Genome-wide association analysis of seedling root development in maize (Zea mays L.)

Background

Plants rely on the root system for anchorage to the ground and the acquisition and absorption of nutrients critical to sustaining productivity. A genome wide association analysis enables one to analyze allelic diversity of complex traits and identify superior alleles. 384 inbred lines from the Ames panel were genotyped with 681,257 single nucleotide polymorphism markers using Genotyping-by-Sequencing technology and 22 seedling root architecture traits were phenotyped.

Results

Utilizing both a general linear model and mixed linear model, a GWAS study was conducted identifying 268 marker trait associations (p ≤ 5.3×10^-7). Analysis of significant SNP markers for multiple traits showed that several were located within gene models with some SNP markers localized within regions of previously identified root quantitative trait loci. Gene model GRMZM2G153722 located on chromosome 4 contained nine significant markers. This predicted gene is expressed in roots and shoots.

Conclusion

This study identifies putatively associated SNP markers associated with root traits at the seedling stage. Some SNPs were located within or near (<1 kb) gene models. These gene models identify possible candidate genes involved in root development at the seedling stage. These and respective linked or functional markers could be targets for breeders for marker assisted selection of seedling root traits.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1226-9) contains supplementary material, which is available to authorized users.     

松嫩平原不同株型玉米品种根系分布特征比较研究

采用土柱模拟栽培法与大田试验相结合的方法,对松嫩平原不同株型玉米的根系分布特征进行了比较。结果表明,平展型玉米和紧凑型玉米根干重最大值出现的时期不同,二者根干重分别在抽丝后15d和抽丝后30d时达到最大值,成熟时紧凑型玉米根干重比平展型高12．2％,二者根系垂直分布有明显的差异,在20cm以下的根干重比率,平展型玉米在19％以下,而紧凑型玉米高于23％,紧凑型玉米的深层根量较多,在深40～100cm土层内根干重比率比平展型高42．3％,二者的根系水平分布也不同,紧凑型玉米根系水平分布较集中,在距植株0～10cm水平范围内,根系分布比率比平展型玉米高9．6％,紧凑型玉米深层根量较多,水平分布集中,耐密植,是易获得高产的重要原因之一。     

Response of maize seedling roots to changing ethylene concentrations

Maize roots (Zea mays, cv. DK 626) growing in aerated solutions showed striking variations in the amount of ethylene produced during different stages of development. As endogenous ethylene increases, root elongation decreases. Exogenous 1-aminocyclopropane-1-carboxylic acid (ACC) supplied to these roots also inhibited their elongation and increased both the fresh weight of the apex and the ethylene produced. The inhibitor of ethylene biosynthesis, 2-aminoethoxyvinyl glycine (AVG), and the inhibitor of ethylene action, silver thiosulfate (STS), also reduced growth and increased swelling. As growth diminishes at reduced ethylene concentrations or with impeded ethylene action, these results support the view that ethylene is necessary for root growth. As ACC treatment also inhibited root elongation, it appears that ethylene was inhibitory at both low and high concentrations. Whereas ACC stimulated ethylene production 4 h after the beginning of treatment, inhibition of root elongation and promotion of fresh weight advanced slowly and needed 24 h to be established. At that time, root elongation reached a maximum response of 60% inhibition and 50% increase in weight. At 48 h, higher doses of ACC were required to provoke the same response as at 24 h. This suggests that the root growth progressively accomodates to higher ethylene concentrations. Published in Russian in Fiziologiya Rastenii, 2009, Vol. 56, No. 4, pp. 539–545. This text was submitted by the authors in English.     

Cell wall-associated malate dehydrogenase activity from maize roots

Isolated cell walls from maize (Zea mays L.) roots exhibited ionically and covalently bound NAD-specific malate dehydrogenase activity. The enzyme catalyses a rapid reduction of oxaloacetate and much slower oxidation of malate. The kinetic and regulatory properties of the cell wall enzyme solubilized with 1 M NaCl were different from those published for soluble, mitochondrial or plasma membrane malate dehydrogenase with respect to their ATP, Pi, and pH dependence. Isoelectric focusing of ionically-bound proteins and specific staining for malate dehydrogenase revealed characteristic isoforms present in cell wall isolate, different from those present in plasma membranes and crude homogenate. Much greater activity of cell wall-associated malate dehydrogenase was detected in the intensively growing lateral roots compared to primary root with decreased growth rates. Presence of Zn²⁺ and Cu²⁺ in the assay medium inhibited the activity of the wall-associated malate dehydrogenase. Exposure of maize plants to excess concentrations of Zn²⁺ and Cu²⁺ in the hydroponic solution inhibited lateral root growth, decreased malate dehydrogenase activity and changed isoform profiles. The results presented show that cell wall malate dehydrogenase is truly a wall-bound enzyme, and not an artefact of cytoplasmic contamination, involved in the developmental processes, and detoxification of heavy metals.     

Mapping of QTL associated with waterlogging tolerance during the seedling stage in maize

BACKGROUND AND AIMS: Soil waterlogging is a major environmental stress that suppresses maize (Zea mays) growth and yield. To identify quantitative trait loci (QTL) associated with waterlogging tolerance at the maize seedling stage, a F2 population consisting of 288 F(2:3) lines was created from a cross between two maize genotypes, 'HZ32' (waterlogging-tolerant) and 'K12' (waterlogging-sensitive). METHODS: The F2 population was genotyped and a base-map of 1710.5 cM length was constructed with an average marker space of 11.5 cM based on 177 SSR (simple sequence repeat) markers. QTL associated with root length, root dry weight, plant height, shoot dry weight, total dry weight and waterlogging tolerance coefficient were identified via composite interval mapping (CIM) under waterlogging and control conditions in 2004 (EXP.1) and 2005 (EXP.2), respectively. KEY RESULTS AND CONCLUSIONS: Twenty-five and thirty-four QTL were detected in EXP.1 and EXP.2, respectively. The effects of each QTL were moderate, ranging from 3.9 to 37.3 %. Several major QTL determining shoot dry weight, root dry weight, total dry weight, plant height and their waterlogging tolerance coefficient each mapped on chromosomes 4 and 9. These QTL were detected consistently in both experiments. Secondary QTL influencing tolerance were also identified and located on chromosomes 1, 2, 3, 6, 7 and 10. These QTL were specific to particular traits or environments. Although the detected regions need to be mapped more precisely, the findings and QTL found in this study may provide useful information for marker-assisted selection (MAS) and further genetic studies on maize waterlogging tolerance.     

High-value products from transgenic maize

Maize (also known as corn) is a domesticated cereal grain that has been grown as food and animal feed for tens of thousands of years. It is currently the most widely grown crop in the world, and is used not only for food/feed but also to produce ethanol, industrial starches and oils. Maize is now at the beginning of a new agricultural revolution, where the grains are used as factories to synthesize high-value molecules. In this article we look at the diversity of high-value products from maize, recent technological advances in the field and the emerging regulatory framework that governs how transgenic maize plants and their products are grown, used and traded.     

Suberin lamella development in maize seedling roots grown in aerated and stagnant conditions

Hypoxia can stimulate the development of a suberized exodermis in aquatic plants; however, its influence on this aspect of terrestrial root development is sparsely documented. To determine the effects of hypoxia on maize (Zea mays cv. Seneca Horizon) roots, seedlings were grown in vermiculite (VERM), aerated hydroponics (AER), stagnant hydroponics with agar (STAG), or aerated hydroponics with agar (AERAG). The endo- and exodermis were examined for wall modifications. Lateral root emergence and aerenchyma formation were documented qualitatively. The endodermal Casparian band formation was unaffected by treatment. Endodermal and exodermal suberin lamella formation was earliest and most extensive in VERM. Suberization, especially in the exodermis of aerated treatments, was depressed in all hydroponic media. In comparison with AER, STAG exodermal lamellae were increased, but endodermal lamellae were decreased. Since the suberized exodermis forms a barrier to radial oxygen loss from roots to the medium, its stimulation in STAG roots (which also developed extensive aerenchyma) would help retain oxygen in the root. The reduction of endodermal lamellae should facilitate oxygen diffusion into the stele. Clearly, the response to environmental conditions is variable within individual cortical cell layers. Additionally, the observed patterns of lamellae, aerenchyma and lateral root development indicate a tight radial co-ordination of root development.     

Phytotoxic effects of fumonisin B1 on maize seedling growth

Fumonisin B₁ toxin is produced by the fungusFusarium moniliforme Sheldon, which is systemic to maize (Zea mays L.) and maize seeds. The effects of zero to 100 parts per million fumonisin B₁ on the germination process of maize seeds was determined. The presence of fumonisin had no effect on percent seed germination, but fumonisin inhibited radicle elongation by up to 75% after 48 hours of imbibition. An analysis of amylase secretion in the maize endosperm indicated that fumonisins inhibited amylase production in the germinating seed. Isoelectric focusing of endosperm extracts indicated that secretion of the low pI class of amylases was affected more that other amylase isozymes. The results suggested that the presence of high levels of fumonisin in maize seed may have deleterious effects on seedling emergence.     

施用缓/控释尿素对玉米苗期土壤生物学活性的影响

采用盆栽试验,模拟田间生态环境,研究了施用不同种缓/控释氮素底肥对玉米苗期土壤硝酸还原酶、脲酶活性及微生物量碳、氮的影响.结果表明,施用硝化抑制剂(双氰胺)和脲酶抑制剂(n-丁基硫代磷酰三胺)涂层大颗粒尿素肥料的土壤硝酸还原酶活性最高;施用大颗粒尿素,脲酶活性最强,微生物量碳、氮最高.施用醋酸酯淀粉包膜大颗粒尿素、包膜双氰胺涂层大颗粒尿素、丙烯酸树脂包膜双氰胺涂层大颗粒尿素与不施氮肥土壤脲酶活性较高;每种处理微生物量碳与氮变化完全一致.施用醋酸酯淀粉包膜硝化和脲酶抑制剂涂层大颗粒尿素肥料,土壤微生物量碳、氮最低.同种膜材料包膜抑制剂涂层大颗粒尿素制成的缓/控释氮肥,对土壤生物学活性的影响效果好于直接包膜大颗粒尿素;丙烯酸树脂包膜大颗粒尿素制成的缓/控释氮肥,对氮素的控释效果明显好于醋酸酯淀粉包膜.     

Cloning and characterization of miRNAs from maize seedling roots under low phosphorus stress

MicroRNAs (miRNAs) are a class of small, non-coding regulatory RNAs that regulate gene expression by guiding target mRNA cleavage or translational inhibition in plants and animals. In this study, a small RNA library was constructed to identify conserved miRNAs as well as novel miRNAs in maize seedling roots under low level phosphorus stress. Twelve miRNAs were identified by high throughput sequencing of the library and subsequent analysis, two belong to conserved miRNA families (miRNA399b and miRNA156), and the remaining ten are novel and one of latter is conserved in gramineous species. Based on sequence homology, we predicted 125 potential target genes of these miRNAs and then expression patterns of 7 miRNAs were validated by semi-RT-PCR analysis. MiRNA399b, Zma-miR3, and their target genes (Zmpt1 and Zmpt2) were analyzed by real-time PCR. It is shown that both miRNA399b and Zma-miR3 are induced by low phosphorus stress and regulated by their target genes (Zmpt1 and Zmpt2). Moreover, Zma-miR3, regulated by two maize inorganic phosphate transporters as a newly identified miRNAs, would likely be directly involved in phosphate homeostasis, so was miRNA399b in Arabidopsis and rice. These results indicate that both conserved and maize-specific miRNAs play important roles in stress responses and other physiological processes correlated with phosphate starvation, regulated by their target genes. Identification of these differentially expressed miRNAs will facilitate us to uncover the molecular mechanisms underlying the progression of maize seedling roots development under low level phosphorus stress.     

苗期水分亏缺对玉米根系发育及解剖结构的影响

利用盆栽试验,研究了不同水分亏缺[土壤含水量分别为田间持水量的75%～85%(对照)、65%～75%(轻度)、55%～65%(中度)、45%～55%(重度)]对玉米苗期根系发育及解剖结构的影响.结果表明:干旱抑制了植株生长,随着水分亏缺程度的加重,根系长度缩短、根直径变细、总生物量降低;而根系活力、根冠比、根尖多糖含量均增加;侧根根毛长度、根毛密度、根毛总长度在中度水分亏缺条件下达到最大.组织切片观察结果表明,根直径变细主要是由于根的中柱面积减小、导管直径缩小所致,不同水分亏缺处理间导管的数量差异不大,但水分亏缺使导管壁变得不规整.根尖多糖含量的增加主要表现在表皮细胞和根冠细胞内,在表皮细胞内多糖主要以游离形式分布,在根冠细胞内主要以淀粉粒形式分布.总之,在水分亏缺条件下,玉米通过改变导管结构、增加表皮细胞与根冠细胞内多糖的含量及扩大根毛总表面积,来调节根系对水分的吸收能力,增强玉米植株的抗旱性,但根毛并不随着亏缺程度的加重而无限制的增长,在过度干旱条件下,根毛会受到抑制或损伤.     

Respiration rate in maize roots is related to concentration of reduced nitrogen and proliferation of lateral roots

The relationship between specific rate of respiration (respiration rate per unit root dry weight) and concentration of reduced nitrogen was examined for maize ( Zea mays L.) roots. Plants with 2 primary nodal root axes were grown for 8 days in a split-root hydroponic system in which NO-₃ was supplied to both axes at 1.0 mol m⁻³, to one axis at 1.0 mol m⁻³ and the other axis at 0.0 mol m⁻³ or to both axes at 0.0 mol m⁻³ Respiration rates and root characteristics were measured at 2-day intervals. Specific rate of respiration was positively correlated in a nonlinear relationship with concentration of reduced nitrogen. The lowest specific rates of respiration occurred when neither axis received exogenous NO⁻³ and the concentration of reduced nitrogen in the axes was less than 9 mg g⁻¹. The greatest rates occurred in axes that were actively absorbing NO⁻³ and contained more than 35 mg g⁻¹ of reduced nitrogen. At 23 mg g⁻¹ of reduced nitrogen, below which initiation of lateral branches was decreased by 30–50%. specific rate of respiration was 17% greater for roots actively absorbing NO⁻³ than for roots not absorbing NO⁻³ Increases in specific rate of respiration associated with concentrations of reduced nitrogen greater than 23 mg g⁻¹ were concluded to be attributable primarily to proliferation of lateral branches.     

Proteomic changes in maize roots after short-term adjustment to saline growth conditions

It is of fundamental importance to understand adaptation processes leading to salt resistance. The initial effects on maize roots in the first hour after the adjustment to saline conditions were monitored to elucidate initial responses. The subsequent proteome change was monitored using a 2‐D proteomic approach. We found several new salt‐inducible proteins, whose expression has not been previously reported to be modulated by salt. A set of phosphoproteins in maize was detected but only ten proteins were phosphorylated and six proteins were dephosphorylated after the application of 25 mM NaCl for 1 h. Some of the phosphorylated maize proteins such as fructokinase, UDP‐glucosyl transferase BX9, and 2‐Cys‐peroxyredoxine were enhanced, whereas an isocitrate‐dehydrogenase, calmodulin, maturase, and a 40‐S‐ribosomal protein were dephosphorylated after adjustment to saline conditions. The initial reaction of the proteome and phosphoproteome of maize after adjustment to saline conditions reveals members of sugar signalling and cell signalling pathways such as calmodulin, and gave hint to a transduction chain which is involved in NaCl‐induced signalling. An alteration of 14‐3‐3 proteins as detected may change plasma membrane ATPase activity and cell wall growth regulators such as xyloglucane endotransglycosylase were also found to be changed immediately after the adjustment to salt stress.     

Sloughing of cap cells and carbon exudation from maize seedling roots in compacted sand

Sloughing of root cap cells and exudation of mucilage plays an important role in the penetration of compacted soils by roots. For the first time we have quantified the rate of sloughing of root cap cells in an abrasive growth medium that was compacted to create mechanical impedance to root growth. The number of maize ( Zea mays ) root cap cells sloughed into sand increased as a result of compaction, from 1930 to 3220 d⁻¹ per primary root. This represented a 12-fold increase in the number of cells sloughed per mm root extension (from 60 to >700). We estimated that the whole of the cap surface area was covered with detached cells in compacted sand, compared with c . 7% of the surface area in loose sand. This lubricating layer of sloughed cells and mucilage probably decreases frictional resistance to soil penetration. The total carbon deposited by the root was estimated at c . 110 μg g⁻¹ sand d⁻¹. Sloughed cells accounted for <10% of the total carbon, the vast majority of carbon being contained in mucilage exudates.     

Partitioning of reduced nitrogen derived from exogenous nitrate in maize roots: Initial priority for protein synthesis

Summary When roots of five day-old maize seedlings were exposed to¹⁵N-nitrate, a constant (25–29%) proportion of the reduced¹⁵N derived from the entering¹⁵N-nitrate accumulated as insoluble¹⁵N nitrogen. Constancy was established by two hours and lasted through 12 hours at ambient¹⁵N-nitrate concentrations of 0.05 mM to 20.0 mM. Even when little¹⁵N nitrate had been reduced (<2 moles), there was a linear relationship between accumulation of insoluble¹⁵N (but not accumulation or translocation of soluble reduced¹⁵N) and total reduced¹⁵N. It is proposed that protein synthesis from the entering nitrate occurs in close association with nitrate reduction.Paper No. 9764 of the Journal Series of the North Carolina Agricultural Research Service, Raleigh, NC, 27695-7619, USA. This research was supported by Grant No. PCM-8118661 from the National Science Foundation.Use of trade names in this publication does not imply endorsement by the North Carolina Agricultural Research Service of the product's name or criticisms of similar ones not mentioned.     

Auxin gradient along the root of the maize seedling

[5-³H]Indol-3yl-acetic acid (IAA) applied to the shoot apices of intact 6-day-old maize (Zea mays L.) plants moved into the primary root and accumulated at the root apex. IAA from the shoot could partially satisfy the requirement of the primary root for IAA for growth.Abbreviation IAA indol-3yl-acetic acid     

Proteomic analysis of heterosis during maize seed germination

Heterosis is observed for most phenotypic traits and developmental stages in many plants. In this study, the embryos, from germinating seeds after 24 h of soaking, for five elite maize hybrids and their parents were selected to unravel the genetic basis of heterosis using 2‐D proteomic method. In total, 257 (80.06%), 363 (58.74%), 351 (79.95%), 242 (54.50%), and 244 (46.30%) nonadditively expressed proteins were identified in hybrids Zhengdan 958, Nongda 108, Yuyu 22, Xundan 20, and Xundan 18, respectively. The nonadditive proteins were divided into above high‐parent (++; 811, 55.66%), high‐parent (+; 121, 8.30%), partial dominance (+?; 249, 17.09%), low‐parent (?; 30, 2.06%), below low‐parent (? ?; 62, 4.26%), and D (different; 184, 12.63%) expression patterns. The observed patterns indicate the important roles of dominance, partial dominance, and overdominance in regulating seed germination in maize. Additionally, 54 different proteins were identified by mass spectrometry and classified into nine functional groups: metabolism (9), cell detoxification (8), unknown functional proteins (8), chaperones (7), signal transduction (6), development process (5), other (5), transporter (3), and stress response (3). Of these, the most interesting are those involved with germination‐related hormone signal transduction and the abscisic acid and gibberellin regulation networks.     

Cyanidin as endogenous chelator of metal ions in maize seedling roots

The property of cyanidin complexation with different metal ions in maize seedlings roots was established using parameters of reflectance spectroscopy and colorimetry. The spectral criteria of pigment association with metals in vivo were evaluated.