Genomic prediction of hybrid performance in maize with models incorporating dominance and population specific marker effects

Identifying high performing hybrids is an essential part of every maize breeding program. Genomic prediction of maize hybrid performance allows to identify promising hybrids, when they themselves or other hybrids produced from their parents were not tested in field trials. Using simulations, we investigated the effects of marker density (10, 1, 0.3 marker per mega base pair, Mbp(-1)), convergent or divergent parental populations, number of parents tested in other combinations (2, 1, 0), genetic model (including population-specific and/or dominance marker effects or not), and estimation method (GBLUP or BayesB) on the prediction accuracy. We based our simulations on marker genotypes of Central European flint and dent inbred lines from an ongoing maize breeding program. To simulate convergent or divergent parent populations, we generated phenotypes by assigning QTL to markers with similar or very different allele frequencies in both pools, respectively. Prediction accuracies increased with marker density and number of parents tested and were higher under divergent compared with convergent parental populations. Modeling marker effects as population-specific slightly improved prediction accuracy under lower marker densities (1 and 0.3?Mbp(-1)). This indicated that modeling marker effects as population-specific will be most beneficial under low linkage disequilibrium. Incorporating dominance effects improved prediction accuracies considerably for convergent parent populations, where dominance results in major contributions of SCA effects to the genetic variance among inter-population hybrids. While the general trends regarding the effects of the aforementioned influence factors on prediction accuracy were similar for GBLUP and BayesB, the latter method produced significantly higher accuracies for models incorporating dominance.     

Identification of proteins regulated by ABA in response to combined drought and heat stress in maize roots

We adopted a proteomics approach to identify and analyze the differential expression of maize root proteins associated with abscisic acid (ABA) regulation under combined drought and heat stress. Using mass spectrometry, we identified 22 major proteins that were significantly up-regulated under combined drought and heat stress. These 22 proteins were classified into 6 functional categories: disease/defense (8), metabolism (3), cell growth/division (3), signal transduction (2), transporters (2) and unclassified (4). Our previous reports showed that ABA regulates the expression of several small heat-shock proteins (sHSPs) in maize leaves subjected to the combination of drought and heat stress; however, no sHSPs were identified among the root proteins up-regulated in this study. RT-PCR and western blot analyses were used to identify six known sHSPs. The maize roots were pretreated with 100 μM of ABA, and subsequently, the expression of the 22 up-regulated proteins and 6 sHSPs was examined. 11 proteins were up-regulated in an ABA-dependent manner, 13 proteins were up-regulated in an ABA-independent manner, and 4 proteins were up-regulated but inhibited by ABA. The up-regulated proteins are interesting candidates for further physiological and molecular investigations of combination stress tolerance in maize.     

Proteomic evaluation of wound‐healing processes in potato (Solanum tuberosum L.) tuber tissue

Proteins from potato (Solanum tuberosum L.) tuber slices, related to the wound‐healing process, were separated by 2‐DE and identified by an MS analysis in MS and MS/MS mode. Slicing triggered differentiation processes that lead to changes in metabolism, activation of defence and cell‐wall reinforcement. Proteins related to storage, cell growth and division, cell structure, signal transduction, energy production, disease/defence mechanisms and secondary metabolism were detected. Image analysis of the 2‐DE gels revealed a time‐dependent change in the complexity of the polypeptide patterns. By microscopic observation the polyalyphatic domain of suberin was clearly visible by D4, indicating that a closing layer (primary suberisation) was formed by then. A PCA of the six sampling dates revealed two time phases, D0–D2 and D4–D8, with a border position between D2 and D4. Moreover, a PCA of differentially expressed proteins indicated the existence of a succession of proteomic events leading to wound‐periderm reconstruction. Some late‐expressed proteins (D6–D8), including a suberisation‐associated anionic peroxidase, have also been identified in the native periderm. Despite this, protein patterns of D8 slices and native periderm were still different, suggesting that the processes of wound‐periderm formation are extended in time and not fully equivalent. The information presented in this study gives clues for further work on wound healing‐periderm formation processes.     

Proteomic studies on the white matter of human brain

Limited information on the protein expression profiles of the different components of mammalian brain is available to date. In the present study, proteomic analysis was performed on 32 white matter samples obtained from 8 different regions of brains of four post mortem cases. Proteins were separated by 2D gel electrophoresis and identified by mass spectrometry. Most of the protein spots (98%) are reproducibly present in all the samples analyzed. A total of 64 different proteins were identified and divided into seven functional groups. These include metabolic proteins (33%), structural proteins (9%), proteins involved in signal transduction (9%), blood proteins (8%), stress related proteins (23%), and proteins involved in the ubiquitin mediated proteolysis (6%). This protein database obtained from the white matter of human brain contributes to deepen our knowledge on the molecular mechanisms that control several pathologies affecting this key component of the brain.     

Analysis of nonadditive protein accumulation in young primary roots of a maize (Zea mays L.) F(1)-hybrid compared to its parental inbred lines

Heterosis describes the superior performance of heterozygous F(1)-hybrids compared to their homozygous parental inbred lines. Heterosis is already manifested during early maize (Zea mays L.) primary root development. In this study, the most abundant soluble proteins have been investigated before the phenotypic manifestation of heterosis in 3.5-day-old primary roots in the flint inbred line UH002, the dent inbred line UH301 and the corresponding hybrid UH301 x UH002. In CBB-stained 2-DE gels, 150 of 304 detected proteins (49%) were accumulated in a nonadditive fashion in the hybrid compared to the average of their parental inbred lines (Student's t-test: p < 0.05). Remarkably, expression of 51% (76/150) of the nonadditively accumulated proteins exceeded the high parent or was below the low parent. ESI-MS/MS identified 75 of the 76 proteins that belonged to these expression classes. The most abundant functional classes among the 75 proteins that were encoded by 60 different genes were metabolism (58%) and disease and defense (19%). Nonadditive protein accumulation in primary roots of maize hybrids might be associated with heterosis manifestation. Identification of these proteins could therefore contribute to the better understanding of the molecular basis of heterosis.     

Proteomic analysis of colonic mucosa in a rat model of irritable bowel syndrome

Irritable bowel syndrome (IBS) is one of the most common functional disorders of the gastrointestinal tract. It is characterized by abdominal pain and changes in bowel habits. Various studies have investigated the pathophysiologic processes underlying IBS, but the mechanism remains poorly understood. In the present study, we established an IBS model and identified differentially expressed proteins in colon tissue of IBS rats compared with healthy controls by 2‐D gel electrophoresis, MALDI‐TOF‐MS, and Western blot analysis. Our results showed that 13 of the 1396 protein spots on 2‐D gel were differently expressed between the IBS and control groups. Ontological analysis of these proteins revealed primary roles in catalytic activity (protein disulfide‐isomerase A3, glyoxalase I, cathepsin S, α‐enolase), structural support (cytokeratin 8), antioxidant activity (peroxiredoxin‐6), protein binding (transgelin, serpin peptidase inhibitor B5), and signal transduction (40S ribosomal protein SA). Protein disulfide‐isomerase A3 and cytokeratin 8 overexpression in IBS were confirmed by Western blot. The findings indicate that multiple proteins are involved in IBS processes that influence intestinal tract immunity, inflammation, and nerve regulation. Our study provides useful candidate genes and proteins for further investigation.     

玉米杂种与亲本穗分化期功能叶基因差异表达与杂种优势

为探讨玉米杂种优势的分子机理,以10个玉米自交系及其组配的38个杂交种为材料,利用cDNA-AFLP技术,分析杂种与亲本在玉米雌穗小穗分化期功能叶片的基因差异表达类型与主要农艺性状的杂种表现及杂种优势的关系。研究表明：（1）杂种的基因相对于其双亲,存在质和量的表达差异,其中质的差异表达类型包括：单亲沉默表达,双亲沉默表达,亲本显性表达和杂种特异表达等类型。（2）在雌穗小穗分化期,同一差异表达类型中不同杂交组合间差异很大;从总体平均看,杂种特异表达类型占25.22%,亲本显性表达类型占21.46%,双亲沉默表达类型占8.27%,单亲沉默表达类型占33.49%。（3）单亲沉默表达与株高的杂种表现呈显著正相关;双亲沉默表达与穗粗的杂种优势呈显著负相关,显性表达与行粒数和单株粒重的杂种优势呈显著负相关,其余表达类型与所有农艺性状杂种表现及杂种优势均不相关,并对结果进行了讨论。     

Identification of Indica rice chromosome segments for the improvement of Japonica inbreds and hybrids

Exploitation of heterosis has brought significant advance in plant breeding and agricultural production, although its genetic basis is still poorly understood. In this study, a total of 66 chromosome segment substitution (CSS) lines, derived from a cross between japonica rice inbred line Asominori (as the recurrent parent) and indica rice inbred line IR24 (as the donor parent), were used to investigate the genetic basis of heterosis in indica × japonica inter-subspecific rice hybrids. Each CSS line was crossed with the background parent Asominori, and the heterosis of F(1) hybrids was estimated by comparing the F(1) performance with its two parental lines. Field experiments were carried out across six different environments to evaluate yield and yield-related traits in the 66 CSS lines and their 66 corresponding F(1) hybrids. Quantitative trait loci (QTL) analyses were conducted using a likelihood ratio test based on the stepwise regression. Thirty-six QTL were identified with significant effects in CSSL, 21 with significant effects in hybrids and 13 with significant effects in both. On the basis of average dominance degree, of all the 70 QTL affecting yield-related agronomic traits, 28.6% (20) showed an overdominance, 35.7% (25) a partial dominance and 30% (21) an additive effect, indicating that all effects contribute to trait variation in japonica-indica rice hybrids. Effects of these QTL were examined to identify Indica rice chromosome segments of interest for the improvement of japonica inbred lines and hybrids.     

A low molecular weight proteome comparison of fertile and male sterile 8 anthers of Zea mays

During maize anther development, somatic locular cells differentiate to support meiosis in the pollen mother cells. Meiosis is an important event during anther growth and is essential for plant fertility as pollen contains the haploid sperm. A subset of maize male sterile mutants exhibit meiotic failure, including ms8 (male sterile 8) in which meiocytes arrest as dyads and the locular somatic cells exhibit multiple defects. Systematic proteomic profiles were analysed in biological triplicates plus technical triplicates comparing ms8 anthers with fertile sibling samples at both the premeiotic and meiotic stages; proteins from 3.5 to 20 kDa were fractionated by 1‐D PAGE, cleaved with Lys‐C and then sequenced using a LTQ Orbitrap Velos MS paradigm. Three hundred and 59proteins were identified with two or more assigned peptides in which each of those peptides were counted at least two or more times (0.4% peptide false discovery rate (FDR) and 0.2% protein FDR); 2761 proteins were identified with one or more assigned peptides (0.4% peptide FDR and 7.6% protein FDR). Stage‐specific protein expression provides candidate stage markers for early anther development, and proteins specifically expressed in fertile compared to sterile anthers provide important clues about the regulation of meiosis. 49% of the proteins detected by this study are new to an independent whole anther proteome, and many small proteins missed by automated maize genome annotation were validated; these outcomes indicate the value of focusing on low molecular weight proteins. The roles of distinctive expressed proteins and methods for mass spectrometry of low molecular weight proteins are discussed.     

Comparative proteomic analysis reveals similar and distinct features of proteins in dry and wet stigmas

Angiosperm stigma supports compatible pollen germination and tube growth, resulting in fertilization and seed production. Stigmas are mainly divided into two types, dry and wet, according to the absence or presence of exudates on their surfaces. Here, we used 2DE and MS to identify proteins specifically and preferentially expressed in the stigmas of maize (Zea Mays, dry stigma) and tobacco (Nicotiana tabacum, wet stigma), as well as proteins rinsed from the surface of the tobacco stigma. We found that the specifically and preferentially expressed proteins in maize and tobacco stigmas share similar distributions in functional categories. However, these proteins showed important difference between dry and wet stigmas in a few aspects, such as protein homology in "signal transduction" and "lipid metabolism," relative expression levels of proteins containing signal peptides and proteins in "defense and stress response." These different features might be related to the specific structures and functions of dry and wet stigmas. The possible roles of some stigma-expressed proteins were discussed. Our results provide important information on functions of proteins in dry and wet stigmas and reveal aspects of conservation and divergence between dry and wet stigmas at the proteomic level.     

Cis-transcriptional variation in maize inbred lines B73 and Mo17 leads to additive expression patterns in the F1 hybrid

Microarray analysis of gene expression patterns in immature ear, seedling, and embryo tissues from the maize inbred lines B73 and Mo17 identified numerous genes with variable expression. Some genes had detectable expression in only one of the two inbreds; most of these genes were detected in the genomic DNA of both inbreds, indicating that the expression differences are likely caused by differential regulation rather than by differences in gene content. Gene expression was also monitored in the reciprocal F1 hybrids B73xMo17 and Mo17xB73. The reciprocal F1 hybrid lines did not display parental effects on gene expression levels. Approximately 80% of the differentially expressed genes displayed additive expression patterns in the hybrids relative to the inbred parents. The approximately 20% of genes that display nonadditive expression patterns tend to be expressed at levels within the parental range, with minimal evidence for novel expression levels greater than the high parent or less than the low parent. Analysis of allele-specific expression patterns in the hybrid suggested that intraspecific variation in gene expression levels is largely attributable to cis-regulatory variation in maize. Collectively, our data suggest that allelic cis-regulatory variation between B73 and Mo17 dictates maintenance of inbred allelic expression levels in the F1 hybrid, resulting in additive expression patterns.     

Nonadditive protein accumulation patterns in Maize (Zea mays L.) hybrids during embryo development

Heterosis describes the superior performance of heterozygous F(1)-hybrid plants compared to their homozygous parental inbred lines. In the present study, heterosis was detected for length, weight, and the time point of seminal root primordia initiation in maize (Zea mays L.) embryos of the reciprocal F(1)-hybrids UH005xUH250 and UH250xUH005. A two-dimensional gel electrophoresis (2-DE) proteome survey of the most abundant proteins of the reciprocal hybrids and their parental inbred lines 25 and 35 days after pollination revealed that 141 of 597 detected proteins (24%) exhibited nonadditive accumulation in at least one hybrid. Approximately 44% of all nonadditively accumulated proteins displayed an expression pattern that was not distinguishable from the low parent value. Electrospray ionization-tandem mass spectrometry (ESI-MS/MS) analyses and subsequent functional classification of the 141 proteins revealed that development, protein metabolism, redox-regulation, glycolysis, and amino acid metabolism were the most prominent functional classes among nonadditively accumulated proteins. In 35-day-old embryos of the hybrid UH250xUH005, a significant up-regulation of enzymes related to glucose metabolism which often exceeded the best parent values was observed. A comparison of nonadditive protein accumulation between rice and maize embryo data sets revealed a significant overlap of nonadditively accumulated proteins suggesting conserved organ- or tissue-specific regulatory mechanisms in monocots related to heterosis.     

Proteomic Analysis Demonstrates that Elongation of Below-Ear Internodes in Maize is Related to Three Different Hormones

In many grain crops, the length of internodes below ears is related to lodging resistance in the field. To clarify the relationship between internode morphological differentiation and internode proteins during primary elongation stages in maize (Zea mays L.), we used proteomics analysis to explore factors regulating internodes in eight elite inbred maize lines: Zong3, Yu87-1, Xun9058, Xun928, Chang7-2, Zheng58, P2, and A50—the parents of four commercial hybrids in China (Yuyu22, Xundan20, Zhengdan958, and Jinsai6850). A total of 66 protein spots corresponding to 48 non-redundant proteins were identified in developing seventh to ninth leaf internodes. Of these spots, seven spots corresponding to six non-redundant proteins were related to the gibberellin (GA) pathway. Nineteen protein spots corresponding to 13 non-redundant proteins were related to the auxin (IAA) pathway, and 31 protein spots corresponding to 20 non-redundant proteins were associated with ethylene biosynthesis. A correlation analysis revealed that GA and IAA contents are negatively correlated with internode length, with the first hormone more strongly length-correlated than the second.     

Distinctive expression and functional regulation of the maize (Zea mays L.) TOR kinase ortholog

TOR (Target of rapamycin) kinase is a central component of a signal transduction pathway that regulates cellular growth in response to nutrients, mitogens and growth factors in eukaryotes. Knowledge of the TOR pathway in plants is scarce, and reports in agronomical relevant plants are lacking. Previous studies indicate that Arabidopsis thaliana TOR (AtTOR) activity is resistant to rapamycin whereas maize TOR (ZmTOR) is not, suggesting that plants might have different regulation mechanisms for this signal transduction pathway. In the present work maize ZmTOR cDNA was identified and its expression regulation was analyzed during germination on different tissues at various stages of differentiation and by the main ZmTOR regulators. Our results show that ZmTOR contains all functional domains characteristic of metazoan TOR kinase. ZmTOR expression is highly regulated during germination, a critical plant development period, but not on other tissues of contrasting physiological characteristics. Bioinformatic analyses indicated that maize FKBP12 and rapamycin form a functional structure capable of targeting the ZmTOR protein, similar to other non-plant eukaryotes, further supporting its regulation by rapamycin (in contrast with the rapamycin insensitivity of Arabidopsis thaliana) and the conservation of rapamycin regulation through plant evolution.     

Effects of S-Abscisic Acid (S-ABA) on Seed Germination,Seedling Growth,and Asr1 Gene Expression Under Drought Stress in Maize

The objective of this study was to evaluate the ability of the phytohormone S-abscisic acid (S-ABA) to protect maize seedlings grown under drought stress and to measure their increased drought tolerance. The maize hybrids ‘Zhengdan 958’ (ZD958; drought tolerant) and ‘Xundan 20’ (XD20; drought sensitive) were treated with nutrient solutions of different concentrations (1, 2, 4, 8, and 10 mg/kg) of S-ABA under polyethylene glycol (PEG, 15% w/v, MW 6000) simulated drought stress. Optimal concentrations of S-ABA were designed to be sprayed onto the leaves of seedlings, and their effect on endogenous ABA, malondialdehyde (MDA), osmotic substances, antioxidant enzyme activities, and Asr1 gene expression in seedlings were studied. Results indicated that, under drought stress, S-ABA treatment significantly improved maize seed germination rate (GR), germination energy (GE), and seedling biomass (p < 0.05). After spraying 4 mg/kg S-ABA onto leaves, the endogenous hormone ABA, osmotic substances, antioxidant enzyme activities, and expressive quantity of the Asr1 gene were extended and MDA content dropped significantly (p < 0.05). Moreover, ZD 958 endogenous ABA content, osmotic substances content, antioxidant enzyme activity and Asr1 gene expressive quantity were higher than that of XD 20 (p < 0.05). In conclusion, S-ABA treatment increased the content of endogenous ABA, induced an increase in antioxidant enzyme activity and Asr1 gene expression level, reduced the oxidative damage caused by drought to maize leaves, and improved the adaptability of maize seedlings to withstand drought stress. The promoting effect of S-ABA on the drought-tolerant variety ZD 958 was more obvious (p < 0.05). These results serve as a reference for the use of S-ABA in mitigating drought stress in maize.