水稻柱头外露率的QTL分析

利用高柱头外露率的籼稻窄叶青8号(ZYQ8)和极低外露率的粳稻京系17(JX17)以及由它们构建的加倍单倍体(DH)群体,在海南对各DH株系的柱头外露率进行调查,并使用该群体的分子连锁图谱进行数量性状座位(QTL)分析。共检测到2个控制水稻柱头外露率的QTL(qPES-2,qPES-3),分别位于第2、第3染色体;并发现控制柱头单边外露率的QTL与柱头外露率完全一致,而控制柱头双边外露率的QTL在第2染色体上检测到;其增效基因均来源于ZYQ8。同时定位的控制穗粒数的QTL位于第6染色体和第8染色体上,与柱头外露率之间没有连锁关系。     

水稻叶片叶绿素和过氧化氢含量的QTL检测及上位性分析

研究水稻叶片叶绿素和过氧化氢含量的遗传规律,对探讨光合代谢产物遗传规律和开展高产育种具有重要指导意义。利用由日本晴／Kasalath∥日本晴的杂交组合衍生的98个回交重组自交家系(BC1F9)所组成的BIL(backcross inbred lines)群体,在第1、2、3和10染色体上分别检测出5个与叶绿素含量相关的QTL和2个影响剑叶过氧化氢含量的QTL,其中位于第1染色体的RFLP标记C86和C813之间的q-Chll对叶绿素含量的影响最为显著,对表型变异的贡献率达22％,其增效基因来自粳稻品种日本晴;同时在该区间检测到1个与剑叶过氧化氢含量相关的QTL:q-H2O2I,对过氧化氢含量的减效基因来自日本晴品种。上位性分析结果显示影响叶绿素含量及过氧化氢含量的非等位QTL之间存在显著的上位性效应。具有上位性效应的QTL分布于第2、6、11和12染色体上,未检测到与q-Chll或q-H2O2I互作的位点。暗示日本晴品种的RFLP标记C86和C813之间存在1个能够提高叶绿素含量,同时又能降低过氧化氢含量的主效QTL,其加性效应显著而不存在上位性效应。     

A generalized estimating equations approach to quantitative trait locus detection of non-normal traits

To date, most statistical developments in QTL detection methodology have been directed at continuous traits with an underlying normal distribution. This paper presents a method for QTL analysis of non-normal traits using a generalized linear mixed model approach. Development of this method has been motivated by a backcross experiment involving two inbred lines of mice that was conducted in order to locate a QTL for litter size. A Poisson regression form is used to model litter size, with allowances made for under- as well as over-dispersion, as suggested by the experimental data. In addition to fixed parity effects, random animal effects have also been included in the model. However, the method is not fully parametric as the model is specified only in terms of means, variances and covariances, and not as a full probability model. Consequently, a generalized estimating equations (GEE) approach is used to fit the model. For statistical inferences, permutation tests and bootstrap procedures are used. This method is illustrated with simulated as well as experimental mouse data. Overall, the method is found to be quite reliable, and with modification, can be used for QTL detection for a range of other non-normally distributed traits.     

Dynamic root growth and architecture responses to limiting nutrient availability: linking physiological models and experimentation

In recent years the study of root phenotypic plasticity in response to sub-optimal environmental factors and the genetic control of these responses have received renewed attention. As a path to increased productivity, in particular for low fertility soils, several applied research projects worldwide target the improvement of crop root traits both in plant breeding and biotechnology contexts. To assist these tasks and address the challenge of optimizing root growth and architecture for enhanced mineral resource use, the development of realistic simulation models is of great importance. We review this research field from a modeling perspective focusing particularly on nutrient acquisition strategies for crop production on low nitrogen and low phosphorous soils. Soil heterogeneity and the dynamics of nutrient availability in the soil pose a challenging environment in which plants have to forage efficiently for nutrients in order to maintain their internal nutrient homeostasis throughout their life cycle. Mathematical models assist in understanding plant growth strategies and associated root phenes that have potential to be tested and introduced in physiological breeding programs. At the same time, we stress that it is necessary to carefully consider model assumptions and development from a whole plant-resource allocation perspective and to introduce or refine modules simulating explicitly root growth and architecture dynamics through ontogeny with reference to key factors that constrain root growth. In this view it is important to understand negative feedbacks such as plant–plant competition. We conclude by briefly touching on available and developing technologies for quantitative root phenotyping from lab to field, from quantification of partial root profiles in the field to 3D reconstruction of whole root systems. Finally, we discuss how these approaches can and should be tightly linked to modeling to explore the root phenome.     

Effect and mode of action of the Texel muscling QTL (TM-QTL) on carcass traits in purebred Texel lambs

TM-QTL is a quantitative trait locus (QTL) on ovine chromosome 18 (OAR18) known to affect loin muscling in Texel sheep. Previous work suggested that its mode of inheritance is consistent with paternal polar overdominance, but this has yet to be formally demonstrated. This study used purebred Texel sheep segregating for TM-QTL to confirm its presence in the chromosomal region in which it was first reported and to determine its pattern of inheritance. To do so, this study used the first available data from a Texel flock, which included homozygote TM-QTL carriers (TM/TM; n=34) in addition to homozygote non-carriers (+/+; n=40 and, heterozygote TM-QTL-carriers inheriting TM-QTL from their sire (TM/+; n=53) or their dam (+/TM; n=17). Phenotypes included a wide range of loin muscling, carcass composition and tissue distribution traits. The presence of a QTL affecting ultrasound muscle depth on OAR18 was confirmed with a paternal QTL effect ranging from +0.54 to +2.82 mm UMD (s.e. 0.37 to 0.57 mm) across the sires segregating for TM-QTL. Loin muscle width, depth and area, loin muscle volume and dissected M. longissimus lumborum weight were significantly greater for TM/+ than +/+ lambs (+2.9% to +7.9%; P<0.05). There was significant evidence that the effect of TM-QTL on the various loin muscling traits measured was paternally polar overdominant (P<0.05). In contrast, there was an additive effect of TM-QTL on both live weight at 20 weeks and carcass weight; TM/TM animals were significantly (P<0.05) heavier than +/+ (+11.1% and +7.3%, respectively) and +/TM animals (+11.9% and +11.7%, respectively), with TM/+ intermediate. Weights of the leg, saddle and shoulder region (corrected for carcass weight) were similar in the genotypic groups. There was a tendency for lambs inheriting TM-QTL from their sire to be less fat with slightly more muscle than non-carriers. For example, carcass muscle weight measured by live animal CT-scanning was 2.8% higher in TM/TM than +/+ lambs (P<0.05), carcass muscle weight measured by carcass CT-scanning was 1.36% higher in TM/+ than +/+ lambs (P<0.05), and weight of fat trimmed from the carcass cuts was significantly lower for TM/+ than +/+ lambs (−11.2%; P<0.05). No negative effects of TM-QTL on carcass traits were found. Optimal commercial use of TM-QTL within the sheep industry would require some consideration, due to the apparently different mode of action of the two main effects of TM-QTL (on growth and muscling).     

Morphological integration and pleiotropy in the adaptive body shape of the snail‐feeding carabid beetle Damaster blaptoides

The snail‐feeding carabid beetle Damaster blaptoides exhibits diverse head and thorax morphologies, and these morphotypes are linked with two alternative feeding behaviours. Stout‐shaped beetles feed on snails by crushing the shells, whereas slender‐shaped beetles consume snails by inserting their heads into the shells. A trade‐off exists between these feeding strategies. Because intermediate‐shaped beetles are less proficient in these two behaviours, stout–slender morphological divergence occurs between related species feeding on land snails. To examine the genetic basis of these morphotypes, we conducted morphological analyses and quantitative trait locus (QTL) mapping using backcross offspring between the stout and slender subspecies. The morphological analyses showed that the width and length of the beetle body parts were correlated with each other; in particular, the head width (HW) and thorax length (TL) were strongly negatively correlated. QTL mapping showed that QTLs for HW and TL are located in close proximity to one another on the longest linkage group and that they have positive and negative additive genetic effects. Our results suggest that the adaptive phenotypic sets of a wide head and short thorax and a narrow head and long thorax are based on the closeness of these QTLs. Morphological integration between the head and thorax may play an important role in the adaptive divergence of these beetles.     

A Graphical Weighted Power Improving Multiplicity Correction Approach for SNP Selections

Controlling for the multiplicity effect is an essential part of determining statistical significance in large-scale single-locus association genome scans on Single Nucleotide Polymorphisms (SNPs). Bonferroni adjustment is a commonly used approach due to its simplicity, but is conservative and has low power for large-scale tests. The permutation test, which is a powerful and popular tool, is computationally expensive and may mislead in the presence of family structure. We propose a computationally efficient and powerful multiple testing correction approach for Linkage Disequilibrium (LD) based Quantitative Trait Loci (QTL) mapping on the basis of graphical weighted-Bonferroni methods. The proposed multiplicity adjustment method synthesizes weighted Bonferroni-based closed testing procedures into a powerful and versatile graphical approach. By tailoring different priorities for the two hypothesis tests involved in LD based QTL mapping, we are able to increase power and maintain computational efficiency and conceptual simplicity. The proposed approach enables strong control of the familywise error rate (FWER). The performance of the proposed approach as compared to the standard Bonferroni correction is illustrated by simulation and real data. We observe a consistent and moderate increase in power under all simulated circumstances, among different sample sizes, heritabilities, and number of SNPs. We also applied the proposed method to a real outbred mouse HDL cholesterol QTL mapping project where we detected the significant QTLs that were highlighted in the literature, while still ensuring strong control of the FWER.