Why is Madagascar special? The extraordinarily slow evolution of pelican spiders (Araneae,Archaeidae)

Although Madagascar is an ancient fragment of Gondwana, the majority of taxa studied thus far appear to have reached the island through dispersal from Cenozoic times. Ancient lineages may have experienced a different history compared to more recent Cenozoic arrivals, as such lineages would have encountered geoclimatic shifts over an extended time period. The motivation for this study was to unravel the signature of diversification in an ancient lineage by comparing an area known for major geoclimatic upheavals (Madagascar) versus other areas where the environment has been relatively stable. Archaeid spiders are an ancient paleoendemic group with unusual predatory behaviors and spectacular trophic morphology that likely have been on Madagascar since its isolation. We examined disparities between Madagascan archaeids and their non‐Madagascan relatives regarding timing of divergence, rates of trait evolution, and distribution patterns. Results reveal an increased rate of adaptive trait diversification in Madagascan archaeids. Furthermore, geoclimatic events in Madagascar over long periods of time may have facilitated high species richness due to montane refugia and stability, rainforest refugia, and also ecogeographic shifts, allowing for the accumulation of adaptive traits. This research suggests that time alone, coupled with more ancient geoclimatic events allowed for the different patterns in Madagascar.     

Evolutionary dynamics of ecological niche in three Rhinogobio fishes from the upper Yangtze River inferred from morphological traits

In the past decades, it has been debated whether ecological niche should be conserved among closely related species (phylogenetic niche conservatism, PNC) or largely divergent (traditional ecological niche theory and ecological speciation) and whether niche specialist and generalist might remain in equilibrium or niche generalist could not appear. In this study, we employed morphological traits to describe ecological niche and test whether different niche dimensions exhibit disparate evolutionary patterns. We conducted our analysis on three Rhinogobio fish species (R. typus, R. cylindricus, and R. ventralis) from the upper Yangtze River, China. Among the 32 measured morphological traits except body length, PCA extracted the first four principal components with their loading scores >1.000. To find the PNC among species, Mantel tests were conducted with the Euclidean distances calculated from the four principal components (representing different niche dimensions) against the pairwise distances calculated from mitochondrial cytochrome b sequence variations. The results showed that the second and the third niche dimension, both related to swimming ability and behavior, exhibited phylogenetic conservatism. Further comparison on niche breadth among these three species revealed that the fourth dimension of R. typus showed the greatest width, indicating that this dimension exhibited niche generalism. In conclusion, our results suggested that different niche dimensions could show different evolutionary dynamic patterns: they may exhibit PNC or not, and some dimensions may evolve generalism.     

优良单株家系辣木叶的表型性状分析

为挖掘辣木(Moranga oleifera)优良种质资源,对30个优良单株家系的叶片表型性状进行研究。结果表明,除叶形外,辣木不同家系间的叶柄和叶片颜色、复叶数、复叶柄长度和直径、复叶间距、叶长、叶宽均存在不同程度的差异。复叶数与复叶柄长度和直径、复叶间距、叶长、叶宽呈极显著正相关;主成分分析表明,叶长、叶宽、复叶柄长度和直径、复叶间距、叶柄和叶片颜色是区分辣木不同家系最主要的叶片性状指标。聚类分析结果表明,30个辣木家系可分为3大类,叶片表型性状存在显著差异的家系的遗传距离较远。因此,叶柄和叶片颜色、复叶数、复叶柄长度和直径、复叶间距、叶长、叶宽将为直观区分辣木家系提供参考。     

QTL detection on porcine chromosome 12 for fatty-acid composition and association analyses of the fatty acid synthase, gastric inhibitory polypeptide and acetyl-coenzyme A carboxylase alpha genes

Refinement of previous QTL on porcine chromosome 12 for fatty-acid composition and a candidate gene association analysis were conducted using an Iberian × Landrace cross. The concentrations of ten fatty acids were assayed in backfat tissue from which four metabolic ratios were calculated for 403 F₂ animals. Linkage analysis identified two significant QTL. The first QTL was associated with the average chain length ratio and the percentages of myristic, palmitic and gadoleic acids. The second QTL was associated with percentages of palmitoleic, stearic and vaccenic acids. Based upon its position on SSC12, fatty acid synthase was tested as a candidate gene for the first QTL and no significant effects were found. Similarly, gastric inhibitory polypeptide ( GIP ) and acetyl-coenzyme A carboxylase alpha ( ACACA ) were tested as candidate genes for the second QTL using three SNPs in GIP and 15 synonymous SNPs in ACACA cDNA sequences. Two missense SNPs in GIP showed significant effects with palmitoleic and stearic fatty-acid concentration. Highly significant associations were found for two SNPs in ACACA with stearic, palmitoleic and vaccenic fatty-acid concentrations. These associations could be due to linkage disequilibrium with the causal mutations.     

QTL modulating ear size and erectness in pigs

Ear size and erectness are important conformation measurements in pigs. An F(2) population established by crossing European Large White (small, erect ears) with Chinese Meishan (large, flop ears) was used to study the genetic influence of the two ear traits for the first time. A linkage map incorporating 152 markers on 18 autosomal chromosomes was utilised in a genome scan for QTL. Significant QTL were found on SSC1, 5, 7, 9 and 12 for the two traits. The QTL on SSC5 and SSC7 had major effects and were significant at the genome-wide level (P < 0.01). The QTL on SSC1 for ear erectness also had a major effect and was genome-wide significant (P < 0.01). The 95% confidence interval (CI) of the ear size QTL on SSC5 spanned only 4 cM. The QTL on SSC7 for the two ear traits each had a CI of <20 cM, and their positions overlapped with those of the major QTL affecting subcutaneous fat depths on the same chromosome. This study provides insights on the complex genetic influences underlying pig ear traits and will facilitate positional candidate gene analysis to identify causative DNA variants.     

Consistent detection of QTLs for crown rust resistance in Italian ryegrass (<Emphasis Type="Italic">Lolium multiflorum</Emphasis> Lam.) across environments and phenotyping methods

Crown rust, caused by Puccinia coronata f. sp. lolii, is one of the most important diseases of temperate forage grasses, such as ryegrasses (Lolium spp.), affecting yield and nutritional quality. Therefore, resistance to crown rust is a major goal in ryegrass breeding programmes. In a two-way pseudo-testcross population consisting of 306 Lolium multiflorum individuals, multisite field evaluations as well as alternative methods based on artificial inoculation with natural inoculate in controlled environments were used to identify QTLs controlling resistance to crown rust. Disease scores obtained from glasshouse and leaf segment test (LST) evaluations were highly correlated with scores from a multisite field assessment (r = 0.66 and 0.79, P < 0.01, respectively) and thus confirmed suitability of these methods for crown rust investigations. Moreover, QTL mapping based on a linkage map consisting of 368 amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) markers revealed similar results across different phenotyping methods. Two major QTLs were consistently detected on linkage group (LG) 1 and LG 2, explaining up to 56% of total phenotypic variance (V _p). Nevertheless, differences between position and magnitude of QTLs were observed among individual field locations and suggested the existence of specific local pathogen populations. The present study not only compared QTL results among crown rust evaluation methods and environments, but also identified molecular markers closely linked to previously undescribed QTLs for crown rust resistance in Italian ryegrass with the potential to be applied in marker-assisted forage crop breeding. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Genome-wide association study for flowering time,maturity dates and plant height in early maturing soybean (Glycine max) germplasm

Background

Soybean (Glycine max) is a photoperiod-sensitive and self-pollinated species. Days to flowering (DTF) and maturity (DTM), duration of flowering-to-maturity (DFTM) and plant height (PH) are crucial for soybean adaptability and yield. To dissect the genetic architecture of these agronomically important traits, a population consisting of 309 early maturity soybean germplasm accessions was genotyped with the Illumina Infinium SoySNP50K BeadChip and phenotyped in multiple environments. A genome-wide association study (GWAS) was conducted using a mixed linear model that involves both relative kinship and population structure.

Results

The linkage disequilibrium (LD) decayed slowly in soybean, and a substantial difference in LD pattern was observed between euchromatic and heterochromatic regions. A total of 27, 6, 18 and 27 loci for DTF, DTM, DFTM and PH were detected via GWAS, respectively. The Dt1 gene was identified in the locus strongly associated with both DTM and PH. Ten candidate genes homologous to Arabidopsis flowering genes were identified near the peak single nucleotide polymorphisms (SNPs) associated with DTF. Four of them encode MADS-domain containing proteins. Additionally, a pectin lyase-like gene was also identified in a major-effect locus for PH where LD decayed rapidly.

Conclusions

This study identified multiple new loci and refined chromosomal regions of known loci associated with DTF, DTM, DFTM and/or PH in soybean. It demonstrates that GWAS is powerful in dissecting complex traits and identifying candidate genes although LD decayed slowly in soybean. The loci and trait-associated SNPs identified in this study can be used for soybean genetic improvement, especially the major-effect loci associated with PH could be used to improve soybean yield potential. The candidate genes may serve as promising targets for studies of molecular mechanisms underlying the related traits in soybean.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1441-4) contains supplementary material, which is available to authorized users.     

狭域还是广域：杂色山雀和 大山雀行为特征比较

动物行为是个体与社群适应内外环境变化（刺激）所作出的动态反应。动物的行为特征对其适合度以及进化有着重要意义,但关于鸟类行为特征对扩散以及分布的研究还较少,本文以杂色山雀（Sittiparus varius）和大山雀（Parus cinereus）这两种生活史策略相似、分布范围差异显著的雀形目鸟类为例,采用经典新环境测试法对两物种探索性、活跃性、冒险性三种行为进行比较。Mann-Whitney U-test结果显示,大山雀的探索性（Z =﹣2.582,P < 0.01）、活跃性（Z =﹣5.148,P < 0.001）、冒险性（Z =﹣2.046,P < 0.05）得分均显著高于杂色山雀,证明广域分布的大山雀探索性、活跃性及冒险性明显强于狭域分布的杂色山雀。我们由此猜想鸟类行为特征可能会与种群的分布范围相关;通过对鸟类行为特征的探究或许可以间接预测种群未来的发展方向,为种群的保护提供指导。     

粪食性金龟的行为及其适应演化

粪食性金龟的行为简单分为3类:粪居型(endocoprid或dwelling behaviour)、直接掘洞型(paracoprid或tunnelling behaviour)和滚粪球型(telocoprid或rolling behaviour)。文章详细阐述各类型的特点,探讨粪食性金龟行为的进化趋势和过程,并进一步阐述粪食性金龟的适应演化。     

培矮64S/爪哇稻F1农艺性状表现和对照优势分析

本文报道了利用原始爪哇稻资源与光温敏雄性不育系培矮64S配制的27个籼爪交组合在长沙的农艺性状和杂种优势表现.从总体上来看,籼爪交组合与对照相比在每穗实粒数和理论产量上无显著差异,在其它性状上均有极显著的差异;籼爪交组合在秆高、穗长、每穗总粒数、每穗实粒数和千粒重方面有正向对照优势,在播始历期、有效分蘖数、结实率、理论产量和实际产量上存在负向对照优势.从个体上来看,籼爪交组合理论产量对照优势＞40%的比例为11.1%.实际产量对照优势＞40%的机率为3.7%,说明爪哇稻资源在籼爪交杂种优势利用中具有利用价值.本文还对爪哇稻资源在籼爪杂种优势利用中的一些问题进行了讨论.