RNAi技术及在植物功能基因组研究中的应用

RNAi,即RNA干扰,是通过外源或内源性的双链RNA在细胞内诱导同源序列的基因表达受抑的现象,自RNAi现象在上世纪90年代中期被发现以来,它就被利用到基因组功能的分析研究之中,成为分子生物学研究的热点。本文简要阐述了RNAi的作用机制,并通过将RNAi方法与其他功能基因组研究方法的对比,阐述了RNAi作为高通量植物功能基因组研究方法的优点,同时综述了利用RNAi技术在植物功能基因组研究中的应用进展。     

Multivariate study of different beef quality traits from local Spanish cattle breeds

Different raw beef quality traits from four local Spanish cattle breeds were studied using correlation, factorial, discriminant and multiple regression analysis. The following variables were studied after 0, 5, 10 and 15 days of storage under 60% O₂, 30% CO₂ and 10% N₂ modified atmosphere packaging (MAP): colour physical variables, meat pigments, sensory degradation of odour and colour, microbial counts, thiobarbituric acid (TBA), pH, drip loss, lipid composition and volatile compounds. The degradation of raw beef quality was related to the increase in 2,3,3-trimethylpentane, 2,2,5-trimethylhexane, 3-methyl-2-heptene, 2-octene, 3-octene, 2-propanone, Enterobacteriaceae and aerobial plate counts (APC), metmyoglobin (MMb), lightness (L*), yellowness (b*), drip loss and TBA. Among these variables, TBA, b* and MMb may be useful in evaluating raw beef quality. No variables related to fat, except for TBA, including pH were limiting factors of the colour and odour shelf-life of raw beef under MAP. Each breed had some characteristics that were unique and these differences may influence the stability of meat to oxidation depending on myoglobin concentration and the polyunsaturated fatty acid (PUFA)/saturated fatty acid (SFA) ratio.     

RNA干扰文库在功能基因组学研究中的发展及应用

RNA干扰（RNAi）是双链RNA分子在mRNA水平上诱发的序列特异性转录后基因表达沉默,从基因组水平设计针对多个靶基因的RNAi序列,建立RNAi文库进行系统性、大规模的筛选工作是功能基因组学研究的有力工具。目前RNAi文库主要包括质粒（或病毒）文库、siRNA表达盒文库、寡核苷酸文库和随机RNAi文库,已经被成功应用于基因功能鉴别、信号转导途径解析和药物靶标筛选等研究领域。近年来,这一领域发展迅速,本文就RNAi文库的发展应用以及存在的问题与展望进行综述。     

Recent advances in conifer somatic embryogenesis: improving somatic embryo quality

Somatic embryogenesis of coniferous species was first reported more than 20 years ago. Since then, there has been an explosion of research aimed at developing and optimizing protocols for efficient regeneration of plantlets. Although routinely used both as a means of propagation, as well as a valuable model system for investigating the structural, physiological, and molecular events occurring during embryo development, in vitro embryogenesis is still problematic for some coniferous species. Major problems include: low number of embryos generated; and low frequency of mature embryos able to convert into viable plantlets. Until recent years, despite the fact that embryogenesis is comprised of a sequence of defined steps which include proliferation of embryogenic tissue, embryo maturation, and germination, attempts at improving the whole procedure have been made almost exclusively during the maturation stage. This strategy was based on the assumption that successful regeneration is related to treatments provided during the development of the embryos. Major optimizations of the maturation medium have involved judicious selections of type and concentration of growth regulators, namely abscisic acid, and adjustments of the osmoticum of the culture medium. Extensive work has been conducted in defining the effects of plasmolysing and non-plasmolysing osmoticum agents during maturation, as well as in improving desiccation techniques required for the completion of the maturation program. In the last 2 years, however, work on spruce has clearly demonstrated that the early events in embryogenesis are crucial for the successful completion of the overall embryogenic program. The use of cell tracking techniques, implemented by physiological and molecular studies, has revealed that manipulations of the culture conditions early in the process can increase both number and quality of embryos produced in culture. Additional manipulations of the germination medium can also enhance germination and conversion frequency of somatic embryos matured in a sub-optimal environment. These new findings, together with the unraveling of molecular mechanisms involved in the control/regulation of embryo development hold considerable promise for clonal propagation in conifers.     

Origin and assessment of bruises in beef cattle at slaughter

Studies of bruises, as detected on carcasses at the slaughterhouse, may provide useful information about the traumatic situations the animals endure during the pre-slaughter period. In this paper, we review scientific data on the prevalence, risk factors and estimation of the age of bruises in beef cattle. Risk factors such as animal characteristics, transport conditions, stocking density, livestock auction and handling of the animals are discussed. Investigation of the age of bruises could provide information on when in the meat chain bruises occur and, could help to pinpoint where preventive measures should be taken, from the stage of collecting the animals on the farm until slaughter. We review the methods available to assess the age of the bruises; data on human forensic research are also included. The feasibility to identify traumatic episodes during the pre-slaughter period, in order to improve animal welfare is discussed.     

Breed variation and genetic parameters for growth and body development in diverse beef cattle genotypes

Conformation scores can account for more than 20% of cattle price variation at Australian livestock sales. However, there are limited available references which define genetic factors relating objective live developmental traits to carcass composition. Weaning and post-weaning weight, height, length, girth, muscle (ratio of stifle to hip width) and fat depth of 1202 progeny from mature Hereford cows (637) mated to seven sire breeds (Jersey, Wagyu, Angus, Hereford, South Devon, Limousin and Belgian Blue) were examined for growth and development across ages. Crossbred Wagyu and Jersey were both lighter in weight and smaller in size (height, length and girth) than purebred Hereford and crossbred Angus, South Devon, Limousin and Belgian Blue. Within the five larger crossbreds, there were significant changes in relative weight from weaning to 600 days. Sire breeds differed in fat depth, with Angus being the fattest (9% on average fatter than Hereford and Wagyu), and Jersey 5% less fat than Hereford, followed by South Devon and Limousin (19% lower than Hereford) and Belgian Blue (39% lower than Hereford). Direct heritability ranged from 19 to 42% and was higher than the proportion of total phenotypic variance accounted for by maternal effects (which ranged from 0 to 17%) for most body measurement traits except for weight (38 v. 18%) and girth (36 v. 9%) traits at weaning, an indication of maternal effect on some body conformation traits at early ages. Muscularity (19 to 44%) and fat depth (26 to 43%) were moderately to highly heritable across ages. There were large differences for growth and the objective measures of body development between crossbreds with a degree of overlap among the progeny of the seven sire breeds. The variation between genetic (positive) and environmental (negative) correlations for dry versus wet season average daily gains in weight and fat, suggested the potential use of live-animal conformation traits for within breed selection of genetically superior animal in these traits across seasons.     

Effects of castration and time-on-feed on Mertolenga breed beef quality

Physicochemical characteristics were determined in the longissimus lumborum muscle, after 8 days of ageing of steers (n=12) and bulls (n=12) from Mertolenga breed slaughtered directly from pasture (day 0) or after a finishing period of 50, 100 and 150 days in a feed-lot facility. Bulls and steers presented similar live weight (averaging 388 kg), carcass weight (CW; averaging 213 kg), dressing percentage (averaging 60%), carcass fatness (11.9% CW) and carcass fat thickness (averaging 3.03 mm). Live weight, CW, carcass fatness and fat thickness increased along time-on-feed. Gender only had a negligible effect on meat characteristics, with b* and h* being the only parameters of colour affected by gender, also presenting a significant interaction gender×time-on-feed. Nevertheless, both the genders presented a high-quality grade concerning tenderness (Warner–Bratzler shear force (WBSF)). L* increased until 50 days on feed and decreased afterwards, whereas a* and C* values increased along time-on-feed. Pigment content was also affected by time-on-feed and showed a gender×time-on-feed interaction. Beef colour became darker and redder along time-on-feed, but still in a colour range highly acceptable by Portuguese consumers. Despite the increase in intramuscular fat and myofibrillar fragmentation index, as well as the decrease in collagen content of steers and bulls along time-on-feed, it did not affect the tenderness/hardness, indicating a small effect of time-on-feed in meat characteristics. Despite only small differences in carcass characteristics and meat-quality parameters that have been noticed along time-on-feed, those differences were only significant after 100 days on feed. Principal component analysis (PCA) was performed. The first PC axis (39.6% of the total variance) included colour variables a*, b* and C*, and carcass fatness, fat thickness, CW and live weight, whereas the second one (12.7% of the total variance) included h*, cooking losses and dressing-out. The principal component (PC) analysis confirmed the lack of differences between bulls and steers and indicates a differentiation of the first two periods of feeding (0 and 50 days on feed) from the two latter (100 and 150 days on feed) periods of feeding.     

Approaches to functional genomics in filamentous fungi

The study of gene function in filamentous fungi is a field of research that has made great advances in very recent years. A number of transformation and gene manipulation strategies have been developed and applied to a diverse and rapidly expanding list of economically important filamentous fungi and oomycetes. With the significant number of fungal genomes now sequenced or being sequenced, functional genomics promises to uncover a great deal of new information in coming years. This review discusses recent advances that have been made in examining gene function in filamentous fungi and describes the advantages and limitations of the different approaches.     

Physiologic and innate immunity responses to bacterial lipopolysaccharide administration in beef heifers supplemented with OmniGen-AF

Nutritional alternatives to strengthen animal immunocompetence are critical for welfare and productivity in livestock systems, such as beef cattle operations. This experiment evaluated physiological and innate immunity effects of supplementing an immunomodulatory feed ingredient (Omnigen-AF; Phibro Animal Health, Teaneck, NJ, USA) to beef heifers administered bacterial lipopolysaccharide (LPS). In total, 8 non-pregnant, non-lactating nulliparous Angus×Hereford heifers (676±4 days of age) were ranked by BW (473±8 kg), and assigned to crossover design containing two periods of 34 days each. Heifers were housed in individual pens and had ad libitum access to meadow foxtail (Alopecurus pratensis L.) hay, water and a granulated commercial vitamin+mineral mix. Within each period, heifers received (as-fed basis) 227 g/day of dried distillers grains including (OMN) or not (CON) 56 g of Omnigen-AF for 34 days. On day 28 of each period (0800 h), heifers received an intravenous bolus dose (0.5 μg/kg of BW, diluted in 5 ml of 0.9% sterile saline) of bacterial LPS (Escherichia coli 0111:B4). Hay DM intake was recorded daily from day 0 to 34. Blood was collected at −1, 0, 0.5, 1, 1.5, 2, 2.5, 3, 4, 5, 6, 24, 48, 72, 96, 120 and 144 h relative to LPS administration. Heifer intravaginal temperature was recorded every 10 min from −0.5 to 10 h relative to LPS administration. No treatment effect was detected (P=0.35) for hay DM intake during the experiment. No treatment effects were detected (P⩾0.64) for intravaginal temperature and plasma concentrations of tumor necrosis-α, cortisol and haptoglobin, which increased (time effect, P<0.01) for OMN and CON heifers and peaked at 4.5, 2, 4 and 48 h, respectively, after LPS administration. No treatment effects were detected (P⩾0.35) for whole blood mRNA expression of chemokine ligand 5, tumor necrosis-α, cyclooxygenase 2 and interleukin 8, which also increased (time effect, P<0.01) for OMN and CON heifers and peaked at 0.5, 1.5, 2 and 2.5 h, respectively, after LPS administration. Whole blood mRNA expression of interleukin 8 receptor and L-selectin were also similar (P⩾0.61) between OMN and CON heifers, and decreased (time effect, P<0.01) for both treatments reaching nadir levels at 1 and 2.5 h, respectively, after LPS administration. Collectively, OMN supplementation did not modulate the physiological and innate immunity responses of beef heifers to bacterial LPS administration.     

Prediction of beef eating quality in France using the Meat Standards Australia system

An experiment was set up for (i) comparing Australian and French consumer preferences to beef and to (ii) quantify how well the Meat Standards Australia (MSA) grading model could predict the eating quality of beef in France. Six muscles from 18 Australian and 18 French cattle were tested as paired samples. In France, steaks were grilled ‘medium’ or ‘rare’, whereas in Australia ‘medium’ cooking was used. In total, 360 French consumers took part in the ‘medium’ cooking test, with each eating half Australian beef and half French beef and 180 French consumers tested the ‘rare’ beef. Consumers scored steaks for tenderness (tn), juiciness (ju), flavour liking (fl) and overall liking (ov). They also assigned a quality rating to each sample: ‘unsatisfactory’, ‘satisfactory everyday quality’ (3*), ‘better than everyday quality’ (4*) or ‘premium quality’ (5*). The prediction of the final ratings (3*, 4*, 5*) by the French consumers using the MSA-weighted eating quality score (0.3 tn + 0.1 ju + 0.3 fl + 0.3 ov) was over 70%, which is at least similar to the Australian experience. The boundaries between ‘unsatisfactory’, 3*, 4* and 5* were found to be ca. 38, 61 and 80, respectively. The differences between extreme classes are therefore slightly more important in France than in Australia. On average, even though it does not have predictive equations for bull meat, the mean predicted scores calculated by the MSA model deviated from observed values by a maximum of 5 points on a 0 to 100 scale except for the Australian oyster blade and the French topside, rump and outside (deviating by <15). Overall, the data indicate that it would be possible to manage a grading system in France as there is high agreement and consistency across consumers. The ‘rare’ and ‘medium’ results are also very similar, indicating that a common set of weightings and cut-offs can be employed.     

香蕉品质相关功能基因组学的研究进展

香蕉是重要的热带水果之一,是热区人民脱贫致富的主要经济来源。香蕉品质一直是人们关注的焦点。文章综述了近年来香蕉果实品质如成熟、软化、糖代谢及香气相关功能基因分离和鉴定等方面的最新研究进展,将有助于从源头上对香蕉进行创新性的探索与研究,支撑香蕉品质改良和新品种培育。     

Detection of quantitative trait loci for meat quality traits in cattle

A whole-genome scan was carried out to detect quantitative trait loci (QTL) affecting sensory, organoleptic, physical and chemical properties of meat. The study used phenotypic data from 235 second-generation cross-bred bull calves of a Charolais × Holstein experimental population. Loin muscle samples were evaluated for yield force, intramuscular fat and nitrogen contents, myofibrillar fragmentation index, haem pigment concentration, moisture content and pH at 24 h postmortem. A sensory assessment was performed on grilled loin and roasted silverside joints by trained panellists. A linear regression analysis based on 165 markers revealed 35 QTL at the 5% chromosome-wide significance level (20 for sensory traits and 15 for physical and chemical traits), five of which were highly significant ( F -value: ≥9). The most significant QTL was located on chromosome 6 (with the best likely position at 39 cM) and affected haem pigment concentration. The Holstein allele for this QTL was associated with an increase of 0.53 SD in the haem scores. A QTL for pH_24h was identified on chromosome 14 (at 40 cM) and a QTL for moisture content was identified on chromosome 22 (at 21 cM). Two highly significant QTL were identified for sensory panel-assessed traits: beef odour intensity (grilled sample) on chromosome 10 (at 119 cM), and juiciness (roast sample) on chromosome 16 (at 70 cM). The proportion of phenotypic variance explained by the significant QTL ranged from 3.6% (for nitrogen content on chromosome 10) to 9.5% (for juiciness, roast sample on chromosome 16).     

Effects of replacing grass silage with maize silages differing in inclusion level and maturity on the performance,meat quality and concentrate-sparing effect of beef cattle

The effects of maturity of maize at harvest, level of inclusion and potential interactions on the performance, carcass composition, meat quality and potential concentrate-sparing effect when offered to finishing beef cattle were studied. Two maize silages were ensiled that had dry matter (DM) concentrations of 217 and 304 g/kg and starch concentrations of 55 and 258 g/kg DM, respectively. Grass silage was offered as the sole forage supplemented with either 4 or 8 kg concentrate/steer daily or in addition with one of the two maize silages at a ratio 0.5 : 0.5, on a DM basis, maize silage : grass silage supplemented with 4 kg concentrate daily. The two maize silages were also offered as the sole forage supplemented with 4 kg concentrate/steer daily. The forages were offered ad libitum. The six diets were offered to 72 steers (initial live weight 522 s.d. 23.5 kg) for 146 days. There were significant interactions (P < 0.05) between maize maturity and inclusion level for food intake, fibre digestibility and daily gain. For the grass silage supplemented with 4 or 8 kg concentrate, and the maize silages with DM concentrations of 217 and 304 g/kg offered as 0.5 or 1.0 of the forage component of the diet, total DM intakes were 8.3, 9.8, 8.9, 8.2, 9.2 and 9.8 kg DM/day (s.e. 0.27); live-weight gains were 0.74, 1.17, 0.86, 0.71, 0.88 and 1.03 kg/day (s.e. 0.057); and carcass gains were 0.48, 0.73, 0.56, 0.46, 0.56 and 0.63 kg/day (s.e. 0.037), respectively. Increasing the level of concentrate (offered with grass silage), maize maturity and level of maize inclusion reduced (P < 0.05) fat b* (yellowness). The potential daily concentrate-sparing effect, as determined by carcass gain, for the maize silages with DM concentrations of 217 and 304 g/kg offered as 0.5 and 1.0 of the forage component of the diet were 1.3, −0.3, 1.3 and 2.4 kg fresh weight, respectively. It is concluded that the response, in animal performance, including maize silage is dependent on the stage of maturity and level of inclusion in the diet. Maize silage with a DM of 304 g/kg offered ad libitum increased carcass gain by 31%, because of a combination of increased metabolizable energy (ME) intake and improved efficiency of utilization of ME, and produced carcasses with whiter fat.     

High-throughput RNAi in Caenorhabditis elegans: genome-wide screens and functional genomics

The phenomenon of RNA-mediated interference (RNAi) was first discovered in the nematode Caenorhabditis elegans, in which introduction of double-stranded RNA causes specific inactivation of genes with corresponding sequences. Technical advances in RNAi methodology and the availability of the complete genome sequence have enabled the high-throughput, genome-wide RNAi analysis of this organism. Several groups have used large-scale RNAi to systematically examine every C. elegans gene for knock-down phenotypes, providing basal information to be mined in more detailed studies. Now, in addition to functional genomic RNAi analyses, high-throughput RNAi is also routinely used for rapid, genome-wide screens for genes involved in specific biological processes. The integration of high-throughput RNAi experiments with other large-scale data, such as DNA microarrays and protein-protein interaction maps, enhances the speed and reliability of such screens. The accumulation of RNAi phenotype data dramatically accelerates our understanding of this organism at the genetic level.     

The effects of grain treatment, grain feed level and grass silage feed value on the performance of and meat quality from, finishing beef cattle

A completely randomised design study involving 132 continental crossbred beef steers was undertaken to evaluate the effects of method of grain treatment and feed level, and grass silage feed value on animal performance, carcass characteristics and meat quality of beef cattle. Winter wheat was harvested and the grain was stored either ensiled crimped and treated with 4.5 l/t of a proprietary acid-based additive (crimped), ensiled whole and treated with 20 kg feed-grade urea per t (urea) or stored conventionally in an open bin treated with 3 l propionic acid per t. Two grass silages, of contrasting feed value (L and H) were ensiled. For the conventional, crimped and urea treatments, grain dry matter (DM) concentrations were 802, 658 and 640 g/kg, respectively. For the L- and H-feed value silages, DM concentrations were 192 and 240 g/kg and D values were 671 and 730 g/kg DM, respectively. The silages were offered as the sole forage supplemented with either conventional, crimped or urea-treated grain-based concentrate at either 3.5 or 6.0 kg DM per steer per day. The grain supplement consisted of 850 and 150 g/kg DM of grain and citrus pulp, respectively. For the conventional, urea and crimped treatments, DM intakes were 8.85, 9.43 and 9.04 kg/day (standard error (s.e.) = 0.129); estimated carcass gains were 0.60, 0.55 and 0.61 kg/day (s.e. = 0.020), respectively. For the low- and high- feed value grass silages, estimated carcass gains were 0.56 and 0.61 kg/day (s.e. = 0.014), respectively. For the low and high grain feed levels, estimated carcass gains were 0.56 and 0.61 kg/day, respectively. Grain treatment, grain feed level or silage feed value did not alter (P > 0.05) meat quality, lean colour or fat colour. There were significant silage feed value × grain feed level interactions (P < 0.05) for final live weight (LW) and daily live-weight gain (DLWG). Increasing grain feed level increased final LW and DLWG when offered with the low-feed value silage, however, grain feed level had no effect on final LW or DLWG when offered with the high-feed value silage. It is concluded that urea treatment of grain increased silage intake and feed conversion ratio (kg DM intake per kg carcass) and tended to decrease carcass gain. Crimping provides a biologically equally effective method to store grain as conventional methods. Improving grass silage feed value had a greater impact on animal performance than increasing grain feed level by 2.4 kg DM per day.     

Genetic mapping of quantitative trait loci for meat quality and muscle metabolic traits in cattle

A whole‐genome scan was carried out in New Zealand and Australia to detect quantitative trait loci (QTL) for live animal and carcass composition traits and meat quality attributes in cattle. Backcross calves (385 heifers and 398 steers) were generated, with Jersey and Limousin backgrounds. The New Zealand cattle were reared and finished on pasture, whilst Australian cattle were reared on grass and finished on grain for at least 180 days. This paper reports on meat quality traits (tenderness measured as shear force at 4–5 ages on two muscles as well as associated traits of meat colour, pH and cooking loss) and a number of metabolic traits. For meat quality traits, 18 significant QTL (P < 0.05), located in nine linkage groups, were detected on a genome‐wise basis, in combined‐sire (seven QTL) or within‐sire analyses (11 QTL). For metabolic traits, 11 significant QTL (P < 0.05), located in eight linkage groups, were detected on a genome‐wise basis, in combined‐sire (five QTL) or within‐sire analyses (six QTL). BTA2 and BTA3 had QTL for both metabolic traits and meat quality traits. Six significant QTL for meat quality and metabolic traits were found at the proximal end of chromosome 2. BTA2 and BTA29 were the most common chromosomes harbouring QTL for meat quality traits; QTL for improved tenderness were associated with Limousin‐derived and Jersey‐derived alleles on these two chromosomes, respectively.     

Understandings and future challenges in soybean functional genomics and molecular breeding

Soybean(Glycine max) is a major source of plant protein and oil.Soybean breeding has benefited from advances in functional genomics.In particular,the release of soybean reference genomes has advanced our understanding of soybean adaptation to soil nutrient deficiencies,the molecular mechanism of symbiotic nitrogen(N) fixation,biotic and abiotic stress tolerance,and the roles of flowering time in regional adaptation,plant architecture,and seed yield and quality.Nevertheless,many challenges remain...