A robust,high‐throughput method for computing maize ear,cob, and kernel attributes automatically from images

Grain yield of the maize plant depends on the sizes, shapes, and numbers of ears and the kernels they bear. An automated pipeline that can measure these components of yield from easily‐obtained digital images is needed to advance our understanding of this globally important crop. Here we present three custom algorithms designed to compute such yield components automatically from digital images acquired by a low‐cost platform. One algorithm determines the average space each kernel occupies along the cob axis using a sliding‐window Fourier transform analysis of image intensity features. A second counts individual kernels removed from ears, including those in clusters. A third measures each kernel's major and minor axis after a Bayesian analysis of contour points identifies the kernel tip. Dimensionless ear and kernel shape traits that may interrelate yield components are measured by principal components analysis of contour point sets. Increased objectivity and speed compared to typical manual methods are achieved without loss of accuracy as evidenced by high correlations with ground truth measurements and simulated data. Millimeter‐scale differences among ear, cob, and kernel traits that ranged more than 2.5‐fold across a diverse group of inbred maize lines were resolved. This system for measuring maize ear, cob, and kernel attributes is being used by multiple research groups as an automated Web service running on community high‐throughput computing and distributed data storage infrastructure. Users may create their own workflow using the source code that is staged for download on a public repository.     

弱光胁迫对不同耐荫型玉米果穗发育及内源激素含量的影响

2010—2011年以耐荫性较弱的玉米杂交种豫玉22和耐荫性较强的玉米杂交种郑单958为材料,在抽雄前3 d开始进行弱光胁迫处理,吐丝后10 d恢复自然光照,研究弱光胁迫及光恢复对不同耐荫型玉米果穗生长发育及其内源激素含量的影响。结果表明:弱光胁迫下,玉米果穗生长发育明显减缓,穗长、穗粗和果穗干物质积累显著减小,秃尖度变大;穗行数、穗粒数和籽粒库容显著降低;吐丝期果穗顶部小穗子房发育停滞,已有败育迹象的籽粒在恢复自然光照后无明显改善;豫玉22果穗和籽粒性状在处理间的差异程度均大于郑单958。弱光胁迫下,两玉米杂交种果穗的ABA和ZR含量均升高,而GA含量和GA/ABA比值均降低;IAA含量和IAA/ABA比值在郑单958果穗中表现为升高,而豫玉22则表现为下降。     

Can genetic variability for nitrogen metabolism in the developing ear of maize be exploited to improve yield?

Quantitative trait loci (QTLs) for the main steps of nitrogen (N) metabolism in the developing ear of maize (Zea mays L.) and their co-localization with QTLs for kernel yield and putative candidate genes were searched in order to identify chromosomal regions putatively involved in the determination of yield. During the grain-filling period, the changes in physiological traits were monitored in the cob and in the developing kernels, representative of carbon and N metabolism in the developing ear. The correlations between these physiological traits and traits related to yield were examined and localized with the corresponding QTLs on a genetic map. Glycine and serine metabolism in developing kernels and the cognate genes appeared to be of major importance for kernel production. The importance of kernel glutamine synthesis in the determination of yield was also confirmed. The genetic and physiological bases of N metabolism in the developing ear can be studied in an integrated manner by means of a quantitative genetic approach using molecular markers and genomics, and combining agronomic, physiological and correlation studies. Such an approach leads to the identification of possible new regulatory metabolic and developmental networks specific to the ear that may be of major importance for maize productivity.     

Suppressor of sessile spikelets1 (Sosl): a dominant mutant affecting inflorescence development in maize

Suppressor of sessile spikeletsl (Sos1) is a dominant mutant of maize that blocks branching of the spikelet-pair primordium to form the sessile spikelet during ear development. As a result, Sos1 mutant ears and tassels possess single spikelets as opposed to the normal condition of paired spikelets, one sessile and the other pedicellate. Sos1 also causes a reduction in the number of tassel branches and the number of orthostichies (or cupule ranks) in the ear. The sos1 genetic locus maps to the short arm of maize chromosome 4. The Sos1 single spikelet phenotype appears similar to the single spikelet phenotype found in teosinte, the probable progenitor of maize. This similarity invites the hypothesis that sos1 had a role in the evolution of maize from teosinte. However, genetic mapping data and a comparison of the developmental basis of the single spikelet condition in the Sos1 mutant and teosinte demonstrate that their similar phenotypes result from distinct genetic-developmental mechanisms. These results indicate that sos1 was not involved in the evolution of maize and caution against drawing conclusions of homology based solely on similar adult phenotypes.     

玉米抗镰刀菌穗腐病接种方法及抗病资源筛选研究

对玉米抗穗腐病性鉴定中采用的牙签法与花丝通道注射法进行比较研究表明,牙签法接种果穗的发病程度重于花丝通道注射法接种。牙签法接种病菌于果穗子粒与穗轴之间,有利于病原菌的发育扩展,是一种比较理想的、容易操作的接种方法。采用牙签法接种串珠镰刀菌,对178份玉米自交系和15份杂交种进行抗穗腐病鉴定,筛选出高抗(HR)自交系1份、抗病(R)玉米自交系34份、抗病(R)玉米杂交种12份。     

玉米雌穗性状遗传分析与形成机制*

雌穗是玉米重要的生殖器官,雌穗发育决定成熟果穗大小及单穗粒重,进而直接影响玉米产量。雌穗性状主要包括穗长、穗粗、穗行数、行粒数、穗重、单穗粒重等,均为多基因控制的数量遗传性状,且其遗传结构各不相同。解析雌穗性状的遗传基础,优化雌穗结构,是玉米增产的重要途径。前人通过数量性状位点(quantitative trait locus mapping,QTL)定位和全基因组关联分析(genome-wide association study, GWAS)等方法,已经鉴定出较多雌穗性状相关的遗传位点,但是目前已鉴定功能的基因较少,所建立的遗传位点一致性图谱并不完整,因此难以全面揭示雌穗性状遗传结构。通过综合前人雌穗性状遗传定位进展,现将已鉴定QTL位点和显著关联SNP整合至玉米B73参考基因组V4版本,并鉴定出雌穗性状定位热点区间,对深入解析雌穗性状遗传结构、指导雌穗性状基因克隆和理解雌穗发育分子机制均具有重要意义。     

Candidate gene identification of existing or induced mutations with pipelines applicable to large genomes

Bulked segregant analysis (BSA) is used to identify existing or induced variants that are linked to phenotypes. Although it is widely used in Arabidopsis and rice, it remains challenging for crops with large genomes, such as maize. Moreover, analysis of huge data sets can present a bottleneck linking phenotypes to their molecular basis, especially for geneticists without programming experience. Here, we identified two genes of maize defective kernel mutants with newly developed analysis pipelines that require no programing skills and should be applicable to any large genome. In the 1970s, Neuffer and Sheridan generated a chemically induced defective kernel (dek) mutant collection with the potential to uncover critical genes for seed development. To locate such mutations, the dek phenotypes were introgressed into two inbred lines to take advantage of maize haplotype variations and their sequenced genomes. We generated two pipelines that take fastq files derived from next‐generation (nextGen) paired‐end DNA and cDNA sequencing as input, call on several well established and freely available genomic analysis tools to call SNPs and INDELs, and generate lists of the most likely causal mutations together with variant index plots to locate the mutation to a specific sequence position on a chromosome. The pipelines were validated with a known strawberry mutation before cloning the dek mutants, thereby enabling phenotypic analysis of large genomes by next‐generation sequencing.     

Effects of red and blue light on the composition and morphology of maize kernels grown in vitro

Growth and development of plants are known to be affected by exposure to red and blue light. Mechanisms by which light quality influences gene expression in maize (Zea mays L.) embryos have not been explored. Maize kernels can be cultured in vitro allowing experimental manipulation of environmental factors during seed development. We used the in vitro kernel culture system to investigate the response of developing maize seeds, which normally develop without exposure to light, to controlled light quality. Kernels grown under red light accumulated more dry weight than those grown in darkness, whereas kernels grown under blue light accumulated less. Reciprocal color shift experiments showed that light quality during the first week in culture had more influence on kernel weight than during the subsequent three weeks in culture. Soluble sugars were higher in both light treatments than in darkness. Blue-grown kernels had higher amino acid and lower lipid levels than red-or dark-grown kernels. Embryo morphology was markedly affected by red light, under which the upper shoot axis was longer than under blue light or in darkness. Embryo morphology was influenced by light quality during the later stages of development rather than the first week. We suggest, based on these results, that gene expression in the embryo and endosperm of developing maize seeds is sensitive to light quality, and the mechanism and time dependence of this effect warrant further study. In vitro maize kernel culture affords a convenient system for such light quality experiments.     

粗缩病对玉米产量和籽粒品质的影晌

以6个对玉米粗缩病（MRDV）表现不同抗性的玉米品种为材料,研究了粗缩病对玉米产量性状和籽粒品质的影响。结果表明,在供试品种中,‘青农105’和‘青农8’为抗病品种,‘登海3622’和‘农大108’为中抗品种,‘先玉335’和‘郑单958’为感病品种。感病后,玉米果穗穗长、行粒数、穗粒重和产量显著降低,且损失程度表现为抗病品种〈中抗品种〈感病品种：籽粒中粗淀粉含量显著降低,粗蛋白含量升高,粗脂肪含量变化不明显。回归分析表明,通过旃情指数可以准确预测玉米粗缩病导致的产量损失。     

A program system for interactive measurements on digitized cell images.

Using a high precision image scanner and a PDP-8/F minicomputer, we have developed a program system for interactive measurements on microscopic images. By giving simple keyboard commands, the operator can run the image scanner and manipulate the digitized images. The interface between the operator and the microscope-computer system is a Tektronix 4010 graphic terminal. The system allows objects to be isolated and parameters to be calculated from each object, e.g., parameters characterizing shape of the object, irregularity in light transmission over the object, area, integrated light transmission, etc. Objects are isolated and parameters are calculated under complete operator control using interactive computer graphics technique. Calculated parameters may be stored in dedicated data records, which are stored in files for later statistical analysis. The system also includes a statistical evaluation part. Technically, the system consists of a command scanner, which translates commands into internal representation, a parser, which checks the syntax of the commands, and an interpreter, which executes the commands. The system is designed so that new commands can be added easily.     

Robustness of central carbohydrate metabolism in developing maize kernels

The central carbohydrate metabolism provides the precursors for the syntheses of various storage products in seeds. While the underlying biochemical map is well established, little is known about the organization and flexibility of carbohydrate metabolic fluxes in the face of changing biosynthetic demands or other perturbations. This question was addressed in developing kernels of maize (Zea mays L.), a model system for the study of starch and sugar metabolism. ¹³C-labeling experiments were carried out with inbred lines, heterotic hybrids, and starch-deficient mutants that were selected to cover a wide range of performances and kernel phenotypes. In total, 46 labeling experiments were carried out using either [U-¹³C₆]glucose or [U-¹³C₁₂]sucrose and up to three stages of kernel development. Carbohydrate flux distributions were estimated based on glucose isotopologue abundances, which were determined in hydrolysates of starch by using quantitative ¹³C-NMR and GC-MS. Similar labeling patterns in all samples indicated robustness of carbohydrate fluxes in maize endosperm, and fluxes were rather stable in response to glucose or sucrose feeding and during development. A lack of ADP-glucose pyrophosphorylase in the bt2 and sh2 mutants triggered significantly increased hexose cycling. In contrast, other mutations with similar kernel phenotypes had no effect. Thus, the distribution of carbohydrate fluxes is stable and not determined by sink strength in maize kernels.     

Factoring distribution and prevalence of Fall armyworm in southwest China

Host plant growth changing with environmental conditions can impact the distribution of herbivores. The generalist herbivore fall armyworm (FAW), Spodoptera frugiperda (J. E. Smith) (Lepidoptera: Noctuidae), is an invasive pest rapidly spreading across the world and has recently invaded southern China. We studied effects of environmental factors on the distribution of the fall armyworm and its host (maize) plant growth in the tropical mountainous area of Huize County, province of Yunnan, southwest China. Moreover, the relationships among the FAW distribution, environmental factors (altitude, temperature and humidity) and plant growth (mean kernel weight, kernel number per ear and ear weight) were analysed. The results showed that FAW predominated at altitude 1,243.3 m, temperature 21.4°C and humidity 82.1%. The host plant grew best at 1,200–1,312 m, 21.0–21.7°C and 81.2%–82.0%. Environmental factors indirectly influenced the distribution of FAW via the host plant growth. Compared with environmental factors, the host plant growth had a simplistic positive linear relationship with the density of FAW. FAW is less impacted by abiotic factors rather it determined by host plant prevalence, and thus the locations where maize plants grow best are preferred by FAW and should be the focus of insecticide applications. Understanding the distribution of FAW under various environmental conditions provides a valuable reference for Chinese maize production and food security.     

Fusarium species complex and mycotoxins in grain maize from maize hybrid trials and from grower's fields

Aims: To quantify and to compare the occurrence of Fusarium species in maize kernels and stalk pieces, to analyse mycotoxins in kernels and maize crop residues, to evaluate two approaches to obtain kernel samples and to compare two methods for mycotoxin analyses. Methods and Results: The occurrence of Fusarium species in maize kernels and stalk pieces from a three‐year maize hybrid trial and 12 kernel samples from grower’s fields was assessed. Nine to 16 different Fusarium species were detected in maize kernels and stalks. In kernels, F. graminearum, F. verticillioides and F. proliferatum were the most prevalent species whereas in stalks, they were F. equiseti, F. proliferatum and F. verticillioides. In 2006, 68% of the kernel samples exceeded the recommended limit for pig feed for deoxynivalenol (DON) and 42% for zearalenone (ZON), respectively. Similarly, 75% of the samples from grower’s fields exceeded the limits for DON and 50% for ZON. In maize crop residues, toxin concentrations ranged from 2·6 to 15·3 mg kg^?1 for DON and from 0·7 to 7·4 mg kg^?1 for ZON. Both approaches to obtain maize kernel samples were valid, and a strong correlation between mycotoxin analysis using ELISA and LC‐MS/MS was found. Conclusions: The contamination of maize kernels, stalk pieces and remaining crop residues with various mycotoxins could pose a risk not only to animal health but also to the environment. With the hand‐picked sample, the entire Fusarium complex can be estimated, whereas combine harvested samples are more representative for the mycotoxin contents in harvested goods. Significance and Impact of the Study: This is the first multi‐year study investigating mycotoxin contamination in maize kernels as well as in crop residues. The results indicate a high need to identify cropping factors influencing the infection of maize by Fusarium species to establish recommendations for growers.     

Transposition of the En/Spm transposable element system in maize (Zea mays L.): reciprocal crosses of a1-m(Au) and a1-m(r) alleles uncover developmental patterns

Transposition studies of the transposon, En/Spm, have dealt with general aspects of the timing of the excision event with regard to DNA replication and plant development, but without describing details of the process. By following the excision events of an En transposon inserted at the a1 locus [a1-m(Au)], several features of this process can be elucidated. In progenies from reciprocal crosses between the a1-m(Au) allele containing an En insert, and a nonautonomous En allele, [a1-m(r) is a deficiency derivative of En], several features of the En at the a1-m(Au) allele can be observed taking place during ear development and during microsporogenesis. First, it has long been known that the distribution of mutant kernel phenotypes on an ear indicates that En transposes late in most of the events during ear development. Second, the phase change of En (presence and absence of activity) is observed during cob development. Third, discordant kernel phenotypes of two ears, reported herein, resulting from a reciprocal cross with the parental phenotype can be deduced to arise from the transposition of En during microsporogenesis and subsequent fertilization, leading to a discordant genotype between endosperm and embryo. The phase change and discordance lead us to conclude that these events can arise from transposition after host DNA replication. It can also be concluded that the activity of the En inserted in this a1-m(Au) allele is not limited to a specific stage or timing during plant development. Further, this study illustrates the power of genetic analysis in the determination of cellular events. Received: 26 May 1999 / Accepted: 11 November 1999     

Performance evaluation of a machine vision system for insect pests identification of field crops using artificial neural networks

Feature extraction is a crucial part of advanced image recognition systems. In this research, an autonomous detection device was designed and developed for insect pest detection to improve the ability of intelligent systems in order to annihilate harmful insect pests in agricultural crop fields. Device included a dark chamber, a CCD digital camera, a LDR lightening module and a personal computer. The proposed programme for precise insect pest detection was based on an image processing algorithm and artificial neural networks (ANNs). After image acquisition, the insect pests’ images were extracted from original images with Canny filtration. Afterwards, four morphological and three textural features from the obtained images were measured and normalised. Performance of ANN model was tested successfully for Beet armyworm (Spodoptera exigua) recognition in images using back-propagation supervised learning method and inspection data. Results showed that proposed system was able to identify S. exigua in the images from other species. Such this machine vision system can be used in autonomous field robots to achieve a modern farmer’s assistant.     

Cloning and characterization of a putative GS3 ortholog involved in maize kernel development

The GS3 gene was the first identified gene controlling the grain size in rice. It has been proven to be involved in the evolution of grain size during domestication. We isolated the maize ortholog, ZmGS3 and investigated its role in the evolution of maize grain size. ZmGS3 has five exons encoding a protein with 198 amino acids, and has domains in common with the rice GS3 protein. Compared with teosinte, maize has reduced nucleotide diversity at ZmGS3, and the reduction is comparable to that found in neutrally evolving maize genes. No positive selection was detected along the length of the gene using either the Hudson–Kreitman–Aguadé or Tajima’s D tests. Phylogenetic analysis reveals a distribution of maize sequences among two different clades, with one clade including related teosinte sequences. The nucleotide polymorphism analysis, selection test and phylogenetic analysis reveal that ZmGS3 has not been subjected to selection, and appears to be a neutrally evolving gene. In maize, ZmGS3 is primarily expressed in immature ears and kernels, implying a role in maize kernel development. Association mapping analysis revealed one polymorphism in the fifth exon that is significantly associated with kernel length in two environments. Also one polymorphism in the promoter region was found to affect hundred kernel weight in both environments. Collectively, these results imply that ZmGS3 is involved in maize kernel development but with different functional polymorphisms and thus, possibly different mechanisms from that of the rice GS3 gene.     

Stenocarpella maydis (Berk.) Sutton Colonization of Maize Ears

A study was undertaken to determine the ramification of maize shank, cob and kernel tissues by Stenocarpella maydis. Trials consisting of inoculated and uninoculated treatments were planted at two localities. Shank, cob and kernels of each treatment were divided into segments and S. maydis colonization was determined. Infection of the pedicel portion of maize kernels was significantly higher than the apical portion. Preferential colonization of the embryo's of kernels was observed. Colonization of cobs occurred primarily at the attachment end of the cob, with sclerenchymatous tissues showing the greatest re-isolation frequency. Shank segments did not show significant differences in S. maydis re-isolation frequency, although a tendency for higher re-isolations was observed at the stalk-attachment end. It is concluded that S. maydis colonization occurs at the base of the ear with mycelial ramification toward the tip of the ear. The sclerenchyma and placentae were the primary colonized cob tissues. as were the embryos in the kernels.     

Quantitative trait locus analysis of drought tolerance and yield in Maize in China

Drought accounts for significant yield losses in crops. Maize (Zea mays L.) is particularly sensitive to water stress at reproductive stages, and breeding to improve drought tolerance has been a challenge. By use of a linkage map with 121 single sequence repeat (SSR) markers, quantitative trait loci (QTLs) for grain yield and yield components were characterized in the population of the cross X178×B73 under water-stressed and well-watered conditions. Under the well-watered regime, 2, 4, 4, 1, 2, 2, and 3 QTLs were identified for grain yield, 100-kernel weight, kernel number per ear, cob weight per ear, kernel weight per ear, ear weight, and ear number per plant, respectively, whereas under the water-stressed conditions, 1, 5, 2, 6, 1, 3, and 2 QTLs, respectively, were found. The significant phenotypic correlations among yield and yield components to some extent were observed under both water conditions, and some overlaps between the corresponding QTLs were also found. QTLs for grain yield and kernel weight per ear under well-watered conditions and ear weight under both well-watered and water-stressed conditions over-lapped, and all were located on chromosome 1.03 near marker bnlg176. Two other noticeable QTL regions were on chromosome 9.05 and 9.07 near markers umc1657 and bnlg1525; the first corresponded to grain yield, kernel weight per ear, and ear weight under well-watered conditions and kernel number per ear under both water conditions, and the second to grain yield and cob weight per ear under water-stressed conditions and ear number per plant under both water conditions. A comparative analysis of the QTLs herein identified with those described in previous studies for yield and yield components in different maize populations revealed a number of QTLs in common. These QTLs have potential use in molecular marker-assisted selection.