Genome-wide association study identified genetic variations and candidate genes for plant architecture component traits in Chinese upland cotton

Key message

Thirty significant associations between 22 SNPs and five plant architecture component traits in Chinese upland cotton were identified via GWAS. Four peak SNP loci located on chromosome D03 were simultaneously associated with more plant architecture component traits. A candidate gene, Gh_D03G0922, might be responsible for plant height in upland cotton.

Abstract

A compact plant architecture is increasingly required for mechanized harvesting processes in China. Therefore, cotton plant architecture is an important trait, and its components, such as plant height, fruit branch length and fruit branch angle, affect the suitability of a cultivar for mechanized harvesting. To determine the genetic basis of cotton plant architecture, a genome-wide association study (GWAS) was performed using a panel composed of 355 accessions and 93,250 single nucleotide polymorphisms (SNPs) identified using the specific-locus amplified fragment sequencing method. Thirty significant associations between 22 SNPs and five plant architecture component traits were identified via GWAS. Most importantly, four peak SNP loci located on chromosome D03 were simultaneously associated with more plant architecture component traits, and these SNPs were harbored in one linkage disequilibrium block. Furthermore, 21 candidate genes for plant architecture were predicted in a 0.95-Mb region including the four peak SNPs. One of these genes (Gh_D03G0922) was near the significant SNP D03_31584163 (8.40 kb), and its Arabidopsis homologs contain MADS-box domains that might be involved in plant growth and development. qRT-PCR showed that the expression of Gh_D03G0922 was upregulated in the apical buds and young leaves of the short and compact cotton varieties, and virus-induced gene silencing (VIGS) proved that the silenced plants exhibited increased PH. These results indicate that Gh_D03G0922 is likely the candidate gene for PH in cotton. The genetic variations and candidate genes identified in this study lay a foundation for cultivating moderately short and compact varieties in future Chinese cotton-breeding programs.

     

High-Resolution Genetic Map of the Human Glutamyl Aminopeptidase Gene (ENPEP)

The murine B-lymphocyte differentiation antigen BP-1/6C3 has been identified as glutamyl aminopeptidase (EAP), the gene symbol for which isENPEP.Using genomic DNA encoding for human EAP as a probe, we identified theENPEPgene location on human chromosome 4q25 by polymerase chain reaction analysis of a human/rodent somatic cell hybrid mapping panel and by fluorescencein situhybridization. Using a radiation hybrid panel, the gene order aroundENPEPwas determined to be centromere–D4S1236–(570 kb)–ENPEP–(210 kb)–D4S262–(270 kb)–D4S953–(270 kb)–D4S474–(570 kb)–IF. The linkage ofENPEPto complement factor I (IF) confirms the human chromosome band 4q25 localization predicted from the chromosomal location of murineENPEP.HumanENPEPthus provides an additional marker for the long arm of chromosome 4 that should facilitate studies of this genomic region.     

华山松吸收光谱及叶绿素荧光特性的地理变异

利用分离的叶绿体作实验材料,发现华山松(Pinus armandi Franch.)南方种源的4阶导数吸收光谱在680nm处峰值较大,在670nm处峰值较小,而北方种源中出现了在680nm处峰值较在670nm峰值小的类群,推断北方种群反应中心活力有下降趋势。南、北种源之间的低温(77K)荧光发射光谱有明显差异,PSⅠ、PSⅡ发射峰位置出现地理变动。低温荧光激发光谱分析表明,地理变异主要发生在叶绿素a的分子状态上。研究还表明,完整的针叶因为有角质层、松脂等物质干扰,检测不出光谱的差异,不是理想的实验材料。     

EVALUATING THE IMPACT OF INSECT COMMUNITY ON PINE CATERPILLAR DENSITY IN DIFFERENT STAND CONDITIONS

Abstract  Natural enemies play an important role in inhibiting population growth of pine caterpillar, but they are difficult to be used in systematic management models. This paper attempts to use some forest stand factors to substitute the effect of natural enemies, which could be used in management models. Through the studies from more than 200 stand plots with different stand conditions in Qu County, Changshan County, and Longyou County of Zhejiang Province, 16 predominant species groups from insect community were selected, and the canonical correlation coefficient between the diversity index, species number, individual number of predominant species and the stand factors was analyzed. The results indicated that the canopy density and ground vegetation were the key stand factors for characterizing the function of insect community. The forest area was divided into four types according to the variation of canopy and vegetation conditions by using cluster analysis. The regression models between the rate of variation of pine caterpillar density and the forest factors including canopy density and vegetation covers were developed in each type of forests. There were significant differences in diversity index, species number, individual number of insect community and population density of pine caterpillar among four types of forests, and correlation coefficients of the four regression models were rather high ( r =0. 924 — 0. 964). This means that the classification of the forest stands is reasonable and the stand factors can characterize the effect of natural enemies in practice.     

OxLDL-induced macrophage cytotoxicity is mediated by lysosomal rupture and modified by intralysosomal redox-active iron

Oxidized low density lipoprotein (oxLDL) is believed to play a central role in atherogenesis. LDL is oxidized in the arterial intima by mechanisms that are still only partially understood. OxLDL is then taken up by macrophages through scavenger receptor-mediated endocytosis, which then leads to cellular damage, including apoptosis. The complex mechanisms by which oxLDL induces cell injury are mostly unknown. This study has demonstrated that oxLDL-induced damage of macrophages is associated with iron-mediated intralysosomal oxidative reactions, which cause partial lysosomal rupture and ensuing apoptosis. This series of events can be prevented by pre-exposing cells to the iron-chelator, desferrioxamine (DFO), whereas it is augmented by pretreating the cells with a low molecular weight iron complex. Since both DFO and the iron complex would be taken up by endocytosis, and thus directed to the lysosomal compartment, the results suggest that the normal contents of lysosomal low molecular weight iron may play an important role in oxLDL-induced cell damage, presumably by catalyzing intralysosomal fragmentation of lipid peroxides and the formation of toxic aldehydes and oxygen-centered radicals.     

Identification of trait-improving quantitative trait loci alleles from a wild rice relative,Oryza rufipogon.

Wild species are valued as a unique source of genetic variation, but they have rarely been used for the genetic improvement of quantitative traits. To identify trait-improving quantitative trait loci (QTL) alleles from exotic species, an accession of Oryza rufipogon, a relative of cultivated rice, was chosen on the basis of a genetic diversity study. An interspecific BC2 testcross population (V20A/O. rufipogon//V20B///V20B////Ce64) consisting of 300 families was evaluated for 12 agronomically important quantitative traits. The O. rufipogon accession was phenotypically inferior for all 12 traits. However, transgressive segregants that outperformed the original elite hybrid variety, V20A/Ce64, were observed for all traits examined. A set of 122 RFLP and microsatellite markers was used to identify QTL. A total of 68 significant QTL were identified, and of these, 35 (51%) had beneficial alleles derived from the phenotypically inferior O. rufipogon parent. Nineteen (54%) of these beneficial QTL alleles were free of deleterious effects on other characters. O. rufipogon alleles at two QTL on chromosomes 1 and 2 were associated with an 18 and 17% increase in grain yield per plant, respectively, without delaying maturity or increasing plant height. This discovery suggests that the innovative use of molecular maps and markers can alter the way geneticists utilize wild and exotic germplasm.     

双色FISH和DNA纤维FISH方法的建立与应用

在构建了含毛细胞白血病相关的结构性倒位inv (5) (p13.1q13.3)的细胞系后,为了确定该新建细胞系在建株过程中其倒位断裂点关键区遗传物质是否发生改变,以生物素或地高辛标记的cCI5-216 和cCI5-267黏粒DNA为探针,进行染色体中期、间期和DNA纤维3种双色荧光原位杂交的分析。结果表明：该新建细胞系的3种双色荧光原位杂交结果,均与该细胞系的原代细胞的完全相同,证实了该细胞系倒位断裂点关键区的遗传物质结构未发生改变。该细胞系是揭示毛细胞白血病发病的分子机理的重要研究材料。     

Enhancement of antidepressant potency by a potentiator of AMPA receptors

1. AMPA receptor potentiators (ARPs) exhibit antidepressant-like activity in preclinical tests (for example, the forced swim test) that are highly predictive of efficacy in humans. Unlike most currently used antidepressants, ARPs do not elevate extracellular levels of biogenic amines (e.g., 5HT, NE) in prefrontal cortex at doses that are active in the forced swim test.2. The present series of experiments examined the effects of combining the ARP, LY 392098, with biogenic amine-based antidepressants in the forced swim test. Male, NIH Swiss mice were placed in a cylinder of water and observed for attempted escape behaviors and immobility.3. LY 392098 dose-dependently decreased immobility as did a range of classical antidepressants. At doses of LY 392098 below those that decreased immobility, this compound significantly increased the potency with which fluoxetine and citalopram (SSRI antidepressants), imipramine (tricyclic antidepressant), duoxetine (norepinephrine/serotonin uptake blocker), nisoxetine (norepinephrine uptake inhibitor), and rolipram (PDE4 inhibitor) decreased immobility in the forced swim test with potency shifts upward of 5-fold (fluoxetine, imipramine, and rolipram). Likewise, ineffective doses of the traditional antidepressants potentiated the effects LY 392098 with shifts in the dose-effect functions that were 10-fold or more for citalopram, fluoxetine, imipramine, and duloxetine.4. Combined with other evidence for a role of AMPA receptors in the efficacy of antidepressants, the current data suggest that the addition of an ARP may augment the activity and perhaps the onset of the therapeutic effects of biogenic amine and second messenger-based antidepressants.     

HaploBlockFinder: haplotype block analyses

Recent studies have unveiled discrete block-like structures of linkage disequilibrium (LD) in the human genome. We have developed a set of computer programs to analyze the block-like LD structures (haplotype blocks) based on haplotype data. Three definitions of haplotype block are supported, including minimal LD range, no historic recombination, and chromosome coverage. Tagged SNPs that uniquely distinguish common haplotypes are identified. A greedy algorithm was used to improve the efficiency. Two separate utilities were also provided to assist visual inspection of haplotype block structure and pattern of linkage disequilibrium. AVAILABILITY: A web interface for the HaploBlockFinder is available at http://cgi.uc.edu/cgi-bin/kzhang/haploBlockFinder.cgi the source codes are also freely available on the web site.     

蚯蚓纤溶酶的分离纯化及部分序列的测定

以新鲜蚯蚓为原料,经过保温抽提、乙醇沉淀、DEAE-SepharoseFastFlow离子交换层析、Lysine-Sepharose4B亲和层析以及SDS-PAGE制备电泳等纯化步聚,得到一种纯度达95％以上的蚯蚓纤溶酶．该酶具有强烈的溶解纤维蛋白的作用及蛋白酶活性,平板法测得其比活性为90OUK单位／毫克蛋白,TAME法测得其比活性为2500O单位／毫克蛋白．酶学性质研究表明其最适反应温度为65℃,最适反应PH值为8．5．该酶的分子量为33kD,等电点为pH3．5．还对该酶进行了氨基酸组成分析,并测定了其N端部分序列．