Calibration and validation of SiBcrop Model for simulating LAI and surface heat fluxes of winter wheat in the North China Plain

The accurate representation of surface characteristic is an important process to simulate surface energy and water flux in land-atmosphere boundary layer.Coupling crop growth model in land surface model is an important method to accurately express the surface characteristics and biophysical processes in farmland.However,the previous work mainly focused on crops in single cropping system,less work was done in multiple cropping systems.This article described how to modify the sub-model in the SiBcrop to realize the accuracy simulation of leaf area index(LAI),latent heat flux(LHF)and sensible heat flux(SHF)of winter wheat growing in double cropping system in the North China Plain(NCP).The seeding date of winter wheat was firstly reset according to the actual growing environment in the NCP.The phenophases,LAI and heat fluxes in 2004–2006 at Yucheng Station,Shandong Province,China were used to calibrate the model.The validations of LHF and SHF were based on the measurements at Yucheng Station in 2007–2010 and at Guantao Station,Hebei Province,China in 2009–2010.The results showed the significant accuracy of the calibrated model in simulating these variables,with which the R2,root mean square error(RMSE)and index of agreement(IOA)between simulated and observed variables were obviously improved than the original code.The sensitivities of the above variables to seeding date were also displayed to further explain the simulation error of the SiBcrop Model.Overall,the research results indicated the modified SiBcrop Model can be applied to simulate the growth and flux process of winter wheat growing in double cropping system in the NCP.

Genome sequences of horticultural plants:past,present,and future

Horticultural plants play various and critical roles for humans by providing fruits,vegetables,materials for beverages,and herbal medicines and by acting as ornamentals.They have also shaped human art,culture,and environments and thereby have influenced the lifestyles of humans.With the advent of sequencing technologies,there has been a dramatic increase in the number of sequenced genomes of horticultural plant species in the past decade.The genomes of horticultural plants are highly diverse and complex,often with a high degree of heterozygosity and a high ploidy due to their long and complex history of evolution and domestication.Here we summarize the advances in the genome sequencing of horticultural plants,the reconstruction of pan-genomes,and the development of horticultural genome databases.We also discuss past,present,and future studies related to genome sequencing,data storage,data quality,data sharing,and data visualization to provide practical guidance for genomic studies of horticultural plants.Finally,we propose a horticultural plant genome project as well as the roadmap and technical details toward three goals of the project.

Mapping of Mutant Gene prbs Controlling Poly-Row-and-Branched Spike in Barley (Hordeum vulgare L.)

A row-type mutant of barley named poly-row-and-branched spike （prbs） was previously obtained from a two-rowed cultivar Pudamai-2 after treated by inflorescence soaking in maize total DNA solution. The mutant produces branched spikes with irregular multiple rows. Genetic analysis indicated that the mutant phenotype was caused by a recessive gene prbs, and the PRBS locus had a recessive epistatic effect on an independent locus （denoted as Vrsx） conferring the variation of two-rowed spike vs. six-rowed spike. This study aimed to map PRBS as well as Vrsx using simple sequence repeats （SSR） markers. We developed an F2 population from a cross between the prbs mutant and a six-rowed cultivar Putianwudu for the gene mapping. As the two target loci interacted to result in a segregation ratio of two-rowed type：six-rowed type：prbs=9：3：4 in the population, we adopted a special strategy to map the two loci. PRBS was mapped between SSR markers HvLTPPB and Bmag0508A on the short arm of chromosome 3H, with distances of 24.7 and 14.3 cM to the two markers, respectively. Vrsx was mapped between SSR markers Bmag0125 and Bmag0378 on chromosome 2H, with distances of 6.9 and 15.3 cM to the two markers, respectively. This suggests that Vrsx should be the known locus Vrs1, which predominantly controls row-type variation in barley cultivars, and PRBS is a new locus related to the row type of spikes in barley.

Exogenous Application of Abscisic Acid (ABA)Enhances Chilling Tolerance in Seedlings ofNapier Grass (Pennisetum purpureum Schum.)

Napier grass, an important forage crop with potentials in multi-purpose applications, is widely grown throughout the tropics and subtropics. Low temperature severely limits its productivity and geographical distribution in temperate regions of the world. In this study, we investigated the effect of exogenous abscisic Acid(ABA) on chilling tolerance of napier grass(Pennisetum purpureum Schum.) seedlings. Seven-day-old napier grass seedlings were cultured in dd H_2O or ABA solution at different concentrations and exposed to 1 ℃ for different time durations. The chilling injury, membrane stability index(MSI) and proline content were estimated from leaf samples. The results showed that there was obvious morphological injury of leaf blighting and restrained growth for the seedlings under chilling stress, but this damage can be largely reduced(by 2/3) when the seedlings were treated by 100 μmol/L ABA in the culture solution, and that the application of exogenous ABA can help to maintain a good stability of leaf cell membrane as expressed by a high MSI value and a low level of proline in leaf cells. These results suggested that exogenous ABA can significantly alleviate chilling injury in napier grass seedlings by maintaining the stability of leaf cell membrane during chilling stress, and that the chilling tolerance was not ensured by a proline accumulation although a passive accumulation of proline was observed in the seedlings under chilling stress. Our results lay a preliminary foundation for future investigations on the molecular mechanisms of ABA induced chilling or freezing tolerance in napier grass.

Determination of Heterotic Groups and Heterosis Analysis of Yield Performance in indica Rice

To compare the heterosis levels among various groups of parental lines used extensively in China, identify foundational heterotic groups in parental pools and understand the relationship between genetic distance and heterosis performance, 16 parental lines with extensive genetic variation were selected from various sub-groups, and 39 hybrid combinations were generated and evaluated in Fujian and Hainan Provinces of China. The main results were as follows： （1） The 16 parental lines can be grouped into 7 sub-groups consisting of 1 maintainer sub-group and 6 restorer sub-groups; （2） Mean grain yield of the restorer lines was higher than that of the maintainer lines, and mean yield of parental lines was higher than that of the hybrid combinations; （3） The two best heterotic patterns were II-32A × G5 and II-32A × G6, moreover, the order of restorer sub-groups according to grain yield, from the highest to lowest, was G7, G6, G5, G4, G3 and G2; High specific combining ability values were observed for combinations of II-32A × G5, II-32A × G6 and Tianfeng A × G7; （4） Hybrid combinations derived from II-32A crossed with 13 restorer lines had higher yield trait values （mid-parent heterosis, better-parent heterosis, standard heterosis over check and specific combining ability） than any other combinations; （5） Genetic distance was positively correlated with panicle number, grain length and length-to-width ratio （P 〈 0.05） and negatively correlated with grain width, grain yield, seed-setting rate, as well as mid-parent heterosis, standard heterosis over check, and specific combining ability for grain yield （P 〈 0.01）. These heterotic groups and patterns and their argonomic traits will provide useful information for future hybrid rice breeding programs.

Sugarcane mosaic virus infection of model plants Brachypodium distachyon and Nicotiana benthamiana

Sugarcane mosaic virus (SCMV;genus Potyvirus, family Potyviridae) is a causal pathogen of sugarcane mosaic disease, and it is widespread in regions where sugarcane (Saccharum spp. hybrids) is grown. It is difficult to investigate the molecular mechanism of pathogen infection in sugarcane because of limited genomic information. Here, we demonstrated that SCMV strain FZ1 can systemically infect Brachypodium distachyon inbred line Bd21 and Nicotiana benthamiana through inoculation, double antibody sandwich enzyme-linked immunosorbent, transmission electron microscopy, and reverse transcription PCR assays. The leaves of Bd21 developed mosaic symptoms, while the leaves of N. benthamiana showed no obvious symptoms under the challenge of SCMV-FZ1. We concluded that B. distachyon inbred line Bd21 is a promising experimental model plant compared with N. benthamiana for study on the infectivity of SCMV. This is the first report on the SCMV infection of model plants B. distachyon inbred line Bd21 and N. benthamiana, which will shed light on the mechanism of SCMV infection of sugarcane and benefit sugarcane breeding against sugarcane mosaic disease.

Minor-effect QTL for heading date detected in crosses between indica rice cultivar Teqing and near isogenic lines of IR24

Identification of quantitative trait loci(QTL) having small effects on heading date(HD) is important for fine-tuning flowering time in rice(Oryza sativa L.). In this study, minor-effect QTL for HD were identified using five segregating rice populations, including a recombinant inbred line population derived from crosses between indica cultivar Teqing and near isogenic lines of IR24,and four populations derived from residual heterozygotes identified in the original population.HD data from these populations were obtained in multiple years or at two locations with different photoperiods. A total of 11 QTL were detected; they had small additive effects ranging from 0.21 to1.63 days. The QTL were all detected in different populations, locations and/or years, having consistent allelic effects across experiments and a stable magnitude across years at the same location. These QTL, and other minor-effect QTL that have been cloned or fine-mapped, generally do not have strong photoperiod sensitivity, and thus can be used in a wide range of ecogeographical conditions. Seven of the 11 QTL were different from those that have been cloned or fine-mapped, providing new candidates for gene cloning and marker-assisted breeding. Allelic effects of QTL corresponding to those that had been cloned or fine-mapped, were much smaller in this study than previously reported. The results supported the assumption that qualitative and quantitative genes may be different alleles at the same loci, suggesting that it may be promising to identify minor-effect QTL from major heading date genes/QTL that have been cloned.

Cloning and Characterization of Full Length cDNA of a CC-NBS-LRR Resistance Gene in Sweetpotato

Conserved domain such as nucleotide binding site （NBS） was found in several cloned plant disease resistance genes. Based on the NBS domain, resistance gene analogues （RGAs） have been isolated. A full-length cDNA, SPR1 was obtained by rapid amplification of cDNA ends （RACE） method. Sequence analysis indicated that the length of SPR1 was 3 066 bp, including a complete open reading frame of 2 667 bp encoding SPR1 protein of 888 amino acids. Compared with known NBS-LRR genes, it presented relatively high amino acid sequence identity. The polypeptide has a typical structure of nonT1R-NBS-LRR genes, with NB-ARC, CC, and LRR domains. The SPR1-related sequences belonged to multicopy gene family in sweetpotato genome according to the result of Southern blotting. Semi-quantitative RT-PCR analysis showed SPR1 expressed in all tested tissues. The cloning of putative resistance gene from sweetpotato provides a basis for studying the structure and function of sweetpotato disease-resistance relating genes and disease resistant genetic breeding in sweetpotato. The gene has been submitted to the GenBank database, and the accession number is EF428453.

Comprehensive cytological characterization of the Gossypium hirsutum genome based on the development of a set of chromosome cytological markers

Cotton is the world's most important natural fiber crop. It is also a model system for studying polyploidization, genomic organization, and genome-size variation. Integrating the cytological characterization of cotton with its genetic map will be essential for understanding its genome structure and evolution, as well as for performing further genetic-map based mapping and cloning. In this study, we isolated a complete set of bacterial artificial chromosome clones anchored to each of the 52 chromosome arms of the tetraploid cotton Gossypium hirsutum. Combining these with telomere and centromere markers, we constructed a standard karyotype for the G. hirsutum inbred line TM-1. We dissected the chromosome arm localizations of the 45 S and 5S r DNA and suggest a centromere repositioning event in the homoeologous chromosomes AT09 and DT09. By integrating a systematic karyotype analysis with the genetic linkage map, we observed different genome sizes and chromosomal structures between the subgenomes of the tetraploid cotton and those of its diploid ancestors. Using evidence of conserved coding sequences, we suggest that the different evolutionary paths of non-coding retrotransposons account for most of the variation in size between the subgenomes of tetraploid cotton and its diploid ancestors. These results provide insights into the cotton genome and will facilitate further genome studies in G. hirsutum.

A Method for Upscaling Genetic Parameters of CERES-Rice in Regional Applications

To upscale the genetic parameters of CERES-Rice in regional applications, Jiangsu Province, the second largest rice producing province in China, was taken as an example. The province was divided into four rice regions with different rice variety types, and five to six sites in each region were selected. Then the eight genetic parameters of CERES-Rice, particularly the four parameters related to the yield, were modified and validated using the Trial and Error Method and the local statistical data of rice yield at a county level from 2001 to 2004, combined with the regional experiments of rice varieties in the province as well as the local meteorological and soil data （Method 1）. The simulated results of Method 1 were compared with those of other three traditional methods upscaling the genetic parameters, i.e., using one-site experimental data from a local representative rice variety （Method 2）, using local long-term rice yield data at a county level after deducting the trend yield due to progress of science and technology （Method 3）, and using rice yield data at a super scale, such as provincial, ecological zone, country or continent levels （Method 4）. The results showed that the best fitness was obtained by using the Method 1. The coefficients of correlation between the simulated yield and the statistical yield in the Method 1 were significant at 0.05 or 0.01 levels and the root mean squared error （RMSE） values were less than 9% for all the four rice regions. The method for upscaling the genetic parameters of CERES-Rice presented is not only valuable for the impact studies of climate change, but also favorable to provide a methodology for reference in crop model applications to the other regional studies.

Advances of Allelopathic Autotoxicity in Rehmannia glutinosa L.

Allelopathic autotoxicity occurs when a plant releases toxic chemical substances into the environment which inhibits development and growth of the same plant species.Rehmannia glutinosa L.( R.glutinosa ) is one of the most common traditional Chinese medicines,whose productivity and quality,however,are seriously impacted by consecutive monoculture obstacle.Allelopathic autotoxicity is one reason for consecutive monoculture obstacle.In this paper,we reviewed the categories of allelochemicals,the methods of allelochemicals identification,and the mechanisms of allelopathic autotoxicity,which provides clues for further study of the molecular mechanisms of allelopathic autotoxicity and consecutive monoculture obstacle.

Evaluation of the Liver Cancer Prevention of Anthocyanin Extracts from Mulberry (<i>Morus alba</i>L.) Variety PR-01

This study aims to evaluate the preventive effects of anthocyanins extracts (MAEs) from mulberry variety PR-01 against N-nitrosodiethylamine (NDEA)-induced hepatocarcinogenesis in rats. It was found that 150 mg·kg-1 MAEs treatment significantly reduced the NDEA-induced hepatic nodules incidence and hepatocellular carcinoma incidence by 58.30% and 41.70% compared to the model group. Meanwhile, MAEs significantly restored the elevated the liver function enzymes, inhibited the tumor necrosis factor alpha and interleukin-6 levels, elevated the serum interleukin-10 and interferon-γ and increased hepatic glutathione-S-transferase and UDP-glucuronosyltransferase 2B1 enzyme activity. Moreover, 150 mg·kg-1 MAEs supplement enhanced glutathione content and the activities of superoxide dismutase, catalase, glutathione peroxidase activities but reduced the malondialdehyde and thiobarbituric acid-reactive substances content by 37.90% and 44.52%. Furthermore, MAEs pretreatment maintained nuclear factor erythroid 2-related factor 2 (Nrf2), Kelch-like ECH-associated protein 1, heme oxygenase-1, and NAD(P)H: quinine oxidoreductase1 stimulation and inhibited the expression of TNF-α, nuclear factor-kappaB (NF-κB), and cyclooxygenase-2 (COX-2), indicating that MAEs exhibit effectively prevention effects against liver cancer via decreased lipid peroxidation, induced Nrf2-mediated antioxidant enzymes and attenuating the inflammatory mediators COX-2 through NF-κB pathway. Thus, MAEs of mulberry variety PR-01 may be used as a good functional dietary supplement against liver cancer.

Recent amplification of Osr4 LTR-retrotransposon caused rice D1 gene mutation and dwarf phenotype

A novel rice d1 mutant was identified using map-based cloning and comparative analysis of known dl mutants.The mutant[d1-a) shows a mild dwarf trait,which differs only slightly from the wildtype in plant height at the tillering stage.The dl-a mutant is different from other dl mutants.We found that it was interrupted by an Osr4 long terminal repeat(LTR)-retrotransposon,which resulted in the loss of exon 7 in the mutant D1 mRNA.A paralog of the D1 gene.D1-like,was revealed.D1-like is a truncated gene that might have resulted from recombination between retrotransposons.We identified 65 Osr4LTR-retrotransposons in Nipponbare,and found more LTR variants in contrast to coding DNA sequence(CDS) in the retrotransposons.We also identified five possible regulatory motifs in LTRs which may control the expression of the retrotransposons.In addition,we predicted six putative functional Osr4 retrotransposons that contain complete CDSs and all important elements.Osr4 retrotransposons were classified into 4 groups,and this type of retrotransposon only appears to be present in monocots.Members of group 1-1,which included all putative functional retrotransposons,showed a high similarity with each other.The retrotransposons were expressed in all tissues,at especially higher levels in some leaves and seeds.These findings imply that transpositions of group 1-1 members might have occurred frequently and recently.

Effects of Suppressing OsCRY1a Gene Expression on Rice Agronomic Traits

Using primers designed according to the published sequence of rice OsCRY1a gene, we obtained part of the gene fragment by PCR and constructed an RNA interference expression vector with it. To down-regulate the expression level of the gene or lead to the loss-of-function of the gene, the vector was then introduced into rice via Agrobacterium-mediated transformation. Based on the performance of the transgenic plants, the functions of the gene were analyzed and deduced. The results indicated that suppressing the expression of the gene retarded flowering for 16 d in rice with the plant height and grain length significantly increasing whereas other important agronomic traits observed remained unchanged apparently.

Analysis of Genetic Similarity for Improved Japonica Rice Varieties from Different Provinces and Cities in China

To provide a genetic basis for japonica rice breeding, the genetic similarity and cluster of 139 accessions of improved japonica rice varieties from 12 provinces and cities of China were analyzed using 34 SSR markers. Totally 198 alleles were detected among these improved japonica rice varieties with the average number of alleles per pair of primers was 5.3235. RM320, RM531, RM1, RM286, and RM336 showed more alleles, which were 15, 12, 11, 9, and 9, respectively. RM320, RM336, RM286 and RM531 showed higher genetic diversity indexes; which were 2.3324, 2.0292, 1.8996, and 1.7820, respectively. The range of genetic similar index among improved japonica rice varieties from different provinces was from 0.321 to 0.914, with the average of 0.686. There was a high genetic similarity among improved japonica rice varieties from Heilongjiang, Jilin, Liaoning, Ningxia, and Yunnan, which were located in similar latitude or similar ecological environment, while there was a low genetic similarity between improved japonica rice varieties from Guizhou and Jiangsu, and other provinces which were located in more different latitudes and ecological environments. The markers of RM320, RM531, RM1, RM286, and RM336 fit to be used in analysis of genetic diversity for improved japonica rice variety. The genetic similarity among improved japonica rice varieties from different provinces was closely associated with genetic basis of parents, and was also correlated with latitude and ecological environment where the varieties were bred.

Statistical Method for Block in Replication Design and Its SAS Program

Large-scale genetic population used for genetic breeding researches covers a large area in the field experiment,and the effect of local control would be gradually weakened.The block in replication(BIR)design is suitable for large population,which is applied to the field experiment of genetic population.The statistical methods of analysis of variance(ANOVA)and heritability estimation in single and multiple environments were derived and implemented using the statistical analysis system(SAS)program for the analysis of BIR.As a work example,a comparison of statistical analysis between BIR design and the completely random block(CRB)design were conducted for the protein content from a panel containing 455 soybean germplasms.The results indicated the different estimates of average heritability in multiple environments.The research results provided technical support for the application of BIR design in genetics and breeding studies.

Genetic diversity and DNA fingerprinting in jute(Corchorus spp.) based on SSR markers

Genetic diversity analysis and DNA finger printing are very useful in breeding programs,seed conservation and management. Jute(Corchorus spp.) is the second most important natural fiber crop after cotton. DNA fingerprinting studies in jute using SSR markers are limited. In this study, 58 jute accessions, including two control varieties(Huangma 179 and Kuanyechangguo) from the official variety registry in China were evaluated with 28 pairs of SSR primers. A total of 184 polymorphic loci were identified. Each primer detected 3 to 15 polymorphic loci, with an average of 6.6. The 58 jute accessions were DNA-fingerprinted with 67 SSR markers from the 28 primer pairs. These markers differentiated the 58 jute accessions from one another, with Co SSR305-120 and Co SSR174-195 differentiating Huangma 179 and Kuanyechangguo, respectively. NTSYS-pc2.10 software was used to analyze the genetic diversity in the 58 jute accessions. Their genetic similarity coefficients ranged from 0.520 to 0.910 with an average of 0.749, indicating relatively great genetic diversity among them. The 58 jute accessions were divided into four groups with the coefficient 0.710 used as a value for classification, consistent with their species and pedigrees. All these results may be useful both for protection of intellectual property rights of jute accessions and for jute improvement.

Development of an efficient expression system with large cargo capacity for interrogation of gene function in bamboo based on bamboo mosaic virus

Bamboo is one of the fastest growing plants among monocotyledonous species and is grown extensively in subtropical regions.Although bamboo has high economic value and produces much biomass quickly,gene functional research is hindered by the low efficiency of genetic transformation in this species.We therefore explored the potential of a bamboo mosaic virus(BaMV)-mediated expression system to investigate genotype-phenotype associations.We determined that the sites between the triple gene block proteins(TGBps)and the coat protein(CP)of BaMV are the most efficient insertion sites for the expression of exogenous genes in both monopodial and sympodial bamboo species.Moreover,we validated this system by individually overexpressing the two endogenous genes ACE1 and DEC1,which resulted in the promotion and suppression of intemode elongation,respectively.In particular,this system was able to drive the expression of three 2A-linked betalain biosynthesis genes(more than 4 kb in length)to produce betalain,indicating that it has high cargo capacity and may provide the prerequisite basis for the development of a DNA-free bamboo genome editing platform in the future.Since BaMV can infect multiple bamboo species,we anticipate that the system described in this study will greatly contribute to gene function research and further promote the molecular breeding of bamboo.

Simple Sequence Repeat Analysis of Genetic Diversity in Primary Core Collection of Peach(Prunus persica)

In this study, the genetic diversity of 51 cultivars in the primary core collection of peach （Prunus persica （L.） Batsch） was evaluated by using simple sequence repeats （SSRs）. The phylogenetic relationships and the evolutionary history among different cultivars were determined on the basis of SSR data. Twenty-two polymorphic SSR primer pairs were selected, and a total of 111 alleles were identified in the 51 cultivars, with an average of 5 alleles per locus. According to traditional Chinese classification of peach cultivars, the 51 cultivars in the peach primary core collection belong to six variety groups. The SSR analysis revealed that the levels of the genetic diversity within each variety group were ranked as Sweet peach 〉 Crisp peach 〉 Flat peach 〉 Nectarine 〉 Honey Peach 〉 Yellow fleshed peach. The genetic diversity among the Chinese cultivars was higher than that among the introduced cultivars. Cluster analysis by the unweighted pair group method with arithmetic averaging （UPGMA） placed the 51 cultivars into five linkage clusters. Cultivar members from the same variety group were distributed in different UPGMA clusters and some members from different variety groups were placed under the same cluster. Different variety groups could not be differentiated in accordance with SSR markers. The SSR analysis revealed rich genetic diversity in the peach primary core collection, representative of genetic resources of peach.