Identification and verification of QTL associated with growth traits in two genetic backgrounds of Barramundi (Lates calcarifer)

Quantitative trait loci (QTL) affecting growth traits have previously been mapped in linkage groups (LG) 2, 3 and 23 of Barramundi ( Lates carcalifer ), but these QTL have not been verified in different genetic backgrounds and environments. Here, we report the identification and verification of QTL for growth traits on LG2, 3, 10 and 23 in F₁ families constructed using brooders from the Singapore Marine Aquaculture Center (MAC) and from wild stocks collected in Thailand (THAI). The previously detected QTL for body weight and length linked to marker Lca371 on LG2 were confirmed in both the MAC and THAI families, whereas other QTL previously mapped to LG3 and 23 were only detected in one of the two families. QTL for body weight and length were identified in the MAC family, but not in the THAI family, in a region where the insulin-like growth factor 2 ( IGF2 ) and tyrosine hydroxylase 1 ( TH1 ) genes are located on LG10. Significant epistatic interactions were identified between markers Lca287 on LG2 and IGF2 on LG10 for growth trait QTL in the MAC family, but not in the THAI family. Effects of the IGF2 , TH1 and parvalbumin 1 candidate genes were family-specific. Our results indicate that some but not all QTL are family-specific in Barramundi.     

线虫耐寒性研究进展

对于分布在温带和寒带的线虫,它们只有战胜冬季寒冷的挑战,才能有利于种群的存在与发展。因此,耐寒性是线虫生物学研究中不可忽视的内容。综述了关于线虫在低温胁迫下的耐寒性测定方法、耐寒对策及耐寒机制等方面的研究进展。线虫的耐寒性和昆虫一样,可通过过冷却点和低温存活率两种指标进行评价,但在具体的实验方法上,线虫耐寒性研究有其不同之处。线虫的耐寒对策和耐寒机制具有多样化。耐寒对策主要有耐冻和避冻,二者能共同渗透于线虫的耐寒过程中。耐寒机制包括特殊发育阶段的形成、低温驯化作用、低分子量抗冻物质的聚集、以及高分子量抗冻蛋白和热休克蛋白的产生,等等。此外,还强调应从多个角度研究线虫的耐寒性,如寒冷敏感型线虫的研究、寄生线虫的耐寒对策研究以及交叉胁迫的研究。     

Antifreeze proteins in Alaskan insects and spiders

Prior to this study, antifreeze proteins (AFPs) had not been identified in terrestrial arthropods from the Arctic or anywhere in Alaska. The hemolymph of 75 species of insects and six spiders from interior and arctic Alaska were screened for thermal hysteresis (a difference between the freezing and melting points), characteristic of the presence of AFPs. Eighteen species of insects and three spiders were shown to have AFPs. Ten of the insects with AFPs were beetles including the first species from the families Chrysomelidae, Pythidae, Silphidae and Carabidae. In addition, the first Neuropteran to have AFPs was identified, the lacewing Hemerobius simulans together with the second and third Diptera (the first Tipulids) and the second and third Hemiptera, the stinkbug Elasmostethus interstinctus (the first Pentatomid), and the water strider Limnoporus dissortis (the first Gerrid). Prior to this study, 33 species of insects and three spiders had been reported to have AFPs. Most AFP-producing terrestrial arthropods are freeze avoiding, and the AFPs function to prevent freezing. However, some of the AFP- producing insects identified in this study are known to be freeze tolerant (able to survive freezing) to very low temperatures (-40 to -70 degrees C).     

Genetic analysis of post-flowering drought tolerance and components of grain development in Sorghum bicolor (L.) Moench

Drought is a serious agronomic problem and the single greatest factor contributing to crop yield loss in the world today. This problem may be alleviated by developing crops that are well adapted to dry-land environments. Sorghum (Sorghum bicolor (L.) Moench) is one of the most drought-tolerant grain crops and is an excellent crop model for evaluating mechanisms of drought tolerance. In this study, a set of 98 recombinant inbred (RI) sorghum lines was developed from a cross between two genotypes with contrasting drought reactions, TX7078 (pre-flowering-tolerant, post-flowering susceptible) and B35 (pre-flowering susceptible, post-flowering-tolerant). The RI population was characterized under drought and non-drought conditions for the inheritance of traits associated with post-flowering drought tolerance and for potentially related components of grain development. Quantitative trait loci (QTL) analysis identified 13 regions of the genome associated with one or more measures of post-flowering drought tolerance. Two QTL were identified with major effects on yield and 'staygreen under post-flowering drought. These loci were also associated with yield under fully irrigated conditions suggesting that these tolerance loci have pleiotropic effects on yield under non-drought conditions. Loci associated with rate and/or duration of grain development were also identified. QTL analysis indicated many loci that were associated with both rate and duration of grain development. High rate and short duration of grain development were generally associated with larger seed size, but only two of these loci were associated with differences in stability of performance under drought.     

陆地棉遗传图谱构建与纤维品质性状QTL定位

以陆地棉(Gossypium hirsutum L.)品种Bar19/1和Acala1517-77杂交的108个F2单株为材料,应用85个标记(70个SSR标记和15个AFLP标记)构建了总长为814cM的遗传图谱,覆盖棉花基因组的18.3%。该图谱包含25个连锁群,分别对应到17条染色体和4个未知连锁群。应用复合区间作图法分析了该组合的108个F2单株和F3家系纤维品质性状,从遗传图谱上检测到19个纤维品质数量性状基因座(QTL),包括5个纤维长度、6个纤维比强度、4个伸长率及4个马克隆值QTL,分别解释各性状表型变异的15.11%~28.45%、8.46%~24.51%、11.08%~27.55%和9.23%~42.21%。纤维长度和伸长率的QTL以部分显性为主,少数具有超显性,比强度QTL以加性和部分显性为主,4个马克隆值QTL中有3个表现为超显性。研究结果表明,陆地棉Bar19/1和Acala1517-77间多态性位点丰富,有利于构建高密度遗传图谱,纤维品质性状的QTL分析从分子水平上揭示了纤维品质的遗传基础。     

Using QTL mapping to investigate the relationships between abiotic stress tolerance (drought and salinity) and agronomic and physiological traits

Background

Drought and salinity are two major abiotic stresses that severely limit barley production worldwide. Physiological and genetic complexity of these tolerance traits has significantly slowed the progress of developing stress-tolerant cultivars. Marker-assisted selection (MAS) may potentially overcome this problem. In the current research, seventy two double haploid (DH) lines from a cross between TX9425 (a Chinese landrace variety with superior drought and salinity tolerance) and a sensitive variety, Franklin were used to identify quantitative trait loci (QTL) for drought and salinity tolerance, based on a range of developmental and physiological traits.

Results

Two QTL for drought tolerance (leaf wilting under drought stress) and one QTL for salinity tolerance (plant survival under salt stress) were identified from this population. The QTL on 2H for drought tolerance determined 42% of phenotypic variation, based on three independent experiments. This QTL was closely linked with a gene controlling ear emergency. The QTL on 5H for drought tolerance was less affected by agronomic traits and can be effectively used in breeding programs. A candidate gene for this QTL on 5H was identified based on the draft barley genome sequence. The QTL for proline accumulation, under both drought and salinity stresses, were located on different positions to those for drought and salinity tolerance, indicating no relationship with plant tolerance to either of these stresses.

Conclusions

Using QTL mapping, the relationships between QTL for agronomic and physiological traits and plant drought and salinity tolerance were studied. A new QTL for drought tolerance which was not linked to any of the studied traits was identified. This QTL can be effectively used in breeding programs. It was also shown that proline accumulation under stresses was not necessarily linked with drought or salinity tolerance based on methods of phenotyping used in this experiment. The use of proline content in breeding programs can also be limited by the accuracy of phenotyping.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1243-8) contains supplementary material, which is available to authorized users.     

The Complete Mitochondrial Genome Sequence and Characterization of Single-Nucleotide Polymorphisms in the Control Region of the Asian Seabass (Lates calcarifer)

We determined the complete mtDNA nucleotide sequence of Lates calcarifer using the shotgun sequencing method. The mitochondrial DNA (mtDNA) was 16,535 base pairs (bp) in length, and contained 13 protein coding genes, 22 transfer RNAs, 2 ribosomal RNAs, and one major noncoding control region (CR). The CR was unusually short at only 768 bp. A striking feature of the mitochondrial genome was the high G+C content (46.1%), which is among the highest in fish. The gene order was identical to that of a typical vertebrate. Phylogenetic analyses using concatenated amino acid sequences of 12 protein-coding genes of 30 fish species representing 14 suborders clearly showed Lates calcarifer was located in the cluster of fish species from the order Perciformes, supporting the traditional systematic classification. We characterized single-nucleotide polymorphisms (SNPs) in the CR by sequencing the complete CR of 25 individuals obtained from Australia and Singapore. A total of 68 SNPs were detected. Eighteen SNPs were fixed with alternative nucleotides in Australian and Singapore seabass, and these SNPs could be used for differentiating fish from the two countries.     

植物耐冷性基因工程

温度决定物种的分布,同时还影响作物的产量和品质。植物耐冷的机制涉及到许多方面,包括膜脂组成的变化、可混溶溶质的积累、抗氧化酶活性的提高、低温相关基因的诱导表达等。由于植物的耐冷性状由多基因控制,采用传统的育种方法往往难以取得理想的结果,而植物基因工程技术的发展及应用则提供了另外可能的途径,可以通过转移耐冷性状形成的关键基因从而对植物进行改良。本文从膜脂组成、可混溶溶质、抗冻蛋白、抗氧化酶和诱导植物低温相关基因的转录因子等方面对植物耐冷性的基因工程研究进行了综述,以期为植物育种者和从事冷胁迫机制研究的工作者提供参考。     

Expression of a synthetic antifreeze protein in potato reduces electrolyte release at freezing temperatures

A synthetic antifreeze protein gene was expressed in plants and reduced electrolyte leakage from the leaves at freezing temperatures. The synthetic AFP was expressed as a fusion to a signal peptide, directing it to the extracytoplasmic space where ice crystallization first occurs. The gene was introduced to Solanum tuberosum L. cv. Russet Burbank by Agrobacterium-mediated transformation. Transformants were identified by PCR screening and expression of the introduced protein was verified by immunoblot. Electrolyte-release analysis of transgenic plant leaves established a correlation between the level of transgenic protein expression and degree of tolerance to freezing. This is the first identification of a phenotype associated with antifreeze protein expression in plant tissue.     

快速冷耐受比冷驯化更能提高越冬松针瘿蚊 (Thecodiplosis japonensis)幼虫的耐寒力(英文)

松针瘿蚊以三龄老熟幼虫在浅层土表越冬。本文比较两种温度处理过程 ,快速冷耐受 (rapidcoldhardening)和冷驯化 (coldacclimation)对松针瘿蚊获得耐寒性的能力。发现 3龄越冬幼虫具有一种特殊的生物学现象 -快速冷耐受。当越冬幼虫直接从 2 7℃转入 - 1 5℃ 3小时 ,其存活率仅为 1 7 9% ,然而在 - 1 5℃暴露之前 ,经 4℃ ,2h短暂处理 ,其存活率升高至 40 0 % ,而短时间 (1 5分钟 ) 2 7℃能抑制快速冷耐受的表达。快速冷耐受比冷驯化更能提高越冬松针瘿蚊幼虫的耐寒力。文中还讨论了快速冷耐受和冷驯化提高松针瘿蚊耐寒能力的不同机制     

Differential allelic expression of IL13 and CSF2 genes associated with asthma

An important area of genetic research is the identification of functional mechanisms in polymorphisms associated with diseases. A highly relevant functional mechanism is the influence of polymorphisms on gene expression levels (differential allelic expression, DAE). The coding single nucleotide polymorphisms (SNPs) CSF2^rs25882 and IL13^rs20541 have been associated with asthma. In this work, we investigated whether the mRNA expression levels of CSF2 or IL13 were correlated with these SNPs. Samples were analyzed by mass spectrometry-based quantification of gene expression. Both SNPs influenced gene expression levels (CSF2^rs25882: p_overall = 0.008 and p_{DAE samples} = 0.00006; IL13^rs20541: p_overall = 0.059 and p_{DAE samples} = 0.036). For CSF2, the expression level was increased by 27.4% (95% CI: 18.5%–35.4%) in samples with significant DAE in the presence of one copy of risk variant CSF2^rs25882-T. The average expression level of IL13 was increased by 29.8% (95% CI: 3.1%–63.4%) in samples with significant DAE in the presence of one copy of risk variant IL13^rs20541-A. Enhanced expression of CSF2 could stimulate macrophages and neutrophils during inflammation and may be related to the etiology of asthma. For IL-13, higher expression could enhance the functional activity of the asthma-associated isoform. Overall, the analysis of DAE provides an efficient approach for identifying possible functional mechanisms that link disease-associated variants with altered gene expression levels.     

甘蔗耐寒相关miRNA的生物信息学分析及其靶基因预测

为了解不同基因型甘蔗(Saccharum officinarum)响应低温胁迫的分子机制,该研究以低温胁迫4 ℃处理 24 h 后的3个不同耐寒性甘蔗品种的叶片为材料进行Illumina HiSeqTM 2000 高通量测序,构建了18个低温胁迫前后sRNA文库。结果表明:(1)共获得分属于84个家族的322个已知miRNA及预测得到110个新miRNA,并在已知miRNA中筛选出100个差异表达miRNA(61个上调,39个下调),新miRNA中筛选出37个差异表达 miRNA(15个上调, 22个下调)。(2)利用psRNATarget、TargetFinder、Tapirhybrid软件对所获得的差异表达miRNA进行靶基因预测,得到1 844个靶基因并进行GO分析揭示其主要功能类别,即分子功能、细胞组分与生物过程。(3)为验证高通量测序数据的可靠性,筛选14个miRNA及其靶基因进行qRT-PCR验证,结果显示这些miRNA均被检测发现且大多表达结果与测序结果一致。(4)鉴定出部分差异表达miRNA的靶基因,这些基因参与植物生长、发育及低温胁迫反应。综上认为,耐寒型甘蔗体内miRNA直接或间接作用靶基因实现表达调控相关代谢途径,对其重要农艺性状均起着关键的调控作用。     

水稻耐盐碱性生理和遗传研究进展

水稻是对盐碱中度敏感的作物,其耐盐碱性因品种、生育阶段、器官、土壤盐碱类型等而存在差异。盐碱胁迫对水稻的伤害主要表现为延迟种子发芽时间、降低发芽率、抑制生育进程、阻碍幼穗分化、推迟分蘖时间、减少分蘖数、降低产量和品质。本文论述了近年来在水稻耐盐碱生理机理、转运蛋白、遗传和数量性状位点的分子检测、分子信号传导以及基因克隆转化方面的研究进展,并对今后的研究工作提出了建议。