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Genetic dissection of crown root traits and their relationships with aboveground agronomic traits in maize
SHA Xiao-qian, GUAN Hong-hui, ZHOU Yu-qian, SU Er-hu, GUO Jian, LI Yong-xiang, ZHANG Deng-feng, LIU Xu-yang, HE Guan-hua, LI Yu, WANG Tian-yu, ZOU Hua-wen, LI Chun-hui
2023, 22 (11): 3394-3407.   DOI: 10.1016/j.jia.2023.04.022
Abstract238)      PDF in ScienceDirect      
The crown root system is the most important root component in maize at both the vegetative and reproductive stages.  However, the genetic basis of maize crown root traits (CRT) is still unclear, and the relationship between CRT and aboveground agronomic traits in maize is poorly understood.  In this study, an association panel including 531 elite maize inbred lines was planted to phenotype the CRT and aboveground agronomic traits in different field environments.  We found that root traits were significantly and positively correlated with most aboveground agronomic traits, including flowering time, plant architecture and grain yield.  Using a genome-wide association study (GWAS) coupled with resequencing, a total of 115 associated loci and 22 high-confidence candidate genes were identified for CRT.  Approximately one-third of the genetic variation in crown root was co-located with 46 QTLs derived from flowering and plant architecture.  Furthermore, 103 (89.6%) of 115 crown root loci were located within known domestication- and/or improvement-selective sweeps, suggesting that crown roots might experience indirect selection in maize during domestication and improvement.  Furthermore, the expression of Zm00001d036901, a high-confidence candidate gene, may contribute to the phenotypic variation in maize crown roots, and Zm00001d036901 was selected during the domestication and improvement of maize.  This study promotes our understanding of the genetic basis of root architecture and provides resources for genomics-enabled improvements in maize root architecture.

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Evaluation of drought tolerance in ZmVPP1-overexpressing transgenic inbred maize lines and their hybrids
JIA Teng-jiao, LI Jing-jing, WANG Li-feng, CAO Yan-yong, MA Juan, WANG Hao, ZHANG Deng-feng, LI Hui-yong
2020, 19 (9): 2177-2187.   DOI: 10.1016/S2095-3119(19)62828-5
Abstract140)      PDF in ScienceDirect      
The vacuolar proton-pumping pyrophosphatase gene (VPP) is often used to enhance plant drought tolerance via genetic engineering.  In this study, the drought tolerance of four transgenic inbred maize lines overexpressing ZmVPP1 (PH4CV-T, PH6WC-T, Chang7-2-T, and Zheng58-T) and their transgenic hybrids was evaluated at various stages.  Under normal and drought conditions, the height and fresh weight were greater for the four transgenic inbred maize lines than for the wild-type (WT) controls at the germination and seedling stages.  Additionally, the transgenic plants exhibited enhanced photosynthetic efficiency at the seedling stage.  In irrigated and non-irrigated fields, the four transgenic lines grew normally, but with increased ear weight and yield compared with the WT plants.  Moreover, the ear weight and yield of the transgenic hybrids resulting from the PH4CV-T×PH6WC-W and Chang7-2-T×Zheng58-W crosses increased in the non-irrigated field.  Our results demonstrated that the growth and drought tolerance of four transgenic inbred maize lines with improved photosynthesis were enhanced by the overexpression of ZmVPP1.  Moreover, the Chang7-2 and PH4CV transgenic lines may be useful for future genetic improvements of maize hybrids to increase drought tolerance.
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Genome-wide identification and comparative analysis of drought related genes in roots of two maize inbred lines with contrasting drought tolerance by RNA sequencing
HAO Lu-yang, LIU Xu-yang, ZHANG Xiao-jing, SUN Bao-cheng, LIU Cheng, ZHANG Deng-feng, TANG Huai-jun, LI Chun-hui, LI Yong-xiang, SHI Yun-su, XIE Xiao-qing, SONG Yan-chun, WANG Tian-yu, LI Yu
2020, 19 (2): 449-464.   DOI: 10.1016/S2095-3119(19)62660-2
Abstract174)      PDF in ScienceDirect      
Drought is one of the most important abiotic stresses affecting maize growth and development and therefore resulting in yield loss.  Thus it is essential to understand molecular mechanisms of drought stress responses in maize for drought tolerance improvement.  The root plays a critical role in plants sensing water deficit.  In the present study, two maize inbred lines, H082183, a drought-tolerant line, and Lv28, a drought-sensitive line, were grown in the field and treated with different water conditions (moderate drought, severe drought, and well-watered conditions) during vegetative stage.  The transcriptomes of their roots were investigated by RNA sequencing.  There were 1 428 and 512 drought-responsive genes (DRGs) in Lv28, 688 and 3 363 DRGs in H082183 under moderate drought and severe drought, respectively.  A total of 31 Gene Ontology (GO) terms were significantly over-represented in the two lines, 13 of which were enriched only in the DRGs of H082183.  Based on results of Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis, “plant hormone signal transduction” and “starch and sucrose metabolism” were enriched in both of the two lines, while “phenylpropanoid biosynthesis” was only enriched in H082183.  Further analysis revealed the different expression patterns of genes related to abscisic acid (ABA) signal pathway, trehalose biosynthesis, reactive oxygen scavenging, and transcription factors might contribute to drought tolerance in maize.  Our results contribute to illustrating drought-responsive molecular mechanisms and providing gene resources for maize drought improvement.
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Transcriptomic profiling of sorghum leaves and roots responsive to drought stress at the seedling stage
ZHANG Deng-feng, ZENG Ting-ru, LIU Xu-yang, GAO Chen-xi, LI Yong-xiang, LI Chun-hui, SONG Yan-chun, SHI Yun-su, WANG Tian-yu, LI Yu
2019, 18 (9): 1980-1995.   DOI: 10.1016/S2095-3119(18)62119-7
Abstract145)      PDF in ScienceDirect      
Drought stress affects the growth and productivity of crop plants including sorghum.  To study the molecular basis of drought tolerance in sorghum, we conducted the transcriptomic profiling of sorghum leaves and roots under drought stress using RNA-Seq method.  A total of 510, 559, and 3 687 differentially expressed genes (DEGs) in leaves, 3 368, 5 093, and 4 635 DEGs in roots responding to mild drought, severe drought, and re-watering treatments were identified, respectively.  Among them, 190 common DEGs in leaves and 1 644 common DEGs in roots were responsive to mild drought, severe drought, and re-watering environment.  Gene Ontology (GO) enrichment analysis revealed that the GO categories related to drought tolerance include terms related to response to stimulus especially response to water deprivation, abscisic acid stimulus, and reactive oxygen species.  The major transcription factor genes responsive to drought stress include heat stress transcription factor (HSF), ethylene-responsive transcription factor (ERF), Petunia NAM, Arabidopsis ATAF1/2 and CUC2 (NAC), WRKY transcription factor (WRKY), homeodomain leucine zipper transcription factor (HD-ZIP), basic helix-loop-helix transcription factor (bHLH),  and V-myb myeloblastosis viral oncogene homolog transcription facotr (MYB).  Functional protein genes for heat shock protein (HSPs), late-embryogenesis-abundant protein (LEAs), chaperones, aquaporins, and expansins might play important roles in sorghum drought tolerance.  Moreover, the genomic regions enriched with HSP, expansin, and aquaporin genes responsive to drought stress could be used as powerful targets for improvement of drought tolerance in sorghum and other cereals.  Overall, our results provide a genome-wide analysis of DEGs in sorghum leaves and roots under mild drought, severe drought, and re-watering environments.  This study contributes to a better understanding of the molecular basis of drought tolerance of sorghum and can be useful for crop improvement.
 
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Simple nonlinear model for the relationship between maize yield and cumulative water amount
LIU Cheng SUN Bao-cheng, TANG Huai-jun, WANG Tian-yu LI Yu, ZHANG Deng-feng, XIE Xiao-qing, SHI Yun-su, SONG Yan-chun, YANG Xiao-hong, LI Jian-sheng
2017, 16 (04): 858-866.   DOI: 10.1016/S2095-3119(16)61493-4
Abstract794)      PDF in ScienceDirect      
Both the additive and multiplicative models of crop yield and water supply are polynomial equations, and the number of parameters increases linearly when the growing period is specified.  However, interactions among multiple parameters occasionally lead to unreasonable estimations of certain parameters, which were water sensitivity coefficients but with negative value.  Additionally, evapotranspiration must be measured as a model input.  To facilitate the application of these models and overcome the aforementioned shortcomings, a simple model with only three parameters was derived in this paper based on certain general quantitative relations of crop yield (Y) and water supply (W).  The new model, Y/YmWk/(Wk+whk), fits an S or a saturated curve of crop yield with the cumulative amount of water.  Three parameters are related to biological factors: the yield potential (Ym), the water requirement to achieve half of the yield potential (half-yield water requirement, wh), and the water sensitivity coefficient (k).  The model was validated with data from 24 maize lines obtained in the present study and 17 maize hybrids published by other authors.  The results showed that the model was well fit to the data, and the normal root of the mean square error (NRMSE) values were 2.8 to 17.8% (average 7.2%) for the 24 maize lines and 2.7 to 12.7% (average 7.4%) for the 17 maize varieties.  According to the present model, the maize water-sensitive stages in descending order were pollen shedding and silking, tasselling, jointing, initial grain ?lling, germination, middle grain ?lling, late grain ?lling, and end of grain ?lling.  This sequence was consistent with actual observations in the maize field.  The present model may be easily used to analyse the water use efficiency and drought tolerance of maize at specific stages.
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Genome-Wide Transcriptional Analysis of Yield and Heterosis-Associated Genes in Maize (Zea mays L.)
ZHANG Ti-fu, LI Bo, ZHANG Deng-feng, JIA Guan-qing, LI Zhi-yong, WANG Shou-cai
2012, 12 (8): 1245-1256.   DOI: 10.1016/S1671-2927(00)8653
Abstract1376)      PDF in ScienceDirect      
Heterosis has contributed greatly to yield in maize, but the nature of its contribution is not completely clear. In this study, two strategies using whole-genome oligonucleotide microarrays were employed to identify differentially expressed genes (DEGs) associated with heterosis and yield. The analysis revealed 1 838 heterosis-associated genes (HAGs), 265 yieldassociated genes (YAGs), and 85 yield heterosis-associated genes (YHAGs). 37.1% of HAGs and 22.4% of YHAGs expressed additively. The remaining genes expressed non-additively, including those with high/low-parent dominance and over/under dominance, which were prevalent in this research. Pathway enrichment analysis and quantitative trait locus (QTL) co-mapping demonstrated that the metabolic pathways for energy and carbohydrates were the two main enriched pathways influencing heterosis and yield. Therefore, the DEGs participating in energy and carbohydrate metabolism were considered to contribute to heterosis and yield significantly. The investigation of potential groups of HAGs, YAGs, and YHAGs might provide valuable information for exploiting heterosis to improve yield in maize breeding. In addition, our results support the view that heterosis is contributed by multiple, complex molecular mechanisms.
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