January 2014, Volume 56 Issue 1, Pages 2每101.


Cover Caption: Genome Variations in Sorghum
About the cover: The Presence and Absence Variants (PAVs) are a major source of genome structural variations that are useful in functional genomics and plant breeding. Using the next generation sequencing technology, Zhang et al. (pp. 24每37) identified a large number of PAVs in the C4-model plant Sorghum bicolour. They characterized 51 large-sized PAVs (>30 kb) that affect a total size of 2.92 Mb and contain 202 genes in a panel of 96 sorghum inbred lines.

 

          Editorial
New year, new look, and new goals  
Author: Chun-Ming Liu
Journal of Integrative Plant Biology 2014 56(1): 2每3
Published Online: January 15, 2014
DOI: 10.1111/jipb.12146
Abstract (Browse 878)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
          Commentary
Yes indeed, most Americans do eat GMOs every day!  
Author: Maarten J. Chrispeels
Journal of Integrative Plant Biology 2014 56(1): 4每6
Published Online: January 15, 2014
DOI: 10.1111/jipb.12147
Abstract (Browse 2950)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
          New Technology
Conventional digital cameras as a tool for assessing leaf area index and biomass for cereal breeding  
Author: Jaume Casadesús and Dolors Villegas
Journal of Integrative Plant Biology 2014 56(1): 7每14
Published Online: December 16, 2013
DOI: 10.1111/jipb.12117
      
    

Affordable and easy-to-use methods for assessing biomass and leaf area index (LAI) would be of interest in most breeding programs. Here, we describe the evaluation of a protocol for photographic sampling and image analysis aimed at providing low-labor yet robust indicators of biomass and LAI. In this trial, two genotypes of triticale, two of bread wheat, and four of tritordeum were studied. At six dates during the growing cycle, biomass and LAI were measured destructively, and digital photography was taken on the same dates. Several vegetation indices were calculated from each image. The results showed that repeatable and consistent values of the indices were obtained in consecutive photographic samplings on the same plots. The photographic indices were highly correlated with the destructive measurements, though the magnitude of the correlation was lower after anthesis. This work shows that photographic assessment of biomass and LAI can be fast, affordable, have good repeatability, and can be used under bright and overcast skies. A practical vegetation index derived from pictures is the fraction of green pixels over the total pixels of the image, and as it shows good correlations with all biomass variables, is the most robust to lighting conditions and has easy interpretation.

Casadesús J, Villegas D (2014) Conventional digital cameras as a tool for assessing leaf area index and biomass for cereal breeding. J Integr Plant Biol 56: 7–14. doi: 10.1111/jipb.12117

Abstract (Browse 980)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
          Research Articles
Identification and expression profiling of Vigna mungo microRNAs from leaf small RNA transcriptome by deep sequencing  
Author: Sujay Paul, Anirban Kundu and Amita Pal
Journal of Integrative Plant Biology 2014 56(1): 15每23
Published Online: December 19, 2013
DOI: 10.1111/jipb.12115
      
    

MicroRNAs (miRNAs) represent a class of small non-coding RNA molecules that play a crucial role in post-transcriptional gene regulation. Several conserved and species-specific miRNAs have been characterized to date, predominantly from the plant species whose genome is well characterized. However, information on the variability of these regulatory RNAs in economically important but genetically less characterized crop species are limited. Vigna mungo is an important grain legume, which is grown primarily for its protein-rich edible seeds. miRNAs from this species have not been identified to date due to lack of genome sequence information. To identify miRNAs from V. mungo, a small RNA library was constructed from young leaves. High-throughput Illumina sequencing technology and bioinformatic analysis of the small RNA reads led to the identification of 66 miRNA loci represented by 45 conserved miRNAs belonging to 19 families and eight non-conserved miRNAs belonging to seven families. Besides, 13 novel miRNA candidates in V. mungo were also identified. Expression patterns of selected conserved, non-conserved, and novel miRNA candidates have been demonstrated in leaf, stem, and root tissues by quantitative polymerase chain reaction, and potential target genes were predicted for most of the conserved miRNAs. This information offers genomic resources for better understanding of miRNA mediated post-transcriptional gene regulation.

Paul S, Kundu A, Pal A (2014) Identification and expression profiling of Vigna mungo microRNAs from leaf small RNA transcriptome by deep sequencing. J Integr Plant Biol 56: 15–23. doi: 10.1111/jipb.12115

Abstract (Browse 920)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Genome-wide patterns of large-size presence/absence variants in sorghum  
Author: Li-Min Zhang, Hong Luo, Zhi-Quan Liu, Yi Zhao, Jing-Chu Luo, Dong-Yun Hao and Hai-Chun Jing
Journal of Integrative Plant Biology 2014 56(1): 24每37
Published Online: January 15, 2014
DOI: 10.1111/jipb.12121
      
    

The presence/absence variants (PAVs) are a major source of genome structural variation and have profound effects on phenotypic and genomic variation in animals and humans. However, little is understood about PAVs in plant genomes. Our previous resequencing effort on three sorghum (Sorghum bicolour L.) genomes, each 12× coverage, uncovered 5 364 PAVs. Here, we report a detailed characterization of 51 large-size (>30 kb) PAVs. These PAVs spanned a total size of 2.92 Mb of the sorghum genome containing 202 known and predicted genes, including 38 genes annotated to encode cell death and stress response genes. The PAVs varied considerably for repeat sequences and mobile elements with DNA transposons as the major components. The frequency and distribution of these PAVs differed substantially across 96 sorghum inbred lines, and the low- and high frequency PAVs differed in their gene categories. This report shed new light on the occurrence and diversity of PAVs in sorghum genomes. Our research exemplifies a new perspective to explore genome structural variation for genetic improvement in plant breeding.

Zhang LM, Luo H, Liu ZQ, Zhao Y, Luo JC, Hao DY, Jing HC (2014) Genome坼wide patterns of large坼size presence/absence variants in sorghum. J Integr Plant Biol 56: 24–37. doi: 10.1111/jipb.12121

Abstract (Browse 798)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Genome-wide analysis and molecular dissection of the SPL gene family in Salvia miltiorrhiza  
Author: Linsu Zhang, Bin Wu, Degang Zhao, Caili Li, Fenjuan Shao and Shanfa Lu
Journal of Integrative Plant Biology 2014 56(1): 38每50
Published Online: November 20, 2013
DOI: 10.1111/jipb.12111
      
    

SQUAMOSA promoter binding protein-likes (SPLs) are plant-specific transcription factors playing vital regulatory roles in plant growth and development. There is no information about SPLs in Salvia miltiorrhiza (Danshen), a significant medicinal plant widely used in Traditional Chinese medicine (TCM) for >1,700 years and an emerging model plant for TCM studies. Through genome-wide identification and subsequent molecular cloning, we identified a total 15 SmSPLs with divergent sequence features, gene structures, and motifs. Comparative analysis showed sequence conservation between SmSPLs and their Arabidopsis counterparts. A phylogenetic tree clusters SmSPLs into six groups. Many of the motifs identified commonly exist in a group/subgroup, implying their functional redundancy. Eight SmSPLs were predicted and experimentally validated to be targets of miR156/157. SmSPLs were differentially expressed in various tissues of S. milltiorrhiza. The expression of miR156/157-targeted SmSPLs was increased with the maturation of S. miltiorrhiza, whereas the expression of miR156/157 was decreased, confirming the regulatory roles of miR156/157 in SmSPLs and suggesting the functions of SmSPLs in S. miltiorrhiza development. The expression of miR156/157 was negatively correlated with miR172 during the maturation of S. miltiorrhiza. The results indicate the significance and complexity of SmSPL-, miR156-, and miR172-mediated regulation of developmental timing in S. miltiorrhiza.

Zhang L, Wu B, Zhao D, Li C, Shao F, Lu S (2014) Genome坼wide analysis and molecular dissection of the SPL gene family in Salvia miltiorrhiza. J Integr Plant Biol 56: 38–50. doi: 10.1111/jipb.12111

Abstract (Browse 911)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Association analysis of fiber quality traits and exploration of elite alleles in Upland cotton cultivars/accessions (Gossypium hirsutum L.)  
Author: Caiping Cai, Wenxue Ye, Tianzhen Zhang and Wangzhen Guo
Journal of Integrative Plant Biology 2014 56(1): 51每62
Published Online: January 15, 2014
DOI: 10.1111/jipb.12124
      
    

Exploring the elite alleles and germplasm accessions related to fiber quality traits will accelerate the breeding of cotton for fiber quality improvement. In this study, 99 Gossypium hirsutum L. accessions with diverse origins were used to perform association analysis of fiber quality traits using 97 polymorphic microsatellite marker primer pairs. A total of 107 significant marker-trait associations were detected for three fiber quality traits under three different environments, with 70 detected in two or three environments and 37 detected in only one environment. Among the 70 significant marker-trait associations, 52.86% were reported previously, implying that these are stable loci for target traits. Furthermore, we detected a large number of elite alleles associated simultaneously with two or three traits. These elite alleles were mainly from accessions collected in China, introduced to China from the United States, or rare alleles with a frequency of less than 5%. No one cultivar contained more than half of the elite alleles, but 10 accessions were collected from China and the two introduced from the United States did contain more than half of these alleles. Therefore, there is great potential for mining elite alleles from germplasm accessions for use in fiber quality improvement in modern cotton breeding.

Cai C, Ye W, Zhang T, Guo W (2014) Association analysis of fiber quality traits and exploration of elite alleles in Upland cotton cultivars/accessions (Gossypium hirsutum L.). J Integr Plant Biol 56: 51–62. doi:
10.1111/jipb.12124

Abstract (Browse 875)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
LeCDJ1, a chloroplast DnaJ protein, facilitates heat tolerance in transgenic tomatoes  
Author: Fanying Kong, Yongsheng Deng, Guodong Wang, Jieru Wang, Xiaoqing Liang and Qingwei Meng
Journal of Integrative Plant Biology 2014 56(1): 63每74
Published Online: January 15, 2014
DOI: 10.1111/jipb.12119
      
    

The roles of a tomato (Lycopersicon esculentum) chloroplast-targeted DnaJ protein (LeCDJ1) were investigated using wild-type (WT) and sense transgenic tomatoes. The LeCDJ1 expression was upregulated by 38 °C, 42 °C, 45 °C, NaCl, PEG, methyl viologen (MV) and hydrogen peroxide (H2O2), but not by 30 °C and 35 °C. Meanwhile, LeCDJ1 was involved in the response of plants to abscisic acid (ABA). Under heat stress, the sense plants showed better growth, higher chlorophyll content, lower malondialdehyde (MDA) accumulation and relative electrical conductivity (REC), and also less PSII photoinhibition than WT. Interestingly, the sense plants treated with streptomycin (SM), an inhibitor of organellar translation, still showed higher maximum photochemistry efficiency of PSII (Fv/Fm) and D1 protein levels than the SM-untreated WT, suggesting that the protective effect of LeCDJ1 on PSII was, at least partially, independent of D1 protein synthesis. Furthermore, the relatively lower superoxide radical (O2•−) and H2O2 levels in the sense plants were considered to be due to the higher ascorbate peroxidase (APX) and superoxide dismutase (SOD) activity, which seemed unlikely dependent on their transcription level. These results indicated that LeCDJ1 overexpression facilitated heat tolerance in transgenic tomatoes.

Kong F, Deng Y, Wang G, Wang J, Liang X, Meng Q (2014) LeCDJ1, a chloroplast DnaJ protein, facilitates heat tolerance in transgenic tomatoes.J Integr Plant Biol 56: 63–74. doi: 10.1111/jipb.12119

Abstract (Browse 990)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Genomic regions underlying agronomic traits in linseed (Linum usitatissimum L.) as revealed by association mapping  
Author: Braulio J. Soto-Cerda, Scott Duguid, Helen Booker, Gordon Rowland, Axel Diederichsen and Sylvie Cloutier
Journal of Integrative Plant Biology 2014 56(1): 75每87
Published Online: January 15, 2014
DOI: 10.1111/jipb.12118
      
    

The extreme climate of the Canadian Prairies poses a major challenge to improve yield. Although it is possible to breed for yield per se, focusing on yield-related traits could be advantageous because of their simpler genetic architecture. The Canadian flax core collection of 390 accessions was genotyped with 464 simple sequence repeat markers, and phenotypic data for nine agronomic traits including yield, bolls per area, 1,000 seed weight, seeds per boll, start of flowering, end of flowering, plant height, plant branching, and lodging collected from up to eight environments was used for association mapping. Based on a mixed model (principal component analysis (PCA) + kinship matrix (K)), 12 significant marker-trait associations for six agronomic traits were identified. Most of the associations were stable across environments as revealed by multivariate analyses. Statistical simulation for five markers associated with 1000 seed weight indicated that the favorable alleles have additive effects. None of the modern cultivars carried the five favorable alleles and the maximum number of four observed in any accessions was mostly in breeding lines. Our results confirmed the complex genetic architecture of yield-related traits and the inherent difficulties associated with their identification while illustrating the potential for improvement through marker-assisted selection.

Soto坼Cerda BJ, Duguid S, Booker H, Rowland G, Diederichsen A, Cloutier S (2014) Genomic regions underlying agronomic traits in linseed (Linum usitatissimum L.) as revealed by association mapping. J Integr Plant Biol 56: 75–87. doi: 10.1111/jipb.12118

Abstract (Browse 879)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
Iron deprivation results in a rapid but not sustained increase of the expression of genes involved in iron metabolism and sulfate uptake in tomato (Solanum lycopersicum L.) seedlings  
Author: Anna Rita Paolacci, Silvia Celletti, Giulio Catarcione, Malcolm J. Hawkesford, Stefania Astolfi and Mario Ciaffi
Journal of Integrative Plant Biology 2014 56(1): 88每100
Published Online: November 25, 2013
DOI: 10.1111/jipb.12110
      
    

Characterization of the relationship between sulfur and iron in both Strategy I and Strategy II plants, has proven that low sulfur availability often limits plant capability to cope with iron shortage. Here it was investigated whether the adaptation to iron deficiency in tomato (Solanum lycopersicum L.) plants was associated with an increased root sulfate uptake and translocation capacity, and modified dynamics of total sulfur and thiols accumulation between roots and shoots. Most of the tomato sulfate transporter genes belonging to Groups 1, 2, and 4 were significantly upregulated in iron-deficient roots, as it commonly occurs under S-deficient conditions. The upregulation of the two high affinity sulfate transporter genes, SlST1.1 and SlST1.2, by iron deprivation clearly suggests an increased root capability to take up sulfate. Furthermore, the upregulation of the two low affinity sulfate transporter genes SlST2.1 and SlST4.1 in iron-deficient roots, accompanied by a substantial accumulation of total sulfur and thiols in shoots of iron-starved plants, likely supports an increased root-to-shoot translocation of sulfate. Results suggest that tomato plants exposed to iron-deficiency are able to change sulfur metabolic balance mimicking sulfur starvation responses to meet the increased demand for methionine and its derivatives, allowing them to cope with this stress.

Paolacci AR, Celletti S, Catarcione G, Hawkesford MJ, Astolfi S, Ciaffi M (2014) Iron deprivation results in a rapid but not sustained increase of the expression of genes involved in iron metabolism and sulfate uptake in tomato (Solanum lycopersicum L.) seedlings. J Integr Plant Biol 56: 88–100. doi: 10.1111/jipb.12110

Abstract (Browse 881)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
          Erratum
Erratum  
Author:
Journal of Integrative Plant Biology 2014 56(1): 101-101
Published Online: December 10, 2013
DOI: 10.1111/jipb.12143
Abstract (Browse 533)  |  References  |  Full Text HTML  |  Full Text PDF  |  Cited By       
 

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