Isolation of mitochondrial DNA from cytoplasmic male sterile and maintainer lines of pearl millet,Pennisetum americanum (L.) Leeke

Summary Mitochondrial DNA has been isolated from paired lines of pearl millet maintainer and cytoplasmic male sterile plants. Evaluation of the DNA by agarose gel electrophoresis shows that good quality DNA of high molecular weight can be obtained from mitochondria of both maintainer and male sterile pearl millet.     

Synthesis of Ogura male sterile rapeseed (Brassica napus L.) with cold tolerance by protoplast fusion and effects of atrazine resistance on seed yield

Twenty-one cold-tolerant, male sterile Brassica napus somatic hybrids were produced by protoplast fusion. The fusion partners were a coldsensitive, Ogura cytoplasmic male sterile cauliflower inbred (B. oleracea var. botrytis inbred NY7642A) and a cold-tolerant, fertile canola-type B. rapa cv. Candle. Hybridity was confirmed by morphology, isozyme expression, flow cytometry, and DNA hybridization. Organellar analyses revealed a very strong bias for Brassica over Raphanus chloroplasts. Cold tolerance was confirmed by cold chamber studies and chloroplast DNA analyses. Good female fertility with 21.4 ± 3.1 seeds/pod was observed in the field using natural pollination vectors. Total seed yield was significantly greater for the atrazine-sensitive somatic hybrids produced in this study than for atrazine-resistant isolines.Abbreviations CMS cytoplasmic male sterility - IA iodoacetate - cpDNA chloroplast DNA     

Comparative analysis of the chloroplast proteomes of a wheat (Triticum aestivum L.) single seed descent line and its parents

To understand the photosynthetic basis in a single seed descent line 10 (SSDL10) of wheat contained high ATP in leaves, the chloroplast proteome was compared to SSDL10 and its parents using a combination of 2-DE and MALDI-TOF MS and MS/MS. More than 300 protein spots could be reproducibly detected in the 2D gel. 18 spots were differentially expressed between SSDL10 and the parents, 16 of which were identified by MS with the localization in chloroplasts. These proteins are grouped into diverse functional categories, including Calvin cycle and electron transport in photosynthesis, redox homeostasis, metabolism, and regulation. In addition to Rubisco large subunit, the content of photosynthetic electron transfers such as chlorophyll a-b binding protein, ATP synthase δ subunit, ferredoxin-NADP⁺ oxidoreductase (FNR) was higher in SSDL10 than in its parents. Furthermore, cyclic electron transfer around photosystem I (CET) was faster in SSDL10 than in the parents. Analysis of NADPH-NBT oxidoreductase activity combined with immuno-detection further revealed that, the activity of two high molecular mass protein complexes containing FNR probably involved, the CET appeared higher in SSDL10 than in the parents. The possible mechanism for the regulative role of CET in photosynthesis in SSDL10 is discussed.     

胞质雄性不育白菜叶绿体ndhJ-trnF区域序列发生变异

以来自Polima胞质甘蓝型油菜雄性不育源转育获得的不育白菜‘Bpol97-05A’和其回交亲本即保持系‘Bajh97-01B’为材料，利用cDNA扩增片段长度多态性(cDNA-AFLP)技术获得一条长约330 bp的特异片段P1708，RT-PCR验证确认该序列为不育白菜材料所特有，经测序和BLAST比对，发现该片段除54 bp的插入序列外，其余部分与大白菜和甘蓝叶绿体ndhJ-trnF基因之间的一段序列完全一致. 根据基因区域两端的保守部位设计引物，以Polima不育白菜DNA和可育甘蓝型油菜的DNA为模板，分别获得了长约1 900 bp的序列，比较序列发现：不育白菜与可育白菜、甘蓝型油菜的DNA序列存在一定差异，‘Bpol97-05A’中除多个位点发生变异外，另有108 bp的插入序列，该插入由2个长度为54 bp的重复序列组成，重复序列中除5′端3个碱基CTT外，其余部分均与trnF基因3′端51 bp完全相同.     

Comparative analysis of mitochondrial genomes between the hau cytoplasmic male sterility (CMS) line and its iso-nuclear maintainer line in Brassica juncea to reveal the origin of the CMS-associated gene orf288

Background

Cytoplasmic male sterility (CMS) is not only important for exploiting heterosis in crop plants, but also as a model for investigating nuclear-cytoplasmic interaction. CMS may be caused by mutations, rearrangement or recombination in the mitochondrial genome. Understanding the mitochondrial genome is often the first and key step in unraveling the molecular and genetic basis of CMS in plants. Comparative analysis of the mitochondrial genome of the hau CMS line and its maintainer line in B. juneca (Brassica juncea) may help show the origin of the CMS-associated gene orf288.

Results

Through next-generation sequencing, the B. juncea hau CMS mitochondrial genome was assembled into a single, circular-mapping molecule that is 247,903 bp in size and 45.08% in GC content. In addition to the CMS associated gene orf288, the genome contains 35 protein-encoding genes, 3 rRNAs, 25 tRNA genes and 29 ORFs of unknown function. The mitochondrial genome sizes of the maintainer line and another normal type line “J163-4” are both 219,863 bp and with GC content at 45.23%. The maintainer line has 36 genes with protein products, 3 rRNAs, 22 tRNA genes and 31 unidentified ORFs. Comparative analysis the mitochondrial genomes of the hau CMS line and its maintainer line allowed us to develop specific markers to separate the two lines at the seedling stage. We also confirmed that different mitotypes coexist substoichiometrically in hau CMS lines and its maintainer lines in B. juncea. The number of repeats larger than 100 bp in the hau CMS line (16 repeats) are nearly twice of those found in the maintainer line (9 repeats). Phylogenetic analysis of the CMS-associated gene orf288 and four other homologous sequences in Brassicaceae show that orf288 was clearly different from orf263 in Brassica tournefortii despite of strong similarity.

Conclusion

The hau CMS mitochondrial genome was highly rearranged when compared with its iso-nuclear maintainer line mitochondrial genome. This study may be useful for studying the mechanism of natural CMS in B. juncea, performing comparative analysis on sequenced mitochondrial genomes in Brassicas, and uncovering the origin of the hau CMS mitotype and structural and evolutionary differences between different mitotypes.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-322) contains supplementary material, which is available to authorized users.     

Cytoplasmic male sterility in hybrids of sterile wild beet (Beta vulgaris ssp. maritima) and O-type fertile sugar beet (Beta vulgaris L.): molecular analysis of mitochondrial and nuclear genomes

The organization of the mitochondrial genome of B3, B4 and B5generations of hybrids created by backcrossing sterile wild beet Betamaritima with a fertile O-type sugar beet line was studied usingrestriction fragment length polymorphism (RFLP) analysis. Random amplifiedpolymorphic DNA (RAPD) analysis was used to study restoration of the fertile(O-type) sugar beet genotype in hybrids after multiple backcrossings.Restriction of mtDNAs from the cytoplasm of B. maritimaandhybrids revealed BamHI, EcoRI andXhoI restriction patterns different from those for sterileand fertile sugar beet lines. The most conspicuous feature of our accession ofsterile wild beet mtDNA was the absence of the 10.7-kbEcoRI fragment detected in the cytoplasm of S-type sterileB. maritima and sugar beet. The hybridization of digestedmtDNAs with coxII, atpA andatp6 homologous probes revealed alterations within thesegene loci that distinguished wild beet and hybrids from sugar beets.Characteristic hybridization profiles for the wild beet and B3, B4 and B5hybrids were observed for all probes regardless of the restrictase used todigest mtDNA. Notable changes in atpA andatp6 genes resulted when probes that comprised the5flanking sequences of these genes and a small part of the coding sequences wereused. RFLP analysis of the sterile B. maritimamitochondrial genome further supported the unique character of this source ofwild beet sterility. The genotypic differences between hybrids and parentalaccessions were determined by scoring PCR-RAPD reaction products for nineselected primers. The diversity of the B. maritimagenotyperesulted in a lower genetic similarity index in comparison with hybrids,sterileand fertile lines of sugar beet. The dendrogram obtained after cluster analysisdistinguished hybrids as a group that differed from wild beet and themaintainersugar beet line used for backcrossing. These results may indicate incompleterestoration of the fertile sugar beet genotype in hybrids.     

Growth stage-based modulation in antioxidant defense system and proline accumulation in two hexaploid wheat (Triticum aestivum L.) cultivars differing in salinity tolerance

Changes in the antioxidant defense system and proline accumulation were examined at different growth stages (vegetative, boot and reproductive) in plants of two hexaploid spring wheat cultivars (S-24, salt tolerant; MH-97, salt sensitive), grown in hydroponics and salinity-affected with 0, 50, 100 and 150 mM of NaCl. Salt stress provoked a marked decline in plant dry mass and ascorbic acid contents, and increased proline, total soluble proteins and H₂O₂ contents in both wheat cultivars at all growth stages. However, higher accumulation of proline and H₂O₂ contents was recorded at the vegetative and boot stages, respectively, in both wheat cultivars. Salt stress caused a consistent rise in the activities of some key antioxidant enzymes (CAT, SOD, POD, and APX) at all growth stages only in the salt tolerant cultivar S-24, whereas such pattern of enhanced activities of enzymatic antioxidants in cv. MH-97 was found only at the vegetative stage under saline regimes. Maximum activities of various enzymatic antioxidants were observed at the vegetative stage in both wheat cultivars under varying external salt treatments. The results showed that high salinity tolerance of cv. S-24, as manifested by lower decrease in its dry matter under salt stress, was associated with higher activities of antioxidant enzymes, increased accumulation of proline, and lower levels of H₂O₂, as compared with cv. MH-97 at all growth stages under saline regimes.     

DNA methylation changes in photoperiod-thermo-sensitive male sterile rice PA64S under two different conditions

Epigenetic modification can occur at a high frequency in crop plants and might generate phenotypic variation without changes in DNA sequences. DNA methylation is an important epigenetic modification that may contribute to environmentally-induced phenotypic variations by regulating gene expression. Rice Photoperiod-Thermo-Sensitive Genic Male Sterile (PTGMS) lines can transform from sterility to fertility under lower temperatures and short-day (SD) conditions during anther development. So far, little is known about the DNA methylation variation of PTGMS throughout the genome in rice. In this study, we investigated DNA cytosine methylation alterations in the young panicles of PTGMS line PA64S under two different conditions using methylation sensitive amplified polymorphism (MSAP) method. Compared with the DNA methylation level of PA64S under lower temperatures and SD conditions (fertility), higher methylation was observed in PA64S (sterility). The sequences of 25 differentially amplified fragments were successfully obtained and annotated. Three methylated fragments, which are homologous to D2, NAD7 and psaA, were confirmed by bisulfite sequencing and their expression levels were also evaluated by qPCR. Real time quantitative PCR analysis revealed that five of the six selected methylated genes were downregulated in PA64S (sterility). These results suggested that DNA methylation may be involved in the sterility–fertility transition of PA64S under two different environmental conditions.     

盐胁迫下不同基因型冬小麦渗透及离子的毒害效应

以4种不同基因型冬小麦为试验材料,利用分根法研究了盐胁迫对小麦的渗透胁迫和离子毒害的效应。结果表明,在盐胁迫下,小麦既受渗透胁迫,也受盐离子胁迫。渗透胁迫效应比较快,大约在处理后1-2d内发生;离子毒害效应比较缓慢,大约需3-4d时间。在一半盐胁迫(200mmol/L NaCl)和一半非盐胁迫的分根条件下,小麦没有明显的渗透胁迫效应,小麦植株地上部Na⁺ 累积到毒性水平之前盐处理对小麦生长无抑制效应。小麦具有将Na⁺ 从盐胁迫一侧转移非盐一侧的能力,说明小麦吸收的Na⁺ 有一部分可以从地上部回流到根系中,回流率可达76%-89%。无水分胁迫(不加入PEG)的回流率大于水分胁迫(加入PEG)的回流率。不同基因型小麦在盐分吸收累积和回流,及渗透和离子胁迫的速度和程度等方面具有明显差异。NR 9405和小偃6号的Na⁺ 累积速度要少于陕229和RB 6;NR 9405根系排Na⁺ 能力强于陕229和RB 6。因此,NR 9405和小偃6号的耐盐性高于陕229和RB 6。     

The use of a Spacer DNA fragment insulates the tissue-specific expression of a cytotoxic gene (barnase) and allows high-frequency generation of transgenic male sterile lines in Brassica juncea L.

Male-sterile lines were generated in oilseed mustard (Brassica juncea) with a cytotoxic gene (barnase) in conjunction with either of two tapetum-specific promoters, TA29 and A9. Several transformation vectors based on different promoter and marker gene combinations were developed and tested for their efficacy in generating agronomically viable male-sterile lines. Use of strong constitutive promoters (e.g. CaMV 35S or its double-enhancer variant) to express the marker gene (bar) in barnase constructs generated male-sterile plants at an extremely low frequency with most plants showing abnormalities in vegetative morphology, poor female fertility, low seed germination frequencies and/or distortion in segregation ratios of transgenes. Such abnormalities were considerably reduced on using weaker promoters (e.g. nos) to drive the marker gene (nptII) in barnase constructs and could therefore be attributed to leaky expression of the barnase gene under enhancing effects of strong constitutive promoters. We show that the use of a Spacer DNA fragment between the barnase gene (driven by a tapetum-specific promoter) and the CaMV 35S promoter-driven bar gene insulates tissue-specific expression of the barnase gene over all developmental stages of transgenic plants and significantly enhances recovery of agronomically viable male-sterile lines. All TA29-barnase male-sterile lines containing the Spacer DNA fragment exhibited normal morphology, growth and seed set on backcrossing as observed for wild-type plants. Around 75% of single-copy events tested further also showed proper segregation of the marker gene/male-sterile phenotype among backcross progeny. Constructs based on the use of Spacer DNA fragments as insulators could be successfully used to alleviate limitations associated with transformation of plant systems using cytotoxic genes for development of agronomically viable male-sterile lines in crop plants and for cell/tissue ablation studies in general.     

小麦Ven型胞质雄性不育植株与可育植株花药蛋白质组差异研究

普通小麦具有偏凸山羊草（Ae. ventricosa）细胞质的不育系为Ven型胞质雄性不育系（Ven cytoplasmic male sterility, Ven CMS）,是粘类小麦CMS的一种类型。该研究对小麦Ven型雄性不育系冀5418A及其同型保持系冀5419B的单核期和二核期的花药进行差异蛋白质组学分析,探讨小麦质核互作雄性不育的分子机制。通过双向电泳分离花药蛋白,基质辅助激光解析飞行时间串联质谱（MALDI TOF TOF）对差异表达蛋白进行质谱鉴定,利用生物信息学进行差异表达蛋白鉴定和功能注释分析。结果表明,在分子量19.0～100.0 kD、等电点4～7线性范围内,共检测到约2 000个蛋白点。2个时期共检测到差异蛋白98个,其中两个时期差异表达变化一致的蛋白点56个;数据库搜索获得鉴定的蛋白点41个,其中18个蛋白的表达量在冀5418A 中显著下调,23个在冀5418B 中明显下调。在不育系和可育系中均有参与能量代谢、活性氧代谢、核糖体合成、花粉物质合成的差异蛋白。GO分析预测差异蛋白生物学过程多涉及电子传递和能量代谢、核糖体代谢、活性氧代谢等,细胞组成主要是在膜区域和线粒体,分子功能主要是DNA和RNA结合功能和水解酶等。KEGG分析表明,较多蛋白分布于碳水化合物代谢、活性氧代谢和蛋白组装和折叠途径。推测不育系冀5418A 的雄性不育性除了涉及能量代谢、活性氧清除过程,核糖体蛋白、伴侣蛋白等也有重要作用,雄性不育性可能还与蛋白质加工、物质合成过程的紊乱有关。     

The mitochondrial genome of the Russian wheat aphid Diuraphis noxia: Large repetitive sequences between trnE and trnF in aphids

To characterize aphid mitochondrial genome (mitogenome) features, we sequenced the complete mitogenome of the Russian wheat aphid, Diuraphis noxia. The 15,784-bp mitogenome with a high A + T content (84.76%) and strong C skew (− 0.26) was arranged in the same gene order as that of the ancestral insect. Unlike typical insect mitogenomes, D. noxia possessed a large tandem repeat region (644 bp) located between trnE and trnF. Sequencing partial mitogenome of the cotton aphid (Aphis gossypii) further confirmed the presence of the large repeat region in aphids, but with different repeat length and copy number. Another motif (58 bp) tandemly repeated 2.3 times in the control region of D. noxia. All repeat units in D. noxia could be folded into stem-loop secondary structures, which could further promote an increase in copy numbers. Characterization of the D. noxia mitogenome revealed distinct mitogenome architectures, thus advancing our understanding of insect mitogenomic diversities and evolution.     

Effectiveness of potassium sulfate in mitigating salt-induced adverse effects on different physio-biochemical attributes in sunflower (Helianthus annuus L.)

To assess whether foliar application of K+S as potassium sulfate (K₂SO₄) could alleviate the adverse effects of salt on sunflower (Helianthus annuus L. cv. SF-187) plants, a greenhouse experiment was conducted. There were two NaCl levels (0 and 150 mM) applied to the growth medium and six levels of K+S as K₂SO₄ (NS (no spray), WS (spray of water+0.1% Tween 20 solution), 0.5% K+0.21% S, 1.0% K+0.41% S, 1.5% K+0.62% S, and 2.0% K+0.82% S in 0.1% Tween-20 solution) applied two times foliarly to non-stressed and salt-stressed sunflower plants. Salt stress markedly repressed the growth, yield, photosynthetic pigments, water relations and photosynthetic attributes, quantum yield (F_v/F_m), leaf and root K⁺, Mg²⁺, P, Ca²⁺, N as well as K⁺/Na⁺ ratios, while it enhanced the cell membrane permeability, and leaf and root Na⁺ and Cl⁻ concentrations. Foliar application of potassium sulfate significantly improved growth, achene yield, photosynthetic and transpiration rates, stomatal conductance, water use efficiency, leaf turgor and enhanced shoot and leaf K⁺ of the salt-stressed sunflower plants, but it did not improve leaf and root Na⁺, Cl⁻, Mg²⁺, P, Ca²⁺, N as well as K⁺/Na⁺ ratios. The most effective dose of K+S for improving growth and achene yield was found to be 1.5% K+0.62% S and 1% K+0.41% S, respectively. Improvement in growth of sunflower plants due to exogenously applied K₂SO₄ was found to be linked to enhanced photosynthetic capacity, water use efficiency, leaf turgor and relative water content.     

Association between the melanopsin gene polymorphism OPN4*Ile394Thr and sleep/wake timing in Japanese university students

Background

In our previous studies, we found that the Ile394Thr SNP in the melanopsin gene (OPN4) was functionally associated with the pupillary light reflex. This indicates the possibility that OPN4*Ile394Thr is associated with other non-image forming responses. The aim of this study was therefore to determine whether OPN4*Ile394Thr is associated with sleep/wake timing.

Methods

A total of 348 healthy Japanese university students participated in this study. Scalp hair was used to genotype the Ile394Thr SNP of OPN4. Sleep habits, including bedtime, wake time and sleep duration, were assessed separately for weekdays and weekends. A total of 328 samples, including 223 samples with TT genotype, 91 with TC genotype and 14 with CC genotype, were used for statistical analysis. No significant difference in age or male/female distribution was found among the three genotype groups.

Results

There was no significant difference in circadian preference among the genotype groups. During weekdays, bedtime, wake time and midpoint of sleep for CC subjects were significantly later than those for TT and TC subjects. However, there was no difference between TT and TC subjects in any of their sleep habits. During weekends, bedtime of CC subjects was significantly later than those of TT and TC subjects, and the midpoint of sleep of CC subjects was significantly later than that of TC subjects.

Conclusions

Our findings demonstrated that OPN4*Ile394Thr is associated with sleep/wake timing. We also found that the sleep/wake timing of subjects with the CC genotype was later than that of subjects with the TT or TC genotype.     

Genomic regions for yield and yield parameters in Chinese winter wheat (Triticum aestivum L.) genotypes tested under varying environments correspond to QTL in widely different wheat materials

Field trials with a population of 108 doubled haploid (DH) lines of bread wheat (Triticum aestivum L.) derived from a cross between the Chinese winter wheat cultivars CA9613 and H1488 were carried out at Beijing (China) in 2000/2001 and 2001/2002. In addition, a field trial and a pot experiment were carried out at the experimental field stations of Giessen University (Germany) in the vegetation periods 2004/2005 and 2006/2007. Phenotypic data for major agronomic yield-related traits, i.e. grain weight per ear (GWE), grain number per ear (GNE), plant height and thousand-grain weight (TGW), were recorded in all experiments. In addition, biomass weight per tiller and ear weight were evaluated in the two field trials at Beijing. Based on the phenotypic data and a genetic map comprising 168 SSR markers, an analysis of quantitative trait loci (QTL) was carried out for yield and yield parameters using the composite interval mapping (CIM) approach. A total of 30 QTL were detected for these traits across four environments. Five of these QTL located on chromosomes 1A, 1B, 2B, 2D and 7D exhibited pleiotropic effects. Such pleiotropic gene loci will be very useful for understanding the homologous/homeologous relationships among QTL and designing an appropriate marker-assisted breeding programme including multi-trait selection in order to accumulate (“pyramide”) favorable alleles at different genetic loci.     

In sacco degradation kinetics of fresh and field-cured peanut (Arachis hypogaea L.) forage harvested at different maturities

There is interest in growing peanut (Arachis hypogaea L.) for forage, but little is known about the nutritive value and forage quality of modern cultivars. The objective of this study was to compare the chemical composition and in sacco degradation kinetics of three cultivars of peanuts (cv. ‘C99-R’, ‘Georgia-01R’, and ‘York’) at either stage 2 or 8 maturities when fresh and field-cured. Herbage yield was at least 3000 kg DM/ha for all cultivars at both maturities. Crude protein (CP) was greater (P < 0.0001) at R2 stage than at R8 stage; whereas, neutral detergent fiber (aNDF), acid detergent fiber, and Lignin (sa) were greater (P < 0.01) at R8 than R2 maturity stages. Water soluble carbohydrate and acid detergent insoluble nitrogen was not different (P > 0.07) among cultivars, maturity stage, or harvest forms. In vitro true digestibility was greatest (P < 0.02) for C99-R and least for York. Undegradable intake protein concentration was greatest (P < 0.04) in York and least for C99-R. Maturity had a greater effect on the degradation kinetics than harvest form or cultivar. The dry matter (DM) and CP in the soluble wash fraction (A) and insoluble but degradable fraction (B) and the effective ruminal degradability were greater among all cultivars and both harvest forms of the R2 maturity stage than the R8. The undegradable DM, aNDF, and CP in the undegradable fraction were greatest (P < 0.002) for all three cultivars at R8 maturity. The rate of degradation of DM and CP in the B fraction was faster (P < 0.001) at R2 stage than at R8 stage; whereas, rate of aNDF degradation was not different (P > 0.09) among treatments. Lag of DM, aNDF, or CP degradation was not different (P > 0.1) among treatments. The cultivars C99-R and Georgia-01R are recommended for further feeding trials.