestication of B. oleracea focused on leaf or stem development. Gene flows resulting from agricultural practices and variety improvement were detected among different morphotypes. Selective-sweep and pan-genome analyses identified an auxin-responsive small auxin up-regulated RNA gene and a CLAVATA3/ESR-RELATED family gene as crucial players in leaf-stem differentiation during the early stage of B. oleracea domestication and the BoKAN1 gene as instrumental in shaping the leafy heads of cabbage and Brussels sprouts. Our pan-genome and functional analyses further revealed that variations in the BoFLC2 gene play key roles in the divergence of vernalization and flowering characteristics among different morphotypes, and variations in the first intron of BoFLC3 are involved in fine-tuning the flowering process in cauliflower. This study provides a comprehensive understanding of the pan-genome of B. oleracea and sheds light on the domestication and differential organ development of this globally important crop species.

Contouring Analysis on Synthetic Contrast-Enhanced MR from GRMM-GAN and Implications on MR-Guide Radiation Therapy

PURPOSE/OBJECTIVE(S)

MR-guided linear accelerators have been commercialized making MR-only planning and adaptation an appealing alternative circumventing MR-CT registration. However, obtaining daily contrast-enhanced MR images can be prohibitive due to the increased risk of side effects from repeated contrast injections. In this work, we evaluate the quality of contrast-enhanced multi-modal MR image synthesis network GRMM-GAN (gradient regularized multi-modal multi-discrimination sparse-attention fusion generative adversarial network) for MR-guided radiation therapy.

MATERIALS/METHODS

With IRB approval, we trained the GRMM-GAN based on 165 abdominal MR studies from 65 patients. Each study included T2, T1 pre-contrast (T1pre), and T1 contrast enhanced (T1ce) images. The two pre-contrast MR modalities, T2 and T1pre images were adopted as inputs for GRMM-GAN, and the T1ce image at the portal venous phase was used as an output. Ten MR scans containing 21 liver tumors were selected for contouring analysis. A Turing test was first given to six radiation oncologists, in which 100 real T1ce and synthetic T1ce image slices are randomly given to the radiation oncologists to determine the authenticity of the synthesis. We then invited two radiation oncologists (RadOnc 1 and RadOnc2) to manually contour the 21 liver tumors independently on the real T1ce images. RadOnc2 then performed contouring on the respective synthetic T1ce MRs. DICE coefficient (defined as the intersection over the average of two volumes) and Hausdorff distance (HD, measuring how far two volumes are from each other) were used as analysis metrics. The DICE coefficients were calculated from the two radiation oncologists' contours on the real T1ce MR for each tumor. The DICE coefficients were also calculated from RadOnc 2's contours on real and synthetic MRs. Besides, tumor center shifts were extracted. The tumor center of mass coordinates was extracted from real and synthetic volumes. The difference in the coordinates indicated the shifts in the superior-inferior (SI), right-left (RL), and anterior-posterior (AP) directions between real and synthetic tumor volumes.

RESULTS

An average of 52.3% test score was achieved from the six radiation oncologists, which is close to random guessing. RadOnc 1 and RadOnc 2, who had participated in the contouring analysis, achieved an average DICE of 0.91±0.02 from tumor volumes drawn on the real T1ce MRs. This result sets the inter-operator uncertainty baseline in the real clinical setting. RadOnc 2 achieved an average DICE (real vs. synth) of 0.90±0.04 and HD of 4.76±1.82 mm. Only sub-millimeter (SI: 0.67 mm, RL: 0.41 mm, AP: 0.39 mm) tumor center shifts were observed in all three directions.

CONCLUSION

The GRMM-GAN method has the potential for MR-guided liver radiation when contrast agents cannot be administered daily and provide synthetic contrast-enhanced MR for better tumor targeting. The network can produce synthetic MR images with satisfactory contour agreement and geometric integrity.

High species diversity in Diaporthe associated with citrus diseases in China

Species in Diaporthe have broad host ranges and cosmopolitan geographic distributions, occurring as endophytes, saprobes and plant pathogens. Previous studies have indicated that many Diaporthe species are associated with Citrus. To further determine the diversity of Diaporthe species associated with citrus diseases in China, we conducted extensive surveys in major citrus-producing areas from 2017-2020. Diseased tissues were collected from leaves, fruits, twigs, branches and trunks showing a range of symptoms including melanose, dieback, gummosis, wood decay and canker. Based on phylogenetic comparisons of DNA sequences of the internal transcribed spacer regions (ITS), calmodulin (cal), histone H3 (his3), translation elongation factor 1-alpha (tef1) and beta-tubulin (tub2), 393 isolates from 10 provinces were identified as belonging to 36 species of Diaporthe, including 32 known species, namely D. apiculata, D. biconispora, D. biguttulata, D. caryae, D. citri, D. citriasiana, D. compacta, D. discoidispora, D. endophytica, D. eres, D. fusicola, D. fulvicolor, D. guangxiensis, D. hongkongensis, D. hubeiensis, D. limonicola, D. litchii, D. novem, D. passifloricola, D. penetriteum, D. pescicola, D. pometiae, D. sackstonii, D. sennicola, D. sojae, D. spinosa, D. subclavata, D. tectonae, D. tibetensis, D. unshiuensis, D. velutina and D. xishuangbanica, and four new species, namely D. gammata, D. jishouensis, D. ruiliensis and D. sexualispora. Among the 32 known species, 14 are reported for the first time on Citrus, and two are newly reported from China. Among the 36 species, D. citri was the dominant species as exemplified by its high frequency of isolation and virulence. Pathogenicity tests indicated that most Diaporthe species obtained in this study were weakly aggressive or non-pathogenic to the tested citrus varieties. Only D. citri produced the longest lesion lengths on citrus shoots and induced melanose on citrus leaves. These results further demonstrated that a rich diversity of Diaporthe species occupy Citrus, but only a few species are harmful and D. citri is the main pathogen for Citrus in China. The present study provides a basis from which targeted monitoring, prevention and control measures can be developed. Citation: Xiao XE, Liu YD, Zheng F, et al. 2023. High species diversity in Diaporthe associated with citrus diseases in China. Persoonia 51: 229-256. doi: 10.3767/persoonia.2023.51.06.

TaTPP-7A positively feedback regulates grain filling and wheat grain yield through T6P-SnRK1 signalling pathway and sugar-ABA interaction

Grain size and filling are two key determinants of grain thousand-kernel weight (TKW) and crop yield, therefore they have undergone strong selection since cereal was domesticated. Genetic dissection of the two traits will improve yield potential in crops. A quantitative trait locus significantly associated with wheat grain TKW was detected on chromosome 7AS flanked by a simple sequence repeat marker of Wmc17 in Chinese wheat 262 mini-core collection by genome-wide association study. Combined with the bulked segregant RNA-sequencing (BSR-seq) analysis of an F₂ genetic segregation population with extremely different TKW traits, a candidate trehalose-6-phosphate phosphatase gene located at 135.0 Mb (CS V1.0), designated as TaTPP-7A, was identified. This gene was specifically expressed in developing grains and strongly influenced grain filling and size. Overexpression (OE) of TaTPP-7A in wheat enhanced grain TKW and wheat yield greatly. Detailed analysis revealed that OE of TaTPP-7A significantly increased the expression levels of starch synthesis- and senescence-related genes involved in abscisic acid (ABA) and ethylene pathways. Moreover, most of the sucrose metabolism and starch regulation-related genes were potentially regulated by SnRK1. In addition, TaTPP-7A is a crucial domestication- and breeding-targeted gene and it feedback regulates sucrose lysis, flux, and utilization in the grain endosperm mainly through the T6P-SnRK1 pathway and sugar-ABA interaction. Thus, we confirmed the T6P signalling pathway as the central regulatory system for sucrose allocation and source-sink interactions in wheat grains and propose that the trehalose pathway components have great potential to increase yields in cereal crops.

Fast integration and accumulation of beneficial breeding alleles through an AB-NAMIC strategy in wheat

Wheat (Triticum aestivum) is among the most important staple crops for safeguarding the food security of the growing world population. To bridge the gap between genebank diversity and breeding programs, we developed an advanced backcross-nested association mapping plus inter-crossed population (AB-NAMIC) by crossing three popular wheat cultivars as recurrent founders to 20 germplasm lines from a mini core collection. Selective backcrossing combined with selection against undesirable traits and extensive crossing within and between sub-populations created new opportunities to detect unknown genes and increase the frequency of beneficial alleles in the AB-NAMIC population. We performed phenotyping of 590 AB-NAMIC lines and a natural panel of 476 cultivars for six consecutive growing seasons and genotyped these 1066 lines with a 660K SNP array. Genome-wide association studies of both panels for plant development and yield traits demonstrated improved power to detect rare alleles and loci with medium genetic effects in AB-NAMIC. Notably, genome-wide association studies in AB-NAMIC detected the candidate gene TaSWEET6-7B (TraesCS7B03G1216700), which has high homology to the rice SWEET6b gene and exerts strong effects on adaptation and yield traits. The commercial release of two derived AB-NAMIC lines attests to its direct applicability in wheat improvement. Valuable information on genome-wide association study mapping, candidate genes, and their haplotypes for breeding traits are available through WheatGAB. Our research provides an excellent framework for fast-tracking exploration and accumulation of beneficial alleles stored in genebanks.

A chromosome-scale genome assembly of Dasypyrum villosum provides insights into its application as a broad-spectrum disease resistance resource for wheat improvement

Dasypyrum villosum is one of the most valuable gene resources in wheat improvement, especially for disease resistance. The mining of favorable genes from D. villosum is frustrated by the lack of a whole genome sequence. In this study, we generated a doubled-haploid line, 91C43^DH, using microspore culture and obtained a 4.05-GB high-quality, chromosome-scale genome assembly for D. villosum. The assembly contains39 727 high-confidence genes, and 85.31% of the sequences are repetitive. Two reciprocal translocation events were detected, and 7VS-4VL is a unique translocation in D. villosum. The prolamin seed storage protein-coding genes were found to be duplicated; in particular, the genes encoding low-molecular-weight glutenin at the Glu-V3 locus were significantly expanded. RNA sequencing (RNA-seq) analysis indicated that, after Blumeria graminearum f.sp tritici (Bgt) inoculation, there were more upregulated genes involved in the pattern-triggered immunity and effector-triggered immunity defense pathways in D. villosum than in Triticum urartu. MNase hypersensitive sequencing (MH-seq) identified two Bgt-inducible MH sites (MHSs), one in the promoter and one in the 3' terminal region of the powdery mildew resistance (Pm) gene NLR1-V. Each site had two subpeaks and they were termed MHS1 (MHS1.1/1.2) and MHS2 (MHS2.1/2.2). Bgt-inducible MHS2.2 was uniquely present in D. villosum, and MHS1.1 was more inducible in D. villosum than in wheat, suggesting that MHSs may be critical for regulation of NLR1-V expression and plant defense. In summary, this study provides a valuable genome resource for functional genomics studies and wheat-D. villosum introgression breeding. The identified regulatory mechanisms may also be exploited to develop new strategies for enhancing Pm resistance by optimizing gene expression in wheat.

Genomic footprints of Kam Sweet Rice domestication indicate possible migration routes of the Dong people in China and provide resources for future rice breeding

The Dong people are one of China's 55 recognized ethnic minorities, but there has been a long-standing debate about their origins. In this study, we performed whole-genome resequencing of Kam Sweet Rice (KSR), a valuable, rare, and ancient rice landrace unique to the Dong people. Through comparative genomic analyses of KSR and other rice landraces from south of the Yangtze River Basin in China, we provide evidence that the ancestors of the Dong people likely originated from the southeast coast of China at least 1000 years ago. Alien introgression and admixture in KSR demonstrated multiple migration events in the history of the Dong people. Genomic footprints of domestication demonstrated characteristics of KSR that arose from artificial selection and geographical adaptation by the Dong people. The key genes GS3, Hd1, and DPS1 (related to agronomic traits) and LTG1 and MYBS3 (related to cold tolerance) were identified as domestication targets, reflecting crop improvement and changes in the geographical environment of the Dong people during migration. A genome-wide association study revealed a candidate yield-associated gene, Os01g0923300, a specific haplotype in KSR that is important for regulating grain number per panicle. RNA-sequencing and quantitative reverse transcription-PCR results showed that this gene was more highly expressed in KSR than in ancestral populations, indicating that it may have great value in increasing yield potential in other rice accessions. In summary, our work develops a novel approach for studying human civilization and migration patterns and provides valuable genomic datasets and resources for future breeding of high-yield and climate-resilient rice varieties.

Resistance of QYm.nau-2D to wheat yellow mosaic virus was derived from an alien introgression into common wheat

The QYm.nau-2D locus conferring wheat yellow mosaic virus resistance is an exotic introgression and we developed 11 diagnostic markers tightly linked to QYm.nau-2D. Wheat yellow mosaic virus (WYMV) is a serious disease of winter wheat in China. Breeding resistant varieties is the most effective strategy for WYMV control. A WYMV resistant locus QYm.nau-2D on the chromosome arm 2DL has been repeatedly reported but the mapped region is large. In the present study, we screened recombinants using a biparental population and mapped QYm.nau-2D into an 18.8 Mb physical interval. By genome-wide association studies of 372 wheat varieties for WYMV resistance in four environments, we narrowed down QYm.nau-2D into a 16.4 Mb interval. Haplotype analysis indicated QYm.nau-2D were present as six different states due to recombination during hybridization breeding. QYm.nau-2D was finally mapped into a linkage block of 11.2 Mb. Chromosome painting using 2D specific probes and collinearity analysis among the published sequences corresponding to QYm.nau-2D region indicated the block was an exotic introgression. The Illumina-sequenced reads of four diploid Aegilops species were mapped to the sequence of Fielder, a variety having the introgression. The mapping reads were significantly increased at the putative introgression regions of Fielder. Ae. uniaristata (NN) had the highest mapping reads, suggesting that QYm.nau-2D was possibly an introgression from genome N. We investigated the agronomic performances of different haplotypes and observed no linkage drag of the alien introgression for the 15 tested traits. For marker-assisted selection of QYm.nau-2D, we developed 11 diagnostic markers tightly linked to the locus. This research provided a case study of an exotic introgression, which has been utilized in wheat improvement for WYMV resistance.

Genomic insights into historical improvement of heterotic groups during modern hybrid maize breeding

Single-cross maize hybrids display superior heterosis and are produced from crossing two parental inbred lines belonging to genetically different heterotic groups. Here we assembled 1,604 historically utilized maize inbred lines belonging to various female heterotic groups (FHGs) and male heterotic groups (MHGs), and conducted phenotyping and genomic sequencing analyses. We found that the FHGs and MHGs have undergone both convergent and divergent changes for different sets of agronomic traits. Using genome-wide selection scans and association analyses, we identified a large number of candidate genes that contributed to the improvement of agronomic traits of the FHGs and MHGs. Moreover, we observed increased genetic differentiation between the FHGs and MHGs across the breeding eras, and we found a positive correlation between increasing heterozygosity levels in the differentiated genes and heterosis in hybrids. Furthermore, we validated the function of two selected genes and a differentiated gene. This study provides insights into the genomic basis of modern hybrid maize breeding.

Resilience Factors Preventing Schizophrenia in Ultra-high Risk Patients: Lessons from Genetics

Over the past decades, researchers and psychiatrists in the field of psychosis have moved from a conception of a chronic presentation to a more dynamic paradigm. Accordingly, schizophrenia is now conceptualized as a progressive illness that typically emerges during late adolescence and follows different stages: early vulnerability, ultra-high risk state, first episode of psychosis, and chronic disease. Only one-quarter of the ultra-high risk patients will convert to a full-blown psychotic episode within 3 years while the others, called non-converters, will remain at-risk, develop other psychiatric disorders, or fully recover. The reasons for this differential outcome are not yet understood but this concept opens the way to scientific research to determine the protective factors involved in resilience for non-converters. Based on the Gene X Environment interaction model, schizophrenia results from genetic vulnerability and environmental aggressions which can have an impact on the epigenome and gene expression. Recent studies have shown that genetic variants play a role in the resilience of psychosis. Polygenic risk scores, computed as the addition of genetic polymorphisms, can modulate the effects of genetic at-risk deletions (i.e. del22q11) that predispose to psychosis and may also influence the cognitive symptoms of ultra-high risk patients. Resilience, defined as the ability to withstand adversity, is not only related to external skills or psychotherapeutic care but could also be explained by internal molecular factors. Identifying the genetic factors of resilience might help to stratify the risk and to develop precision medicine in psychiatry.

Wheat breeding history reveals synergistic selection of pleiotropic genomic sites for plant architecture and grain yield

Diversity surveys of crop germplasm are important for gaining insights into the genomic basis for plant architecture and grain yield improvement, which is still poorly understood in wheat. In this study, we exome sequenced 287 wheat accessions that were collected in the past 100 years. Population genetics analysis identified that 6.7% of the wheat genome falls within the selective sweeps between landraces and cultivars, which harbors the genes known for yield improvement. These regions were asymmetrically distributed on the A and B subgenomes with regulatory genes being favorably selected. Genome-wide association study (GWAS) identified genomic loci associated with traits for yield potential, and two underlying genes, TaARF12 encoding an auxin response factor and TaDEP1 encoding the G-protein γ-subunit, were located and characterized to pleiotropically regulate both plant height and grain weight. Elite single-nucleotide haplotypes with increased allele frequency in cultivars relative to the landraces were identified and found to have accumulated over the course of breeding. Interestingly, we found that TaARF12 and TaDEP1 function in epistasis with the classical plant height Rht-1 locus, leading to propose a "Green Revolution"-based working model for historical wheat breeding. Collectively, our study identifies selection signatures that fine-tune the gibberellin pathway during modern wheat breeding and provides a wealth of genomic diversity resources for the wheat research community.

Species of Botryosphaeriaceae associated with citrus branch diseases in China

Citrus is an important and widely cultivated fruit crop in South China. Although the species of fungal diseases of leaves and fruits have been extensively studied, the causal organisms of branch diseases remain poorly known in China. Species of Botryosphaeriaceae are known as important fungal pathogens causing branch diseases on citrus in the USA and Europe. To determine the diversity of Botryosphaeriaceae species associated with citrus branch diseases in China, surveys were conducted in the major citrus-producing areas from 2017 to 2020. Diseased tissues were collected from twigs, branches and trunks with a range of symptoms including cankers, cracking, dieback and gummosis. Based on morphological characteristics and phylogenetic comparison of the DNA sequences of the internal transcribed spacer region (ITS), the translation elongation factor 1-alpha gene (tef1), the β-tubulin gene (tub2) and the DNA-directed RNA polymerase II second largest subunit (rpb2), 111 isolates from nine provinces were identified as 18 species of Botryosphaeriaceae, including Botryosphaeria dothidea, B. fabicerciana, Diplodia seriata, Dothiorella alpina, Do. plurivora, Lasiodiplodia citricola, L. iraniensis, L. microconidia, L. pseudotheobromae, L. theobromae, Neodeightonia subglobosa, Neofusicoccum parvum, and six previously undescribed species, namely Do. citrimurcotticola, L. guilinensis, L. huangyanensis, L. linhaiensis, L. ponkanicola and Sphaeropsis linhaiensis spp. nov. Botryosphaeria dothidea (28.8 %) was the most abundant species, followed by L. pseudotheobromae (23.4 %), which was the most widely distributed species on citrus, occurring in six of the nine provinces sampled. Pathogenicity tests indicated that all 18 species of Botryosphaeriaceae obtained from diseased citrus tissues in this study were pathogenic to the tested Citrus reticulata shoots in vitro, while not all species are pathogenic to the tested Cocktail grapefruit (C. paradisi × C. reticulata) shoots in vivo. In addition, Lasiodiplodia was the most aggressive genus both in vitro and in vivo. This is the first study to identify Botryosphaeriaceae species related to citrus branch diseases in China and the results provide a theoretical basis for the implementation of prevention and control measures. Citation: Xiao XE, Wang W, Crous PW, et al. 2021. Species of Botryosphaeriaceae associated with citrus branch diseases in China. Persoonia 47: 106-135. https://doi.org/10.3767/persoonia.2021.47.03.

Species of Botryosphaeriaceae associated with citrus branch diseases in China

Citrus is an important and widely cultivated fruit crop in South China. Although the species of fungal diseases of leaves and fruits have been extensively studied, the causal organisms of branch diseases remain poorly known in China. Species of Botryosphaeriaceae are known as important fungal pathogens causing branch diseases on citrus in the USA and Europe. To determine the diversity of Botryosphaeriaceae species associated with citrus branch diseases in China, surveys were conducted in the major citrus-producing areas from 2017 to 2020. Diseased tissues were collected from twigs, branches and trunks with a range of symptoms including cankers, cracking, dieback and gummosis. Based on morphological characteristics and phylogenetic comparison of the DNA sequences of the internal transcribed spacer region (ITS), the translation elongation factor 1-alpha gene (tef1), the β-tubulin gene (tub2) and the DNA-directed RNA polymerase II second largest subunit (rpb2), 111 isolates from nine provinces were identified as 18 species of Botryosphaeriaceae, including Botryosphaeria dothidea, B. fabicerciana, Diplodia seriata, Dothiorella alpina, Do. plurivora, Lasiodiplodia citricola, L. iraniensis, L. microconidia, L. pseudotheobromae, L. theobromae, Neodeightonia subglobosa, Neofusicoccum parvum, and six previously undescribed species, namely Do. citrimurcotticola, L. guilinensis, L. huangyanensis, L. linhaiensis, L. ponkanicola and Sphaeropsis linhaiensis spp. nov. Botryosphaeria dothidea (28.8 %) was the most abundant species, followed by L. pseudotheobromae (23.4 %), which was the most widely distributed species on citrus, occurring in six of the nine provinces sampled. Pathogenicity tests indicated that all 18 species of Botryosphaeriaceae obtained from diseased citrus tissues in this study were pathogenic to the tested Citrus reticulata shoots in vitro, while not all species are pathogenic to the tested Cocktail grapefruit (C. paradisi × C. reticulata) shoots in vivo. In addition, Lasiodiplodia was the most aggressive genus both in vitro and in vivo. This is the first study to identify Botryosphaeriaceae species related to citrus branch diseases in China and the results provide a theoretical basis for the implementation of prevention and control measures. Citation: Xiao XE, Wang W, Crous PW, et al. 2021. Species of Botryosphaeriaceae associated with citrus branch diseases in China. Persoonia 47: 106-135. https://doi.org/10.3767/persoonia.2021.47.03.

Identification of rice (Oryza sativa L.) genes involved in sheath blight resistance via a genome-wide association study

Rice sheath blight (RSB) is an economically significant disease affecting rice yield worldwide. Genetic resistance to RSB is associated with multiple minor genes, with each providing a minor phenotypic effect, but the underlying dominant resistance genes remain unknown. A genome-wide association study (GWAS) of 259 diverse rice varieties, with genotypes based on a single nucleotide polymorphism (SNP) and haplotype, was conducted to assess their sheath blight reactions at three developmental stages (seedlings, tillering and booting). A total of 653 genes were correlated with sheath blight resistance, of which the disease resistance protein RPM1 (OsRSR1) and protein kinase domain-containing protein (OsRLCK5) were validated by overexpression and knockdown assays. We further found that the coiled-coil (CC) domain of OsRSR1 (OsRSR1-CC) and full-length OsRLCK5 interacted with serine hydroxymethyltransferase 1 (OsSHM1) and glutaredoxin (OsGRX20), respectively. It was found that OsSHM1, which has a role in the reactive oxygen species (ROS) burst, and OsGRX20 enhanced the antioxidation ability of plants. A regulation model of the new RSB resistance though the glutathione (GSH)-ascorbic acid (AsA) antioxidant system was therefore revealed. These results enhance our understanding of RSB resistance mechanisms and provide better gene resources for the breeding of disease resistance in rice.

Genome-wide association study-based identification genes influencing agronomic traits in rice (Oryza sativa L.)

Rice is one of the most important cereal crops, providing the daily dietary intake for approximately 50% of the global human population. Here, we re-sequenced 259 rice accessions, generating 1371.65 Gb of raw data. Furthermore, we performed genome-wide association studies (GWAS) on 13 agronomic traits using 2.8 million single nucleotide polymorphisms (SNPs) characterized in 259 rice accessions. Phenotypic data and best linear unbiased prediction (BLUP) values of each of the 13 traits over two years of each trait were used for the GWAS. The results showed that 816 SNP signals were significantly associated with the 13 agronomic traits. Then we detected candidate genes related to target traits within 200 kb upstream and downstream of the associated SNP loci, based on linkage disequilibrium (LD) blocks in the whole rice genome. These candidate genes were further identified through haplotype block constructions. This comprehensive study provides a timely and important genomic resource for breeding high yielding rice cultivars.

Resequencing of 145 Landmark Cultivars Reveals Asymmetric Sub-genome Selection and Strong Founder Genotype Effects on Wheat Breeding in China

Controlled pedigrees and the multi-decade timescale of national crop plant breeding programs offer a unique experimental context for examining how selection affects plant genomes. More than 3000 wheat cultivars have been registered, released, and documented since 1949 in China. In this study, a set of 145 elite cultivars selected from historical points of wheat breeding in China were re-sequenced. A total of 43.75 Tb of sequence data were generated with an average read depth of 17.94× for each cultivar, and more than 60.92 million SNPs and 2.54 million InDels were captured, based on the Chinese Spring RefSeq genome v1.0. Seventy years of breeder-driven selection led to dramatic changes in grain yield and related phenotypes, with distinct genomic regions and phenotypes targeted by different breeders across the decades. There are very clear instances illustrating how introduced Italian and other foreign germplasm was integrated into Chinese wheat programs and reshaped the genomic landscape of local modern cultivars. Importantly, the resequencing data also highlighted significant asymmetric breeding selection among the three sub-genomes: this was evident in both the collinear blocks for homeologous chromosomes and among sets of three homeologous genes. Accumulation of more newly assembled genes in newer cultivars implied the potential value of these genes in breeding. Conserved and extended sharing of linkage disequilibrium (LD) blocks was highlighted among pedigree-related cultivars, in which fewer haplotype differences were detected. Fixation or replacement of haplotypes from founder genotypes after generations of breeding was related to their breeding value. Based on the haplotype frequency changes in LD blocks of pedigree-related cultivars, we propose a strategy for evaluating the breeding value of any given line on the basis of the accumulation (pyramiding) of beneficial haplotypes. Collectively, our study demonstrates the influence of "founder genotypes" on the output of breeding efforts over many decades and also suggests that founder genotype perspectives are in fact more dynamic when applied in the context of modern genomics-informed breeding.

Ethyl methanesulfonate mutant library construction in Gossypium hirsutum L. for allotetraploid functional genomics and germplasm innovation

As the gene pool is exposed to both strain on land resources and a lack of diversity in elite allotetraploid cotton, the acquisition and identification of novel alleles has taken on epic importance in facilitating cotton genetic improvement and functional genomics research. Ethyl methanesulfonate (EMS) is an excellent mutagen that induces genome-wide efficient mutations to activate the mutagenic potential of plants with many advantages. The present study established, determined and verified the experimental procedure suitable for EMS-based mutant library construction as the general reference guide in allotetraploid upland cotton. This optimized method and procedure are efficient, and abundant EMS mutant libraries (approximately 12 000) in allotetraploid cotton were successfully obtained. More than 20 mutant phenotypes were observed and screened, including phenotypes of the leaf, flower, fruit, fiber and plant architecture. Through the plants mutant library, high-throughput and high-resolution melting technology-based variation evaluation detected the EMS-induced site mutation. Additionally, based on overall genome-wide mutation analyses by re-sequencing and mutant library assessment, the examination results demonstrated the ideal quality of the cotton EMS-treated mutant library constructed in this study with appropriate high mutation density and saturated genome. What is more, the collection is composed of a broad repertoire of mutants, which is the valuable resource for basic genetic research and functional genomics underlying complex allotetraploid traits, as well as cotton breeding.

Prophylaxis of implant-related infections by local release of vancomycin from a hydrogel in rabbits

Local prophylaxis with antibiotic-loaded bone cement is a successful method to prevent post-operative infections in patients receiving orthopaedic implants. No comparable method is available for uncemented implants. Therefore, a hydrogel consisting of hyaluronic and polylactic acids was evaluated in a rabbit model for delivery of antimicrobial agents to prevent post-operative infections. In a pilot study, the suitability of the in vivo model was assessed by testing the hydrogel as carrier material for antimicrobial agents.In the main study, the antimicrobial-agent-loaded hydrogel was evaluated for infection prophylaxis. Rabbits received a titanium rod intramedullary in the tibia after contamination with Staphylococcus aureus. The rods were coated with unloaded hydrogel (Gel), hydrogel loaded with 2 % (Van2) or 5 % vancomycin (Van5), bioactive glass (BAG) or N-acetyl-L-cysteine (NAC). To analyse the infection severity after 28 d, histopathological, bacteriological, micro-computed tomographic and haematological analyses were performed. In the pilot study, the Van5 group had less infection (0/6 infected) as compared to the Gel group (5/5, p = 0.000) and the in vivo model was deemed suitable. In the main study, in the Van2 and Van5 groups, the number of infected animals was lower [1/6 (p = 0.006) and 2/6 (p = 0.044) infected, respectively]. In contrast, BAG and NAC groups showed no infection reduction (5/6 both groups, p = 0.997). The hydrogel can be used as a local carrier of vancomycin for prophylaxis of implant-related infections.The present study showed promising results for local delivery of antibacterial agents by hydrogel to prevent implant-related infections.

[Mid-to-long term outcomes and influence factors of postoperative concurrent chronic ankle instability and posterior ankle impingement]

OBJECTIVE

To investigate the mid-to-long-term efficacy of patients with chronic ankle instability combined with posterior impingement syndrome after 3-9 years of follow-up, and to analyze the influencing factors.

METHODS

From February 2010 to December 2015, 46 patients underwent concurrent lateral ankle ligament repair with posterior ankle arthroscopic surgery at the Institute of Sports Medicine, Peking University Third Hospital. The patient was first placed in a prone position and underwent arthroscopic debridement for the posterior impingement. After finishing the posterior arthroscopy, the surgeon and assistants first translated the patient to the affected side, then turned to the healthy side, and changed the position to the supine position. During the turning over, another assistant held the arthroscope and the instrument to ensure that it was sterile and could be used without replacement. The anterior ankle arthroscopy was operated if necessary and the lateral ankle ligament repair was anatomic repaired with anchors. The 42 patients were followed up, including 26 males and 16 females. The average age was (28.9±10.0) years. The patient's clinical symptoms, joint stability, mobility and motor function were compared by questionnaire and physical examination. The preoperative and postoperative visual analogue scale (VAS) scores, American Orthopaedic Foot and Ankle Society (AOFAS) scores, Tegner scores were compared, and the clinical scores and the patient age, gender, height and weight were compared. The correlations between body mass index (BMI), preoperative duration, surgery duration, and cartilage injury were analyzed.

RESULTS

The mean follow-up time was (71.8±22.8) months. The postoperative VAS scores (1.0 vs. 5.0, P<0.001), AOFAS scores (92 vs. 80, P<0.001), and Tegner scores (6.5 vs. 2, P<0.001) were significantly superior to the preoperative levels. The excellent and good rate was 97.6%. The postoperative VAS score (t=2.719, P=0.10), AOFAS score (t=-2.853, P=0.10), Tegner score (t=-3.443, P=0.001) and time to return exercise (t=2.814, P=0.008) were negatively correlated with the patient age, and the postoperative VAS score was negatively correlated with cartilage injury (Z=-2.195, P=0.028).

CONCLUSION

The mid-to-long-term clinical outcomes of the chronic ankle ligament instability combined with the posterior impingement were good. The age of the patients was negatively correlated with the clinical outcome. The combined cartilage injury could aggravate the postoperative pain.

[Retrospective analysis of modified Karlsson surgery for chronic calcaneofibular ligament injury]

Objective: To retrospectively evaluate the therapeutic effect and influencing factors of the modified Karlsson operation (anchor method) in treating chronic rupture of the calcaneofibular ligament (CFL). Methods: From August 2010 to May 2014, the data of 24 patients with calcaneofibular ligament rupture treated in Institute of Sports Medicine, Third Hospital of Peking University were retrospectively analyzed. All cases were repaired with modified Karlsson operation (anchor method). There were 14 males and 10 females, with an average age of (30±9) years, and the average body mass index (BMI) was (25±5) kg/m(2). Visual analogue pain score (VAS), American Foot and Ankle Surgery Association score (AOFAS), Tegner knee motion score, ankle stability and mobility were followed up and analyzed. The paired t test was used to compare the normal distribution data before and after the operation. Results: The average follow-up time was (41±13) months. Compared with pre-operation, VAS score decreased significantly at the last follow-up [0(0,7) vs 5(0,8), Z=4.13,P=0.000], AOFAS score increased significantly (94±10 vs 70±14, t=8.94, P<0.05), Tegner score increased significantly (4.7±1.5 vs 2.8±1.3, t=6.87, P<0.05), all improved significantly. AOFAS score was excellent in 19 cases, good in 4 cases and moderate in 1 case, the excellent and good rate was 95.8%. Among them, 20 cases (83.3%) were satisfied with the recovery effect after the operation. Postoperative sprain occurred in 5 cases (20.8%) and ankle mobility was limited in 3 cases (12.5%). Conclusions: The modified Karlsson operation (anchor method) can restore the stability of the ankle joint by treating the chronic rupture of CFL. It is an effective therapy for lateral ankle instability.

[Reconstruction of neglected Achilles tendon rupture: flexor hallucis longus transfer versus gastrocnemius turn-down flaps]

Objective: To compare the outcome of either flexor hallucis longus transfer or turn-down of proximal Achilles tendon tissue repair in treating chronic Achilles tendon rupture. Methods: The clinical data of 21 patients who underwent repair of Myerson type Ⅲ chronic Achilles tendon rupture at Peking University Sports Medicine Research Institute from May 2012 to March 2015 were retrospectively analyzed. Among them, 11 cases were treated with flexor hallucis longus (FHL) transfer, and 10 cases were treated with gastrocnemius turn-down flaps repair. The American Orthopedic Foot & Ankle Society (AOFOS) hindfoot score and Tegner motor function score before and after surgery were recorded and compared between the two groups. Data comparison between groups was performed with t test. Results: The patients in the both group were followed up for an average of (21±7) months. The postoperative AOFOS hindfoot score in the long flexor and gastrocnemius groups were both significantly higher than those before surgery, and the differences were statistically significant (97.7±2.6 vs 72.0±8.1 and 96.0±5.5 vs 78.5±6.4, t=10.70, 6.42, both P<0.05).The postoperative Tegner scores of the two groups were also significantly higher than those before surgery (4.2±1.4 vs 0.7±0.4 and 4.1±0.8 vs 0.6±0.5,t=7.29, 9.35, both P<0.05). There were no significant differences in postoperative AOFOS hindfoot scores and Tegner motor function scores between the two groups (both P>0.05). Conclusion: The flexor hallucis longus transfer and turn-down of proximal Achilles tendon tissue repair can both get satisfactory results in treating chronic Achilles tendon rupture.

Evolutionary conservation of candidate osmoregulation genes in plant phloem sap-feeding insects

The high osmotic pressure generated by sugars in plant phloem sap is reduced in phloem-feeding aphids by sugar transformations and facilitated water flux in the gut. The genes mediating these osmoregulatory functions have been identified and validated empirically in the pea aphid Acyrthosiphon pisum: sucrase 1 (SUC1), a sucrase in glycoside hydrolase family 13 (GH13), and aquaporin 1 (AQP1), a member of the Drosophila integral protein (DRIP) family of aquaporins. Here, we describe molecular analysis of GH13 and AQP genes in phloem-feeding representatives of the four phloem-feeding groups: aphids (Myzus persicae), coccids (Planococcus citri), psyllids (Diaphorina citri, Bactericera cockerelli) and whiteflies (Bemisia tabaci MEAM1 and MED). A single candidate GH13-SUC gene and DRIP-AQP gene were identified in the genome/transcriptome of most insects tested by the criteria of sequence motif and gene expression in the gut. Exceptionally, the psyllid Ba. cockerelli transcriptome included a gut-expressed Pyrocoelia rufa integral protein (PRIP)-AQP, but has no DRIP-AQP transcripts, suggesting that PRIP-AQP is recruited for osmoregulatory function in this insect. This study indicates that phylogenetically related SUC and AQP genes may generally mediate osmoregulatory functions in these diverse phloem-feeding insects, and provides candidate genes for empirical validation and development as targets for osmotic disruption of pest species.

Expression of a GDP-L-galactose phosphorylase-like gene in a Chinese wild Vitis species induces responses to Erysiphe necator and defense signaling molecules

Using rapid amplification of cDNA ends, a full-length cDNA sequence of a GDP-L-galactose phosphorylase-like gene was isolated from leaves infected by Erysiphe necator in the Chinese wild (Vitis pseudoreticulata) clone, 'Baihe-35-1', an E. necator-resistant genotype. The full-length cDNA, designated as VpVTC, comprised 1943 bp and putatively encodes a 453-amino acid polypeptide containing an HIT motif. The deduced amino acid sequence showed high similarity with that of VTC genes from other plants. The expression of VpVTC, determined by reverse transcriptase-polymerase chain reaction, was induced by E. necator and defense signaling molecules, including salicylic acid, methyl jasmonate, and ethephon, in 'Baihe-35-1', the V. quinquangularis genotype 'Shang-24', and the E. necator-susceptible V. pseudoreticulata genotype, 'Hunan-1'. Transcript levels of VpVTC correlated well with the degree of disease resistance in the 3 genotypes. Maximum induction of VpVTC by E. necator (>7-fold at 96 h post-inoculation) occurred in 'Baihe-35-1', which also showed the fastest response to signaling molecules. Upregulating the expression of VpVTC in 'Baihe-35-1' resulted in a gradual increase in the ascorbic acid concentration of leaves inoculated with E. necator. Furthermore, VpVTC was expressed in leaves, stems, inflorescence, tendrils, and fruit at all developmental stages, with the highest level occurring in fruit 35 days after flowering.

The chemokine (C-X-C motif) receptor 4 inhibitor AMD3100 accelerates blood flow restoration in diabetic mice

AIMS/HYPOTHESIS

Bone marrow cell mobilisation potently induces vascular growth in ischaemic tissue, possibly by mobilising endothelial cell progenitors. Thus, mobilising agents might not be therapeutic when endothelial cell progenitors are dysfunctional, as in diabetes mellitus. Local injection of autologous endothelial cell progenitors also stimulates vascular growth in ischaemic tissue, but endothelial cell progenitors from people with multiple cardiovascular risk factors and from obese diabetic mice are marginally therapeutic or inhibitory. We sought to identify possible strategies to improve vascularisation in patients with diabetes mellitus by determining if (1) mobilisation accelerates neovascularisation in diabetic animals, and (2) mobilised cells from a non-diabetic source accelerate vascularisation in diabetic animals.

METHODS

We tested whether systemic administration of the chemokine (C-X-C motif) receptor 4 inhibitor AMD3100 or local injection of human CD34(+) circulating cells mobilised by AMD3100 could speed or enhance blood flow restoration in ischaemic limbs of diabetic mice. The small-molecule-mobilising drug AMD3100 was selected because mobilisation and apheresis can be done on the same day.

RESULTS

Systemic administration of AMD3100 and local injection of cells mobilised by AMD3100 greatly accelerated the restoration of blood flow to ischaemic limbs of diabetic mice. CD34(+) cells mobilised by AMD3100 appeared to be more potent growth stimulators than their unmobilised counterparts.

CONCLUSIONS/INTERPRETATION

Unlike other mobilising agents requiring multi-day mobilisation, AMD3100 enables mobilised donors to undergo mobilisation and apheresis on the same day. The combination of excellent therapeutic benefits as well as ease of use indicates that AMD3100 could be a powerful tool to ameliorate tissue ischaemia in the diabetic environment.

Alterations in grip strength during male sexual arousal

Although it is known that alterations in grip strength occur under a number of conditions, little is known about relationships between grip strength and sexual arousal. This relationship was investigated in 30 healthy heterosexual males, who viewed both erotic and nonerotic videos. A questionnaire was used to assess the extent of sexual arousal. The grip strengths of both hands were measured with a five-position (P1-P5) dynamometer, before and after watching the videos. After watching the erotic video, there was a statistically significant reduction in grip strength for the P2 position, with nonsignificant overall reductions in grip strength for all other positions tested. No such effect was observed in control tests. The results indicate that during sexual arousal, the neural system is likely to reduce the output to muscles not directly related to sexual function, presumably to enhance the physiological responses of sexual arousal.

CD34- blood-derived human endothelial cell progenitors

A subset of adult peripheral blood leukocytes functions as endothelial cell progenitors called angioblasts. They can incorporate into the vasculature in animal models of neovascularization and accelerate the restoration of blood flow to mouse ischemic limbs. Earlier reports suggested that CD34-expressing (CD34+) but not CD34+ cell-depleted (CD34-) leukocytes can differentiate into endothelial cells (EC) in vitro and in vivo. Recent findings suggest that CD14+ cells, which are typically CD34-, also have angioblast-like properties in vitro. To determine the identity of angioblasts, the potential of CD34+, CD34-, CD34- CD14+, and CD34- CD14- cells to produce EC was compared. We show that a subset of monocyte (CD34- CD14+)-enriched cells can take on an EC-like phenotype in culture, but that the EC-like cells also express dendritic cell antigens. These findings suggest that monocytes differentiate into macrophages, dendritic cells, or EC depending on environmental cues. The data also demonstrate that angioblasts are more abundant in the blood than previously thought. Finally, we demonstrate that CD34- and CD34- CD14+ cells incorporate into the endothelium of blood vessels in mouse ischemic limbs. However, incorporation of these cells requires co-injection with CD34+ cells, indicating that leukocyte-leukocyte interactions may play a critical role in governing angioblast behavior in vivo.

Blood-derived angioblasts accelerate blood-flow restoration in diabetic mice

Endothelial cell progenitors, angioblasts, have been detected in the peripheral blood of adult humans, mice, and rabbits. These cells have been shown to incorporate into the endothelium of newly forming blood vessels in pathological and nonpathological conditions. Here we investigated the possibility that the CD34-expressing leukocytes (CD34(+) cells) that appear to be enriched for angioblasts could be used to accelerate the rate of blood-flow restoration in nondiabetic and diabetic mice undergoing neovascularization due to hindlimb ischemia. CD34(+) cells did not accelerate the restoration of flow in nondiabetic mice, but dramatically increased it in diabetic mice. Furthermore, CD34(+) cells derived from type 1 diabetics produced fewer differentiated endothelial cells in culture than did their type 2 diabetic- or nondiabetic-derived counterparts. In vitro experiments suggest that hyperglycemia per se does not alter the ability of angioblasts to differentiate or of angioblast-derived endothelial cells to proliferate. In contrast, hyperinsulinemia may enhance angioblast differentiation but impair angioblast-derived endothelial cell survival or proliferation. Our findings suggest that CD34(+) cells may be a useful tool for therapeutic angiogenesis in diabetics.

Lecithin vesicular carriers for transdermal delivery of cyclosporin A

Two kinds of vesicles with and without the presence of sodium cholate (flexible vesicles and conventional vesicles) were prepared, using cyclosporin A as model drug. When applied onto the excised abdominal skin of mice non-occlusively, the enhancing effects of vesicles on the penetration of cyclosporin A were assessed by an in vitro permeation technique. The effect of sodium cholate micelles was also studied. In vivo study was carried out by topical application of vesicles onto the mice skin and drug serum concentration was detected. Results showed that after 8 h of administration, flexible vesicles transported 1.16 microg of cyclosporin A through per cm(2) mice skin and amounted to 1.88 microg 24 h later. The residual amount in the skin was 1.78+/-0.51 microg/cm(2). However, flexible vesicles failed to transport measurable amount of drug through pre-hydrated skin while deposited 2.39+/-0.26 microg/cm(2) into the skin. Conventional vesicles failed to transfer cyclosporin A into the receiver while accumulated 0. 72+/-0.19 microg/cm(2) of drug in the skin. Furthermore, 1 and 40% sodium cholate micelles precluded the transport of cyclosporin A. In vivo studies indicated that with the application of flexible vesicles, serum drug concentration of 53.43+/-9.24 ng/ml was detected 2 h later. After the stratum corneum of mouse skin has been destroyed by shaving, flexible vesicles transferred large amount of drug into blood, up to 187.32+/-53.21 ng/ml after 1 h of application. Conventional vesicles failed to deliver measurable amount of drug into the blood under normal skin condition. In conclusion, flexible vesicle is better than conventional vesicle as the carrier for transdermal delivery of cyclosporin A. Penetration and fusion have been suggested to be two major functional mechanisms. Hydration is detrimental to the enhancement effect. Stratum corneum constitutes main barrier to the transport of lipophilic cyclosporin A.