利用DH或RIL群体检测QTL体系并估计其遗传效应

利用ＤＨ和ＲＩＫＬ群体并结合重复内分组随机区组设计对和物产量等遗传率较低的数量性状进行分离分析可提高遗传分析的精度。根据混合分布理论菜了利用ＤＨ或ＲＩＬ群体重复实验数据鉴定数量性状混合遗传模型的分离分析法,特别是２对链锁主基因＋多基因模型。该方法可鉴定数量性状的遗传模型和主基因的作用方式,估计主基因、多基因的遗传疚和遗传方差,在两主基因存在连锁可可估计其重组率。下面通过应用举例说明该方法。     

直播条件下水稻6个穗部性状的QTL分析

在大田直播条件下,利用来源于＂Lemont/特青＂的重组自交系群体,对水稻6个穗部性状及其相互间遗传相关的分子基础进行了QTL分析,共检测到19个QTL,各性状QTL数为2～4个,单个QTL贡献率为4%～22%。共检测到3个染色体区段能同时影响多个穗部性状,其中第1染色体RM212-RM104和第2染色体RM263-RM221区段的QTL能同时影响单株产量、每穗颖花数、着粒密度和二次枝梗数中的3个或4个性状,且这2个区段的QTL对各性状的效应方向相同,增效等位基因均来自‘特青’,为各性状间表型正相关提供了重要的遗传解释。第11染色体RG1022附近的QTL对着粒密度的效应值为负,来自‘特青’的等位基因增加性状值,而对穗长的效应值为正,来自‘特青’的等位基因降低性状值,为这2个性状间表型负相关也提供了一定的遗传解释。此外,对水稻穗部性状QTL在多种环境和遗传背景下的稳定表达及其在分子标记辅助育种中的应用进行了讨论。     

Nitrogen aboveground turnover and soil stocks to 8 m depth in primary and selectively logged forest in southern Amazonia

Extensive areas of Amazonia undergo selective logging, modifying forest structure and nutrient cycles. Anthropogenic‐accelerated rates of nitrogen (N) turnover could increase N loss and affect regeneration, carbon sequestration and timber production. We quantified leaf area reduction, canopy opening and downed biomass and resultant N flux from reduced impact logging (RIL) activities. We compared canopy reduction, surface soil moisture and nitrate to 8 m depth between logged gaps and intact primary forest to determine if logging activities increase subsoil nitrate. To test long‐term logging effects, we evaluated surface N stocks along a 12‐year postlogging chronosequence. At the harvest rate of 2.6 trees ha^?1, total N additions in logging gaps, including leaves and wood from felled crowns (24.8 kg N ha^?1) and other killed trees (41.9 kg N ha^?1), accounted for over 80% of the total N addition to aboveground necromass from all logging activities (81.9 kg N ha^?1). Despite this N turnover by logging, belowground nitrate storage to 8 m depth did not differ between logging gaps and primary forest at the low harvest rate and disturbance intensity of this study. Soil water depletion also did not differ between gaps and primary forest over 1 year, indicating the impact on belowground inorganic N was low. Compared with primary forest, nitrate concentrations to 8 m depth in logging gaps were only significantly higher at 60–100 cm, suggesting some N redistribution beyond the bulk of the fine roots in logging gaps. Extrapolated to the Amazon Basin scale, we provide a conservative estimate that logging damage and bole export under RIL would turn over 0.14 ± 0.07 to 0.23 ± 0.12 Tg N yr^?1 based on 1999–2002 selective logging rates. Greater damage during conventional selective logging would cause higher N turnover throughout the Amazon Basin than our results based on RIL.     

绿豆种子休眠性和百粒重的QTLs和互作分析

利用绿豆Berken/ACC41重组自交系在北京种植得到的121个F10家系和79个RFLP分子标记,采用改进复合区间作图法对绿豆种子休眠性和百粒重进行数量性状基因定位及上位性互作分析.检测到与发芽势有关的QTL 3个,与发芽率有关的QTL 4个,分别位于第1、11连锁群,解释表型变异的8.17%～12.14%和4.34%～12.69%.检测到与百粒重有关的QTL 5个,分别位于第2、8、9、11连锁群,解释表型变异的4.58%～10.36%.增加发芽率和百粒重的基因效应均来自母本Berken.分别检测到发芽势、发芽率和百粒重的加性×加性上位性互作8、9、9对,对这3个性状的总表型贡献率分别达到66.58%、47.91%、39.90%.本文初步分析了休眠性和百粒重的关系,并与前人的研究结果作了比较,旨在通过分子标记辅助选择,培育适度休眠的优良绿豆品种,进而解决绿豆收获前的荚上子粒发芽问题.     

Identification of enzymatic and regulatory genes of plant metabolism through QTL analysis in Arabidopsis

The biochemical diversity in the plant kingdom is estimated to well exceed 100,000 distinct compounds (Weckwerth, 2003) and 4000 to 20,000 metabolites per species seem likely (Fernie et al., 2004). In recent years extensive progress has been made towards the identification of enzymes and regulatory genes working in a complex network to generate this large arsenal of metabolites. Genetic loci influencing quantitative traits, e.g. metabolites or biomass, may be mapped to associated molecular markers, a method called quantitative trait locus mapping (QTL mapping), which may facilitate the identification of novel genes in biochemical pathways. Arabidopsis thaliana, as a model organism for seed plants, is a suitable target for metabolic QTL (mQTL) studies due to the availability of highly developed molecular and genetic tools, and the extensive knowledge accumulated on the metabolite profile. While intensely studied, in particular since the availability of its complete sequence, the genome of Arabidopsis still comprises a large proportion of genes with only tentative function based on sequence homology. From a total number of 33,518 genes currently listed (TAIR 9, http://www.arabidopsis.org), only about 25% have direct experimental evidence for their molecular function and biological process, while for more than 30% no biological data are available. Modern metabolomics approaches together with continually extended genomic resources will facilitate the task of assigning functions to those genes. In our previous study we reported on the identification of mQTL (Lisec et al., 2008). In this paper, we summarize the current status of mQTL analyses and causal gene identification in Arabidopsis and present evidence that a candidate gene located within the confidence interval of a fumarate mQTL (AT5G50950) encoding a putative fumarase is likely to be the causal gene of this QTL. The total number of genes molecularly identified based on mQTL studies is still limited, but the advent of multi-parallel analysis techniques for measurement of gene expression, as well as protein and metabolite abundances and for rapid gene identification will assist in the important task of assigning enzymes and regulatory genes to the growing network of known metabolic reactions.     

Actin cytoskeleton remodeling by the alternatively spliced isoform of PDLIM4/RIL protein

RIL (product of PDLIM4 gene) is an actin-associated protein that has previously been shown to stimulate actin bundling by interacting with actin-cross-linking protein α-actinin-1 and increasing its affinity to filamentous actin. Here, we report that the alternatively spliced isoform of RIL, denoted here as RILaltCterm, functions as a dominant-negative modulator of RIL-mediated actin reorganization. RILaltCterm is regulated at the level of protein stability, and this protein isoform accumulates particularly in response to oxidative stress. We show that the alternative C-terminal segment of RILaltCterm has a disordered structure that directs the protein to rapid degradation in the core 20 S proteasomes. Such degradation is ubiquitin-independent and can be blocked by binding to NAD(P)H quinone oxidoreductase NQO1, a detoxifying enzyme induced by prolonged exposure to oxidative stress. We show that either overexpression of RILaltCterm or its stabilization by stresses counteracts the effects produced by full-length RIL on organization of actin cytoskeleton and cell motility. Taken together, the data suggest a mechanism for fine-tuning actin cytoskeleton rearrangement in response to stresses.     

Mapping quantitative trait loci associated with selenate tolerance in Arabidopsis thaliana

Selenium is essential for many organisms, but is toxic at higher levels. To investigate the genetic basis of selenate tolerance in Arabidopsis thaliana, quantitative trait loci (QTL) associated with selenate tolerance in accessions Landsberg erecta and Columbia were mapped using recombinant inbred lines (RILs). The selenate tolerance index (TI(D10) = root growth + 30 microm selenate/root growth control x 100%) was fourfold higher for parental line Col-4 (59%) than for parent Ler-0 (15%). Among the 96 F8 RILs, TI(D10) ranged from 11 to 75% (mean 37%). Using composite interval mapping, three QTL were found on chromosomes 1, 3 and 5, which together explained 24% of variation in TI(D10) and 32% of the phenotypic variation for the difference in root length +/- Se (RL(D10)). Highly significant epistatic interactions between the QTL and markers on chromosome 2 explained additional variation for both traits. Potential candidate genes for Se tolerance in each of the QTL regions are discussed. These results offer insight into the genetic basis of selenate tolerance, and may be useful for identification of selenate-tolerance genes.     

应用重组自交系群体定位大豆根重QTL

应用构建的NJRIKY(科丰1号×1138-2)大豆重组自交家系群体,对大豆根重QTL进行8次重复的随机区组分析;以该群体所构成的遗传连锁图谱为基础,采用复合区间作图法(Cartographer V.1.21)检测到3个与根重有关的QTL位于连锁群N3-B1和N6-C2上。其中rw1在N3-B1的端距离是66.31cM,位于A520T～ACCCA-GO5区间,rw2和rw3分别在N6-C2的端距离是169.91cM和179.71cM,并与OPW13和ACGCATO6重叠。LOD值分别是10.34、4.01和3.15,可以解释26.3％、9.2％和6.8％的遗传变异。加性效应估计值分别为-0.514、-0.303和-0.260。     

Genomics and molecular breeding in lesser explored pulse crops: Current trends and future opportunities

Pulses are multipurpose crops for providing income, employment and food security in the underprivileged regions, notably the FAO-defined low-income food-deficit countries. Owing to their intrinsic ability to endure environmental adversities and the least input/management requirements, these crops remain central to subsistence farming. Given their pivotal role in rain-fed agriculture, substantial research has been invested to boost the productivity of these pulse crops. To this end, genomic tools and technologies have appeared as the compelling supplement to the conventional breeding. However, the progress in minor pulse crops including dry beans (Vigna spp.), lupins, lablab, lathyrus and vetches has remained unsatisfactory, hence these crops are often labeled as low profile or lesser researched. Nevertheless, recent scientific and technological breakthroughs particularly the next generation sequencing (NGS) are radically transforming the scenario of genomics and molecular breeding in these minor crops. NGS techniques have allowed de novo assembly of whole genomes in these orphan crops. Moreover, the availability of a reference genome sequence would promote re-sequencing of diverse genotypes to unlock allelic diversity at a genome-wide scale. In parallel, NGS has offered high-resolution genetic maps or more precisely, a robust genetic framework to implement whole-genome strategies for crop improvement. As has already been demonstrated in lupin, sequencing-based genotyping of the representative sample provided access to a number of functionally-relevant markers that could be deployed straight away in crop breeding programs. This article attempts to outline the recent progress made in genomics of these lesser explored pulse crops, and examines the prospects of genomics assisted integrated breeding to enhance and stabilize crop yields.