Soybean oil content QTL mapping and integrating with meta-analysis method for mining genes

Oil content of soybean was a valuable quantitative trait controlled by multiple genes. Eleven QTLs were detected by both CIM and MIM method with the population crossed between Charleston and Dong nong594 in recent 3 years (2007, 2008, 2009). Combining the QTLs collected over the past 20 years, an integrated map of oil-content major QTLs in soybean was established using soymap2, which was published in 2004, as a reference. Using the software BioMercator ver.2.1, QTLs were projected from their own maps onto the reference map. In total, ninety-eight QTLs were integrated into soymap2. A meta-analysis method was used to narrow down the confidence interval, and 20 consensus QTLs and their corresponding markers were obtained. Using a local version of GENSCAN, 10,137 sequences in the consensus QTL intervals were predicted. With BLAST, these predicted genes were compared to the International Protein Index database to mine the related genes. The results offer a basis for gene mining and molecular breeding in soybean.     

Developmental expression of glutathione-S-transferase in maize and its possible connection with herbicide tolerance

Summary Crop improvement for tolerance to specific herbicides is an important breeding target, since molecules performing well with regard to environmental safety are frequently not completely selective for crops. The glutathione (GSH)/glutathione-S-transferase (GST) system is a general mechanism of detoxification that in higher plants may confer tolerance to some herbicides. GSH level and GST activity were measured in different maize inbred lines, in the absence or in the presence of EPTC (a thiocarbamate) and of Alachlor (a chloroacetanilide); a wide genetic variability was observed for these parameters, which appear to be involved in plant tolerance to herbicides. Isozyme analysis was performed on roots, leaves, scutellum, pollen, coleoptile, mesocotyl of the same inbreds: it revealed the presence of many GST forms in maize, showing high polymorphism; they are controlled by at least five genes, the expression of which is developmentally regulated in the different tissues analyzed.     

玉米HD-ZIP I亚家族基因鉴定及表达分析

转录因子是植物响应逆境胁迫的重要调节因子,在其整个生长发育过程中发挥着重要的作用。HD-ZIP家族蛋白是植物中特有的一大类转录因子,包含4个亚家族(HD-ZIP I～IV),其中HD-ZIP I亚家族成员主要参与干旱、渗透压等极端环境和ABA及乙烯等激素处理的响应过程。本文采用隐马可夫模型(HMM)在玉米参考基因组中鉴定到17个HD-ZIP I亚家族成员,这些基因不均匀分布于玉米6条染色体上,与水稻的亲缘关系要近于拟南芥。玉米HDZIP I亚家族基因在玉米7种组织中表现出多种表达模式,具有明显的组织表达特异性。另外, HD-ZIP I亚家族基因对高盐、淹水及冷害等不同的逆境胁迫处理呈现出不同的响应模式及响应程度差异。5种不同激素处理后,玉米HD-ZIP I亚家族基因也表现出复杂的响应模式。这些结果为进一步解析玉米HD-ZIP I亚家族基因的生物学功能和作用机理提供了一定的参考价值。     

Meta-analysis of constitutive and adaptive QTL for drought tolerance in maize

The response of plants to drought stress is very complex and involves expression of a lot of genes and pathways for diverse mechanisms and interactions with environments. Many quantitative trait loci(QTL) mapping experiments have given heterogeneous results due to use of different genotypes and populations tested in various environments. Our purpose was to identify some important constitutive and adaptive QTL using meta-analysis and to find specific genes and their families for speculating on drought tolerance networks. A total of 239 QTL detected under water-stressed conditions and 160 detected under control conditions from 12 populations tested in 22 experiments were compiled and compared, resulting in identification of 39 consensus QTL under water stress, and 36 under control conditions. Of them, 32 consensus QTL were supposed to be adaptive while others were constitutive QTL. The consensus QTL on chromosomes 1, 2, 3, 5, 6 and 9 were highly overlapped with several different traits and could be identified under multiple environments, most of which were related to traits of high phenotypic variance. Moreover, 48 candidate genes related to stress tolerance were located in silico in these consensus QTL regions what should facilitate the construction of QTL networks and help to understand the mechanisms related to drought tolerance.     

Phenotypic assessment of genetic gain from selection for improved drought tolerance in semi-tropical maize populations

Most maize production across the globe is rain-fed, and production is set to be negatively impacted as duration and occurrence of droughts increases due to climate change. Development of water-deficit tolerant maize germplasm has been a major focus for most breeding programmes. Here, we sought to assess the genetic gain for grain yield in two maize populations developed for drought tolerance at CIMMYT by evaluating their cycle progeny through hybrid performance. Inbreds derived from different cycles of the Drought Tolerant Population (DTP) and La Posta Sequia (LPS) were mated to a tester (CML550), and resulting hybrids were evaluated under managed water-deficit stress and well-watered conditions. The difference in yield between water-deficit and well-watered treatments was 27% and 36% for the DTP and LPS, respectively. Genetic gain for grain yield across cycles for the two populations was confirmed in the study. Genetic gain was observed for both treatments indicating that selection for water-deficit stress tolerance simultaneously improves grain yield in well-watered conditions. The DTP population had a genetic gain of 0.07 t ha⁻¹ cycle⁻¹, while the LPS had 0.16 t ha⁻¹ cycle⁻¹ under water-deficit conditions. Significant genetic gain was also observed in the well-watered treatments for both populations. Anthesis to silking interval was significantly reduced under water-deficit stress conditions in both populations. Plant and ear height were reduced in the LPS population in both treatments, while no reductions were observed for the trait in the DTP population. Potential water-deficit stress tolerance donor lines with yields comparable to commercial check varieties were identified.     

Mass selection for improved cold and density tolerance of two maize populations

Summary Data of planting and plant density are two cultural practices influencing grain yield of maize (Zea mays L.). Our study was designed to evaluate the usefulness of a mass selection scheme to improve cold and density tolerance of the BS2 and BS3 maize populations. Populations were planted at an early planting date and a high plant density, and three cycles of mass selection for well-filled ears on erect plants were conducted at earch of three Corn Belt locations (i.e., Waseca, MN; Ames, IA; Portageville, MO).Results showed that selection improved cold tolerance traits of BS3, but not of BS2. Mass selection did not increase density tolerance of either population at any location. Selection did not improve response to planting dates, although the early planting date did improve agronomic performance and grain yield of all entries. We concluded that mass selection at high plant densities and early planting dates at diverse geographical locations did not produce cycles adapted to specific environmental conditions.     

Genotype by environment effects and selection for drought tolerance in tropical maize. II. Three-mode pattern analysis

A selection program in three tropical maize populations aimed to improve tolerance of mid-season to late season drought environments while maintaining grain yield (GY) potential. The selection process employed other attributes that included maintaining a constant anthesis date (AD) and, under drought, shortening the anthesis-silking interval (ASI) and increasing ear number per plant (EPP). Three-mode (genotypes × environments × attributes) pattern analysis, which consists of clustering and ordination, should be able to collectively interpret these changes from ten evaluation trials. Mixture maximum likelihood clustering identified four groups that indicated the populations' performance had changed with selection. Groups containing the advanced cycles of selection were higher yielding in most environments and had lower ASI and higher EPP, particularly in drought environments. Check entries with no selection for drought tolerance remained grouped with the initial cycles of selection. A 3 × 2 × 3 (genotypes by environments by attributes) principal component model explained 70% of the variation. For the first environmental component, ASI was shown to be highly negatively correlated with both GY and EPP while anthesis date (AD) was virtually uncorrelated with other traits. The second environmental component (explaining 10% of the variation) contrasted droughted and well-watered environments and showed that EPP and GY were better indicators of this contrast (in terms of changes in population performance) than were AD or ASI. Three-mode analysis demonstrated that improvements with selection occurred in both droughted and well-watered environments and clearly summarised the overall success of the breeding program. This revised version was published online in July 2006 with corrections to the Cover Date.     

Characterization of correlation between grain moisture and ear rot resistance in maize by QTL meta-analysis

Ear rot (ER) in maize is a prevalent disease worldwide which reduces yield and grain quality. Grain moisture content (GM) is an important factor which impacts the fungal development of ER species. Our purpose was to identify the genomic regions of maize in the control of GM and ER resistance, and the correlations between two traits. A meta-analysis was carried out using 241 quantitative trait loci (QTL) from 29 studies to propose meta-QTL (MQTL) on a high-density genetic linkage map (IBM 2 neighbors 2008). For GM content, 44 MQTL were identified on all chromosomes except for chromosome 9, while 29 MQTL were found for ER resistance, mainly located on chromosomes 3, 6 and 7. Moreover, 14 overlapping domains for GM MQTL and ER MQTL were observed on chromosomes 2, 3, 6 and 7, mainly focused on five active regions (bins 2.08–2.09, 3.04, 3.06, 6.04–6.06 and 7.03–7.03). There were 13 genes in the overlapping domain which could be divided into five classes: stress-related gene, photosystem-related gene, architecture-related gene, dynamic-related gene and seminal-related gene. It was possibly that the five-class genes were simultaneously related with GM and ER.     

玉米不同氮素水平下产量与zmAspAT基因表达分析

研究不同氮素水平下导入系L18和Y478产量及相关性状的差异以及与zmAspAT基因表达模式的关系。考察L18和Y478在低氮和正常供氮条件下的产量及相关性状,利用实时定量PCR技术分析zmAspAT基因的表达变化。在正常供氮条件下L18的单穗产量比Y478高17.21%,显著增加,行粒数极显著增加,百粒重显著减小;低氮条件下,L18单穗粒重比轮回亲本Y478显著减少,达到20.64%,行粒数显著增加,百粒重极显著减小。在低氮胁迫条件下,zmAspAT基因在L18中下调表达,在Y478则上调表达,表达模式不同。L18是氮低效的导入系,由于zmAspAT基因在L18与Y478表达模式不同,导致了L18较低的氮素利用效率和产量,zmAspAT是重要的玉米氮利用效率基因。     

玉米耐深播主效QTL qMES20-10的精细定位及差异表达基因分析

干旱是影响玉米(ZeamaysL.)产量最主要的环境因素之一,具有耐深播特性的玉米种质材料能够吸收土壤深层水分,具有较强的耐旱性,因此研究玉米耐深播性状的遗传机制具有重要的理论和应用价值。本实验室前期已利用耐深播玉米自交系3681-4与普通自交系X178构建的F_2:3群体,在玉米10号染色体上定位到了一个耐深播主效QTLqMES20-10。本研究在此基础上,以X178为轮回亲本,结合前景选择和背景选择,构建了BC₃F_3:4家系,对qMES20-10迚行了确证;幵迚一步利用分子标记辅助选择构建了高代回交群体,将其精细定位于133.3～136.0Mb的区间之内。同时,利用从BC₃F_3:4家系中筛选出的两个近等基因系,迚行差异表达基因分析,发现差异表达基因主要参与了化学性应激反应、氧化还原反应和对氧化胁迫的应激反应。本研究结果为迚一步兊隆耐深播主效QTL qMES20-10奠定了基础。     

Allele mining and haplotype discovery in barley candidate genes for drought tolerance

In the present study, allele mining was conducted on a panel of drought related candidate genes in a set of 96 barley genotypes using EcoTILLING, which is a variant of the targeting induced local lesions in genomes (TILLING) technology. Analyzing approximately 1.5 million basepairs in barley a total number of 94 verified unique haplotypes were identified in 18 amplicons designed for 9 genes. Overall, 185 single nucleotide polymorphisms (SNPs) and 46 insertions/deletions (INDELs) were detected with a mean of 1SNP/92 bp and 1INDEL/372 bp genomic sequence. Based on overlapping haplotype sequences, markers were developed for four candidate genes (HvARH1, HvSRG6, HvDRF1, HVA1), which allows distinguishing between the main haplotypes showing either differences in amino acid sequence or which have larger INDELs in the promoter region. As “proof of concept”, the HvARH1 and HvSRG6 haplotypes were tested for the level of abscisic acid-induced gene expression in subsets of genotypes belonging to different haplotype categories. An integrated database was developed to contain information about the genes, genotypes, and haplotypes analyzed in this study. The database supplies profound information about the natural variation in the tested drought related candidate genes providing a significant asset for further mapping studies dealing with this highly polygenic trait.     

Genetically manipulated pineapple: transgene stability, gene expression and herbicide tolerance under field conditions

Pineapple plants transformed with the bar gene for bialaphos resistance were evaluated for transgene stability, gene expression and tolerance to glufosinate ammonium, the active ingredient of the herbicide Basta^® X, under field conditions. Genetically modified plants of the cv. Phuket were micropropagated, rooted and established in a shade house before transfer to an experimental plot. Seven months after transfer to the field, plants were tolerant to 1600 ml/rai of the herbicide Basta^® X (stock concentration 15% w/v glufosinate ammonium), this being twice the dose recommended for field application of the herbicide. Genetically modified plants remained green and healthy following spraying with the herbicide. In contrast, non‐transformed pineapple plants of the same cv. became necrotic and died within 21 days of spraying with the herbicide at a reduced concentration of 800 ml/rai. Bar gene stability and expression in clonally‐derived plants were assessed by PCR, RT‐PCR and Southern analyses at 120, 210, 240, 270 and 380 days following transfer of the plants to the field. The bar gene was stable and expressed in transgenic plants throughout the duration of the trial. Fruit characteristics and yield were not affected by transgene introduction and expression. Transgenic plants tolerant to glufosinate ammonium should facilitate more effective weed control in pineapple plantations without damage to the crop.     

Variation among Andean races of maize for cold tolerance during heterotrophic and early autotrophic growth

Cold in the initial growth stages is an important stressfactor for maize grown in regions with a temperate climate,particularly in case of early sowing. Sources of tolerancehave been identified in adapted genotypes, but promisinggenes for cold tolerance should also be found in materialdeveloped under the lower-temperature margins of the cropdistribution. This research was conducted in order to testAndean maize accessions for cold tolerance expressed duringboth the heterotrophic and early autotrophic growth stages.Experiments were conducted in controlled environments tostudy cold tolerance traits (germination %, germinationindex and plant growth rate) at continuous 10^°C (heterotrophic growth) and at varying 10–16^°C (autotrophic growth). An experiment was also performed inthe field with early sowing (both heterotrophic and autotrophic growth). In each experiment, a control trialwas conducted in more favourable conditions (i.e. continuous25^°C in a controlled environment or late planting inthe field) so that cold tolerance traits could also beexamined as the ratio between the stress and the controltrial. None of the accessions was superior for all coldtolerance traits. However, several Andean maize accessionsoutperformed the US Corn-belt hybrid checks for one or moretraits, both in heterotrophic and autotrophic growth. Overall, BOZM 855, PMS 636, Poblacion D, Poblacion E andBOZM 696 were the best accessions, suggesting that they canbe a promising source of genes for improving cold toleranceof adapted maize genotypes.     

Screening for frost tolerance in wheat using the expression of dehydrine genes Wcs120 and Wdhn13 at 17°C

Cold induces expression of Cor/Lea genes, in particular of Wcs120 and Wdhn13 . The level of the expression at low temperatures was related to the frost tolerance (FT) of wheat cultivars. We studied the expression in five cultivars very different in the FT, at relatively high temperature of 17 and 25°C, respectively. Significant correlations at the 1% level were found at 17°C between the expression level and FT, characterized by correlation coefficients 0.92** and 0.97** for Wcs120 and Wdhn13 , respectively. These preliminary results could be used for screening of frost tolerant lines.     

The genetic architecture of zinc and iron content in maize grains as revealed by QTL mapping and meta-analysis

Micronutrient malnutrition, especially zinc (Zn) and iron (Fe) deficiency in diets, has aroused worldwide attention. Biofortification of food crops has been considered as a promising approach for alleviating this deficiency. Quantitative trait locus (QTL) analysis was performed to dissect the genetic mechanism of Zn and Fe content in maize grains using a total of 218 F_2:3 families derived from a cross between inbred lines 178 and P53. Meta-analysis was used to integrate genetic maps and detect Meta-QTL (MQTL) across several independent QTL researches for traits related to Zn or Fe content. Five significant QTLs and 10 MQTLs were detected. Two informative genomic regions, bins 2.07 and 2.08, showed a great importance for Zn and Fe content QTLs. The correlation between Zn and Fe level in maize grains was proposed by MQTLs as 8 of the 10 involved both traits. The results of this study suggest that QTL mapping and meta-analysis is an effective approach to understand the genetic basis of Zn and Fe accumulation in maize grains.     

Genotype by environment effects and selection for drought tolerance in tropical maize. I. Two mode pattern analysis of yield

Ten trials evaluated the performance of several late tropical maize populations (La Posta Sequía, Pool 26 Sequía and Tuxpeño Sequía) selected for tolerance to drought during flowering and grain filling and also for yield potential. Families (S₁ or full-sib) had been selected recurrently for six to eight years on an index of traits. Pattern (clustering and ordination) analysis was used to analyse the relative performance of entries that included cycles of selection for drought tolerance in the populations and non-drought tolerant checks. Mean environment (E) yields ranged from 1.0 to 10.4 t ha^-1. Analysis of variance showed that 97.9% of the total sums of squares was accounted for by E, and that, of the remaining sums of squares the G × E (genotype by environment interaction) was almost 3 times that of the contribution of G alone. Cluster analysis separated the checks, the earlier maturing drought tolerant entries and the later maturing drought tolerant entries. This was verified by principal component (PC) analysis of the G × E matrix. Grouping of the environments (i.e. based on entry performance), resulted in the separation of different types of droughts, and of medium and high yielding well-watered environments. The patterns of discrimination observed indicated that the yield gains under drought would have been unlikely to occur if selection had been done only in well-watered environments. Within each population, selection improved broad adaptation (higher mean yield) to both drought and well-watered environments and cycles of selection ‘jumped’ from non-drought-tolerant to drought-tolerant groups as their specific adaptation to drought environments increased.     

Detection of candidate R genes and single nucleotide polymorphisms for downy mildew resistance in maize inbred lines by association analysis

Downy mildew (DM) is a plant disease that strongly limits maize production. The resistance (R) genes for this disease have been identified and characterized and serve as important tools for plant disease evaluation. In this study, partial genes for PIC15, PO145579, and zmcf5 were identified and analyzed in a panel of 60 public and private maize inbred lines using bioinformatics and statistics tools. These candidate R genes exhibited an average nucleotide diversity value of 0.015. The negative Tajima’s D values for these genes suggested that purifying selection has played a role in the evolution of maize DM resistance genes. In addition, linkage disequilibrium among these genes occurred across an extent of ~ 200 bp. Using association analysis methods, a general linear model, and a mixed linear model, five polymorphisms within the partial PIC15 and PO145579 genes were detected and associated with DM disease. These are new polymorphisms that have not previously been reported in association with DM disease traits. Therefore, correlations between these new polymorphisms and DM disease in these germplasm collections could advance the development of a functional marker for marker-assisted selection of DM disease resistance in maize breeding programs.