Population Structure and Domestication Revealed by High-Depth Resequencing of Korean Cultivated and Wild Soybean Genomes

Despite the importance of soybean as a major crop, genome-wide variation and evolution of cultivated soybeans are largely unknown. Here, we catalogued genome variation in an annual soybean population by high-depth resequencing of 10 cultivated and 6 wild accessions and obtained 3.87 million high-quality single-nucleotide polymorphisms (SNPs) after excluding the sites with missing data in any accession. Nuclear genome phylogeny supported a single origin for the cultivated soybeans. We identified 10-fold longer linkage disequilibrium (LD) in the wild soybean relative to wild maize and rice. Despite the small population size, the long LD and large SNP data allowed us to identify 206 candidate domestication regions with significantly lower diversity in the cultivated, but not in the wild, soybeans. Some of the genes in these candidate regions were associated with soybean homologues of canonical domestication genes. However, several examples, which are likely specific to soybean or eudicot crop plants, were also observed. Consequently, the variation data identified in this study should be valuable for breeding and for identifying agronomically important genes in soybeans. However, the long LD of wild soybeans may hinder pinpointing causal gene(s) in the candidate regions.     

Different Effects of Wild and Cultivated Soybean on Rhizosphere Bacteria

Microbiology - Wild varieties of plants have stronger stress resistances than their cultivated relatives, and rhizosphere bacteria play an important role in improving the environmental...     

黑龙江省野生和栽培大豆异黄酮与其组分相关性分析

利用高效液相色谱法（HPLC）检测了黑龙江省556份不同生态区以及不同类型大豆的异黄酮、大豆苷和染料木苷含量,其中野生大豆243份,栽培大豆313份。结果表明：野生大豆异黄酮含量高于栽培大豆,同时筛选出高异黄酮含量种质3份,低异黄酮含量种质2份。异黄酮、大豆苷和染料木苷含量三者问的相关分析表明,大豆异黄酮含量与大豆苷含量及染料木苷含量、大豆苷含量与染料木苷含量均呈极显著正相关。     

Sequencing and Utilization of the Gossypium Genomes

Revealing the genetic underpinnings of cotton productivity will require understanding both the prehistoric evolution of spinnable fibers, and the results of independent domestication processes in both the Old and New Worlds. Progress toward a reference sequence for the smallest Gossypium genome is a logical stepping-stone toward revealing diversity in the remaining seven genomes (A, B, C, E, F, G, K) that permitted Gossypium species to adapt to a wide range of ecosystems in warmer arid regions of the world, and toward identifying the emergent properties that account for the superior productivity and quality of tetraploid cottons. The greatest challenge facing the cotton community is not genome sequencing per se but the conversion of sequence to knowledge.     

Proteomic Analysis of Allergen and Antinutritional Proteins in Wild and Cultivated Soybean Seeds

In this study, profiles of allergen and antinutritional proteins both in wild (Glycine soja) and cultivated (Glycine max) soybean seeds were compared. We used two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) for the separation of proteins at two different pH ranges and applied a combined matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS) and liquid chromatography mass spectrometry (LC-MS/MS) analysis for the identification of proteins. Although overall distribution patterns of the allergen (Gly m Bd 60K, Gly m Bd 30K, Gly m Bd 28K) and antinutritional proteins (trypsin inhibitors and lectin) appeared similar, there was remarkable variation in the number and intensity of the protein spots between wild and cultivated genotypes. The wild genotype showed fifteen polypeptides of Gly m Bd 60K and three polypeptides of trypsin inhibitors. The cultivated genotypes showed twelve polypeptides of Gly m Bd 60K and two polypeptides of trypsin inhibitors. In contrast, the cultivated genotype showed two polypeptides of Gly m Bd 30K and three polypeptides of lectin and the wild genotype showed two and one polypeptides of Gly m Bd 30K and lectin, respectively. Two polypeptides of Gly m Bd 28K were observed in both genotypes. This is the first study reporting the comparative analysis of allergen and antinutritional proteins in both wild and cultivated soybean genotypes using combined proteomic tools.     

Genome-Wide Association Studies Using Single Nucleotide Polymorphism Markers Developed by Re-Sequencing of the Genomes of Cultivated Tomato

With the aim of understanding relationship between genetic and phenotypic variations in cultivated tomato, single nucleotide polymorphism (SNP) markers covering the whole genome of cultivated tomato were developed and genome-wide association studies (GWAS) were performed. The whole genomes of six tomato lines were sequenced with the ABI-5500xl SOLiD sequencer. Sequence reads covering ∼13.7× of the genome for each line were obtained, and mapped onto tomato reference genomes (SL2.40) to detect ∼1.5 million SNP candidates. Of the identified SNPs, 1.5% were considered to confer gene functions. In the subsequent Illumina GoldenGate assay for 1536 SNPs, 1293 SNPs were successfully genotyped, and 1248 showed polymorphisms among 663 tomato accessions. The whole-genome linkage disequilibrium (LD) analysis detected highly biased LD decays between euchromatic (58 kb) and heterochromatic regions (13.8 Mb). Subsequent GWAS identified SNPs that were significantly associated with agronomical traits, with SNP loci located near genes that were previously reported as candidates for these traits. This study demonstrates that attractive loci can be identified by performing GWAS with a large number of SNPs obtained from re-sequencing analysis.     

利用野生大豆资源创新优质抗病大豆新种质

利用野生大豆与栽培大豆种间杂交中间材料与高产栽培大豆回交转育,创新选育出蛋白质含量45％以上,蛋脂总含量63％以上,分别抗大豆疫霉根腐病,抗大豆灰斑病,农艺性状优良的大豆创新种质资源3份。其中,龙品8802-1抗大豆疫霉根腐病兼抗大豆灰斑病,蛋白质含量45．64％,脂肪含量18．42％,蛋脂总含量64．06％;龙品01-757抗大豆灰斑病,蛋白质含量45．99％,脂肪含量19．4％,蛋脂总含量65．39％;龙品9501,中抗大豆灰斑病,蛋白质含量45．11％,脂肪含量18．32％,蛋脂总含量63．43％。研究结果表明,利用含有野生大豆血缘的种间杂交材料与高产栽培大豆回交,是拓宽大豆遗传基础,创新选育优质、抗病、农艺性状优良大豆新种质资源的有效途径。     

The Effect of Ventilation on in vitro Response of Seedlings of the Cultivated Tomato and its Wild Salt-tolerant Relative Lycopersicon pennellii to Salt Stress

Organs or plants grown in vitro do not always exhibit the same responses to salinity as the whole plant of same species grown ex vitro. The response to salinity (100 mM NaCl) of seedlings of the wild tomato species Lycopersicon pennellii acc. Atico (Lpa) and of the cultivated tomato L. esculentum cv. M82 (Lem), the former is known as salt tolerant and the second as relatively salt sensitive under ex vitro conditions, was compared under in vitro conditions with three different ventilation regimes. It was found that under salinity shoots of the wild species accumulated the same or even more dry biomass than the control (roots somewhat less) under all ventilation levels. Growth of shoots and roots of the cultivated species was inhibited under the same conditions especially under the high ventilation. Ventilation reduced some abnormalities of leaf development related to hyperhydricity and consequently ventilated leaves exhibited a more compounded structure, increased area, increased resistance to water loss and stomata functioning. Ventilation increased K⁺, Na⁺ and Cl⁻ accumulation in shoots of both tomato species. This was more pronounced under salinity and in Lpa. This work indicates that differences that characterize whole plants of these species in response to salinity under ex vitro conditions are exhibited also in whole plants grown in vitro under high ventilation. It is suggested that ventilation is needed to evaluate well the response of whole plants to salt stress applied in vitro.     

黑龙江省野生大豆、栽培大豆高异黄酮种质资源筛选

利用改进的高效液相色谱法(HPLC)检测了黑龙江省野生大豆(Glycine soja)、栽培大豆(G. max) 60份种质资源的异黄酮含量.结果表明,不同类型大豆种质资源异黄酮含量有明显遗传差异,变幅为416.2～6808.2μg/g,野生大豆高于栽培大豆,筛选出高异黄酮野生大豆种质资源4份、高异黄酮栽培大豆种质资源2份.     

野生大豆光温反应规律的研究

野生大豆（G .Soja）是栽培大豆的近缘祖光种,利用中国野生大豆分布的广泛性,为我们了解和认识大豆在自然界中光温反应的规律提供了条件。通过对29个纬度区自然生长的野生大豆主要生育阶段光温反应特点的了解,明确了不同纬度区野生大豆在自然环境中出苗温度是13.1～14.7℃,开花期温度是20.5～26.5℃,成熟期温度是10～19℃;初花期临界光照时数是13h15min至16h40min之间。出苗越早的低纬度区野生大豆开花和成熟期越晚,而出苗越晚的高纬度区野生大豆开化和成熟期越早。     

Stomatal Response of some Cultivated and Wild Tuber-bearing Potatoes in Warm Tropics as Influenced by Water Deficits

Leaf resistances of 14 cultivated potato genotypes (Solanumspp) and three tuber-bearing wild Solanum species were comparedwhen plants were grown under water stress at two tropical sitesFactors investigated were diurnal changes in leaf resistance,the effect of plant age, transient drought versus well-wateredconditions of potted and field-grown plants These measurementswere carried out in order to determine the stomatal behaviourof tuber-bearing genotypes and species Significant genotypic differences in leaf resistances were notedwithin the cultivated genotypes All genotypes had higher resistanceswhen water-stressed, but LT-7 appeared to have the lowest leafresistances Genetic differences in stomatal behaviour of tuber-bearingSolanum species were confirmed Abaxial stomatal resistancesof water-stressed plants of the species ranged between 1 74and 13 8 s cm^–1 Stomata of S chacoense were less affectedby drought (three-fold) than S tuberosum (four-fold) The greatesteffect was on S jungasense (five-fold) and on S raphanifoliumThese data show that stomata behaviour among tuber-bearing Solanumspecies is sufficiently different to warrant investigationsof drought-resistance in potato species under dry hot conditions Solanum tuberosum L., Solanum raphanifolium, Solanum chacoense, Solanum jungasense, leaf resistance     

大豆耐盐性种质资源SSR遗传多样性及标记辅助鉴定

本研究利用60对SSR引物对93份大豆1级耐盐种质资源和57份盐敏感种质资源(5级)进行分析,以确定耐盐种质资源和盐敏感种质资源的遗传多样性,以及耐盐相关标记在种质资源耐盐性鉴定中的利用程度.60个位点共检测出等位变异792个,平均13.2个,其中耐盐种质资源特有等位变异133个,盐敏感种质资源特有等位变异106个,但76.0%的等位变异频率低于0.10,仅有1.8%的等位变异出现频率高于0.40.耐盐种质资源多态性信息含量(PIC)平均为0.78(0.47～0.90),盐敏感种质资源PIC平均为0.80(0.46～0.94).根据主成分分析,耐盐和盐敏感种质资源多样性分布规律相似.然而,与耐盐基因相关的一个SSR位点的等位变异分布频率在耐盐和盐敏感种质资源间无显著差异.根据UPGMA聚类分析结果,耐盐种质资源按生态区分为3个类群,类群Ⅰ和Ⅲ分别以东北春大豆和北方春大豆为主,类群Ⅱ为黄淮夏大豆和其他生态类型的混合群.     

Complete Sequencing of Five Araliaceae Chloroplast Genomes and the Phylogenetic Implications

Background

The ginseng family (Araliaceae) includes a number of economically important plant species. Previously phylogenetic studies circumscribed three major clades within the core ginseng plant family, yet the internal relationships of each major group have been poorly resolved perhaps due to rapid radiation of these lineages. Recent studies have shown that phyogenomics based on chloroplast genomes provides a viable way to resolve complex relationships.

Methodology/Principal Findings

We report the complete nucleotide sequences of five Araliaceae chloroplast genomes using next-generation sequencing technology. The five chloroplast genomes are 156,333–156,459 bp in length including a pair of inverted repeats (25,551–26,108 bp) separated by the large single-copy (86,028–86,566 bp) and small single-copy (18,021–19,117 bp) regions. Each chloroplast genome contains the same 114 unique genes consisting of 30 transfer RNA genes, four ribosomal RNA genes, and 80 protein coding genes. Gene size, content, and order, AT content, and IR/SC boundary structure are similar among all Araliaceae chloroplast genomes. A total of 140 repeats were identified in the five chloroplast genomes with palindromic repeat as the most common type. Phylogenomic analyses using parsimony, likelihood, and Bayesian inference based on the complete chloroplast genomes strongly supported the monophyly of the Asian Palmate group and the Aralia-Panax group. Furthermore, the relationships among the sampled taxa within the Asian Palmate group were well resolved. Twenty-six DNA markers with the percentage of variable sites higher than 5% were identified, which may be useful for phylogenetic studies of Araliaceae.

Conclusion

The chloroplast genomes of Araliaceae are highly conserved in all aspects of genome features. The large-scale phylogenomic data based on the complete chloroplast DNA sequences is shown to be effective for the phylogenetic reconstruction of Araliaceae.     

Construction of a Chimeric Thermostable Pyrophosphatase To Facilitate Its Purification and Immobilization by Using the Choline-Binding Tag

The thermophilic inorganic pyrophosphatase (Pyr) from Thermus thermophilus has been produced in Escherichia coli fused to the C terminus of the choline-binding tag (ChB tag) derived from the choline-binding domain (ChBD) of pneumococcal LytA autolysin. The chimeric ChBD-Pyr protein retains its thermostable activity and can be purified in a single step by DEAE-cellulose affinity chromatography. Pyr can be further released from the ChBD by thrombin, using the specific protease recognition site incorporated in the C terminus of this tag. Remarkably, the ChB tag provides a selective and very strong thermostable noncovalent immobilization of ChBD-Pyr in the DEAE-cellulose matrix. The binding of choline or choline analogues, such as DEAE, confers a high thermal stability to this tag; therefore, the immobilized chimeric enzyme can be assayed at high temperature without protein leakage, demonstrating the usefulness of the ChB tag for noncovalent immobilization of thermophilic proteins. Moreover, ChBD-Pyr can be purified and immobilized in a single step on commercial DEAE-cellulose paper. The affinity of the ChB tag for this versatile solid support can be very helpful in developing many biotechnological applications.     

Studies on rDNA ITS1 Regions of Soybean and Its Wild Relatives

The rDNA internal transcribed spacer 1 (ITS1) regions of wild soybean (Glycine soja), semiwild soybean (G. gracillis), perennial wild soybean (G. tomentella, G. tabacina) and two accessions of cultivated soybean (G. max) were amplified by PCR and cloned. The copy number in soybean genome was about 2 × 103. Sequence analysis showed that the G/C content of G. soja (61.40%), G. gracillis (61.40%), G. max (61.40%), G. tabacina (58.11%) and G. tomentella (59.01%) were very similar to that of Phaseolus radiatus (59.81%), and the G/C content of G. tabacina was the lowest one in all known ITS1 re- gions of plants. Maxium-homology analysis proved that the ITS1 sequence of soybean was the most homologous to its counterpart of P. radiatus. It was implied that the homology of ITS1 regions of relative species were related with the genetic relationships among these species. Sequence analysis disclosed that there were two conserved sequences (GACCCGC- GAA) and (GCGCCAAGGAA) in all sequenced ITS1 regions of plants.     

Heteroplasmy in the Mitochondrial Genomes of Human Lice and Ticks Revealed by High Throughput Sequencing

The typical mitochondrial (mt) genomes of bilateral animals consist of 37 genes on a single circular chromosome. The mt genomes of the human body louse, Pediculus humanus, and the human head louse, Pediculus capitis, however, are extensively fragmented and contain 20 minichromosomes, with one to three genes on each minichromosome. Heteroplasmy, i.e. nucleotide polymorphisms in the mt genome within individuals, has been shown to be significantly higher in the mt cox1 gene of human lice than in humans and other animals that have the typical mt genomes. To understand whether the extent of heteroplasmy in human lice is associated with mt genome fragmentation, we sequenced the entire coding regions of all of the mt minichromosomes of six human body lice and six human head lice from Ethiopia, China and France with an Illumina HiSeq platform. For comparison, we also sequenced the entire coding regions of the mt genomes of seven species of ticks, which have the typical mitochondrial genome organization of bilateral animals. We found that the level of heteroplasmy varies significantly both among the human lice and among the ticks. The human lice from Ethiopia have significantly higher level of heteroplasmy than those from China and France (P_t<0.05). The tick, Amblyomma cajennense, has significantly higher level of heteroplasmy than other ticks (P_t<0.05). Our results indicate that heteroplasmy level can be substantially variable within a species and among closely related species, and does not appear to be determined by single factors such as genome fragmentation.