Advances in salinity tolerance of soybean: Genetic diversity, heredity, and gene identification contribute to improving salinity tolerance

Salt stress is one of the major abiotic stresses affecting soybean growth. Genetic improvement for salt tolerance is an effective way to protect soybean yield under salt stress conditions. Successful improvement of salt tolerance in soybean relies on identifying genetic variation that confers tolerance in soybean germplasm and subsequently incorporating these genetic resources into cultivars. In this review, we summarize the progress in genetic diversity and genetics of salt tolerance in soybean, which includes identifying genetic diversity for salt tolerant germplasm; mapping QTLs conferring salt tolerance; map-based cloning; and conducting genome-wide association study（GWAS） analysis in soybean. Future research avenues are also discussed, including high throughput phenotyping technology, the CRISPR/Cas9 Genome-Editing System, and genomic selection technology for molecular breeding of salt tolerance.

Genome-wide identification and co-expression analysis of GDSL genes related to suberin formation during fruit russeting in pear

Glycine-aspartic acid–serine-leucine(GDSL)type lipases/esterases genes play critical roles in plant development and are related to the responses to abiotic and biotic stress.However,little is known about the GDSL family in pear(Pyrus spp.).Studies have shown GDSL-domain proteins play key roles in suberin deposition.Suberin deposition in the fruit epidermis,also called russeting,is an important defect that negatively affects consumer's appeal in some fruit species,such as pear,apple and grapevine.Fruit russeting is mainly associated with cuticle microcracking and suberin accumulation in the inner part of the epidermal cell walls.To gain insight into the role of the GDSL gene family in suberin deposition and russet development in pear,we performed a genome-wide characterization of the GDSL family,including their identification,chromosomal localization,phylogenetic relationships,and expression patterns,in different tissues/organs in pear.One hundred and thirteen GDSL-type lipases/esterases genes were identified in the pear genome,and a phylogenetic analysis revealed that GDSL family can be classified into four distinct groups.Thirty GDSL genes were co-expressed with five homolog pear genes of three well-known suberin biosynthesis Arabidopsis genes(AtGPAT5,AtASFT,and AtCYP86B1)in the transcriptional co-expression network during pear fruit development.Among the 30 co-expressed GDSL genes,twelve genes were further analyzed by quantitative Real-time PCR,and the results showed the expression levels of the 12 genes were different between the russet exocarp and green exocarp of sand pear at different fruit development stages.Our study provides a detailed overview of the GDSL gene family and lays the foundation for future functional characterization of GDSL genes in P.bretschneideri.

Genome-wide identification and characterization of the JAZ gene family and its expression patterns under various abiotic stresses in Sorghum bicolor

The jasmonate ZIM domain(JAZ)protein belongs to the TIFY((TIF[F/Y]XG)domain protein)family,which is composed of several plant-specific proteins that play important roles in plant growth,development,and defense responses.However,the mechanism of the sorghum JAZ family in response to abiotic stress remains unclear.In the present study,a total of 17 JAZ genes were identified in sorghum using a Hidden Markov Model search.In addition,real-time quantification polymerase chain reaction(RT-qPCR)was used to analyze the gene expression patterns under abiotic stress.Based on phylogenetic tree analysis,the sorghum JAZ proteins were mainly divided into nine subfamilies.A promoter analysis revealed that the SbJAZ family contains diverse types of promoter cis-acting elements,indicating that JAZ proteins function in multiple pathways upon stress stimulation in plants.According to RT-qPCR,SbJAZ gene expression is tissuespecific.Additionally,under cold,hot,polyethylene glycol,jasmonic acid,abscisic acid,and gibberellin treatments,the expression patterns of SbJAZ genes were distinctly different,indicating that the expression of SbJAZ genes may be coordinated with different stresses.Furthermore,the overexpression of SbJAZ1 in Escherichia coli was found to promote the growth of recombinant cells under abiotic stresses,such as PEG 6000,NaCl,and 40℃ treatments.Altogether,our findings help us to better understand the potential molecular mechanisms of the SbJAZ family in sorghum in response to abiotic stresses.

Characterizations and identification of the candidate gene of rice thermo-sensitive genic male sterile gene tms5 by mapping

Previous study indicated that the thermo-sensitive genic malesterile(TGMS) gene in rice was regulated by temperature.TGMS rice plays an important role in hybrid rice production,because the application of the TGMS system in two-line breeding is laborsaving,timesaving,simple,inexpensive,efficient,and eliminating the limitations of the cytoplasmic male sterility(CMS) system.'AnnongS' is the first discovered and deeply studied TGMS rice lines in China.'AnnongS-1' and 'Y58S',two derivatives of TGMS line AnnongS,were both controlled by a single recessive gene named tms5,which was genetically mapped on chromosome 2.In this study,three populations('AnnongS-1' × 'Nanjing11','Y58S' × 'Q611',and 'Y58S' × 'Guanghui122') were developed and used for the molecular fine mapping of the tms5 gene.By analyzing recombination events in the sterile individuals using a total of 125 probes covering the tms5 region,the tms5 gene was physically mapped to a 19-kb DNA fragment between two markers 4039-1 and 4039-2,which were located on the BAC clone AP004039.After the construction of the physical map between two markers 4039-1 and 4039-2,a member(ONAC023) of the NAC(NAM-ATAF-CUC-related) gene family was identified as the candidate gene of the tms5 gene.

Genome-wide identification and expression analysis of GDSL esterase/lipase genes in tomato

The GDSL esterase/lipase family contains many functional genes that perform important biological functions in growth and development, morphogenesis, seed oil synthesis, and defense responses in plants. The expression of GDSL esterase/lipase genes can respond to biotic and abiotic stresses. Although GDSL esterase/lipase family genes have been identified and studied in other plants, they have not been identified and their functions remain unclear in tomato. This study is the first to identify 80 GDSL esterase/lipase family genes in tomato, which were named SlGELP1–80. These genes were mapped to their positions on the chromosomes and their physical and chemical properties, gene structure, phylogenetic relationships, collinear relationships, and cis-acting elements were analyzed. The spatiotemporal expression characteristics of the Sl GELP genes in tomato were diverse. In addition, RNA-seq analysis indicated that the expression patterns of the SlGELP genes in tomato differed before and after inoculation with Stemphylium lycopersici. qRT-PCR was used to analyze the expression of five Sl GELP genes after treatments with S. lycopersici, salicylic acid and jasmonic acid. Finally, this study was the first to identify and analyze GDSL esterase/lipase family genes in tomato via bioinformatics approaches, and these findings provide new insights for improving the study of plant disease resistance.

Identification of Differentially Expressed Genes Associated with Cotton Fiber Development in a Chromosomal Substitution Line(CS-B22sh)

One of the impediments in the genetic improvement of cotton fiber is the paucity of information about genes associated with fiber development.Availability of chromosome arm substitution line CS-

TRANSFORMING ACTIVITY OF DNA FROM HUMAN ESOPHAGEAL CANCER AND THE IDENTIFICATION OF THE TRANSFORMING GENE

Rat-1 cells were transfected with DNA from human esophageal cancer 2K, 4K, 6K, 7K. 8K. The transforming foci were obtained and the transforming cell lines were established. The cell lines can form larger colony in soft agar. Those nude mice injected subcutaneously with the cells suffered from larger fibrous sarcoma. This indicates that the cell lines have carcinogenicity. The experimental results suggest that human DNA sequence and human Ha-ras special 616Kb (BamHI) band are present in the DNA of the transforming cells. The over-expression of ras gene products P21 were found in the tissues of exophageal cancer, the tissues adjacent to tumor and the transforming cells.

Identification and Cloning of Resistance Gene Analogues (RGAs) Encoding NBS-LRR Proteins from Gossypium arboreum L.

Plants have developed a complicated defense mechanism during evolution to resist the harmful pathogens they encountered.The mechanism involves the interaction of the plant resistance(R)

Gossypium herbaceum Negative Mutant for Fiber Elongation a Useful Isoline for Identification of Genes for Fiber Elongation

Actin cytoskeleton plays an important role in cell morphogenesis in plants as demonstrated by pharmacological,biochemical,and genetic studies.The actin cytoskeleton may be involved in

Identification of Key Genes in Cotton Fiber

Twenty-eight candidate genes provided by other sub-projects were used to produce transgenic cotton plants.There were over 1000 individuals,and some of them were generation T2 or T3.All

Identification and analysis of differentially expressed genes involved in dark-induced photoperiod response and senescence of soybean leaves by suppression subtractive hybridization

A cDNA subtractive library enriched for dark-induced up-regulated ESTs was constructed by suppression subtractive hybridization(SSH) from leaf tissues of soybean cultivar DongNong L13 treated with short-day(8-h light/16-h dark) and long-day(16-h light/8-h dark) conditions.A total of 148 clones were sequenced,representing 76 unique ESTs which corresponded to about 20% of 738 clones from the cDNA library and showed a significant up-regulation of at least three fold verified by dot blot hybridization.The putative functions of ESTs were predicted by Blastn and Blastx.The 43 differentially expressed genes identified by subtractions were classified according to their putative functions generated by Blast analysis.Genetic functional analysis indicated that putative proteins encoded by these genes were related to diverse functions during organism development,which include biological regulation pathways such as transcription,signal transduction and programmed cell death,protein,nucleic acid and carbohydrate macromolecule degradation,the cell wall modification,primary and secondary metabolism and stress response.Two soybean transcription factors enhanced in SD conditions,GAMYB-binding protein and DNA binding protein RAV cDNAs that may be involved in SD soybean photoperiod response,had been isolated using 5'-and 3'-rapid amplification of cDNA ends(RACE)(Genbank Accession numbers DQ112540 and DQ147914).

Identification of a candidate elongation related gene in rice induced by GA_3

We identified a gibberellin-induced gene frag-ment in rice elongation by using differentialdisplay(DD)of mRNA.The rice seedlingscarried the eui(elongated)gene,named Zhen-chang A,were used,which were sensitive toGAand elongated rapidly after application of

Identification of the DEAD-box RNA helicase family members in grapevine reveals that VviDEADRH25a confers tolerance to drought stress

Grapevine growing areas are increasingly affected by drought,which has greatly limited global wine production and quality.DEAD-box is one of the largest subfamilies of the RNA helicase family,and its members play key roles in the growth and development of plants and their stress responses.Previous studies have shown the potential of DEAD-box genes in the drought stress responses of Arabidopsis and tomato,rice,and other crop species.However,information about DEAD-box genes in grapevine remains limited.In this report,a total of 40 DEAD-box genes were identified in grapevine and their protein sequence characteristics and gene structures were analyzed.By comparing the expression profiles of VviDEADRHs in response to drought stress in different grapevine varieties,nine candidate genes(VviDEADRH10c,-13,-22,-25a,-25b,-33,-34,-36,and-39)were screened based on expression profiling data.Combined with qRTPCR results,Vvi DEADRH25a was selected for functional verification.Heterologous overexpression of Vvi DEADRH25a in Arabidopsis showed the transgenic plants were more sensitive to drought stress than the control.Both electrolyte permeability and malondialdehyde content were significantly increased in transgenic plants,whereas the chlorophyll content and superoxide dismutase(SOD),peroxidase(POD),catalase(CAT),and ascorbate peroxidase(APX)enzyme activities were significantly decreased.Furthermore,VviDEADRH25a-overexpressing plants showed down-regulated expression levels of several drought stress-related marker genes,namely At COR15a,At RD29A,At ERD15,and At P5CS1,which indicated that they participated in the drought stress response.In summary,this study provides new insights into the structure,evolution,and participation of DEAD-box RNA helicase genes in the response to drought stress in grapevines.

Characterization and functional divergence of genes encoding sucrose transporters in oilseeds castor bean

Castor bean(Ricinus communis L.)is an economically important non-edible oilseed crop.Its seed oils are rich in hydroxy fatty acid,which are highly valuable with a wide range of industrial applications.Sucrose transportation is critical in regulating the growth,development and oilseed yield in castor bean.The transporters or carriers(SUTs or SUCs)play a central role in orchestrating sucrose allocation and aiding in plant adaptation to diverse stresses.In this study,based on castor bean genome,three RcSUCs(RcSUC2,RcSUC3 and RcSUC4)were identified and characterized.The expressional profiles of RcSUCs in different tissues such as leaf,stem,root,phloem and seed tissues exhibited a distinct divergence of gene expression,suggesting that the functions of RcSUC2,RcSUC3 and RcSUC4 are differentiated into long or short-distance transportation among tissues.Additionally,under abiotic stresses including hot temperature,low temperature,drought and salt stresses,the sugar allocation among leaf,stem and roots was tested.The expressional changes of Rc SUCs in leaf,stem and root tissues were associated with sugar transportation and allocation.Taken together,the differential expression of Rc SUCs among tissues responsing to abiotic stress suggested functional differences in sucrose transport and redistribution in different tissues.This study is helpful to understand the physiological and molecular mechanisms of sucrose transportation and allocation among tissues in heterotrophic oilseeds,and could provide clues for genetic improvement and optimization of cultivation practices.

The ethanol response gene Cab45 can modulate the impairment elicited by ethanol and ultraviolet in PC12 cells

High consumption of ethanolic beverages facilitates neurodegeneration, but the mechanism of this process still remained elusive. Suppression subtractive hybridization （SSH） is a technique for detection of rare transcripts. With SSH approach, we identified one ethanol response gene Cab45, which was down-regulated by ethanol with time-dependent manner in B104 cells. The full-length sequence of Cab45 gene was obtained by 5＇-RACE （5＇Rapid Amplification of cDNA Ends） for the first time in rat. Based on the sequence of deduced amino acid of rat Cab45, the alignment was conducted with its counterparts in different species and displayed a high conservation. Using different tissues in rat and cell lines, Cab45 was characterized by a ubiquitous expression and differentiation dependent down-regulation. Given that ethanol facilitates some cell differentiation, we hypothesize that Cab45 is involved in ethanol-mediated differentiation. With transient transfection, the function of Cab45 was investigated by up-regulation and down-regulation in PC12 cells. Ethanol treatment and UV exposure were conducted subsequently and cell proliferations were detected by MTT （Methyl Thiazolyl Tetrazolium） approach. It revealed that the up-regulation of Cab45 modulated the impairment elicited by ethanol and UV in transfected cells. As a member of new calcium binding protein family, the exact role of Cab45 still remains unclear.

Cloning of fatty acid elongase1 gene and molecular identification of A and C genome in Brassica species

The fatty acid elongase 1 (FAE1) genes of Brassic napus were cloned from two cultivars, i.e. Zhong- shuan No. 9 with low erucic acid content, and Zhongyou 821 with high erucic acid content, using the degenerate PCR primers. The sequence analysis showed that there was no intron within the FAE1 genes. The FAE1 genes from Zhongyou 821 contained a coding sequence of 1521 nucleotides, and those cloned from Zhongshuan No. 9 contained a 1517 bp coding sequence. Alignment of the FAE1 sequences from Brassica rapa, B. oleracea and B. napus detected 31 single nucleotide polymorphic sites (2.03%), which resulted in 7 amino-acid substitutions. Further analysis indicated that 19 SNPs were genome-specific, of which, 95% were synonymous mutations. The nucleotide substitution at po- sition 1217 in the FAE1 genes led to a specific site of restricted cleavage. An AvrII cleavage site was present only in the C genome genes and absent in the A genome FAE1 genes. Digestion profile of the FAE1 sequences from B. rapa, B. oleracea and B. napus produced with AvrII confirmed that the FAE1 genes of B. oleracea origin was recognized and digested, while that of B. rapa origin could not. The results indicated that by AvrII cleavage it was possible to distinguish B. rapa from B. oleracea and be- tween the A and C genome of B. napus. In addition, the FAE1 genes could be used as marker genes to detect the pollen flow of B. napus, thus providing an alternative method for risk assessment of gene flow.

Identification and Cloning of Differentially Expressed Genes Involved in the Interaction Between Potato and Phytophthora infestans using a Subtractive Hybridization and cDNA-AFLP Combinational Approach

Using a subtractive hybridization （SH）/cDNA-AFLP combinational approach, differentially expressed genes involved in the potato-Phytophthora infestans interaction were identified. These included genes potentially controlling pathogenesis or avr genes in P. infestans as well as those potentially involved in potato resistance or susceptibility to this pathogen. Forty-one differentially expressed transcript, derived fragments （TDFs）, resulting from the interaction, were cloned and sequenced. Two TDFs, suggested as potential pathogenicity factors, have sequence similarity to N-succinyl diaminopimelate aminotransferase and a transcriptional regulator, TetR family gene, respectively. Two other TDFs, suggested as potential avr genes, have sequence similarity to an EST sequence from Avr41Cf.41Avr91Cf- 9 and a P. infestans avirulence-associated gene, respectively. Genes＇ expression and origin were confirmed using Southern blots, Northern blots and qRT-PCR, he., potential resistance gene DL81 was induced at 12 hpi in the moderately resistant cultivar, whereas it was down-regulated as early as 6 hpi in the susceptible cultivar. On the other hand, DL21 was induced at 6 hpi （3.38-fold） in response to the highly aggressive isolate （US8） and strongly up-regulated thereafter （25.13-fold at 120 hpi.）, whereas it was only slightly up-regulated in response to the weakly aggressive isolate US11 （3.82-fold at 96 hpi）, suggesting its potential involvement as a susceptibility gene.

Identification and characterization of genes involved in the jasmonate biosynthetic and signaling pathways in mulberry(Morus notabilis)

Jasmonate （JA） is an important phytohormone regulating growth, development, and environmental response in plants, particularly defense response against herbivorous insects. Recently, completion of the draft genome of the mulberry （Morus notabilis） in conjunction with genome sequencing of silkworm （Bombyx mori） provides an opportuni-ty to study this unique plant-herbivore interaction. Here, we identified genes involved in JA biosynthetic and signaling pathways in the genome of mulberry for the first time, with the majority of samples showing a tissue-biased expression pattern. The analysis of the representative genes 12-oxophy-todienoic acid reductase （OPRs） and jasmonate ZIM-domain （JAZs） was performed and the results indicated that the mulberry genome contains a relatively smal number of JA biosynthetic and signaling pathway genes. A gene encoding an＆amp;nbsp;important repressor, MnNINJA, was identified as an alternative splicing variant lacking an ethylene-responsive element binding factor-associated amphiphilic repression motif. Having this fundamental information wil facilitate future functional study of JA-related genes pertaining to mulberry-silkworm interactions.

Genes functional identification and synthetic biology of natural products

Synthetic biology is one of the rapid developing scientific fields in recent years. Through synthetic biology,we have a better understanding of the natural synthesis process of natural products, which provides a favorable method to research the diversity of natural products, and also provides new tools for us to create new approach for producing natural products, we can synthesize compounds with different structures by artificial combination of different synthesis modules.

EST-based Analysis of Gene Expression in the Porcine Brain

Since pig is an important livestock species worldwide, its gene expressionhas been investigated intensively, but rarely in brain. In order to study gene expression profilesin the pig central nervous system, we sequenced and analyzed 43,122 high-quality 5'' end expressedsequence tags (ESTs) from porcine cerebellum, cortex cerebrum, and brain stem cDNA libraries,involving several different prenatal and postnatal developmental stages. The initial ESTs wereassembled into 16,101 clusters and compared to protein and nucleic acid databases in GenBank. Ofthese sequences, 30.6% clusters matched protein databases and represented function known sequences;75.1% had significant hits to nucleic acid databases and partial represented known function; 73.3%matched known porcine ESTs; and 21.5% had no matches to any known sequences in GenBank. We used thecategories defined by the Gene Ontology to survey gene expression in the porcine brain.