Application of resequencing to rice genomics,functional genomics and evolutionary analysis

Rice is a model system used for crop genomics studies. The completion of the rice genome draft sequences in 2002 not only accelerated functional genome studies, but also initiated a new era of resequencing rice genomes. Based on the reference genome in rice, next-generation sequencing (NGS) using the high-throughput sequencing system can efficiently accomplish whole genome resequencing of various genetic populations and diverse germplasm resources. Resequencing technology has been effectively utilized in evolutionary analysis, rice genomics and functional genomics studies. This technique is beneficial for both bridging the knowledge gap between genotype and phenotype and facilitating molecular breeding via gene design in rice. Here, we also discuss the limitation, application and future prospects of rice resequencing.     

油菜重要性状功能基因研究进展

为实现从传统育种向以基因（或基因组）信息为依据的分子育种转型,研究油菜功能基因组是重要的基础和前提。本文综述了近几年异源四倍体油菜功能基因组研究进展,重点概述了油菜雄性不育、产量、品质和养分代谢等重要性状的功能基因研究结果,并针对我国油菜功能基因组研究和生产育种现状,提出推进功能基因组研究成果应用于育种体系,培育我国自主的高效型油菜重大品种的有关建议,以增强我国生物技术育种的国际竞争力。     

Genomic analysis of isopentenyltransferase genes and functional characterization of TaIPT8 indicates positive effects of cytokinins on drought tolerance in wheat

Cytokinins(CKs) function in plant development and during stress responses, but their role in drought tolerance in wheat is unknown. In the present study, 24 isopentenyltransferase(IPT) genes, encoding ratelimiting enzymes in CK biosynthesis were identified in the wheat genome. The chromosomal locations and structures of the genes, protein properties, and phylogenetic relationships were characterized.ATP/ADP TaIPT genes showed tissue-specific expression. TaIPT2, TaIPT7, and TaIPT8 expression was ...     

Waxy wheat as a functional food for human consumption

Waxy wheat (Triticum aestivum L.), a type of wheat that was first developed in Japan, produces grain amylopectin. I carried out three researches. Firstly, using Japanese adults, we carried out sensory evaluation of three types of mochi (a dumpling-like cake made of steamed and pounded grains) prepared from waxy wheat, normal wheat and waxy rice, and demonstrated that waxy wheat mochi had low adhesiveness and had the greatest ease of swallowing among the samples tested. Secondly, using the members of the JSDR (the Japanese Society of Dysphagia Rehabilitation) who attended the annual meeting, we performed another texture evaluations between waxy wheat and waxy rice mochi. The respondents reported waxy wheat mochi was less sticky and thus easier to chew and swallow than waxy rice mochi.     

Spatial distribution of functional components in the starchy endosperm of wheat grains

The starchy endosperm of the mature wheat grain comprises three major cell types, namely sub-aleurone cells, prismatic cells and central cells, which differ in their contents of functional components: gluten proteins, starch, cell wall polysaccharides (dietary fibre) and lipids. Gradients are established during grain development but may be modified during grain maturation and are affected by plant nutrition, particularly nitrogen application, and environmental factors. Although the molecular controls of their formation are unknown, the high content of protein and low content of starch of sub-aleurone cells, compared to the other starchy endosperm cells types, may result from differences in developmental programming related to the cells having a separate origin (from anticlinal division of the aleurone cells). The gradients within the grain may be reflected in differences in the compositions of mill streams, particularly those streams enriched in the central and outer cells of the starchy endosperm, respectively, allowing the production of specialist flours for specific end uses.     

Improvement on functional properties of wheat gluten by enzymatic hydrolysis and ultrafiltration

Four fractions (100-, 50-, 20-K and permeate) from a proteolytic hydrolysate (DH=2.8%) of wheat gluten were separated using size fractionation on ultrafiltration membranes with molecular weight cut-offs of 100, 50 and 20 kDa and their functional properties evaluated. Proteolysis led to a significant (P<0.05) increase in solubility of gluten fractions at pHs between 2–10 and a shift of the pI value from 6–7 to 5. The solubilities of 100-K, 50-K, 20-K and permeate fractions were significantly (P<0.05) improved compared with the untreated control and the hydrolysate. The 50-K fraction was superior to other three fractions for emulsion activity index between pH 2 and 10. The most stable foam was given by the 100-K fraction which showed 65.8% of initial foam while the control sample gave only 23% of foam, after 60 min resting. Foam stability decreased as the molecular mass of hydrolysate fractions decreased. Furthermore, after proteolysis, the surface hydrophobicity (H₀) of gluten increased significantly (P<0.05) compared with the control except for the permeate fraction. The highest value of H₀ was given by the 100-K fraction, followed by the 50-K, 20-K and permeate fractions. In addition, proteolysis resulted in a decrease in the storage modulus of gels.     

花生基因组资源的开发及应用

花生是世界主要的油料作物,但由于花生本身的遗传特性,导致其基因组资源的开发和利用存在较大难度。花生的高度闭花授粉、初级基因库遗传基础狭窄以及栽培种与二倍体近缘野生种之间的杂交不亲和性,导致花生栽培种的分子遗传多样性偏低,成为花生分子遗传改良的主要瓶颈。然而,近五年来,花生基因组资源开发迅速,分子标记的开发、遗传和物理图谱的构建、表达序列标签（ESTs）的产生、突变体资源的创建和功能基因组学平台的构建促进了QTL的鉴定以及与农艺性状相关的耐/抗生物和非生物胁迫基因的挖掘。本文概述了当前花生基因组资源的研究现状,并对下一步的发展方向进行了展望。     

Effect of wheat bran and enzyme addition on dough functional performance and phytic acid levels in bread

Effects of bran concentration, bran particle size distribution, and enzyme addition – fungal phytase, fungal alpha-amylase – on the mixing and fermentative behaviour of wheat dough and on the amount of phytic acid remaining in bread have been investigated using a factorial design of samples 2⁴. Bran concentration and bran particle size significantly affected all Farinograph parameters, whereas enzyme effects were particularly observed on both the water absorption of the flour and the parameters characterizing the overmixing. Water absorption was maximized in doughs with higher fine bran addition and/or in doughs with no enzymes, and was minimized in blends containing coarse added bran and alpha-amylase and/or alpha-amylase and phytase. alpha-Amylase addition had a significant positive effect on dough development and gassing power parameters during proofing. At low bran addition, phytate hydrolysis takes place to a greater extent than at high bran addition levels. Combination of bran with amylolytic and phytate-degrading enzymes could be advisable for overcoming the detrimental effect of bran on the mineral availability (phytase) or on the technological performance of doughs (alpha-amylase).     

Effect of wheat bran and enzyme addition on dough functional performance and phytic acid levels in bread

Effects of bran concentration, bran particle size distribution, and enzyme addition – fungal phytase, fungal alpha-amylase – on the mixing and fermentative behaviour of wheat dough and on the amount of phytic acid remaining in bread have been investigated using a factorial design of samples 2⁴. Bran concentration and bran particle size significantly affected all Farinograph parameters, whereas enzyme effects were particularly observed on both the water absorption of the flour and the parameters characterizing the overmixing. Water absorption was maximized in doughs with higher fine bran addition and/or in doughs with no enzymes, and was minimized in blends containing coarse added bran and alpha-amylase and/or alpha-amylase and phytase. alpha-Amylase addition had a significant positive effect on dough development and gassing power parameters during proofing. At low bran addition, phytate hydrolysis takes place to a greater extent than at high bran addition levels. Combination of bran with amylolytic and phytate-degrading enzymes could be advisable for overcoming the detrimental effect of bran on the mineral availability (phytase) or on the technological performance of doughs (alpha-amylase).     

Genetic analysis of soft white wheat end-use quality traits in a club by common wheat cross

Improved understanding of the genetic architecture of end-use quality traits and identification of associated quantitative trait loci (QTL) allow breeders to target loci and clarify the complex relationships among these traits. A set of 207 recombinant inbred lines from a ‘Coda’ by ‘Brundage’ soft wheat mapping population was grown in five environments over four years at Aberdeen, ID, Moscow, ID, and Pullman, WA, USA. The population was evaluated for grain, milling, and baking end-use quality traits using AACCI methods. A linkage map consisting of 570 single nucleotide polymorphisms and 136 simple sequence repeat markers was developed using JMP Genomics. This linkage map covered 20 of the 21 wheat chromosomes. Multiple interval mapping with the R/qtl package yielded 71 significant QTL associated with 14 end-use quality traits. QTL on chromosomes 2B, 2D, 4B and 6B were consistently associated with multiple end-use quality traits across multiple environments. Depending on the trait, both Coda and Brundage contributed favorable alleles for end-use quality. For some QTL, both Coda and Brundage contributed favorable alleles, but for different end-use quality traits, indicating these alleles may be linked in repulsion. Combining favorable alleles from each parent into a single line can improve the end-use quality. The identified QTL not only provide breeders with potentially useful markers for selection, but also improve understanding of genetic factors related to soft wheat end-use quality traits.     

Influence of high solid concentrations on enzymatic wheat gluten hydrolysis and resulting functional properties

Enzymatic hydrolysis at increased solid concentrations is beneficial with regard to energy and water consumption. This study examines the influence of the solid concentration on the enzymatic hydrolysis of wheat gluten and the resulting functional properties of the hydrolysate. Wheat gluten was mildly hydrolyzed at a solid concentration varying from 10% to 60% to degrees of hydrolysis (DH%) ranging from 3.2% to 10.2%. The gluten was susceptible to hydrolysis at all solid concentrations but the hydrolysis rate was influenced by increasing solid concentrations. Size-exclusion high-performance liquid chromatography revealed an increase in the ratio of peptides with a molecular mass >25 kDa for solid concentrations of 40% and 60%. The water solubility increased on hydrolysis and was independent of the solid concentration during proteolysis. The foam stability was not influenced by the solid concentration at low DH%. At DH% higher than 8%, high solid concentrations increased the foam stability, which might be related to the presence of more peptides with a molecular mass >25 kDa. In addition, we found increased reactor productivity. The results show the potential of hydrolyzing wheat gluten at high solid concentrations, which could lead to large savings for water and energy when applied industrially.     

Genome assembly of the maize inbred line A188 provides a new reference genome for functional genomics

The current assembled maize genomes cannot represent the broad genetic diversity of maize germplasms.Acquiring more genome sequences is critical for constructing a pan-genome and elucidating the linkage between genotype and phenotype in maize.Here we describe the genome sequence and annotation of A188,a maize inbred line with high phenotypic variation relative to other lines,acquired by single-molecule sequencing and optical genome mapping.We assembled a 2210-Mb genome with a scaffold N50 size of 11.61 million bases(Mb),compared to 9.73 Mb for B73 and 10.2 Mb for Mo17.Based on the B73_Ref Gen_V4 genome,295 scaffolds(2084.35 Mb,94.30%of the final genome assembly)were anchored and oriented on ten chromosomes.Comparative analysis revealed that~30%of the predicted A188 genes showed large structural divergence from B73,Mo17,and W22 genomes,which causes high protein divergence and may lead to phenotypic variation among the four inbred lines.As a line with high embryonic callus(EC)induction capacity,A188 provides a convenient tool for elucidating the molecular mechanism underlying the formation of EC in maize.Combining our new A188 genome with previously reported QTL and RNA sequencing data revealed eight genes with large structural variation and two differentially expressed genes playing potential roles in maize EC induction.     

核盘菌Ss160的基因克隆与功能初探

由核盘菌（Sclerotinia sclerotiorum）引起的菌核病是油菜等十字花科作物的重要病害,对油菜的产量品质造成严重影响。本研究基于转录组数据筛选到一个核盘菌基因Ss160 (Sscle04g035160),发现Ss160在接种油菜的核盘菌中高度表达。生物信息分析表明该基因具有信号肽,且序列在真菌界高度保守。亚细胞定位显示Ss160无特异性的定位,烟草叶片瞬时表达Ss160在核盘菌离体叶接种实验中病斑扩展显著小于表达空载体的和野生型烟草叶片,暗示异源表达Ss160能够提高植物的菌核病抗性。基于酵母系统的体外实验证明Ss160具有转录激活能力。该研究结果为后续Ss160在核盘菌-植物互作中功能机制的研究提供基础,也为油菜菌核病的研究提供借鉴和参考。     

Factorial cross analysis of pre-harvest sprouting resistance in white wheat

The lack of understanding of the genetics of sprouting resistance as well as the lack of white wheat germplasm with sprouting resistance is impeding the development and production of white wheat cultivars. Two sets of factorial crosses were made with 15 white wheat genotypes possessing different origins and different levels of sprouting resistance. These crosses were statistically analyzed to characterize the inheritance of sprouting resistance by assessing sprouting percentage in ears. In experiment I (5 × 10), it was shown that the general combining ability (GCA) effects of resistant (male) and susceptible (female) parents, and specific combining ability (SCA) effects were highly significant based on both single-year analysis and 2-year combined analysis. There was a significant genotype-year interaction, and the performance of F₁ hybrids was more vulnerable to environments than that of the parents. Hybrids have a greater risk of suffering from the sprouting damage than the pure lines. In experiment II (4 × 4), both GCA and SCA effects were significant for F₂s. Cultivars FLXXM, WXBMZ, SNTTM, ZTNEM and Fengchan 3 had higher sprouting resistance and are thus good donors in white wheat breeding programs for sprouting resistance.     

Differential mixing action effects on functional properties and polymeric protein size distribution of wheat dough

A micro Z-arm mixer and a 2g-Mixograph were used to compare the effect of pin and Z-arm-type mixing actions on mixing properties of wheat flour dough. Although the two mixing curves obtained with pin- and Z-arm-type mixing action showed a very similar mixing trace, no significant correlation was found between the two mixers other than the number of revolutions required for optimal dough consistency (peak resistance). Mixing requirement was described by a rate-independent parameter, the number of revolutions to peak dough development and was found to be greater in a Z-arm mixer than in a pin mixer. Mixing requirement showed significant correlation with stability, which is therefore a dough strength parameter. The change in the polymeric structure of gluten proteins of dough as indicated by %UPP (unextractable polymeric protein percentage) was monitored and showed a smaller decrease with Z-arm mixing than with pin mixing. Therefore, pin-mixing action is more energetic than Z-arm mixing. At peak resistance, Z-arm mixing gives a larger quantity of polymeric protein content in the dough relative to pin mixing. The degree of dough development at maximum resistance in the different mixers was shown to be different. A new parameter, delta-_UPPMZ${\mathrm{UPP}}_{\mathrm{MZ}}$ (the difference between %UPP of dough obtained with pin vs Z-arm mixing actions) was identified and proposed to have some relationship to the stability of the polymeric proteins in the dough.     

Milling,functional and thermo-mechanical properties of wheat,rye, triticale,barley and oat

The milling potential of hulled barley, hulled oat, triticale, rye and wheat was studied using a long tempering process and a laboratory four-roller mill. Regardless of the investigated cereal, the results indicated a significant influence (p < 0.05) of volume per surface area ratio on the milling yield and ash contents of the flour. The lowest milling yield was obtained in case of hulled oat. Solvent retention capacity profiles were determined for all investigated whole cereals and flours for predicting the contribution of different polymers to the functionality of samples. For all solvents higher values were obtained for the whole cereals compared to the corresponding flour. Thermo-mechanical properties of the whole cereals and refined flours were also investigated. If in case of wheat the gluten proteins play an essential role on dough behaviour during kneading at 30 °C, in case of triticale, rye, hulled barley and hulled oat, the fibers play a major role as well. Thermo-mechanical properties of starch registered a large variation between cereals and/or flours. The lowest torque value corresponding to starch gelatinization (C3) was registered in case of the hulled oat flour, 1.92 Nm, while the highest value in case of rye flour, 2.65 Nm.     

Intrinsic influence of various plasticizers on functional properties and reactivity of wheat gluten thermoplastic materials

Various compounds, differing in their chemical functions, number of functional group and degree of hydrophobicity, were tested as wheat gluten plasticizers in a thermoplastic process. A low melting point and a moderate hydrophobicity were found to be critical characteristics of a good wheat gluten plasticizer. The influence of five selected plasticizers (water, glycerol, 1,4-butanediol, lactic and octanoic acids) on functional properties of the wheat gluten network was investigated. Dried gluten was used to avoid any plasticization due to hydration water (usually around 10% for commercial gluten). The influence of plasticizer properties and content was studied by dynamic mechanical thermal analysis, size exclusion-high performance liquid chromatography, tensile and water swelling tests. The plasticizing effect, at the same molar content, was found to be identical for water, glycerol and 1,4-butanediol. Lactic and octanoic acids were found to have higher and lower plasticizing effects, respectively. Mechanical properties were mainly related to the thermoplastic state of the materials. Water and lactic acid were found to confer smaller and larger extensibilities, respectively, to gluten materials. Thermo-mechanical reactivity also depended on plasticizer properties. Gluten aggregation, normally induced by heating, was prevented by the acidic environment produced by lactic acid. Water swelling behaviour was found to depend on the hydrophobicity of the plasticizer used, on the degree of gluten crosslinking and on the pH of the gluten-plasticizer blend.