High-Throughput Genomics Enhances Tomato Breeding Efficiency

Tomato (Solanum lycopersicum) is considered a model plant species for a group of economically important crops, such as potato, pepper, eggplant, since it exhibits a reduced genomic size (950 Mb), a short generation time, and routine transformation technologies. Moreover, it shares with the other Solanaceous plants the same haploid chromosome number and a high level of conserved genomic organization. Finally, many genomic and genetic resources are actually available for tomato, and the sequencing of its genome is in progress. These features make tomato an ideal species for theoretical studies and practical applications in the genomics field. The present review describes how structural genomics assist the selection of new varieties resistant to pathogens that cause damage to this crop. Many molecular markers highly linked to resistance genes and cloned resistance genes are available and could be used for a high-throughput screening of multiresistant varieties. Moreover, a new genomics-assisted breeding approach for improving fruit quality is presented and discussed. It relies on the identification of genetic mechanisms controlling the trait of interest through functional genomics tools. Following this approach, polymorphisms in major gene sequences responsible for variability in the expression of the trait under study are then exploited for tracking simultaneously favourable allele combinations in breeding programs using high-throughput genomic technologies. This aims at pyramiding in the genetic background of commercial cultivars alleles that increase their performances. In conclusion, tomato breeding strategies supported by advanced technologies are expected to target increased productivity and lower costs of improved genotypes even for complex traits.Key Words: Solanum lycopersicum, genetic and genomic resources, molecular markers, microarray, resistance to pathogens, fruit quality.     

Phosphorus Enhances Uptake of Dissolved Organic Matter in Boreal Streams

Retention of carbon (C), either by physical mechanisms or microbial uptake, is a key driver of the transformation and storage of C and nutrients within ecosystems. Both the molecular composition and nutrient content of organic matter influence the rate at which it is retained in streams, but the relative influence of these characteristics remains unclear. We estimated the effects of nutrient content and molecular composition of dissolved organic C (DOC) on uptake in boreal streams by measuring rates of C retention, in situ, following introduction of leachates derived from alder, poplar, and spruce trees subject to long-term fertilization with nitrogen (N) or phosphorus (P). Leachate C:N varied approximately twofold, and C:P varied nearly 20-fold across species and nutrient treatments. Uptake of DOC was greatest for leachates derived from trees that had been fertilized with P, a finding consistent with P-limitation of uptake and/or preferential sorption of P-containing molecules. Optical measures indicated that leachates derived from the three tree species varied in molecular composition, but uptake of DOC did not differ across species, suggesting weak constraints on retention imposed by molecular composition relative to nutrient limitation. Observed coupling between P and C cycles highlights the potential for increased P availability to enhance DOC retention in headwater streams.     

Overexpressing CYP71Z2 Enhances Resistance to Bacterial Blight by Suppressing Auxin Biosynthesis in Rice

Background

The hormone auxin plays an important role not only in the growth and development of rice, but also in its defense responses. We’ve previously shown that the P450 gene CYP71Z2 enhances disease resistance to pathogens through regulation of phytoalexin biosynthesis in rice, though it remains unclear if auxin is involved in this process or not.

Methodology and Principal Findings

The expression of CYP71Z2 was induced by Xanthomonas oryzae pv. oryzae (Xoo) inoculation was analyzed by qRT-PCR, with GUS histochemical staining showing that CYP71Z2 expression was limited to roots, blades and nodes. Overexpression of CYP71Z2 in rice durably and stably increased resistance to Xoo, though no significant difference in disease resistance was detected between CYP71Z2-RNA interference (RNAi) rice and wild-type. Moreover, IAA concentration was determined using the HPLC/electrospray ionization/tandem mass spectrometry system. The accumulation of IAA was significantly reduced in CYP71Z2-overexpressing rice regardless of whether plants were inoculated or not, whereas it was unaffected in CYP71Z2-RNAi rice. Furthermore, the expression of genes related to IAA, expansin and SA/JA signaling pathways was suppressed in CYP71Z2-overexpressing rice with or without inoculation.

Conclusions and Significance

These results suggest that CYP71Z2-mediated resistance to Xoo may be via suppression of IAA signaling in rice. Our studies also provide comprehensive insight into molecular mechanism of resistance to Xoo mediated by IAA in rice. Moreover, an available approach for understanding the P450 gene functions in interaction between rice and pathogens has been provided.     

Comparative genetic analysis of Arabidopsis purple acid phosphatases AtPAP10, AtPAP12, and AtPAP26 provides new insights into their roles in plant adaptation to phosphate deprivation

Induction and secretion of acid phosphatases(APases) is thought to be an adaptive mechanism that helps plants survive and grow under phosphate(Pi) deprivation. In Arabidopsis, there are 29 purple acid phosphatase(AtPAP)genes. To systematically investigate the roles of different AtPAPs, we first identified knockout or knock‐down T‐DNA lines for all 29 AtPAP genes. Using these atpap mutants combined with in‐gel and quantitative APase enzyme assays,we demonstrated that AtPAP12 and AtPAP26 are two major intracellular and secreted APases in Arabidopsis while AtPAP10is mainly a secreted APase. On Pi‐deficient(P) medium or Pmedium supplemented with the organophosphates ADP and fructose‐6‐phosphate(Fru‐6‐P), growth of atpap10 was significantly reduced whereas growth of atpap12 was only moderately reduced, and growth of atpap26 was nearly equal to that of the wild type(WT). Overexpression of the AtPAP12 or AtPAP26 gene, however, caused plants to grow better on Por P medium supplemented with ADP or Fru‐6‐P. Interestingly, Pi levels are essentially the same for the WT and overexpressing lines, although these two types of plants have significantly different growth phenotypes. These results suggest that the APases may have other roles besides enhancing internal Pi recycling or releasing Pi from external organophosphates for plant uptake.     

Comparative genetic analysis of,Arabidopsis purple acid phosphatases AtPAP10, AtPAP12, and AtPAP26 provides new insights into their roles in plant adaptation to phosphate deprivation

Induction and secretion of acid phosphatases （APases） is thought to be an adaptive mechanism that helps plants survive and grow under phosphate （Pi） deprivation, in Arabidopsis, there are 29 purple acid phosphatase （AtPAP） genes. To systematically investigate the roles of different AtPAPs, we first identified knockout or knock-down T-DNA lines for all 29 AtPAP genes. Using these atpap mutants combined with in-gel and quantitative APase enzyme assays, we demonstrated that AtPAP12 and AtPAP26 are two major intracellular and secreted APases in Arabidopsis while AtPAPlo is mainly a secreted APase. On Pi-deficient （P-） medium or P- medium supplemented with the organophosphates ADP and fructose-6-phosphate （Fru-6-P）, growth of atpaplo was significantly reduced whereas growth of atpap12 was only moderately reduced, and growth of atpap26 was nearly equal to that of the wild type （WT）. Overexpression of the AtPAP12 or AtPAP26 gene, however, caused plants to grow better on P- or P- medium supplemented with ADP or Fru-6-P. Interest-ingly, Pi levels are essentially the same for the WT and overexpressing lines, although these two types of plants have significantly different growth phenotypes. These results suggest that the APases may have other roles besides enhancing internal Pi recycling or releasing Pi from external organophosphates for plant uptake.     

Molecular and Biochemical Characterization of AtPAP15, a Purple Acid Phosphatase with Phytase Activity,in Arabidopsis

Purple acid phosphatase (PAP) catalyzes the hydrolysis of phosphate monoesters and anhydrides to release phosphate within an acidic pH range. Among the 29 PAP-like proteins in Arabidopsis (Arabidopsis thaliana), AtPAP15 (At3g07130) displays a greater degree of amino acid identity with soybean (Glycine max; GmPHY) and tobacco (Nicotiana tabacum) PAP (NtPAP) with phytase activity than the other AtPAPs. In this study, transgenic Arabidopsis that expressed an AtPAP15 promoter∷β-glucuronidase (GUS) fusion protein showed that AtPAP15 expression was developmentally and temporally regulated, with strong GUS staining at the early stages of seedling growth and pollen germination. The expression was also organ/tissue specific, with strongest GUS staining in the vasculature, pollen grains, and roots. The recombinant AtPAP purified from transgenic tobacco exhibited broad substrate specificity with moderate phytase activity. AtPAP15 T-DNA insertion lines exhibited a lower phytase and phosphatase activity in seedling and germinating pollen and lower pollen germination rate compared with the wild type and their complementation lines. Therefore, AtPAP15 likely mobilizes phosphorus reserves in plants, particularly during seed and pollen germination. Since AtPAP15 is not expressed in the root hair or in the epidermal cells, it is unlikely to play any role in external phosphorus assimilation.At pH in the range of 4 to 7, purple acid phosphatases (PAPs) catalyze the hydrolysis of a wide range of activated phosphoric acid monoesters and diesters and anhydrides (Klabunde et al., 1996). They are distinguished from the other phosphatases by their insensitivity to l-(+) tartrate inhibition and therefore are also known as tartrate-resistant acid phosphatases. Their characteristic pink or purple color derives from a charge transfer transition between a Tyr residue and the “chromophoric” ferric ion in the binuclear Fe(III)-Me(II) center, where the metal (Me) is iron, zinc, or manganese (Schenk et al., 1999). PAP proteins are also characterized by seven conserved amino acid residues (shown in boldface) in the five conserved motifs DXG, GDXXY, GNH(D/E), VXXH, and GHXH, which are involved in the coordination of the dimetal nuclear center (Li et al., 2002).PAPs are widespread in mammals, fungi, bacteria, and plants. Interestingly, while only a few copies of PAP-like genes are present in mammalian and fungal genomes (Mullaney and Ullah, 2003; Flanagan et al., 2006), multiple copies are present in plant genomes (Schenk et al., 2000). For example, 29 PAP-like genes have been identified in the Arabidopsis (Arabidopsis thaliana) genome (Li et al., 2002). It is intriguing that so many PAP-like genes are required for plant metabolism; this diverse portfolio of PAP-like genes implies differential functions for them. Plant PAPs are generally considered to mediate phosphorus acquisition and redistribution based on their ability to hydrolyze phosphorus compounds (Cashikar et al., 1997; Bozzo et al., 2004; Lung et al., 2008). However, additional biological roles have been reported for some plant PAPs. For example, the PAPs AtACP5 (AtPAP17), SAP1, and SAP2 (del Pozo et al., 1999; Bozzo et al., 2002) display not only phosphatase but also peroxidase activity, suggesting their involvement in the removal of reactive oxygen compounds in plant organs. GmPAP3, isolated from salted-stressed soybean (Glycine max), reportedly mediates salt tolerance via NaCl and oxidative stress inductions but not by phosphorus starvation (Liao et al., 2003).Some PAP members can hydrolyze phytic acid (myoinositol hexakisphosphate [InsP6]) to inorganic phosphate and free or lower phosphoric esters of myoinositol. Since the major storage form of phosphorus in plant seeds and pollen grains is phytate, PAPs with phytase activity may play a role in seed and pollen germination. However, not all PAPs exhibit phytase activity. The first plant phytase PAP, GmPHY, was isolated from the cotyledon of germinating soybean seedlings (Hegeman and Grabau, 2001). A tobacco (Nicotiana tabacum) root PAP phytase was identified more recently that is likely involved in mobilizing external organic phosphorus in soil (Lung et al., 2008).Relatively little is known about the biochemical properties and physiological roles of the 29 PAP-like Arabidopsis genes (del Pozo et al., 1999; Veljanovski et al., 2006). An enzyme assay involving the glutathione S-transferase (GST)-AtPAP23 fusion protein revealed that the Arabidopsis PAP AtPAP23 exhibits phytase activity (Zhu et al., 2005). A GUS study showed that AtPAP23 is exclusively expressed in the flower of the Arabidopsis plant. In a recent report, a recombinant AtPAP15 expressed in Escherichia coli was also found to exhibit phytase activity; this PAP potentially modulates plant ascorbate synthesis through supply of myoinositol from the phytate hydrolysis reaction (Zhang et al., 2008). However, the possible physiological roles of AtPAP15 in phosphorus mobilization have not been examined.In this study, AtPAP15 expressed in a plant (tobacco) system was biochemically characterized, and its temporal and spatial expression patterns in Arabidopsis were examined. The physiological roles of AtPAP15 in phosphorus mobilization were also delineated.     

高表达人源SP15对小鼠生长和生殖的影响

目的:探究高表达人源SP15对小鼠生长和生殖的影响,为研究NYD-SP15在生物体中的功能提供动物模型。方法:将人源NYD-SP15 cDNA以及Cre序列插入PCAG启动子下游,构建NYD-SP15转基因表达载体,并通过原核注射,构建全身性表达NYD-SP15的转基因小鼠;将获得的NYD-SP15转基因小鼠与C57/BL6小鼠交配,PCR鉴定转基因小鼠是否有Cre插入,筛选出人源NYD-SP15表达的小鼠,统计转基因小鼠体重变化和后代阳性情况。结果:通过PCR鉴定及公司测序验证,我们成功构建了NYD-SP15转基因过表达载体。并通过PCR鉴定小鼠基因型,筛选出可以表达人NYD-SP15的转基因小鼠。比较转基因小鼠与同窝野生型小鼠体重,发现转基因小鼠体重与同窝野生型小鼠相比无明显区别,说明在体内过表达NYD-SP15对小鼠体重无明显影响。通过对后代阳性小鼠出生情况统计发现F2代阳性小鼠出生率较F1代明显降低。结论:人源NYD-SP15在小鼠体内能正常表达,对其生长无明显影响,但其后代阳性出生率呈逐代下降趋势,推测该原因可能与NYD-SP15在睾丸中表达有关。     

磷胁迫诱导大豆叶片酸性磷酸酶同工酶的表达

通过田间试验对两种磷处理的274个大豆基因型叶片酸性磷酸酶活性进行筛选,并将其中8个进行营养液栽培试验以研究磷胁迫对其叶片酸性磷酸酶同工酶表达的影响.结果表明,大豆叶片酸性磷酸酶活性存在着明显的基因型差异,不施磷处理提高了大部分(约60%)供试基因型叶片酸性磷酸酶的活性.营养液栽培试验表明,低磷处理普遍提高了所有8个供试大豆基因型叶片酸性磷酸酶的活性.等电聚焦电泳结果表明,供试大豆基因型的老叶和新叶中均有6条酸性磷酸酶的同工酶带.低磷处理显著增加了叶片酸性磷酸酶酶带的活性,但是没有诱导新的酸性磷酸酶酶带产生.研究发现叶片酸性磷酸酶活性可作为反映大豆磷胁迫的酶学指标;磷胁迫诱导大豆叶片酸性磷酸酶活性的增加是由于已有同工酶活性的提高而不是由于特异性酶带的产生.     

Slowing Bacterial Translation Speed Enhances Eukaryotic Protein Folding Efficiency

The mechanisms for de novo protein folding differ significantly between bacteria and eukaryotes, as evidenced by the often observed poor yields of native eukaryotic proteins upon recombinant production in bacterial systems. Polypeptide synthesis rates are faster in bacteria than in eukaryotes, but the effects of general variations in translation rates on protein folding efficiency have remained largely unexplored. By employing Escherichia coli cells with mutant ribosomes whose translation speed can be modulated, we show here that reducing polypeptide elongation rates leads to enhanced folding of diverse proteins of eukaryotic origin. These results suggest that in eukaryotes, protein folding necessitates slow translation rates. In contrast, folding in bacteria appears to be uncoupled from protein synthesis, explaining our findings that a generalized reduction in translation speed does not adversely impact the folding of the endogenous bacterial proteome. Utilization of this strategy has allowed the production of a native eukaryotic multidomain protein that has been previously unattainable in bacterial systems and may constitute a general alternative to the production of aggregation-prone recombinant proteins.     

磷胁迫诱导大豆叶片酸性磷酸酶同工酶的表达

通过田间试验对两种磷处理的274个大豆基因型叶片酸性磷酸酶活性进行筛选,行将其中8个进行营养液栽培试验以研究磷胁迫对其叶片酸性磷酸酶同工酶表达的影响。结果表明,大豆叶片酸性磷酸酶活性存在着明显的基因型差异,不施磷处理提高了大部分(约60％)供试基因型叶片酸性磷酸酶的活性。营养液栽培试验表明,低磷处理普遍提高了所有8个供试大豆基因型叶片酸性磷酸酶的活性。等电聚焦电泳结果表明,供试大豆基因型的老叶和新叶中均有6条酸性磷酸酶的同工酶带。低磷处理显著增加了叶片酸性磷酸酶酶带的活性,但是没有诱导新的酸性磷酸酶酶带产生。研究发现叶片酸性磷酸酶活性可作为反映大豆磷肋迫的酶学指标;磷胁迫诱导大豆叶片酸性磷酸酶活性的增加是由于已有同工酶活性的提高而不是由于特异性酶带的产生。     

大豆品种资源子粒中磷含量差异研究

以239份大豆品种资源为试材,研究其子粒中全磷和无机磷含量的差异表现,分析大豆子粒中磷含量水平,并筛选高全磷、高无机磷资源材料。研究结果表明,供试239份大豆品种子粒中的全磷、无机磷含量存在极显著差异;其分布范围分别为全磷6．24～9．56g／kg,无机磷0．12～0．37g／kg;平均含量分别为7．78g／kg,0．20g／kg;无机磷与全磷含量的比值为1．39％～4．94％,平均为2．56％。同时,筛选出子粒中高全磷、高无机磷含量的大豆品种各5个,其中品种洋黄豆、高家营黑豆、绿75、郭柳条青、大毛角为高全磷材料;品种8012混-1、黄豆、白露快、平顶黄、黑大粒为高无机磷材料;     

转铁蛋白基因烟草中内源铁蛋白基因的差异表达及含铁量的变化

铁蛋白是一种由24个亚基组成的高分子贮藏蛋白质,可以储存多达4500个铁原子,在动植物及微生物的新陈代谢中起着非常重要的作用。有研究表明,外源铁蛋白的大量表达可以提高植物储存铁离子的能力。为了明确外源铁蛋白基因转化植物中内源铁蛋白基因差异表达与植物含铁量的关系,本研究在成功获得2个烟草铁蛋白基因的全长cDNA克隆NtFerl（登录号：ay083924）和NtFer2（登录号：ay141105）的基础上,以烟草品种SR-1（Nicotiana tabacum cv．Petit Havana SR-1）为受体,培育了转铁蛋白基因烟草。将双元载体pBI121中的GUS基因用来自大豆的铁蛋白基因SoyFer1（登录号：m64337）置换,利用农杆菌介导法转化烟草叶盘,获得在CaMV35S启动子驱动表达的大豆铁蛋白基因转化烟草植株。Northern杂交和Western杂交分析表明外源铁蛋白基因在转基因烟草中得到了正确表达。比较转基因烟草和非转基因烟草的内源铁蛋白基因表达强度、叶片铁含量、根系铁还原酶活性、株高和鲜重表明,外源铁蛋白基因不但促进了NtFer1的表达,提高转基因植株的储存铁的能力和根系铁还原酶活性,而且促进植株的生长速度。以上结果说明,外源铁蛋白基因转化烟草中内源铁蛋白基因的表达、铁离子的还原吸收及光和作用都得到了进一步的提高。     

Differential Expression of Endogenous Ferritin Genes and Iron Homeostasis Alteration in Transgenic Tobacco Overexpressing Soybean Ferritin Gene

For studying the effects of endogenous ferritin gene expressions (NtFer1, GenBank accession number ay083924; and NtFer2, GenBank accession number ay141105) on the iron homeostasis in transgenic tobacco (Nicotiana tabacum L.) plants expressing soybean (Glycine max Merr) ferritin gene (SoyFer1, GenBank accession number m64337), the transgenic tobacco has been produced by placing soybean ferritin cDNA cassette under the control of the CaMV 35S promoter. The exogenous gene expression was examined by both Northern- and Western-blot analyses. Comparison of endogenous ferritin gene expressions between nontransformant and transgenic tobacco plants showed that the expression of NtFer1 was increased in the leaves of transgenic tobacco plants, whereas the NtFer2 expression was unchanged. The iron concentration in the leaves of transgenic tobacco plants was about 1.5-folds higher than that in nontransformant. Enhanced growth of transgenic tobacco was observed at the early development stages, resulting in plant height and fresh weights significantly greater than those in the nontransformant. These results demonstrated that exogenous ferritin expression induced increased expression of at least one of the endogenous ferritin genes in transgenic tobacco plants by enhancing the ferric chelate reductase activity and iron transport ability of the root, and improved the rate of photosynthesis.     

大豆种子储藏性磷对幼苗适应低磷胁迫的作用

选用种子大小不同、磷效率不同的两个大豆品种‘巴西10号’(B10)和‘本地2号’(L2),在不同供磷条件下进行营养液浇灌沙培,从大豆萌发至2片三出复叶完全展开期测定植株主要器官总磷、可溶性磷浓度、子叶可溶性蛋白、酸性磷酸酶比活性、植酸酶比活性的变化动态,探讨储藏性磷在大豆幼苗期适应磷胁迫中的作用。结果发现:(1)磷效率不同的两个大豆品种的种子中磷含量差异显著。(2)大豆萌发和幼苗生长过程中子叶的磷逐渐转入根、茎、叶中,并以转入叶中的磷最多,其中磷高效品种B10在发芽过程中子叶磷向各个器官转移的总磷量要高于磷低效品种L2,且持续时间长。(3)大豆萌发和幼苗生长过程中外源供磷水平显著影响子叶磷的转移,在外源供磷充足条件下各器官中总磷均高于低供磷条件,子叶中磷和外源磷存在补偿关系。(4)磷高效品种B10子叶中酸性磷酸酶活性在低磷条件下显著高于高磷条件,但磷低效品种L2在高、低磷间无显著差异。研究表明,大豆种子储藏性磷在幼苗期耐低磷能力建立方面具有重要作用。     

植物根构型特性与磷吸收效率

植物根构型,即根系在生长介质中的空间造型和分布,与磷吸收效率密切相关;认识植物根构型,可为植物磷效率的遗传改良提供依据。长期以来,人们试图定量描述植物根构型,确立一个能客观全面地描述根系三维立体构型的综合指标。试验指出,植物主要通过向地性变化和根冠之间的碳源分配来改变根构型,从而影响磷吸收效率;根系向地性变化可由缺磷等因素所诱导,且存在着一定的遗传变异性。有证据表明,根构型对低磷胁迫的适应性变化是     

植物高效吸收和利用磷营养的遗传学研究进展

近些年来,人们对植物营养性状的遗传学背景日益了解,特别是磷素营养。随着分子生物学的快速发展,磷素营养的研究已深入到分子水平并且取得了可喜的成绩。本文从植物体内调控磷吸收利用的相关QTLs定位,缺磷诱导的基因表达,植物体内的磷调控系统,磷转运子及与磷有关的突变体的研究作一概括。     

植物根构型特性与磷吸收效率

植物根构型，即根系在生长介质中的空间造型和分布，与磷吸收效率密切相关；认识植物根构型，可为植物磷效率的遗传改良提供依据。长期以来，人们试图定量描述植物根构型，确立一个能客观全面地描述根系三维立体构型的综合指标。试验指出，植物主要通过向地性变化和根冠之间的碳源分配来改变根构型, 从而影响磷吸收效率；根系向地性变化可由缺磷等因素所诱导，且存在着一定的遗传变异性。有证据表明，根构型对低磷胁迫的适应性变化是受基因调控的一个生理过程，其中乙烯可能是一种重要的生理调节物质。迄今已在一些植物上定位到了部分控制根构型的数量性状座位，为该性状的分子生物学改良提供了基础。随着现代技术的进展，植物根构型研究将取得更大的突破。     

植物高效吸收和利用磷营养的遗传学研究进展

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