Abstract:Alkaline (alkalized) soil refers to a type of soil in which the soil colloid contains a high level of exchangeable sodium (alkalinity > 15%), showing a strong alkaline reaction (pH > 8.5), with poor soil structure, and without a high salt content. Alkaline soils and saline soils often coexist, which are collectively called saline-alkaline soils. Different from the stress caused by neutral salt (NaCl) in the saline soil to the crops, the stress caused by the alkaline salt (NaHCO3 and Na2CO3) in the alkaline soil not only includes ion toxicity and osmotic stress, but also more serious damage to crops due to the high pH outside the roots. The traditional method of “reducing alkaline content with planting rice” can improve alkalized soil on a large scale and increase agricultural land area. Therefore, it is important to understand and master the adaptability of rice to alkali stress, create efficient cultivation technique of rice for alkaline land, and then develop new rice varieties with alkali resistance, which are of great practical significance for improving the utilization rate of alkaline (alkalized) land and ensuring regional food security. Based on recent domestic and foreign progresses reported, this paper reviews the rice alkali-tolerance in aspects of morphology and physiological characteristics, gene location and cloning, germplasm identification and screening, and genetic improvement, and present prospects for future research on alkali tolerance of rice. The purpose of this article is to provide a theoretical basis for the improvement of soil and grain by “reducing alkaline content with planting rice”.

Abstract:Plants with colored foliage provide bright colors and have long viewing periods, which is helpful to improve the ornamental value of urban landscaping. Natural pigments (chlorophyll, carotenoid and anthocyanin) are involved in light-dependent reactions and in response to biotic and abiotic stress, and the changes of their contents and proportions make the leaves show green, yellow, white and purplish-red colors. In this paper, the genetic regulation and external environment factors affecting the biosynthetic pathways of chlorophyll, carotenoids and anthocyanins are reviewed to provide a theoretical basis for explaining the color mechanism of forest tree leaves. The existing studies have shown that environmental factors such as light (photoperiod, light intensity and quality), temperature, drought and salt, and hormone variation stimulate the transcription of transcription factors and the structural genes such as HY5, PIFs and DELLA. Meanwhile, methylated and acetylated chromatin and epigenetic modification after transcription of miRNAs and lncRNAs directly or indirectly regulate the expression of biosynthesis pathway genes of the three pigments. Although the biosynthesis pathways of the three pigments are relatively clear at present, the specific regulatory patterns of the metabolism of the three pigments in colored-leaved forest trees and the environmental signals and hormones still need to be further clarified. In the future, we can construct hybrid populations and Germplasm Resource Bank of colored-leaved plants and make use of genomic, transcriptomic, proteomic, metabonomic, phenomic technologies to create new germplasm of colored leaves.

Abstract:Oat (Avena sativa L.) is receiving increasing appreciation as nutritious diet food due to its nutritional benefits and health-care function. Genomics study of oat will help identify and clone the genes underlying important agronomic traits, thus benefiting for the exploitation of oat germplasm resources. This article reviews the important progresses on oat genomics study from the following aspects: (1) the genome designation，genome size and ploidy level variations in the genus Avena; (2) the oat genetic linkage maps constructed by different types of molecular markers; (3) the sequencing of diploid and hexaploid oat species; (4) functional annotation of genes based on quantitative trait locus (QTL) and genome-wide association study (GWAS) approaches; and (5) population genomics or pan-genome study of oat. The prospects of genomics study in oat are proposed, in order to provide reference information for molecular breeding of oat in future.

Abstract:In order to promote the opening and sharing of agricultural germplasm resources in Jiangsu Province, the construction of Jiangsu Agricultural Germplasm Resources Infrastructure had been initiated in 2005. Taking advantage of the efforts over past ten years, a system on the protection and utilization of agricultural germplasm resources combining "four in one" and "storages" has been preliminarily established. This system integrated the information derived from 30 province-level germplasm banks which conserved the crops, trees, aquatic products and domestic animals, thus strongly supporting the innovation of modern agricultural varieties and the development of industry in Jiangsu. However, due to the interdisciplinary and cross-industry construction of the infrastructure, the germplasm banks cover different regions of the province and involve different responsibility subjects of different nature, the operation and management of the infrastructure has been brought certain difficulties, such as a delay on operation service data, complicated statistical procedures and low management efficiency. To further improve the operation and management efficiency of the infrastructure and promote the utilization of germplasm resources, a Browser/Server mode operation management information system of agricultural germplasm resources infrastructure has been established, which are used for online workflow management, realize unified management of running service data and visual display of running service effectiveness. Collectively, the establishment of the system provided visual data supports for infrastructure management and decision-making.

Abstract:Under the frame of the Third National Action of Crop Germplasm Survey and Collection, a series of rice bean germplasm in Hunan province were collected and subjected for the phenotypic diversity analysis. The results showed that 76 rice bean landraces were mainly distributed in mountainous regions of western and southern areas of Hunan province with an altitude of about 0-600m. The diversity analysis based on 15 phenotypic traits revealed a higher genetic diversity in this collection. The correlation analysis and principal component analysis suggested four principal components including plant height, seed size, yield, flower color and seed coat color, with a cumulative contribution rate of 68.33%. Two main categories were suggested for 76 accessions, consisting of Group I representing prostrate or indeterminate pod, and Group II representing erect or determinate pods. Moreover, Group I was further divided into two subpopulations. The genotypes in Group I-1 generally showed small plant, low yield per plant, and bigger seed, which the accessions from group I-2 showing larger plant, higher yield per plant and smaller seed were predominant. The core collection containing 22 rice bean accessions has been identified by the cluster analysis and the range of quantitative characters, which represented three groups based on the characteristics: erect accessions suitable for machinery harvest, large grain accessions, as well as the accessions with dual end-uses for grain production and biomass.

Abstract:Thirty three tea plant resources from Mangshan in Hunan Province were investigated and collected, 24 of which were studied for biological characters and 27 of which were studied for quality analysis. The 24 resources were mainly small trees with upright habit. The young leaves were mostly glabrous or slightly pubescent, light green or yellow green in color, and the adult leaves were green or dark green, medium-sharply medium-dense- to sparse-serrated and flat at margin, with slightly raised upper surface, acuminate apex, and medium texture. The coefficient of variation of 12 characters ranged from 38.07% to 77.90%, with the average value of 58.70%, and the genetic diversity index was 0.51～1.05, with the average value of 0.81. The variation coefficient of 18 quality components of the 27 resources ranged from 4.86% to 71.32%, with an average of 28.29%; the diversity index ranged from 1.59 to 2.03, with an average of 1.86; the principal component analysis indicated that the cumulative contribution rate of the first 5 principal components was 84.36%. The resources were divided into 5 groups. Group I contained 15 resources, which were divided into two subgroups. Both Group II and Group III contained 5 resources, while Group IV and Group V contained 1 resource each. One low-caffeine and 3 high-caffeine tea plant resources were preliminarily screened out. This study provides a basis for the exploration and utilization of Mangshan tea plant resources and researches in the evolution of tea plants in Hunan Province.

Abstract:SSR primers were developed by using the magnetic bead enrichment method in Cymbidium faberi, and the polymorphic primers were used as research tools to explore the relationship between the genetic diversity and the geographical distribution for nine selected wild populations of Cymbidium from the Chongqing-Guizhou-Sichuan Region in China. The results showed that a total of 53 alleles were amplified by 8 pairs of SSR primers. The average number of alleles per locus was 6.625, and the average percentage of polymorphic fragments (PPF) was 98.6%. Mating imbalance between individual plants of Cymbidium was detected. The range of Nei’s diversity index (H) was 0.3158-0.8661, and the range of Shannon information diversity index (I) was 0.8833-1.3557. The genetic diversity of the Qianjiang populations in Chongqing was the highest, with 79.97% of the genetic differentiation within the population,and 20.03% of the genetic differentiation between the populations, the variation within the population being higher than that between the local populations. The gene flow of Nm<1 indicated that the genetic drift played some role in the genetic differentiation of the Cymbidium. By comparing the relationship between genetic clustering results among the populations and the geographic locations of the Cymbidium plants, it was found that the division of wild Cymbidium populations is greatly affected by geographic factors at the molecular genetic level.

Abstract:Owning to the vast territory, complicated geography and diverse climate, there are abundant soybean germplasm resources in Gansu province. However, classification on the maturity groups (MGs) of soybean varieties remained elusive restricting its use of elite varieties in farming. In this study, 151 soybean cultivars collected from major soybean planting regions across Gansu province and 25 MG 0-V reference varieties introduced from North America were planted at five locations with different ecological regions to evaluate their growth period traits and identify the MGs. The results showed that MGs of soybean varieties from Gansu province ranged from MG 00 to MG VI. MG IV accounted for 44.37% of all the tested varieties, followed by MG V (29.14%), MG III (11.26%), MG II (4.64%), MG 0 (3.31%), MG VI (3.31%), MG 00 (2.65%) and MG I (1.32%). MG III varieties were mainly distributed in Hexi Corridor (HC) occupying 47.62% of varieties in the collection from this region. MG IV varieties were well adapted to the local climate at the Central area of Gansu (CG) and Loess plateau of east Gansu (LP), accounting for 56.67% and 63.83% of the varieties collected from the two regions, respectively. MG V varieties were mainly distributed in the Southern Gansu (SG), which accounted for 63.83% of the local varieties. Based on the regression equation of the MG, longitude and frost-free period of the latest soybean varieties in different areas in Guansu province, we proposed the geographical locations where soybean varieties with different maturation period were adapted. A suggestion for soybean variety introduction was also proposed, which provides a scientific base for soybean breeding and regional planning of varieties in Gansu province.

Abstract:Aegilops tauschii is the donor of wheat D genome and hosts abundant genetic variation in the germplasm resources. The Ae. Tauschii germplasm accessions from China which genetically differ from the resources in Middle East are an important source benefitting for the wheat improvement. In order to better protect and utilize the Ae. tauschii resources, 762 accessions collected from China were subjected for the diversity analysis using the molecular markers and the spike traits. Followed by the grouping results of SSR analysis, the candidate sets of Ae. tauschii core collection were constructed by using 10 spike morphological traits including spike width, spike length, lemma width, lemma length, glume width, glume length, grain width and grain length under different genetic distances and different sampling ratios. Four parameters including mean difference percentage (MD%), coincidence rate of range (CR%), variance difference percentage (VD%) and changeable rate of coefficient of variation (VR%) were deployed to evaluate the usability of the candidate core sets, followed by a test using principal coordinate analysis. As a result, the core collection which was constructed by Euclidean distance and LDSS method with 10% sampling ratio was able to maximize the genetic diversity of Ae. tauschii in China with the smallest number of accessions.

Abstract:In order to effectively utilize wheat germplasm introduced from abroad, Waxy and HMW-GS alleles were detected in 47 introduced wheat materials, and the quality parameters of amylose, amylopectin and wet gluten were analyzed. The results showed that there were three types of Wx-A1a, Wx-A1g and Wx-A1b at the Wx-A1 locus, and 39 materials (82.98%) were mainly of Wx-A1a type. Wx-B1a, Wx-B1e and Wx-B1b were located in the Wx-B1 locus, and 37 materials (78.72%) were mainly of Wx-B1a type. Wx-D1a and Wx-D1b were discovered at Wx-D1 locus, and 46 materials were of Wx-D1a type. A total of 8 Wx-1 allele combinations were identified, and 31 materials (65.96%) were mainly of Wx-A1a/B1a/D1a combination. The results also showed that the Glu-A1 alleles Ax2*, Null and Ax1 were distributed in 18, 18 and 11 materials, respectively. At the Glu-D1 locus, it was found that 23 (48.94%) and 21 (44.68%) materials contained Dx2 and Dx5, respectively; 22 (46.81%) and 20 (42.55%) materials contained Dy12 and Dy10, respectively; 2 materials possessed heterozygous Dy10+Dy12 type. A total of 19 kinds of Glu-A1/D1 allele combinations were identified, and Null/Dx5+Dy12 allele combinations were displayed in 7 materials. The quality analysis showed that the materials with Wx-A1a/B1a/D1a had relatively high amylose and low amylopectin contents, and the materials with Ax1 or Ax2* and Dx5+Dy10 possessed relatively high wet gluten content. Those results suggested that the introduced wheat germplasms were rich in Waxy and HMW-GS alleles, which would provide reference for rational utilization of germplasm resources and quality improvement of modern common wheat.

Abstract:As a sub-project under the frame of the Third National-Wide Investigation of Crop Germplasm Resources Project in China, we conducted the survey and collection of 76 cowpea germplasms in 32 counties in Zhejiang Province, followed by the morphological diversity analysis at 44 agronomic traits in the field trials. Out of 76 accessions, 30 asparagus bean accessions (V. unguiculata ssp. sesquipedialis) and 46 common cowpea accessions (V. unguiculata ssp. unguiculata) have been identified. The large genetic variation on the growth habits, fresh pod characters and yield-related traits in this collection have been observed. Moreover, these accessions were subjected for a genotyping with 101 SNP markers. PCA and phylogenetic tree analysis showed two sub-populations (long-podded vs. short-podded) based on the pod length. The asparagus bean accessions are often detected in the long-podded subpopulation, while common cowpea accessions were predominant in the short-podded subpopulation. Collectively, our results unlocked the genetic diversity of Chinese cowpea germplasms collected from Zhejiang province, which might be valuable resources in the exploration of local cowpea resources and in breeding for new cultivars.

Abstract:As a sub-action of the Third National Survey and Collection of Crop Germplasm Resources, we have carried out the survey and collection of vegetable germplasm in 402 villages of 27 selected counties (or cities or districts) in Jiangxi Province. A total of 1817 vegetable accessions have been collected. The analysis of the geographic distribution and specificity of the collected local vegetable accessions suggested 10 elite accessions with elite traits on the disease resistance, stress resistance, commercial properties, and/or processing flexibility. Moreover, by testing for the disease resistance against F. oxysporum using artificial root-soaking inoculation approach, three bitter gourd accessions with high wilt-resistance have been identified. Collectively, gained from the collection and evaluation of vegetable accessions, this work will provide the vegetable germplasm resource valuable in breeding for new varieties and in theoretical studies.

Abstract:Soybean cyst nematode (SCN, Heterodera glycines Ichinohe) is one of the most yield-limiting diseases of soybean worldwide. Releasing SCN-resistant cultivars are the primary basis for controlling SCN. Identification of parent lines showing major resistant loci and desirable agronomic characteristics are prerequisite for breeding resistant cultivars. In this study, a total of 487 soybean accessions were genotyped using two KASP markers that targeted to two resistance loci rhg1 and Rhg4. The accessions, which were identified harboring resistant alleles, were further subjected for resistance inoculated with race-2, race-4, race-5 and race-X12 in the greenhouse. Twenty accessions were characterized simultaneously harboring rhg1 and Rhg4 loci, while two accessions was found with the Rhg4 locus. Testing for SCN resistance suggested that one accession showed moderate resistant to three races and five accessions showed resistant or moderately resistant to two races. One accession was resistant and four accessions were moderately resistant to race-2. Two accessions showed moderately resistant to race-4. Four accessions showed resistant and fourteen moderately resistant to race-5. However, these accessions were turned out to be moderately susceptible or susceptible against race-X12. Collectively, by taking use of 487 soybean accessions this study identified 20 accessions that harbored two major resistant loci and showed desirable agronomic characteristics, might serve as elite parental lines in breeding for resistant cultivars via pyramiding rhg1 and Rhg4.

Abstract:Rice (Oryza sativa L.) is sensitive extremely to heat stress at the flowering stage. Screening for rice genetic resources with heat tolerance at the flowering stage and identifying the quantitative trait locus (QTL) become important on the improvement of heat tolerance. In this study, 205 rice lines were evaluated for heat tolerance in the field. The rice panicles which flowered under high temperature were tagged for quantifying the spikelet fertility (SF) which was subjected for the genome wide association study(GWAS). The broad variation on the spikelet fertility was observed in heat tolerance among rice accessions, which ranged from 19.0% to 86.6%, with an average of 64.0% and a median of 65.9%. Rice lines such as “06-32”, “Jiandaoqi” and “Louzaoxian No.5” were tolerant against heat stress and they could be used as candidate donor lines in future rice breeding. A total of 18 QTL with 130 SNPs were detected to be significantly associated with heat tolerance. Six QTL were co-localized with the loci which were previously identified. A novel QTL, qHT4-6, with the lowest P-value was selected for the allelic variation analysis. The heat tolerance of rice lines with G-allele of the lead SNP were significantly stronger than those of A-allele lines. As a result, six genes within the interval of qHT4-6 were proposed to be candidate responding to the heat stress.

Abstract:This study reported the identification of a naturally-occurring mutant app1 which shows abnormal (shorter than the lemma, resulting in the unclosed shell or two palea) or absent palea at the reproductive stage. If compared with wild type, this mutant showed 55.52% of the pollen fertility, 6.48% of the seed setting rate, 10.811 gram of the thousand-grain weight as well as 55.21% of the seed germination rate. By generating the F1 and F2 populations crossed with Nipponbare, F1 plants was observed with a wild-type phenotype and F2 individuals were found with a 3:1 segregation, thus indicating that the app1 mutant phenotype is controlled by a single recessive nuclear gene. Genetic mapping suggested that app1 was located on chromosome 3, flanked by molecular markers ID4231 and ID4246, with a genetic distance of 1.3 cM which corresponds to a physical distance of 13.2 kb. The physical interval contained a single complete open reading frame gene LOC_Os03g11614 in which a point mutation and a 245 bp deletion were detected in the promoter region. RT-qPCR analysis revealed a reduction on the transcriptional level in app1 mutant, thus implying that LOC_Os03g11614 is the most strong candidate. LOC_Os03g11614 was known to encode for OsMADS1 that regulates the development of rice floral organs. Mutations in positions led to various phenotypic variations such as leafy glumes, sterility, and smaller grain size. By taking use of 3000 rice seed resources SNP/INDEL mutation database, the mutation in the app1 promoter of OsMADS1is unique and a novel allele, which particularly resulted in a reduction on gene expression. Thus, this study provided a new germplasm resource which is useful to decipher the OsMADS1 function in the formation of rice floral organs.

Abstract:Rice blast is one of the main diseases in rice, and improvement of rice blast resistance is of great significance in rice breeding. In this study, we constructed a new restorer line M630-Pi9 by making crosses in the rice variety 9311-Pi9 that carries the broad-spectrum blast resistance gene Pi9 with the excellent rice restorer line M630, followed by backcrossing combined with molecular marker-assisted selection and background detection. No significant difference on agronomic traits and rice quality was observed in M630-Pi9 and its hybrid Huiliangyou 630-Pi9 if relative to M630 and Huiliangyou 630, respectively. By test for rice blast resistance at the seeding stage was conducted in M630-Pi9 and M630 by using a mixture of predominant isolates from Anhui province, M630-Pi9 represented improved resistance than that of M630. Natural inoculation showed that the improved restorer lines and derived hybrids had significantly improved rice blast resistance. Moreover, a metabolomic analysis was conducted in order to identify the metabolites involved in rice blast resistance. 212 metabolites in M630-Pi9 compared with M630 were found, including 155 down-regulated and 57 up-regulated components. The contents of substances annotated for cell wall and alkaloids which have toxic or immunizing effects on the organism are significantly increased and decreased, respectively. The contents of flavonoids involved in adverse biological process have been modified, implying that the rice blast resistance gene Pi9 trade off the invasion of pathogens via possibly regulating the contents of metabolites. Collectively, this work provided an example of deciphering the mechanism of rice blast resistance and producing new germplasm for rice breeding.

Abstract:In this study, 183 sweet and waxy maize inbred lines were subjected to analyze the flowering time (Days to anthesis, DA), silking time (Days to silking, DS) and Anthesis silking interval (ASI) under Cd-polluted environments, in order to reveal the response and possible regulatory genes at the flowering stage. The results showed that Cd pollution prolonged DA and DS of sweet and waxy maize, especially for DS, which led to the increasing of ASI. The ASI value of waxy maize was found to be lower than that of sweet maize, implying the sensitivity of sweet corn under Cd stress. Three and six SNPs, which were associated with flowering time and silking time, respectively, were detected by Genome-wide association analysis (GWAS). These SNPs were found to be associated with eight genes annotated in maize GDB and NCBI gene databases, including few genes which were reported roles in the flowering time. Collectively, these results might provide theoretical reference for molecular marker assisted breeding and Cd safe breeding of sweet and waxy maize varieties in the future.

Abstract:Kernel ratio (KR) is closely associated with grain yield per ear in maize (Zea mays), and the analysis of genetic mechanism for kernel ratio is important for high yield breeding. We used 309 inbred lines of maize as an association population, and used FarmCPU (fixed and random model circulating probability unification), CMLM (compressed mixed linear model), and MLMM (multiple loci mixed model) to conduct genome-wide association studies for kernel ratio of maize grown in Yuanyang, Dancheng, and Sanya in 2017 and 2019, and best linear unbiased estimate (BLUE). Eighteen significant SNPs for KR were identified (P < 1.72E-05), which were located on Bin1.02(1), Bin1.08(1), Bin1.12(1), Bin2.05(5), Bin2.06(1), Bin2.10(1), Bin4.08(1), Bin4.09(1), Bin5.02(1), Bin5.04(1), Bin5.05(1), Bin6.05(1), Bin8.03(1), and Bin9.04(1). The phenotypic variation explanation for KR of the 18 SNPs ranged from 0.067% to 15.43%. Five SNPs (S1_304584425, S5_11751831, S5_93814060, S5_186385476, and S8_94354503) varied from 10.09% to 15.43%, and were considered as major SNPs. S2_87292896 was detected by CMLM and MLMM in BLUE environment and Yuanyang 2019. S2_111319193 was identified by FarmCPU and MLMM in BLUE environment. S5_93814060 was detected by CMLM and MLMM in Dancheng 2017. Bin1.08, Bin2.06, Bin4.09, and Bin6.05 might be important genomic regions for KR compared with results of previous studies. A total of 32 candidate genes were identified, among which E3 ubiquitin-protein ligase UPL1, DEAD-box ATP-dependent RNA helicase 52 RH52, protein kinase homolog4, SNARE-interacting protein KEULE, and elongation factor (EF1A) may be important genes for KR.

Abstract:Soluble inorganic pyrophosphatase regulates the homeostasis of inorganic pyrophosphate (PPi) in the cytoplasm through hydrolysis. In this study, seven genes encoded for soluble inorganic pyrophosphatase in maize (ZmPPases) were cloned and identified on chromosomes 2, 4, 5, 6, 8, 10, respectively. The relative molecular mass of ZmPPases was varied from 22.8 kDα to 25.6 kDα with the isoelectric point of 4.84 to 6.24. Secondary structure analysis of ZmPPases revealed alpha helix and beta strand motifs. Phylogenetic analysis together with the homozygous proteins in maize, rice, Sorghum, and Arabidopsis suggested three phylogenetic branches of soluble inorganic pyrophosphatases. ZmPPases were localized in the cell membrane and nucleus by transient expression in N. benthamiana. The ZmPPase genes were inducible under salt and drought stress treatments, whereas ZmPPase2.1 (Zm00001d051564) was down-regulated under salt stress treatment. Collectively, this study reported a comprehensive analysis of the sequence and expression of ZmPPases family members, which might provide a theoretical basis for further functional research.

Abstract:The number of vascular bundles in the stem is a key factor that affects the nutrient transport and the lodging resistance in maize. Here we deployed an association panel including 172 maize inbred lines to analyze the difference between the number of small vascular bundles (NSVB) and the number of large vascular bundles (NLVB) in the uppermost internode of maize stem, followed by the multiple comparison analysis to learn about the difference and the trend in the number of vascular bundles among different heterosis groups. The results showed that coefficients of variation of NSVB and NLVB in the uppermost internode in different inbred lines were 17.47%~21.69% and 25.83%~32.19%, respectively. The highly significant differences on either of NSVB and NLVB were revealed in different inbred lines. The broad-sense heritability on NSVB and NLVB was 78.87% and 82.58% respectively, while a significantly positive correlation on NSVB in relative to NLVB was observed. Both NSVB and NLVB represented a similarity on the tendency in different heterotic groups (Lancaster < Reid < P < LRC < TSPT). Collectively, this study represented a preliminary understanding of the genetic variation in the number of vascular bundles in different maize inbred lines, and laid a foundation for future quantitative trail locus (QTL) mapping and gene cloning.

Abstract:Cotton is the most widely cultivated fiber crops in the world. With the improvement of people's living standards and the development of cotton textile industry, the demand for high-quality cotton fiber is constantly increasing. In this study, a large-scale genetic population was generated from a cross of a G. barbadense introgression line ZP171. This line contains the upland cotton (G. hirsutum) variety CCRI 8 genetic background with everal chromosome segments of G. barbadense Pima 90-53. The results revealed significant correlation in fibre length (FL) and fiber strength (FS) if compared with other fiber quality traits, and moderately high broad-sense heritability in FL and FS. Moreover, the variance analysis unlocked abundant genetic variations within the population, which are predictable by using four principal components based on the principal component analysis. Nineteen elite lines with higher fiber length or fiber strength than CCRI 8 were identified across multiple environments, respectively. Collectively, this study provided the elite germplasm resources in fine mapping of functional genes associating with fiber quality and breeding of new cotton varieties.

Abstract:Foxtail millet (Setaria italica (L.) P. Beauv.) is a significant minor crop in China, having the characteristics of drought resistance and infertile soil tolerance, high water use efficiency, wide adaptability, and richly nutritious grains. However, the weeding problem has been restricting intensive cultivation and promotion and development of organic dry farming industry of foxtail millet. In order to quickly select herbicide-resistant foxtail millet varieties, the M2 population of mutants of foxtail millet ‘Jingu 21’ was used as the test materials. The initial selection and re-screening of the ‘Jingu 21’ mutants population were carried out by spraying 0.33% sethoxydim herbicide in order to quickly obtain mutant plants and identify their molecular characteristics. The results showed that 39 mutant plants resistant to sethoxydim were preliminarily selected in the initial screening of 0.33% sethoxydim sprayed at the seedling stage in the field. From these 39 mutant plants, 9 mutants were identified after respraying 0.33% sethoxydim. A total of 15 plants of 3 mutant strains were molecularly identified, and it was found that the 1780th amino acid encoded by the ACCase gene was mutated from isoleucine to leucine in 4 mutant plants, while no change was found in other plants. The results would provide research materials for improvement of the elite millet variety ‘Jingu 21’ and accelerate breeding of herbicide-resistant millet varieties.

Abstract:To clarify the role of VaDREB1A that interplays with rust fungus infection, the gene VaDREB1A from genomic DNA (gDNA) and cDNA were isolated from adzuki bean. VaDREB1A was found without intron and contained a 660-bp full-length coding sequence that encodes 219 amino acids. VaDREB1A was annotated with one AP2 conserved domain, and this belonged to the A1 subclass of DREB/CBF subfamily using amino acid sequence and phylogenic analysis. The promoter of VaDREB1A harbored several cis-elements that are involved in responsive to ethylene, salicylic acid, and biotic and abiotic stresses. RT-qPCR showed that in resistant cultivar the relative expression of VaDREB1A was significantly reduced at 24 h and 120 h post inoculation (hpi) with the rust fungus Uromyces vignae, whereas in the susceptible cultivar the gene was significantly up regulated at 120 and 192 hpi following infection. Moreover, expression of VaDREB1A was significantly inhibited at 24 and 192 hpi in susceptible cultivar if pretreated with 1-aminocyclopropane-1-carboxylic acid (ACC) pretreatment, as observed from the resistant cultivar. Collectively, these results provided a preliminary evidence that supports an involvement of VaDREB1A underlying adzuki bean rust resistance.

Abstract:In order to study the functional basis of Phage shock protein A (PspA), the full-length coding sequence (CDS) of the PspA gene was isolated based on sequence homolog and its expression pattern of PspA from N. flagelliforme under drought stress was studied by RT-qPCR. We further generated a plasmid pCAM35s-GFP-PspA which were subjected for a subcellular localization analysis and a transformation in A. thaliana. PspA contained a 777-bp full-length coding sequence, and this gene was significantly up-regulated in N. flagelliforme upon drought stress treatment. A transient expression of PspA in N. benthamiana suggested a sublocalization on the plasma membrane. Moreover, by transforming this gene in A. thaliana, the transgenic plants showed low copies of the PspA gene using Southern hybridization and expressed the recombination protein by Western blot analysis. The transgenic plants expressing the PspA gene, if compared to the wild type plants, were found to be highly resistant against drought stress. Collectively, the results provided a foundation for further exploring the biological function of the N. flagelliforme PspA gene that interplays with drought stress.

Abstract:Multidrug and toxic compound extrusion transporters (MATE) are able to transport a wide variety of substrates such as metals, hormones and secondary metabolites, and they thus play an important role in growth and development in plant. In this study, the full-length coding sequence of MsMATE1 (NCBI GeneBank accessions: MN547958) and its promoter pMsMATE1 (MT505313) were isolated based on genome and transcriptome sequences of Medicago sativa under iron deficiency. The MsMATE1 is 1470 bp which encodes a putative protein of 489 amino acids. According to bioinformatics analysis, the MsMATE1 protein contains a typical MATE_like superfamily domain, which belongs to the eukaryotic subtype; MsMATE1 is a transmembrane protein, and the main component of its secondary structure is α helix. Phylogenetic analysis showed that MsMATE1 protein is closely related to MtMATE1 (XP013453190.1). The pMsMATE1 is 1598bp which were detected with multiple elements responding to hormone and abiotic stress. MsMATE1 was expressed in roots, shoots and leaves of alfalfa seedlings with the highest abundance in shoots. Under iron-deficient or iron-excess stresses, MsMATE1 was significantly up-regulated in different tissues of alfalfa seedlings, with the highest up-regulation in shoots. In MsMATE1 transgenic tobacco plants if compared with those of wild type plants, the activities of SOD, POD, and CAT, chlorophyll content and soluble protein content were significantly increased, while the significant reduction on content of MDA was observed under iron-deficient or iron-excess conditions, compared with those of wild type plants.The results showed that heterologous expression of MsMATE1 improved the tolerant against iron-deficient or iron-excess stresses in plants. MsMATE1 might be a candidate gene for improving tolerance to iron stress by genetic engineering. Collectively, this study laid a foundation for future deciphering the MsMATE1-involved molecular mechanism upon iron stresses.

Abstract:In this study, three members of the NPR1 family were identified by using the genomic information of Vernicia fordii (tung tree), and were named VfNPR1, VfNPR3 and VfNPR5. The physicochemical properties, subcellular localization, distribution of chromosomes, conservative domain, gene structure, and cis-acting regulatory elements were predicted through bioinformatic methods. The phylogenetic relationship of the NPR1 family in five species of the Euphorbiaceae and Arabidopsis thaliana was analyzed. To understand the expression patterns of the NPR1 family in flowers of different sexualities, in seeds at different phases of development, and in the root system of tung tree under the stress of Fusarium oxysporum, the transcriptional profiles were analyzed by use of the transcriptome sequencing data. The results showed that the NPR1 family members in the five species of the Euphorbiaceae were clearly divided into three subgroups (Clade Ⅰ, Clade Ⅱ, and Clade Ⅲ), and those in Ricinus communis, Jatropha curcas and tung tree showed obvious contraction. The important functional sites of npr1-1 (His334Tyr), npr1-2 (Cys150tyr) and nim1-2 (His300tyr) were quite conservative in the five species of the Euphorbiaceae. The three members of the NPR1 family in tung tree were hydrophobic proteins. VfNPR1, VfNPR3 and VfNPR5 were assigned into chromosomes 8, 10 and 4, respectively. VfNPR1 was located in nuclei, and VfNPR3 and VfNPR5 were located in chloroplasts. The three members of the NPR1 family were significantly differentially expressed in female, male and bisexual flowers, with the highest expression in male flowers. In different development phases of the tung tree seed, VfNPR1 and VfNPR5 had higher expression in the early phase (15 WAF and 10 WAF), while VfNPR3 had higher expression in the late phase (30 WAF). Under the stress of Fusarium oxysporum, the expression of the three members of the NPR1 family was significantly inhibited in the root system of tung tree seedlings at different times of infection, and VfNRP3 was completely inhibited in the late infection period. These results indicate that the three members of the NPR1 family may be involved in the flower and fruit development and the SAR signaling pathway of the root system in tung tree. This study provides important scientific basis for the high-yield cultivation techniques of tung tree, and also provides good genetic resources for the improvement of the tree disease resistance.

Abstract:The production of high quality brown sugar largely depends on the quality of sugarcane. Breeding for sugarcane varieties specifically used for producing brown sugar might be benefited from the sugarcane germplasm resources with rich nutrients. This study was conducted based on 16 representative sugarcane germplasm varieties, which were cultivated widely in China, or often used for the brown sugar production industries at present or in the past. By quantifying the nutrition and quality related traits such as protein, total free amino acid, total polyphenol, sucrose, reducing sugar, ash content, chloride, and colloid content of sugarcane juice, we applied the factor analysis, cluster analysis and grey multidimensional degree comprehensive analysis to evaluate and screen the sugarcane germplasm resources suitable for the brown sugar production. The results showed significant differences in the nutrition and quality indexes in different sugarcane germplasms. Three varieties including Triton, Mintang 69-421 and ROC22, which were detected with the highest contents on protein and amino acids, but a moderate ash content, were qualified for the brown sugar production industry. Considering the demand for the brown sugar production and the nutrient content, five varieties including Triton, Mintang 69-421, Yunzhe 05-51, ROC22 and Chuantang 61-408, have been proposed as the elite germplasm resources in sugarcane breeding.

Abstract:Tetraena mongolica is an endangered species that originated from the Tethys Ocean, and is now endemic to the Eastern Alxa–Western Ordos area. In the recent decades, this species has constantly suffered from environment deterioration and interference of human activities, thus leading to the habitat severely destructed and even disappeared. Rare information of molecular markers has limited the knowledge and protection for this germplasm. In the present study, we sequenced and assembled the transcriptome of T. mongolica, and obtained a dataset that contains 119603 transcribed sequences of the species. Among the assembled transcripts, 25721 Expressed Sequence Tag-Simple Sequence Repeat (EST-SSR) were detected from 21065 Unigenes, with the occurrence frequency of 21.51%. The most abundant motifs type of mononucleotide, dinucleotide, and trinucleotide were A/T, AG/CT, and ATC/ATG, respectively. Of the 39 SSR selected loci, 32 could amplify a total of 140 alleles in 48 individuals. The observed heterozygosity (Ho) ranged from 0.167 to 0.792 and the expected heterozygosity (He) from 0.252 to 0.789, with mean values of 0.462 and 0.579, respectively. The polymorphism information content (PIC) value ranged from 0.218 to 0.746, with an average value of 0.518. Collectively, SSR markers developed in this study might be useful to analyze the genetic structure and adaptive evolutionary mechanisms of T. mongolica, and lay a foundation for conservation, development, and utilization of the germplasm.

Abstract:Rubber tree is an important tropical economic crop. Rubber clones are mainly identified by morphological characters, which is difficult due to the minor morphological differences among them. In order to establish a stable, accurate, and efficient method for rubber clone identification, 5 (out of 426) pairs of SSR primers with clear and stable amplification profiles were selected as core primer sets. Based on these primer sets, high throughput genotyping of 129 rubber tree clones were performed. A total of 71 bands were detected, all of which were polymorphic. The average PIC of the primer pairs was 0.69. According to the polymorphic bands, specific DNA fingerprint of each clone was successfully constructed, and all of the specific DNA fingerprints were converted into quick response (QR) code. The results indicated that an effective method for rubber tree clone identification was constructed, which can provide sufficient technological supports for the protection of rubber tree clone intellectual property.

Abstract:The genus Parrotia C. A. Mey. (Hamamelidaceae) contains just two extant deciduous broad-leaved trees, namely Parrotia subaequalis (H. T. Chang) R. M. Hao & H. T. Wei and P. persica (DC.) C. A. Mey. P. subaequalis, classified as a ‘Grade Ⅰ Key Protected Wild Plant’, is native to eastern China and belongs to East Asian Tertiary relics. Its sibling species, P. persica, is a member of the Arcto-Tertiary relict plant group and is disjunctly distributed in northern Iran. In this study, we estimated for the first time the genome size of the two species of Parrotia using flow cytometry and k-mer analysis, and established and optimized a suitable system for flow cytometric determination of DNA C value of these two plants, selecting Raphanus sativus L. ‘Saxa’ as the internal standard and WPB (woody plant buffer) as the nuclear dissociation solution. Our present research aims to provide a fundamental guidance for whole genome sequencing, genomics research, germplasm resource development and utilization, and species conservation of Parrotia and set an important example for the estimation of the genome size of other genera and species of the Hamamelidaceae. The main findings are as follows: (1) measurement results of the flow cytometry showed that the estimated genome size of P. subaequalis and P. persica was 971.45 ± 13.91 Mb and 890.52 ± 24.69 Mb, respectively; (2) k-mer analysis estimated that the genome size of P. subaequalis was about 951.70 Mb, the hybridity rate was about 1.740%, and the proportion of repeated sequences was about 77.50%; while for P. persica, the genome size, hybridity rate and the percentage of repeated sequences were 858.50 Mb, 0.695% and 74.30%, respectively; (3) the genome of P. subaequalis is classified as a highly heterozygous and highly repeated genome, while the genome of P. persica is a slightly heterozygous and highly repeated genome. Accordingly, the results of this study provide an important database reference for the follow-up work of whole-genome sequencing, assembly and de-redundancy processing of Parrotia based on DNA third-generation high-throughput sequencing technology.