Publications by authors named "Jiquan Xue"

14 Publications

  • Page 1 of 1

New insights into the response of maize to fluctuations in the light environment.

Mol Genet Genomics 2021 May 25;296(3):615-629. Epub 2021 Feb 25.

The Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China.

Light is the most important environmental cue signaling the transition from skotomorphogenesis to photomorphogenesis, thus affecting plant development and metabolic activity. How the light response mechanisms of maize seedlings respond to fluctuations in the light environment has not been well characterized to date. In this study, we built a gene coexpression network from a dynamic transcriptomic map of maize seedlings exposed to different light environments. Coexpression analysis identified ten modules and multiple genes that closely correlate with photosynthesis and characterized hub genes associated with regulatory networks, duplication events, domestication and improvement. In addition, we identified that 38% of hub genes underwent duplication events, 74% of which are related to photosynthesis. Moreover, we captured the dynamic expression atlas of gene sets involved in the chloroplast photosynthetic apparatus and photosynthetic carbon assimilation in different light environments, which should help to elucidate the key mechanisms and regulatory networks that underlie photosynthesis in maize. Insights from this study provide a valuable resource to better understand the genetic mechanisms of the response to fluctuations in the light environment in maize.
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http://dx.doi.org/10.1007/s00438-021-01761-6DOI Listing
May 2021

Identification of Ear Morphology Genes in Maize ( L.) Using Selective Sweeps and Association Mapping.

Front Genet 2020 20;11:747. Epub 2020 Jul 20.

The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Areas of the Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Xianyang, China.

The performance of maize hybrids largely depend on two parental inbred lines. Improving inbred lines using artificial selection is a key task in breeding programs. However, it is important to elucidate the effects of this selection on inbred lines. Altogether, 208 inbred lines from two maize heterosis groups, named Shaan A and Shaan B, were sequenced by the genotype-by-sequencing to detect genomic changes under selection pressures. In addition, we completed genome-wide association analysis in 121 inbred lines to identify candidate genes for ear morphology related traits. In a genome-wide selection scan, the inbred lines from Shaan A and Shaan B groups showed obvious population divergences and different selective signals distributed in 337 regions harboring 772 genes. Meanwhile, functional enrichment analysis showed those selected genes are mainly involved in regulating cell development. Interestingly, some ear morphology related traits showed significant differentiation between the inbred lines from the two heterosis groups. The genome-wide association analysis of ear morphology related traits showed that four associated genes were co-localized in the selected regions with high linkage disequilibrium. Our spatiotemporal pattern and gene interaction network results for the four genes further contribute to our understanding of the mechanisms behind ear and fruit length development. This study provides a novel insight into digging a candidate gene for complex traits using breeding materials. Our findings in relation to ear morphology will help accelerate future maize improvement.
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http://dx.doi.org/10.3389/fgene.2020.00747DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7384441PMC
July 2020

Genome-wide evolutionary characterization and expression analysis of SIAMESE-RELATED family genes in maize.

BMC Evol Biol 2020 07 29;20(1):91. Epub 2020 Jul 29.

Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China.

Background: The SIAMESE (SIM) locus is a cell-cycle kinase inhibitor (CKI) gene that has to date been identified only in plants; it encodes a protein that promotes transformation from mitosis to endoreplication. Members of the SIAMESE-RELATED (SMR) family have similar functions, and some are related to cell-cycle responses and abiotic stresses. However, the functions of SMRs are poorly understood in maize (Zea mays L.).

Results: In the present study, 12 putative SMRs were identified throughout the entire genome of maize, and these were clustered into six groups together with the SMRs from seven other plant species. Members of the ZmSMR family were divided into four groups according to their protein sequences. Various cis-acting elements in the upstream sequences of ZmSMRs responded to abiotic stresses. Expression analyses revealed that all ZmSMRs were upregulated at 5, 20, 25, and 35 days after pollination. In addition, we found that ZmSMR9/11/12 may have regulated the initiation of endoreplication in endosperm central cells. Additionally, ZmSMR2/10 may have been primarily responsible for the endoreplication regulation of outer endosperm or aleurone cells. The relatively high expression levels of almost all ZmSMRs in the ears and tassels also implied that these genes may function in seed development. The effects of treatments with ABA, heat, cold, salt, and drought on maize seedlings and expression of ZmSMR genes suggested that ZmSMRs were strongly associated with response to abiotic stresses.

Conclusion: The present study is the first to conduct a genome-wide analysis of members of the ZmSMR family by investigating their locations in chromosomes, identifying regulatory elements in their promoter regions, and examining motifs in their protein sequences. Expression analysis of different endosperm developmental periods, tissues, abiotic stresses, and hormonal treatments suggests that ZmSMR genes may function in endoreplication and regulate the development of reproductive organs. These results may provide valuable information for future studies of the functions of the SMR family in maize.
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http://dx.doi.org/10.1186/s12862-020-01619-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7389639PMC
July 2020

Comparative transcriptomics reveals the difference in early endosperm development between maize with different amylose contents.

PeerJ 2019 28;7:e7528. Epub 2019 Aug 28.

The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China.

In seeds, the endosperm is a crucial organ that plays vital roles in supporting embryo development and determining seed weight and quality. Starch is the predominant storage carbohydrate of the endosperm and accounts for ∼70% of the mature maize kernel weight. Nonetheless, because starch biosynthesis is a complex process that is orchestrated by multiple enzymes, the gene regulatory networks of starch biosynthesis, particularly amylose and amylopectin biosynthesis, have not been fully elucidated. Here, through high-throughput RNA sequencing, we developed a temporal transcriptome atlas of the endosperms of high-amylose maize and common maize at 5-, 10-, 15- and 20-day after pollination and found that 21,986 genes are involved in the programming of the high-amylose and common maize endosperm. A coexpression analysis identified multiple sequentially expressed gene sets that are closely correlated with cellular and metabolic programmes and provided valuable insight into the dynamic reprogramming of the transcriptome in common and high-amylose maize. In addition, a number of genes and transcription factors were found to be strongly linked to starch synthesis, which might help elucidate the key mechanisms and regulatory networks underlying amylose and amylopectin biosynthesis. This study will aid the understanding of the spatiotemporal patterns and genetic regulation of endosperm development in different types of maize and provide valuable genetic information for the breeding of starch varieties with different contents.
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http://dx.doi.org/10.7717/peerj.7528DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6717500PMC
August 2019

ZmSMR4, a novel cyclin-dependent kinase inhibitor (CKI) gene in maize (Zea mays L.), functions as a key player in plant growth, development and tolerance to abiotic stress.

Plant Sci 2019 Mar 13;280:120-131. Epub 2018 Mar 13.

Key Laboratory of the Biology and Genetic Improvement of Maize in Arid Areas of the Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, China; Maize Engineering and Technology Research Centre of Shaanxi Province, Yangling, Shaanxi, 712100, China. Electronic address:

Endoreduplication is a key cell cycle variant in the developing maize endosperm and has been associated with cell enlargement and dry matter accumulation. Therefore, identification of the key genes associated with endosperm development and endoreduplication would not only lay the groundwork for understanding the biological process of endoreduplication but also be important for maize breeding. Here, we identified 12 putative endoreduplication-related candidate genes as members of the Zea mays L. SIAMESE-RELATED (ZmSMR) gene family and denoted them ZmSMR1-ZmSMR12. Sequence analysis indicated that all the ZmSMR protein sequences exhibited modest sequence similarity to the SIAMESE gene from Arabidopsis. Further analyses suggested that most ZmSMR genes might be associated with the transition from mitosis to endoreduplication because the expression levels of most ZmSMR genes were upregulated in endosperm cells during the phase of switching to an endoreduplication cell cycle. Additionally, the ZmSMRs responded to various abiotic stresses at the transcriptional level. One member of the ZmSMR gene family, the ZmSMR4 (KY946768) gene, was isolated as the first maize endoreduplication-related gene and has been used to develop transgenic Arabidopsis plants. ZmSMR4 was localized to the nucleus and could interact with ZmCDKA and ZmCDKB. Moreover, ZmSMR4 was able to rescue the multicellular trichome phenotype of Arabidopsis sim mutants and enhanced the endoreduplication levels of transgenic Arabidopsis plants. Arabidopsis plants overexpressing ZmSMR4 not only displayed enhanced leaf margin serrations but also showed several interesting breeding phenotypes, such as early blossoming and fuller seeds. Taken together, our data suggest that the ZmSMR4 gene is plant-specific and functions as a key player in the signalling network that controls plant growth, development and responses to abiotic stress by regulating the transition between the mitotic cycle and endoreduplication.
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http://dx.doi.org/10.1016/j.plantsci.2018.03.007DOI Listing
March 2019

The distribution pattern of endopolyploidy in maize.

Theor Appl Genet 2019 May 7;132(5):1487-1503. Epub 2019 Feb 7.

The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China.

Key Message: We discovered that endopolyploidization is common in various organs and tissues of maize at different development stages. Endopolyploidy is not specific in maize germplasm populations. Endopolyploidy is caused by DNA endoreplication, a special type of mitosis with normal DNA synthesis and a lack of cell division; it is a common phenomenon and plays an important role in plant development. To systematically study the distribution pattern of endopolyploidy in maize, flow cytometry was used to determine the ploidy by measuring the cycle (C) value in various organs at different developmental stages, in embryos and endosperm during grain development, in roots under stress conditions, and in the roots of 119 inbred lines from two heterotic groups, Shaan A and Shaan B. Endopolyploidy was observed in most organs at various developmental stages except in expanded leaves and filaments. The endosperm showed the highest C value among all organs. During tissue development, the ploidy increased in all organs except the leaves. In addition, the endopolyploidization of the roots was significantly affected by drought stress. Multiple comparisons of the C values of seven subgroups revealed that the distribution of endopolyploidization was not correlated with the population structure. A correlation analysis at the seedling stage showed a positive relationship between the C value and both the length of the whole plant and the length of main root. A genome-wide association study (GWAS) identified a total of 9 significant SNPs associated with endopolyploidy (C value) in maize, and 8 candidate genes that participate in cell cycle regulation and DNA replication were uncovered in 119 maize inbred lines.
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http://dx.doi.org/10.1007/s00122-019-03294-4DOI Listing
May 2019

Evolutionary, structural and expression analysis of core genes involved in starch synthesis.

Sci Rep 2018 08 24;8(1):12736. Epub 2018 Aug 24.

The key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China.

Starch is the main storage carbohydrate in plants and an important natural resource for food, feed and industrial raw materials. However, the details regarding the pathway for starch biosynthesis and the diversity of biosynthetic enzymes involved in this process are poorly understood. This study uses a comprehensive phylogenetic analysis of 74 sequenced plant genomes to revisit the evolutionary history of the genes encoding ADP-glucose pyrophosphorylase (AGPase), starch synthase (SS), starch branching enzyme (SBE) and starch de-branching enzyme (DBE). Additionally, the protein structures and expression patterns of these four core genes in starch biosynthesis were studied to determine their functional differences. The results showed that AGPase, SS, SBE and DBE have undergone complicated evolutionary processes in plants and that gene/genome duplications are responsible for the observed differences in isoform numbers. A structure analysis of these proteins suggested that the deletion/mutation of amino acids in some active sites resulted in not only structural variation but also sub-functionalization or neo-functionalization. Expression profiling indicated that AGPase-, SS-, SBE- and DBE-encoding genes exhibit spatio-temporally divergent expression patterns related to the composition of functional complexes in starch biosynthesis. This study provides a comprehensive atlas of the starch biosynthetic pathway, and these data should support future studies aimed at increasing understanding of starch biosynthesis and the functional evolutionary divergence of AGPase, SS, SBE, and DBE in plants.
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http://dx.doi.org/10.1038/s41598-018-30411-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6109180PMC
August 2018

Genetic characterization of inbred lines from Shaan A and B groups for identifying loci associated with maize grain yield.

BMC Genet 2018 08 23;19(1):63. Epub 2018 Aug 23.

Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China.

Background: Increasing grain yield is a primary objective of maize breeding. Dissecting the genetic architecture of grain yield furthers genetic improvements to increase yield. Presented here is an association panel composed of 126 maize inbreds (AM126), which were genotyped by the genotyping-by-sequencing (tGBS) method. We performed genetic characterization and association analysis related to grain yield in the association panel.

Results: In total, 46,046 SNPs with a minor allele frequency (MAF) ≥0.01 were used to assess genetic diversity and kinship in AM126. The results showed that the average MAF and polymorphism information content (PIC) were 0.164 and 0.198, respectively. The Shaan B group, with 11,284 unique SNPs, exhibited greater genetic diversity than did the Shaan A group, with 2644 SNPs. The 61.82% kinship coefficient in AM126 was equal to 0, and only 0.15% of that percentage was greater than 0.7. A total of 31,983 SNPs with MAF ≥0.05 were used to characterize population structure, LD decay and association mapping. Population structure analysis suggested that AM126 can be divided into 6 subgroups, which is consistent with breeding experience and pedigree information. The LD decay distance in AM126 was 150 kb. A total of 51 significant SNPs associated with grain yield were identified at P < 1 × 10 across two environments (Yangling and Yulin). Among those SNPs, two loci displayed overlapping regions in the two environments. Finally, 30 candidate genes were found to be associated with grain yield.

Conclusions: These results contribute to the genetic characterization of this breeding population, which serves as a reference for hybrid breeding and population improvement, and demonstrate the genetic architecture of maize grain yield, potentially facilitating genetic improvement.
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http://dx.doi.org/10.1186/s12863-018-0669-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6108135PMC
August 2018

Bivariate flow cytometric analysis and sorting of different types of maize starch grains.

Cytometry A 2018 02 4;93(2):213-221. Epub 2017 Oct 4.

Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China.

Particle-size distribution, granular structure, and composition significantly affect the physicochemical properties, rheological properties, and nutritional function of starch. Flow cytometry and flow sorting are widely considered convenient and efficient ways of classifying and separating natural biological particles or other substances into subpopulations, respectively, based on the differential response of each component to stimulation by a light beam; the results allow for the correlation analysis of parameters. In this study, different types of starches isolated from waxy maize, sweet maize, high-amylose maize, pop maize, and normal maize were initially classified into various subgroups by flow cytometer and then collected through flow sorting to observe their morphology and particle-size distribution. The results showed that a 0.25% Gelzan solution served as an optimal reagent for keeping individual starch particles homogeneously dispersed in suspension for a relatively long time. The bivariate flow cytometric population distributions indicated that the starches of normal maize, sweet maize, and pop maize were divided into two subgroups, whereas high-amylose maize starch had only one subgroup. Waxy maize starch, conversely, showed three subpopulations. The subgroups sorted by flow cytometer were determined and verified in terms of morphology and granule size by scanning electron microscopy and laser particle distribution analyzer. Results showed that flow cytometry can be regarded as a novel method for classifying and sorting starch granules. © 2017 International Society for Advancement of Cytometry.
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http://dx.doi.org/10.1002/cyto.a.23261DOI Listing
February 2018

The effect of salt concentration on swelling power, rheological properties and saltiness perception of waxy, normal and high amylose maize starch.

Food Funct 2017 Oct;8(10):3792-3802

Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, Northwest A & F University, Yangling, 712100, Shaanxi, China.

The effect of salt concentration on swelling power, rheological properties and saltiness perception of waxy, normal and high amylose maize starch was investigated. The swelling power decreased with increasing salt concentration from 0% to 2.0% among all starch samples. Waxy starch showed the highest swelling power at different salt levels, while high amylose starch showed the least swelling power. The salt addition increased the gelatinization temperature of waxy starch and normal starch from 71.3 °C to 77.1 °C and from 72.3 °C to 78.2 °C. Their storage modulus (G'), loss modulus (G''), and viscosity values at lower salt concentration were greater than those at higher salt concentration. The increasing tan δ of waxy and normal starch against frequency sweep indicated liquid-like behavior, while high amylose starch exhibited decreasing tan δ indicating solid-like behavior as it was difficult to gelatinize. When sensory evaluation was conducted by trained panelists, it was found that high amylose starch displayed the highest initial saltiness and in-mouth saltiness intensity, accompanied by the greatest thickness, lubrication and stickiness, while waxy starch displayed the lowest values for saltiness perception and mouthfeel.
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http://dx.doi.org/10.1039/c7fo01041aDOI Listing
October 2017

Transcriptome Dynamics during Maize Endosperm Development.

PLoS One 2016 3;11(10):e0163814. Epub 2016 Oct 3.

The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi, China.

The endosperm is a major organ of the seed that plays vital roles in determining seed weight and quality. However, genome-wide transcriptome patterns throughout maize endosperm development have not been comprehensively investigated to date. Accordingly, we performed a high-throughput RNA sequencing (RNA-seq) analysis of the maize endosperm transcriptome at 5, 10, 15 and 20 days after pollination (DAP). We found that more than 11,000 protein-coding genes underwent alternative splicing (AS) events during the four developmental stages studied. These genes were mainly involved in intracellular protein transport, signal transmission, cellular carbohydrate metabolism, cellular lipid metabolism, lipid biosynthesis, protein modification, histone modification, cellular amino acid metabolism, and DNA repair. Additionally, 7,633 genes, including 473 transcription factors (TFs), were differentially expressed among the four developmental stages. The differentially expressed TFs were from 50 families, including the bZIP, WRKY, GeBP and ARF families. Further analysis of the stage-specific TFs showed that binding, nucleus and ligand-dependent nuclear receptor activities might be important at 5 DAP, that immune responses, signalling, binding and lumen development are involved at 10 DAP, that protein metabolic processes and the cytoplasm might be important at 15 DAP, and that the responses to various stimuli are different at 20 DAP compared with the other developmental stages. This RNA-seq analysis provides novel, comprehensive insights into the transcriptome dynamics during early endosperm development in maize.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0163814PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5047526PMC
June 2017

Genetic basis of maize kernel starch content revealed by high-density single nucleotide polymorphism markers in a recombinant inbred line population.

BMC Plant Biol 2015 Dec 12;15:288. Epub 2015 Dec 12.

National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genomics and Genetic Improvement, China Agricultural University, 100193, Beijing, China.

Background: Starch from maize kernels has diverse applications in human and animal diets and in industry and manufacturing. To meet the demands of these applications, starch quantity and quality need improvement, which requires a clear understanding of the functional mechanisms involved in starch biosynthesis and accumulation. In this study, a recombinant inbred line (RIL) population was developed from a cross between inbred lines CI7 and K22. The RIL population, along with both parents, was grown in three environments, and then genotyped using the MaizeSNP50 BeadChip and phenotyped to dissect the genetic architecture of starch content in maize kernels.

Results: Based on the genetic linkage map constructed using 2,386 bins as markers, six quantitative trait loci (QTLs) for starch content in maize kernels were detected in the CI7/K22 RIL population. Each QTL accounted for 4.7% (qSTA9-1) to 10.6% (qSTA4-1) of the starch variation. The QTL interval was further reduced using the bin-map method, with the physical distance of a single bin at the QTL peak ranging from 81.7 kb to 2.2 Mb. Based on the functional annotations and prior knowledge of the genes in the top bin, seven genes were considered as potential candidate genes for the identified QTLs. Three of the genes encode enzymes in non-starch metabolism but may indirectly affect starch biosynthesis, and four genes may act as regulators of starch biosynthesis.

Conclusions: A few large-effect QTLs, together with a certain number of minor-effect QTLs, mainly contribute to the genetic architecture of kernel starch content in our maize biparental linkage population. All of the identified QTLs, especially the large-effect QTL, qSTA4-1, with a small QTL interval, will be useful for improving the maize kernel starch content through molecular breeding.
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http://dx.doi.org/10.1186/s12870-015-0675-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4676831PMC
December 2015

Producing more grain with lower environmental costs.

Nature 2014 Oct 3;514(7523):486-9. Epub 2014 Sep 3.

College of Resources &Environmental Sciences, China Agricultural University, Beijing 100193, China.

Agriculture faces great challenges to ensure global food security by increasing yields while reducing environmental costs. Here we address this challenge by conducting a total of 153 site-year field experiments covering the main agro-ecological areas for rice, wheat and maize production in China. A set of integrated soil-crop system management practices based on a modern understanding of crop ecophysiology and soil biogeochemistry increases average yields for rice, wheat and maize from 7.2 million grams per hectare (Mg ha(-1)), 7.2 Mg ha(-1) and 10.5 Mg ha(-1) to 8.5 Mg ha(-1), 8.9 Mg ha(-1) and 14.2 Mg ha(-1), respectively, without any increase in nitrogen fertilizer. Model simulation and life-cycle assessment show that reactive nitrogen losses and greenhouse gas emissions are reduced substantially by integrated soil-crop system management. If farmers in China could achieve average grain yields equivalent to 80% of this treatment by 2030, over the same planting area as in 2012, total production of rice, wheat and maize in China would be more than enough to meet the demand for direct human consumption and a substantially increased demand for animal feed, while decreasing the environmental costs of intensive agriculture.
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http://dx.doi.org/10.1038/nature13609DOI Listing
October 2014

[Population physiological indices on density-tolerance of maize in different plant type].

Ying Yong Sheng Tai Xue Bao 2002 Jan;13(1):55-9

Northwest Science & Technology, University of Agriculture and Forestry, Yangling 712100.

Taken maize in two plant types of compact-type and flat-type as research object, the relationships between density-tolerance and light distribution in population, indices of productivity(LAI, NAR, and CGR), and population sink-source were studied synthetically by means of crop growth analysis method. The results showed that light distribution in population was the chief index to measure density-tolerance of different maize varieties. The kinetic rules of LAI, NAR, and CGR were the basic feature reflecting density-tolerance. The correspondent relationship in population sink-source was a comprehensive index to appraise density-tolerance of different maize varieties.
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January 2002
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