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Yin Z.,Yangzhou University | Zhang Z.,Yangzhou University | Deng D.,Yangzhou University | Chao M.,Nanjing Agricultural University | And 6 more authors.
Plant Physiology | Year: 2014

Rubisco activase (RCA) catalyzes the activation of Rubisco in vivo and plays a crucial role in regulating plant growth. In maize (Zea mays), only β-form RCA genes have been cloned and characterized. In this study, a genome-wide survey revealed the presence of an α-form RCA gene and a β-form RCA gene in the maize genome, herein referred to as ZmRCAα and ZmRCAβ, respectively. An analysis of genomic DNA and complementary DNA sequences suggested that alternative splicing of the ZmRCAβ precursor mRNA (premRNA) at its 3' untranslated region could produce two distinctive ZmRCAβ transcripts. Analyses by electrophoresis and matrix-assisted laser desorption/ionization-tandem time-of-flight mass spectrometry showed that ZmRCAα and ZmRCAβ encode larger and smaller polypeptides of approximately 46 and 43 kD, respectively. Transcriptional analyses demonstrated that the expression levels of both ZmRCAα and ZmRCAβ were higher in leaves and during grain filling and that expression followed a specific cyclic day/night pattern. In 123 maize inbred lines with extensive genetic diversity, the transcript abundance and protein expression levels of these two RCA genes were positively correlated with grain yield. Additionally, both genes demonstrated a similar correlation with grain yield compared with three C4 photosynthesis genes. Our data suggest that, in addition to the β-form RCA-encoding gene, the α-form RCA-encoding gene also contributes to the synthesis of RCA in maize and support the hypothesis that RCA genes may play an important role in determining maize productivity. © 2014 American Society of Plant Biologists. All Rights Reserved.


Wang Z.,Zhejiang University | Li Y.,Zhejiang University | Chang S.X.,University of Alberta | Zhang J.,Jiangsu Yanjiang Institute of Agricultural science | And 3 more authors.
Biology and Fertility of Soils | Year: 2014

The effects and associated mechanisms of the application of organic residues or their derived biochar on the dynamics of soil organic C and soil CO2 efflux in planted soils are poorly understood. This paper investigated the impact of bamboo leaf and the derived biochar applications on soil CO2 efflux and labile organic C in an intensively managed Chinese chestnut plantation in a 12-month field study. The treatments studied included Control, application of bamboo leaf (Leaf), and application of biochar (Biochar). The Leaf treatment increased (P < 0.05) soil CO2 efflux and concentrations of water-soluble organic C (WSOC) and microbial biomass C (MBC). The Biochar treatment increased soil CO2 efflux and WSOC and MBC only in the first month after application, but such effects diminished thereafter. The annual cumulative soil CO2 emission was increased by 16 % by the Leaf treatment as compared to the Control, but there was no difference between the Biochar and Control treatments. The soil organic C (SOC) storage was increased by biochar addition but not by bamboo leaf addition. An exponential relationship between soil temperature and soil CO2 efflux was observed regardless of the treatment. Soil CO2 efflux was correlated to soil WSOC (P < 0.05) but not to soil MBC or moisture content. The apparent temperature sensitivity (Q10) of soil CO2 efflux was ranked as Leaf > Biochar > Control. In comparison with the application of fresh bamboo leaf, pyrolyzed bamboo leaf (biochar) application decreased CO2 effluxes and increased C sequestration in the soil. © 2014, Springer-Verlag Berlin Heidelberg.


Hao D.,Nanjing Agricultural University | Hao D.,Jiangsu Yanjiang Institute of Agricultural science | Chao M.,Nanjing Agricultural University | Yin Z.,Yangzhou University | Yu D.,Nanjing Agricultural University
Euphytica | Year: 2012

Chlorophyll fluorescence parameters are generally used to characterize the intrinsic action of photosystem II (PSII), which is interrelated with the photosynthetic capacity. Mapping of quantitative trait loci for chlorophyll fluorescence parameters and associated traits is important for genetic improvement in soybean. In this study, a genome-wide association analysis was conducted to detect key single-nucleotide polymorphisms (SNPs) associated with chlorophyll content (chl) and chlorophyll fluorescence using 1,536 SNPs in a soybean landraces panel. The analysis revealed significant correlations among chl and five chlorophyll fluorescence parameters, including maximum quantum yield of PSII primary photochemistry in the dark-adapted state (Fv/Fm), light energy absorbed per reaction center (ABS/RC), quantum yield for electron transport (ETo/ABS), probability that a trapped exciton moves an electron into the electron transport chain beyond QA - (ETo/TRo), and performance index on absorption basis (PI ABS). Genome-wide association analysis using a mixed linear model detected 51 SNPs associated with chl and chlorophyll fluorescence parameters. Among these identified SNPs, 14 SNPs were co-associated with two or more different traits in this study, and 8 SNPs were co-associated with soybean yield and yield components in our previous study. These significant SNPs will help to better understand the genetic basis of photosynthesis-related physiological traits, and facilitate the pyramiding of favorable alleles for photosynthetic traits in soybean marker assisted selection schemes for high photosynthetic efficiency. © 2012 Springer Science+Business Media B.V.


Hao D.,Nanjing Agricultural University | Hao D.,Jiangsu Yanjiang Institute of Agricultural science | Cheng H.,Nanjing Agricultural University | Yin Z.,Yangzhou University | And 4 more authors.
Theoretical and Applied Genetics | Year: 2012

Genome-wide association analysis is a powerful approach to identify the causal genetic polymorphisms underlying complex traits. In this study, we evaluated a population of 191 soybean landraces in five environments to detect molecular markers associated with soybean yield and its components using 1,536 single-nucleotide polymorphisms (SNPs) and 209 haplotypes. The analysis revealed that abundant phenotypic and genetic diversity existed in the studied population. This soybean population could be divided into two subpopulations and no or weak relatedness was detected between pair-wise landraces. The level of intra-chromosomal linkage disequilibrium was about 500 kb. Genome-wide association analysis based on the unified mixed model identified 19 SNPs and 5 haplotypes associated with soybean yield and yield components in three or more environments. Nine markers were found co-associated with two or more traits. Many markers were located in or close to previously reported quantitative trait loci mapped by linkage analysis. The SNPs and haplotypes identified in this study will help to further understand the genetic basis of soybean yield and its components, and may facilitate future high-yield breeding by marker-assisted selection in soybean. © 2011 Springer-Verlag.


Yin Z.,Nanjing Agricultural University | Yin Z.,Jiangsu Yanjiang Institute of Agricultural science | Meng F.,Nanjing Agricultural University | Song H.,Nanjing Agricultural University | And 3 more authors.
Plant Physiology | Year: 2010

Rubisco activase (RCA) catalyzes the activation of Rubisco in vivo and plays a crucial role in photosynthesis. However, until now, little was known about the molecular genetics of RCA in soybean (Glycine max), one of the most important legume crops. Here, we cloned and characterized two genes encoding the longer α-isoform and the shorter β-isoform of soybean RCA (GmRCAα and GmRCAβ, respectively). The two corresponding cDNAs are divergent in both the translated and 3′ untranslated regions. Analysis of genomic DNA sequences suggested that the corresponding mRNAs are transcripts of two different genes and not the products of a single alternatively splicing pre-mRNA. Two additional possible α-form RCA-encoding genes, GmRCA03 and GmRCA14, and one additional β-form RCA-encoding gene, GmRCA11, were also isolated. To examine the function and modulation of RCA genes in soybean, we determined the expression levels of GmRCAα and GmRCAβ, Rubisco initial activity, photosynthetic rate, and seed yield in 184 soybean recombinant inbred lines. Correlation of gene expression levels with three other traits indicates that RCA genes could play an important role in regulating soybean photosynthetic capacity and seed yield. Expression quantitative trait loci mapping revealed four trans-expression quantitative trait loci for GmRCAα and GmRCAβ. These results could provide a new approach for the modulation of RCA genes to improve photosynthetic rate and plant growth in soybean and other plants. © 2009 American Society of Plant Biologists.


Chao M.,Nanjing Agricultural University | Yin Z.,Yangzhou University | Hao D.,Jiangsu Yanjiang Institute of Agricultural science | Zhang J.,Nanjing Agricultural University | And 4 more authors.
Journal of Experimental Botany | Year: 2014

Understanding the genetic basis of Rubisco activase (RCA) gene regulation and altering its expression levels to optimize Rubisco activation may provide an approach to enhance plant productivity. However, the genetic mechanisms and the effect of RCA expression on phenotype are still unknown in soybean. This work analysed the expression of RCA genes and demonstrated that two RCA isoforms presented different expression patterns. Compared with GmRCA, GmRCAβ was expressed at higher mRNA and protein levels. In addition, GmRCA and GmRCAβ were positively correlated with chlorophyll fluorescence parameters and seed yield, suggesting that changes in expression of RCA has a potential applicability in breeding for enhanced soybean productivity. To identify the genetic factors that cause expression level variation of GmRCAβ, expression quantitative trait loci (eQTL) mapping was combined with allele mining in a natural population including 219 landraces. The eQTL mapping showed that a combination of both cis-and trans-acting eQTLs might control GmRCAβ expression. As promoters can affect both cis-and trans-acting eQTLs by altering cis-acting regulatory elements or transcription factor binding sites, this work subsequently focused on the promoter region of GmRCAβ. Single-nucleotide polymorphisms in the GmRCAβ promoter were identified and shown to correlate with expression level diversity. These SNPs were classified into two groups, A and B. Further transient expression showed that GUS expression driven by the group A promoter was stronger than that by the group B promoter, suggesting that promoter sequence types could influence gene expression levels. These results would improve understanding how variation within promoters affects gene expression and, ultimately, phenotypic diversity in natural populations. © 2013 The Author.


Yin Z.,Nanjing Agricultural University | Yin Z.,Jiangsu Yanjiang Institute of Agricultural science | Meng F.,Nanjing Agricultural University | Song H.,Nanjing Agricultural University | And 3 more authors.
Planta | Year: 2010

Chlorophyll a fluorescence parameters can provide qualitative and quantitative information about photosynthetic processes in chloroplasts. JIP-test and modulated fluorescence (MF) parameters are commonly used chlorophyll a fluorescence parameters. This study was conducted to identify quantitative trait loci (QTLs) associated with JIP-test parameters, MF parameters, and photosynthetic rate (P N), and to examine the relationships among them in soybean (Glycine max (L.) Merr.). Pot and field experiments were performed to evaluate 184 recombinant inbred lines (RILs) for five JIP-test parameters (ABS/RC, TR o/ABS, ET o/TR o, RE o/ET o, and PI ABS), four MF parameters (Fv/Fm, Fv′/Fm′, ΦPSII, and qP), and P N. Significant correlations were commonly observed among JIP-test parameters, MF parameters, and P N. QTL mapping analysis identified 13, 9, and 4 QTLs for JIP-test parameters, MF parameters, and P N, respectively, of which 13 were stable. Four major genomic regions were detected: LG A2 (19. 81 cM) for JIP-test parameters, LG C1 (94.31 and 97. 61 cM) for P N and MF parameters, LG M (100. 51 cM) for JIP-test and MF parameters, and LG O (30.61-49. 91 cM) for P N, JIP-test, and MF parameters. These results indicate that chlorophyll fluorescence parameters, especially ΦPSII and qP, could play an important role in regulating P N, and that JIP-test and MF parameters could be controlled by the same or different genes. The QTLs identified in this study will help in the understanding of the genetic basis of photosynthetic processes in plants. They will also contribute to the development of marker-assisted selection breeding programs for photosynthetic capacity in soybean. © Springer-Verlag 2010.


PubMed | Yangzhou University and Jiangsu Yanjiang Institute of Agricultural science
Type: Journal Article | Journal: Journal of the science of food and agriculture | Year: 2016

The objectives of this study were to: (1) observe the effects of drought stress (DS) on the structural development of endosperm starch granules; (2) investigate the effects of DS on composition and physicochemical properties of starches; and (3) compare the different responses to DS between soft and hard wheat.DS resulted in large A-type starch granules at 12 d after anthesis (DAA) and a high percentage of B-type starch granules at 18 DAA in endosperm cells of the two wheat cultivars. DS decreased the 1000-grain weight, total starch and amylose contents, and amylose-to-amylopectin ratio of both starches. DS also decreased the percentage of B-type starch granules in NM13 and increased the number of hollows on the surface of A-type starch granules in XM33. DS further increased the swelling power and affected pasting properties of both starches. DS also significantly enhanced the hydrolysis degrees of starches by pancreatic -amylase, Aspergillus niger amyloglucosidase, and HCl in NM13. DS altered the contents of rapidly digestible, slowly digestible, and resistant starches in native, gelatinised, and retrograded starches.Overall, DS can affect the development of endosperm starch granules and the physicochemical properties of starches, thus affecting the qualities of the final wheat products. 2015 Society of Chemical Industry.


PubMed | Jiangsu Yanjiang Institute of Agricultural science
Type: Journal Article | Journal: PloS one | Year: 2015

Waxy maize (Zea mays L. var. ceratina) is an important vegetable and economic crop that is thought to have originated from cultivated flint maize and most recently underwent divergence from common maize. In this study, a total of 110 waxy and 110 common maize inbred lines were genotyped with 3072 SNPs to evaluate the genetic diversity, population structure, and linkage disequilibrium decay as well as identify putative loci that are under positive selection. The results revealed abundant genetic diversity in the studied panel and that genetic diversity was much higher in common than in waxy maize germplasms. Principal coordinate analysis and neighbor-joining cluster analysis consistently classified the 220 accessions into two major groups and a mixed group with mixed ancestry. Subpopulation structure in both waxy and common maize sets were associated with the germplasm origin and corresponding heterotic groups. The LD decay distance (1500-2000 kb) in waxy maize was lower than that in common maize. Fourteen candidate loci were identified as under positive selection between waxy and common maize at the 99% confidence level. The information from this study can assist waxy maize breeders by enhancing parental line selection and breeding program design.


PubMed | Jiangsu Yanjiang Institute of Agricultural science, Nanjing Agricultural University and Henan Agricultural University
Type: Journal Article | Journal: Molecular genetics and genomics : MGG | Year: 2015

Soil salinity is a serious threat to agriculture sustainability worldwide. Seed germination is a critical phase that ensures the successful establishment and productivity of soybeans in saline soils. However, little information is available regarding soybean salt tolerance at the germination stage. The objective of this study was to identify the genetic mechanisms of soybean seed germination under salt stress. One natural population consisting of 191 soybean landraces was used in this study. Soybean seeds produced in four environments were used to evaluate the salt tolerance at their germination stage. Using 1142 single-nucleotide polymorphisms (SNPs), the molecular markers associated with salt tolerance were detected by genome-wide association analysis. Eight SNP-trait associations and 13 suggestive SNP-trait associations were identified using a mixed linear model and the TASSEL 4.0 software. Eight SNPs or suggestive SNPs were co-associated with two salt tolerance indices, namely (1) the ratio of the germination index under salt conditions to the germination index under no-salt conditions (ST-GI) and (2) the ratio of the germination rate under salt conditions to the germination rate under no-salt conditions (ST-GR). One SNP (BARC-021347-04042) was significantly associated with these two traits (ST-GI and ST-GR). In addition, nine possible candidate genes were located in or near the genetic region where the above markers were mapped. Of these, five genes, Glyma08g12400.1, Glyma08g09730.1, Glyma18g47140.1, Glyma09g00460.1, and Glyma09g00490.3, were verified in response to salt stress at the germination stage. The SNPs detected could facilitate a better understanding of the genetic basis of soybean salt tolerance at the germination stage, and the marker BARC-021347-04042 could contribute to future breeding for soybean salt tolerance by marker-assisted selection.

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