Quantitative trait loci underlying milk production traits in sheep

Improvement of milk production traits in dairy sheep is required to increase the competitiveness of the industry and to maintain the production of high quality cheese in regions of Mediterranean countries with less favourable conditions. Additional improvement over classical selection could be reached if genes with significant effects on the relevant traits were specifically targeted by selection. However, so far, few studies have been undertaken to detect quantitative trait loci (QTL) in dairy sheep. In this study, we present a complete genome scan performed in a commercial population of Spanish Churra sheep to identify chromosomal regions associated with phenotypic variation observed in milk production traits. Eleven half-sib families, including a total of 1213 ewes, were analysed following a daughter design. Genome-wise multi-marker regression analysis revealed a genome-wise significant QTL for milk protein percentage on chromosome 3. Eight other regions, localized on chromosomes 1, 2, 20, 23 and 25, showed suggestive significant linkage associations with some of the analysed traits. To our knowledge, this study represents the first complete genome scan for milk production traits reported in dairy sheep. The experiment described here shows that analysis of commercial dairy sheep populations has the potential to increase our understanding of the genetic determinants of complex production-related traits.     

Quantitative trait loci for live animal and carcass composition traits in Jersey and Limousin back-cross cattle finished on pasture or feedlot

A quantitative trait locus (QTL) study was carried out in two countries, recording live animal and carcass composition traits. Back-cross calves (385 heifers and 398 steers) were generated, with Jersey and Limousin breed backgrounds. The New Zealand cattle were reared on pasture to carcass weights averaging 229 kg, whilst the Australian cattle were reared on grass and finished on grain (for at least 180 days) to carcass weights averaging 335 kg. From 11 live animal traits and 31 carcass composition traits respectively, 5 and 22 QTL were detected in combined-sire analyses, which were significant ( P  <   0.05) on a genome-wise basis. Fourteen significant traits for carcass composition QTL were on chromosome 2 and these were traits associated with muscling and fatness. This chromosome carried a variant myostatin allele (F94L), segregating from the Limousin ancestry. Despite very different cattle management systems between the two countries, the two populations had a large number of QTL in common. Of the 18 traits which were common to both countries, and which had significant QTL at the genome-wise level, eight were significant in both countries.     

A genome scan for quantitative trait loci affecting three ear traits in a White Duroc × Chinese Erhualian resource population

Chinese Erhualian pigs have larger and floppier ears compared with White Duroc pigs (small, half- or fully-pricked ears). To identify quantitative trait loci (QTL) for ear weight and area as well as erectness, a genome-wide scan with 194 microsatellites was performed in a White Duroc × Chinese Erhualian resource population (>1000 F₂ animals). Twenty-three genome-wide significant QTL and 12 suggestive QTL were identified. All QTL for ear erectness and size detected in two previous studies, bar two on SSC6 and 9, were confirmed here. The 1% genome-wide significant QTL at 70 cM on SSC5 and at 58 cM on SSC7 have profound and pleiotropic effects on the three ear traits, with Erhualian alleles increasing weight and area but decreasing erectness. Notably, the 95% confidence interval of the QTL for weight and area on SSC7 spanned only 3 cM. New QTL reaching 1% genome-wide significance were found on SSC8 (at 37 cM) for all three ear traits, on SSC4 and 16 for weight and area, and on SSCX for area. Unexpectedly, Erhualian alleles at these loci were associated with lighter and smaller or erect ear. Some new suggestive QTL were also found on other chromosome regions. Almost all the QTL for weight and area had essentially additive effects, while the QTL for erectness on SSC2, 5 and 7 showed not only additive effects but also partial dominance effects of Erhualian alleles. The two most significant QTL on SSC7 and SSC5 could be promising targets for fine mapping and identification of the causative mutations.     

Heritabilities and quantitative trait loci for blood gases and blood pH in swine

Maintaining pH and blood gases in a narrow range is essential to sustain normal biochemical reactions. Decreased oxygenation, poor tissue perfusion, disturbance to CO₂ expiration, and shortage of HCO₃⁻ can lead to metabolic acidosis. This is a common situation in swine, and originates from a broad range of medical conditions. pH and blood gases appear to be under genetic control, and populations with physiological traits closer to the pathological thresholds may be more susceptible to developing pathological conditions. However, little is known about the genetic basis of such traits. We have therefore estimated phenotypic and genetic variability and identified quantitative trait loci (QTL) for pH and blood gases in blood samples from 139 F₂ pigs from the Meishan/Pietrain family. Samples were taken before and after challenge with Sarcocystis miescheriana , a protozoan parasite of muscle. Twenty-seven QTL influencing pH and blood gases were identified on nine chromosomes. Five of the QTL were significant on a genome-wide level; 22 QTL were significant on a chromosome-wide level. QTL for pH-associated traits have been mapped to SSC3, 18 and X. QTL associated with CO₂ have been detected on SSC6, 7, 8 and 9, and QTL associated with O₂ on SSC2 and SSC8. QTL showed specific health/disease patterns that were related to the physiological state of the pigs from day 0, to acute disease (day 14), convalescence (day 28) and chronic disease (day 42). The results demonstrate that pH and blood gases are influenced by multiple chromosomal areas, each with relatively small effects.     

The tempo of trait divergence in geographic isolation: Avian speciation across the Marañon Valley of Peru

Geographic isolation is considered essential to most speciation events, but our understanding of what controls the pace and degree of phenotypic divergence among allopatric populations remains poor. Why do some taxa exhibit phenotypic differentiation across barriers to dispersal, whereas others do not? To test factors controlling phenotypic divergence in allopatry, we employed a comparative phylogeographic approach consisting of replicates of ecologically similar Andean bird species isolated across a major biogeographic barrier, the Marañon Valley of Peru. Our study design leverages variation among codistributed taxa in their degree of plumage, morphometric, and vocal differentiation across the Marañon to examine the tempo of phenotypic evolution. We found that substantial plumage differences between populations required roughly two million years to evolve. In contrast, morphometric trait evolution showed greater idiosyncrasy and stasis. Our results demonstrate that despite a large degree of idiosyncrasy in the relationship between genetic and phenotypic divergence across taxa and environments, comparative studies within regions may reveal predictability in the pace of phenotypic divergence. Our results also suggest that social selection is important for driving differentiation of populations found in similar environments.     

Evidence that photoperiodic, dark time measurement in Pharbitis nil involves a circadian rather than a semidian rhythm

Experiments were carried out to determine whether a semidian (12 h) rhythm in flowering response operates in Pharbitis nil as the basis for photoperiodic time measurement. The effect of 5 min far-red light followed by 85 min dark (FRD) given 4, 8,14 and 22 h before the end of a 48 h photoperiod on night-break timing and critical night length was determined. When given 4 h before the end of a 48 h photoperiod, an interruption with FRD advanced the phase of the circadian rhythm in the night-break inhibition of flowering. In contrast, earlier interruptions of the photoperiod had no effect on the phase of the rhythm. The critical night length was modified by FRD given 4 h (shortened) or 8 h (lengthened) before the end of the photo-period; when given at other times FRD did not alter the critical night length. The results are discussed in relation to the basis for photoperiodic timekeeping, with particular reference to suggestions for the involvement of a semidian rhythm. A circadian model based on the concept of limit cycles is described.     

生态系统性状对宏生态研究的启示与挑战

功能性状在器官-物种-种群-群落-生态系统水平都具有其特定的适应或功能优化的意义,但目前对功能性状的测定和研究大都局限于器官或物种水平。然而,当前高速发展的宏生态新研究技术和方法(如遥感观测、通量观测、模型模拟)的研究对象都是在生态系统或区域尺度上,如何将传统功能性状与其相连结并服务于生态环境问题和全球变化问题是科学界的一大难题。为了解决传统性状与宏生态研究"尺度不统一"和"量纲不统一"的难题,研究人员最新发展了"生态系统性状(Ecosystem traits, ESTs)"概念体系,并从"理念-数据源-推导方法-应用"等多角度为后续研究提供了可借鉴案例。生态系统性状将传统性状研究从器官水平拓展到了群落和生态系统水平,以单位土地面积为基础构建了传统性状与宏生态研究(或地学研究)的桥梁,开启了性状研究从"器官到群落"、从"经典理论验证到宏观应用"的美好愿景,为多学科交叉提供了新思路。然而,它在方法学和数据源等方面还存在诸多问题与挑战;在此,我们呼吁相关专家从研究方法、概念体系和应用实践上赋予"生态系统性状"更强大的生命力,尤其从动物群落性状和微生物群落性状等角度。本文在深入解读先前生态性状概念体系、理论意义和潜在挑战的基础上,结合最新进展进行了补充,希望通过广泛讨论,完善生态系统性状概念体系,逐步形成"以性状为基础的生态系统生态学"新研究框架,切实推动宏生态研究和区域生态环境问题的解决。     

Biological traits predict shifts in geographical ranges of freshwater invertebrates during climatic warming and drying

Aim To test the ability of biological traits to predict climate‐related changes in geographical ranges of running‐water invertebrates. Location The Australian state of New South Wales and the Australian Capital Territory. Methods I analysed data from 8928 biomonitoring samples collected during a 16‐year period of generally rising air temperatures and declining precipitation. I used quantile regression to test for expansions and contractions on the climatically cooler, warmer, drier and wetter edges of the ranges of 120 invertebrate taxa, and correlated these shifts with the traits of thermophily (degree of preference for high versus low temperature) and rheophily (preference for flowing versus still water). Results The most commonly inferred range shifts were cool‐edge expansion plus warm‐edge contraction (71 taxa) and wet‐edge expansion plus dry‐edge contraction (71), but contractions from both cool and warm extremes (36) and from both dry and wet extremes (28) were also frequent. High‐temperature preference was associated with cool‐edge expansion and low‐temperature preference with wet‐edge expansion and contraction from all other extremes. A preference for flow was associated with wet‐edge expansion and dry‐edge contraction. Main conclusions Trait analysis has potential for predicting which species will expand their ranges and which will contract, but needs to be coupled with assessment of how the landscape provides each species with opportunities to track or avoid climate change. Improved quantification of climatically relevant traits and integration of trait analysis with species distribution modelling are likely to be beneficial.