Inference of genetic architecture from chromosome partitioning analyses is sensitive to genome variation,sample size,heritability and effect size distribution

Genomewide association studies have contributed immensely to our understanding of the genetic basis of complex traits. One major conclusion arising from these studies is that most traits are controlled by many loci of small effect, confirming the infinitesimal model of quantitative genetics. A popular approach to test for polygenic architecture involves so‐called “chromosome partitioning” where phenotypic variance explained by each chromosome is regressed on the size of the chromosome. First developed for humans, this has now been repeatedly used in other species, but there has been no evaluation of the suitability of this method in species that can differ in their genome characteristics such as number and size of chromosomes. Nor has the influence of sample size, heritability of the trait, effect size distribution of loci controlling the trait or the physical distribution of the causal loci in the genome been examined. Using simulated data, we show that these characteristics have major influence on the inferences of the genetic architecture of traits we can infer using chromosome partitioning analyses. In particular, small variation in chromosome size, small sample size, low heritability, a skewed effect size distribution and clustering of loci can lead to a loss of power and consequently altered inference from chromosome partitioning analyses. Future studies employing this approach need to consider and derive an appropriate null model for their study system, taking these parameters into consideration. Our simulation results can provide some guidelines on these matters, but further studies examining a broader parameter space are needed.     

Inheritance of phenotypic traits in the progeny of a Ceratocystis interspecific cross

Ceratocystis fimbriata is a fungal plant pathogen that causes black rot on Ipomoea batatas. Based on inoculation studies on numerous tree species, the pathogen is known to be host specific. The closely related species, Ceratocystis manginecans, causes severe wilt on a broad range of tree hosts, including Mangifera indica, Acacia mangium and other leguminous tree species. The genetic factors underlying the pathogenicity and host specificity of Ceratocystis species have rarely been investigated. In this study, an F₁ population of 70 recombinant progeny from a cross between C. fimbriata and C. manginecans was generated and the inheritance of various phenotypic traits was investigated. Results showed that colony colour, growth rate, asexual spore production and aggressiveness to I. batatas and A. mangium are all quantitative traits with high levels of heritability. However, conidia production and aggressiveness appeared to be regulated by a small number of genes. No correlation could be found between aggressiveness and other phenotypic traits, suggesting that these are inherited independently. This is the first study to consider genetic inheritance of pathogenicity and host specificity in Ceratocystis species and the results will contribute, in future, to the identification of quantitative trait loci and candidate genes associated with the traits investigated.     

Single step genome-wide association studies based on genotyping by sequence data reveals novel loci for the litter traits of domestic pigs

In this study, data genotyping by sequence (GBS) was used to perform single step GWAS (ssGWAS) to identify SNPs associated with the litter traits in domestic pigs and search for candidate genes in the region of significant SNPs. After quality control, 167,355 high-quality SNPs from 532 pigs were obtained. Phenotypic traits on 2112 gilt litters from 532 pigs were recorded including total number born (TNB), number born alive (NBA), and litter weight born alive (LWB). A single-step genomic BLUP approach (ssGBLUP) was used to implement the genome-wide association analysis at a 5% genome-wide significance level. A total of 8, 23 and 20 significant SNPs were associated with TNB, NBA, and LWB, respectively, and these significant SNPs accounted for 62.78%, 79.75%, and 58.79% of genetic variance. Furthermore, 1 (SSC14: 16314857), 4 (SSC1: 81986236, SSC1: 66599775, SSC1: 161999013, and SSC1: 267883107), and 5 (SSC9: 29030061, SSC2: 32368561, SSC5: 110375350, SSC13: 45619882 and SSC13: 45647829) significant SNPs for TNB, NBA, and LWB were inferred to be novel loci. At SSC1, the AIM1 and FOXO3 genes were found to be associated with NBA; these genes increase ovarian reproductive capacity and follicle number and decrease gonadotropin levels. The genes SLC36A4 and INTU are involved in cell growth, cytogenesis and development were found to be associated with LWB. These significant SNPs can be used as an indication for regions in the Sus scrofa genome for variability in litter traits, but further studies are expected to confirm causative mutations.     

思茅咖啡天牛种群构成与危害的时空特性研究

通过室内饲养和野外调查,本文对思茅市咖啡天牛种群的构成,发生时期危害的时空特性及幼虫蛀孔部位的选择性进行了研究。结果表明,危害思茅地区咖啡的天牛种群由旋皮天牛和灭字虎天牛构成 ,在不同时间两个种群的构成比例不同。施皮天牛是优势种心化高峰期为４月１８－３０日,灭字虎天牛成虫主要在１０－１２月出现;在咖啡树中天牛幼虫的频数分布具有明显特征,１头虫的分布频数最高;     

Adaptive inter-population differences in blue tit life-history traits on Corsica

Few studies of natural populations have investigated how phenotypic variation across populations relates to key factors in the environment and landscape structure. In the blue tits of southern France, inter-population differences in reproductive life-history traits (e.g. laying date and clutch size) are small, whatever the timing of maximum caterpillar availability, a key factor for offspring survival in tits. These small differences are attributed to gene flow between local populations occupying different habitat types. In contrast, in blue tits on the island of Corsica, we noted large differences in reproductive life-history traits between two populations, where each population is synchronized with the peak-date of caterpillar abundance. These occur over a short geographical distance (25km). Considering our study within a framework of long-term population studies in tits, our results support the hypothesis that different blue tit populations on Corsica show adaptive differences in life-history traits, and suggest that landscape structure at a small spatial scale can have profound effects on adaptive between-population differentiation in life-history traits that are closely linked with fitness.     

Partial decline of Arachis hypogaea L. photosynthesis triggered by drought stress

Photosynthetic capacity (PC) of three peanut cultivars (Arachis hypogaea L. cvs. 57-422, 73-30, and GC 8-35) decreased during drought stress (decline in relative water content from ca. 95 to 70 %) and recovered two days after rewatering. Mild water stress was not limiting for the total ribulose-1,5-bisphosphate carboxylase/oxygenase activity, since this enzyme activity increased under drought. Photosystem (PS) 2 and PS1 (the latter only in cv. GC 8-35) electron transport activities decreased under drought. The ratio of the variable to maximal chlorophyll fluorescence (Fv/Fm) decreased mainly in the cv. GC 8-35. All cultivars showed decreases in photochemical quenching (qP) and quantum yield of PS2 electron transport (Φe). Increase of basal fluorescence (F0) was observed in the cvs. 73-30 and GC 8-35, while the cv 57-422 showed a decrease. After rewatering a sharp increase was observed in the majority of the parameters. Thus under the present stress conditions, the cv GC 8-35 was the most affected for all the parameters under study. The cv. 57-422 showed a higher degree of tolerance being gradually affected in photosynthetic capacity (PC) in contrast to the two other cvs. which showed a sharp decrease in PC at the beginning of the drought cycle. This revised version was published online in September 2006 with corrections to the Cover Date.     

Stem Nodulation in Legumes: Diversity,Mechanisms, and Unusual Characteristics

Rhizobia can establish a nitrogen-fixing symbiosis with plants of the Leguminosae family. They elicit on their host plant the formation of new organs, called nodules, which develop on the roots. A few aquatic legumes, however, can form nodules on their stem at dormant root primordia. The stem-nodulating legumes described so far are all members of the genera Aeschynomene, Sesbania, Neptunia, and Discolobium. Their rhizobial symbionts belong to four genera already described: Rhizobium, Bradyrhizobium, Sinorhizobium, and Azorhizobium. This review summarizes our current knowledge on most aspects of stem nodulation in legumes, the infection process and nodule development, the characterization and unusual features of the associated bacteria, and the molecular genetics of nodulation. Potential use as green manure in lowland rice of these stem-nodulating legumes, giving them agronomical importance, is also discussed.     

Decline of photosynthetic capacity with leaf age in relation to leaf longevities for five tropical canopy tree species

The effect of leaf aging on photosynthetic capacities was examined for upper canopy leaves of five tropical tree species in a seasonally dry forest in Panama. These species varied in mean leaf longevity between 174 and 315 d, and in maximum leaf life span between 304 and 679 d. The light-saturated CO2 exchange rates of leaves produced during the primary annual leaf flush measured at 7-8 mo of age were 33-65% of the rates measured at 1-2 mo of age for species with leaf life span of < 1 yr. The negative regression slopes of photosynthetic capacity against leaf age were steeper for species with shorter maximum leaf longevity. In all species, regression slopes were less steep than the slopes predicted by assuming a linear decline toward the maximum leaf age (20-80% of the predicted decline rate). Maximum oxygen evolution rates and leaf nitrogen content declined faster with age for species with shorter leaf life spans. Statistical significance of regression slopes of oxygen evolution rates against leaf age was strongest on a leaf mass basis (r = 0.49-0.87), followed by leaf nitrogen basis (r = 0.48-0.77), and weakest on a leaf area basis (r = 0.35-0.70).