Estimation of coancestry in Iberian pigs using molecular markers

Genetic markers provide a useful tool toestimate pairwise coancestry betweenindividuals in the absence of a known pedigree. Inthe present work 62 pigs from two relatedstrains of Iberian breed, Guadyerbas andTorbiscal, belonging to a conservationprogramme with completely known pedigrees since1945, have been genotyped for 49microsatellites. Four coefficients thatsummarise molecular resemblance betweenindividuals together with eightestimators of coancestry have been calculatedfrom this information. Their values werecompared with the genealogical coancestry,calculated from the complete or partialpedigree. The eight estimations obtained usingmolecular information substantiallyunderestimate the coancestry calculated usingthe genealogical analysis. The correlationbetween the estimates and the genealogicalvalues was also calculated. This correlationwas high, between 0.78 and 0.93 for differentestimators, when all pairwise comparisons amongthe 62 animals were considered. However, thecorrelation decreases remarkably to 0.49–0.69and 0.37–0.47 for the Guadyerbas and Torbiscalpopulations respectively, when they wereanalysed separately. All the correlations weresimilar to those obtained when using simplecoefficients of molecular resemblance such asmolecular coancestry or similarity indexes.Finally, simulations were carried out tofurther explore the results obtained. It isconcluded that lack of information on theallele frequencies in the base population mayexplain the bias of these estimators inpopulations with complex pedigrees.     

Water resources stress assessment and risk early warning–a case of Hebei Province China

In most parts of China, water resources development and utilization has reached or exceeded the international warning level, especially in the northern arid and semi-arid regions, the serious water stress have aroused worldwide concerns. Many issues of water resources are closely and some inseparably associated with human activities. In this study, the water footprint (WF) and related indicators were applied as comprehensive indicators to assess real water use by humans from the consumption perspective. A Fuzzy Comprehensive Evaluation Model (FCE) was used for the evaluation in its role to assess water stress. And the index system of water stress assessment including four aspects, namely water supply and demand balance, socio-economy, agricultural production and ecological environment was established. Taking the case of Hebei province of China where there is serious conflict between water supply and demand, water stress assessment of all eleven administrative areas for the period 2000–2013 was analyzed. The findings showed that water stress was denoted by three levels, namely high water stress (red zone), general water stress (yellow zone) and low water stress (blue zone), which lays the foundation of the further research on water risk warning. According to the results of water stress assessment and the socio-economic development trends of Hebei, a Markov Chain Risk Warning model was built to describe the risk state of water system and to predict the transition probability of future states. This was intended to focus on the possibility that water stress levels might change into higher water stress level. The current study aims at extending earlier research by making a first step from water footprint estimation towards water stress assessment and providing reference for scientific management of water resources in arid and semi-arid regions.     

Life-cycle analysis on biodiesel production from microalgae: Water footprint and nutrients balance

This research examines the life-cycle water and nutrients usage of microalgae-based biodiesel production. The influence of water types, operation with and without recycling, algal species, geographic distributions are analyzed. The results confirm the competitiveness of microalgae-based biofuels and highlight the necessity of recycling harvested water and using sea/wastewater as water source. To generate 1 kg biodiesel, 3726 kg water, 0.33 kg nitrogen, and 0.71 kg phosphate are required if freshwater used without recycling. Recycling harvest water reduces the water and nutrients usage by 84% and 55%. Using sea/wastewater decreases 90% water requirement and eliminates the need of all the nutrients except phosphate. The variation in microalgae species and geographic distribution are analyzed to reflect microalgae biofuel development in the US. The impacts of current federal and state renewable energy programs are also discussed to suggest suitable microalgae biofuel implementation pathways and identify potential bottlenecks.     

Can carbon footprint serve as proxy of the environmental burden from urban consumption patterns?

Carbon footprint (CFP) is widely applied as an indicator when assessing environmental sustainability of products and services. The objective of the present study is to evaluate the validity of CFP as overall environmental indicator for representing the environmental burden of residents from urbanized areas. Applying four different Life Cycle Impact Assessment (LCIA) methods environmental impact profiles were determined for the consumption patterns of 1281 Danish urban residents. Six main consumption components were distinguished including road transport, air travel, food, accommodation (covering consumption of materials for the construction of dwellings) and use of energy in terms of thermal energy, and electricity. The results for the individual consumption components showed a strong correlation between CFP and nearly all other impact indicators for all the applied LCIA methods However, upon aggregation of the indicator results across consumption components, the impact indicators for the total consumption showed no significant correlation between CFP and the other impact scores for any of the four impact assessment methods. These findings suggest that while CFP can be a good indicator of the environmental burden associated with specific activities, this is not the case for more complex activities (such as consumption patterns related to urban life styles). This conclusion discourages the use of CFP as sustainability measure in relation to regulation of private or public consumption.     

Estimation of genetic variability of the founder population in a conservation scheme using microsatellites

In a conservation programme with genealogical records it is possible to estimate the amount of variability of the founder population from a measure of the similarity among the individuals in the current population based on microsatellite markers. Here we compare three available methods and we shown that the one based on the molecular coancestry coefficient should be preferred.     

加工、贮存因素对实验动物颗粒饲料品质的影响

饲料颗粒化是实验动物饲料标准化的重要内容,是实验动物质量控制的重要环节。影响颗粒饲料质量的因素很多,现就饲料加工、贮存环节中对其品质的影响因素加以分析。1 加工工艺对颗粒饲料品质的影响1.1 原料选择的影响因素 饲料的原料,特别是谷物原料,易被野鼠及昆虫污染,可能传播疾病,尤其是沙门氏杆菌。因此在选择、贮存时要引起注意。某些饲料原料含有营养素拮抗因子,如大豆含胰蛋白酶抑制因子、菜籽饼含芥子甙、芥子硷等多种有毒有害物质,影响饲料的营养品质,选择时应尽量不用或少用,或去毒后再用。某些饲料对实验动物的适口性差,如高梁、棉籽饼     

纤维素酶对生长育肥猪饲养效果的影响

本试验选用３２头６７日龄皮大长白杂交生长育肥猪,随机分为两组,试验组日粮在对照组日粮基础上添加０．１％纤维素酶制剂,通过４０天的实验结果表明对照组日增重为３５１．０５克,试验组为４０５．９４克,日增重提高１５．６４％,差异显著（Ｐ〈０．０１）,饲料报酬提高７．２１％,经济效益明显增加。说明该纤维素酶制剂应用于饲喂生长猪是可行的。     

Mapping of the porcine oestrogen receptor 2 gene and association study with litter size in Iberian pigs

Genes encoding the oestrogen receptors (ESR) are considered candidate genes for prolificacy traits due to the key role these molecules play in the regulation of reproductive physiology. In this paper, we report the assignment of the pig ESR2 gene to porcine chromosome 1 by radiation hybrid mapping. Most of the ESR2 cDNA was sequenced from Iberian pig ovarian RNA samples and one A/G single nucleotide polymorphism (SNP) was found at exon 5, being associated with a Met/Val substitution at position 949. This SNP was genotyped using a PCR-RFLP (Hsp92II) protocol and its potential effect on litter size was evaluated in two Iberian pig populations. However, no statistically significant association between the ESR2 polymorphism and litter size was found.     

Feeding level in the period previous to the late fattening phase influences fat composition at slaughter in free-ranged Iberian pigs

Abstract

A group of 11 pigs was fed with 70 g feed per kg of metabolic weight (H pigs) and another group of 11 pigs was fed with 50 g feed per kg of metabolic weight (L pigs). In both experimental groups (H and L pigs), it was observed that the higher initial proportion of C16:0, C18:0 and C18:2 (n-6) in backfat at the beginning of the free-range feeding period, the greater decrease rate of these fatty acid proportions regarding weight gain during the free-range fattening period took place. On the other hand, the greater initial proportion of C18:1 (n-9), the smaller increase rate in the concentration of this fatty acid was observed. The intramuscular neutral lipids from L pigs had higher C18:3 (n-3) and lower proportions of monounsaturated fatty acids (MUFA) than those from H pigs, while intramuscular polar lipids from L pigs had significantly higher proportions of C18:0, PUFA, C18:3 (n-3) and (n-3) and significantly lower MUFA and C18:1 (n-9) proportions than those from H pigs. The α-tocopherol concentration found in Longissimus dorsi from L pigs was significantly higher (p < 0.012) than those from H pigs.     

Comparison of genetic models for analysing the effects of a PvuII polymorphism in the oestrogen receptor 1 (ESR1) gene on prolificacy in an Iberian x Meishan pig population

The effect of a previously reported PvuII polymorphism in oestrogen receptor 1 (ESR1) was analysed in an F(2) population of Iberian x Meishan pigs. We tested three hypotheses: (1) that a causal mutation was fixed in the parental populations, (2) that a causal mutation existed that was in complete linkage disequilibrium with the alleles of the PvuII polymorphism and (3) that a causal mutation existed in linkage disequilibrium within each parental population. The third model was the most plausible based on the available data. ESR1 alleles displayed different patterns of linkage disequilibrium with the causal mutation in each of the parental populations and the PvuII polymorphism was clearly not the causal mutation. As a consequence, the use of the ESR1 mutation for selection must be evaluated for a particular pig population before it is applied.     

Quantifying electricity generation and waste transformations in a low-cost, plug-flow anaerobic digestion system

Methane production, electricity production, and wastewater transformations were quantified for a digestion system that combines biogas from a swine digester and dairy digester in Costa Rica. The low-cost, plug-flow digesters were not heated and were operated in the lower portion of the mesophilic range (25–27 °C).The dairy digester produced 27.5 m³/day of biogas with 62.6% methane and reduced organic matter (COD) by 86%. The swine digester produced 6.0 m³/day of biogas with 76.4% methane and reduced COD by 92%. Combining biogas from a swine and dairy digester, increased electricity production due to the higher biogas production rate of the dairy farm and the higher quality biogas obtained from the swine farm. The farm’s 2-h peak electricity demand (12.9 kW/day) was 81.8% met. The electricity was produced using manure equivalent to the quantity excreted by 5 dairy cows and 40 pigs remaining in corrals 100% of the time.The $21,000 capital cost of the digester project will be recovered in 10.1 years through electricity savings and reductions in wastewater fines. If the generator were more appropriately sized for the farm, the capital recovery time would have been 7.6 years.     

Partial short-read sequencing of a highly inbred Iberian pig and genomics inference thereof

Despite dramatic reduction in sequencing costs with the advent of next generation sequencing technologies, obtaining a complete mammalian genome sequence at sufficient depth is still costly. An alternative is partial sequencing. Here, we have sequenced a reduced representation library of an Iberian sow from the Guadyerbas strain, a highly inbred strain that has been used in numerous QTL studies because of its extreme phenotypic characteristics. Using the Illumina Genome Analyzer II (San Diego, CA, USA), we resequenced ～ 1% of the genome with average 4 × depth, identifying 68,778 polymorphisms. Of these, 55,457 were putative fixed differences with respect to the assembly, based on the genome of a Duroc pig, and 13,321 were heterozygous positions within Guadyerbas. Despite being highly inbred, the estimate of heterozygosity within Guadyerbas was ～ 0.78 kb(-1) in autosomes, after correcting for low depth. Nucleotide variability was consistently higher at the telomeric regions than on the rest of the chromosome, likely a result of increased recombination rates. Further, variability was 50% lower in the X-chromosome than in autosomes, which may be explained by a recent bottleneck or by selection. We divided the whole genome in 500 kb windows and we analyzed overrepresented gene ontology terms in regions of low and high variability. Multi organism process, pigmentation and cell killing were overrepresented in high variability regions and metabolic process ontology, within low variability regions. Further, a genome wide Hudson-Kreitman-Aguadé test was carried out per window; overall, variability was in agreement with neutral expectations.     

Characterization of OCA2 cDNA in different porcine breeds and analysis of its potential effect on skin pigmentation in a red Iberian strain

Although the function of the OCA2 gene product has not been totally clarified, variation in OCA2 has been associated with skin and hair pigmentation in human and mouse. However, its contribution to skin colour in domestic species has not been reported. In this study, cDNA and intron 9 sequences of the porcine OCA2 gene have been characterized in several pig populations. The cDNA sequence alignment of 20 animals from eight porcine populations allowed the identification of 10 single nucleotide polymorphisms (SNPs); five of the 10 SNPs were non-synonymous. The intron 9 sequence alignment of 12 animals belonging to four pig populations revealed four additional SNPs. Skin colour variation was analysed in a red strain of Iberian pigs with segregation of three SNPs forming two OCA2 intragenic haplotypes. Results from this study provide evidence of a suggestive dominant effect of haplotypes on colour intensity and indicate an important contribution of additive polygenic effects (h2 = 0.56 +/- 0.21) to the variance of this trait.