Association mapping for seed cotton yield,yield components and fibre quality traits in upland cotton (Gossypium hirsutum L.) genotypes

Association mapping has revolutionized human genetics and is increasingly used in plant genetics. It is an efficient way of determining the genetic basis of complex traits. In cotton so far numerous association mapping studies are available as compared to many other important crops. In our study, mapping was performed using cotton 63K infinium beadchip with 201 germplasm lines. Through fast STRUCTURE analysis, lines were grouped into 12 subgroups and revealed genome sharing among the groups. The critical value (R²) was set to 0.243 as threshold to claim LD between two loci. About 3.13% marker pairs recorded significantly high LD (R² = 1), and 8.19% of marker pairs were in the range of 0.3 to 0.99 R². In MLM, 349 significant marker–trait associations were detected as against 642 in GLM because of effectiveness in eliminating false associations in MLM. A total of 68 markers explained >10% phenotypic variation for yield and fibre quality traits. Phenotypic variation explained by markers was smaller, suggesting that they might be associated with minor QTLs.     

Genomic analysis of maize lines introduced in the early stages of a breeding programme

The diversity analysis and screening of major genes using genomewide association studies (GWAS) for quantitative traits have been exploited in several grass crops, but in maize it has been neglected. This study was conducted to evaluate the genetic diversity of a collection of lines and the potential of genomic analysis as an initial screening tool. For this purpose, a collection of 470 maize inbred lines were genotyped with 23,153 Dart‐seq markers. The genomewide analysis of ear weight was used aiming to perform an initial screening in our germplasm. The diversity analysis allowed the lines to be separated into distinct groups, and most of the lines were in agreement with previous pedigree information. The GWAS revealed ten regions potentially associated with the ear weight trait, one of which was related to drought stress. The results of a multiple marker analysis confirmed four of these regions, presenting a predictive accuracy of 0.6. Based on the molecular data and the results of GWAS, it is possible to infer the potential use of this genetic background for breeding.     

The potential of genomic‐assisted breeding to improve Fusarium head blight resistance in winter durum wheat

Durum wheat is the most important tetraploid wheat mainly used for semolina and pasta production, but is notorious for its high susceptibility to Fusarium head blight (FHB). Our objectives were to identify and characterize quantitative trait loci (QTL) in winter durum and to evaluate the potential of genomic approaches for the improvement of FHB resistance. Here, we employed an international panel of 170 winter and 14 spring durum lines, phenotyped for Fusarium culmorum resistance at five environments. Heading date, plant height and mean FHB severity showed significant genotypic variation with high heritabilities and FHB resistance was negatively correlated with both heading date and plant height. The dwarfing gene Rht‐B1 significantly affected FHB resistance and the genome‐wide association scan identified eight additional QTL affecting FHB resistance, explaining between 1% and 14% of the genotypic variation. A genome‐wide prediction approach yielded only a slightly improved predictive ability compared to marker‐assisted selection based on the four strongest QTL. In conclusion, FHB resistance in durum wheat is a highly quantitative trait and in breeding programmes may best be tackled by classical high‐throughput recurrent phenotypic selection that can be assisted by genomic prediction if marker profiles are available.     

Signaling pathways involved in mediating mitochondrial damage in diabetic kidney disease

Diabetic kidney disease （DKD） is one of the most common and serious chronic complications of diabetes and has gradually become the main cause of end-stage renal disease （ESRD）. As the center of energy and metabolism in cells, mitochondria have become the focus of the research on the pathogenesis of DKD in recent years. Current studies find that damage to mitochondria, such as DNA mutations, structural damage, oxidative stress imbalance, etc, leads to apoptosis of kidney cells, thus causing the loss of kidney function. In the process of mitochondrial damage, a series of important signaling pathways are involved, and exploring these signaling pathways would help us better understand the pathogenesis of DKD and find new therapeutic targets. In this article, the important signaling pathways associated with mitochondrial damage are reviewed.     

灰毛浆果楝叶绿体基因组密码子使用特征分析

通过分析灰毛浆果楝叶绿体基因组密码子的使用特征,探讨影响其密码子使用偏性的主要因素。从灰毛浆果楝叶绿体基因组中筛选出54条编码序列(CDS),利用Codon W 1.4.2和CUSP软件计算不同基因密码子各位置的GC含量,以明确灰毛浆果楝叶绿体基因组密码子的使用偏性规律。结果显示:灰毛浆果楝叶绿体基因组密码子第3位碱基的GC含量为28.95%,即第3位密码子富含A和U,有效密码子数(Nec)在34.60~61.00之间,Nec值大于45的CDS有39个;相对同义密码子使用度(URSC)值大于1的密码子有29个,其中16个以U结尾,12个以A结尾;中性绘图分析结果显示GC 12和GC 3的相关系数为0.0984,相关性不显著,回归系数(对角线斜率)为0.1379;基因N ec比值大多数分布在-0.05~0.05区间外,即大部分基因N ec值与预期值差距较大;相关关系分析显示,GC 3与GC1、GC2均未达到显著相关,Nec与GC3呈极显著相关。综合分析发现灰毛浆果楝叶绿体基因组密码子偏好性较弱,选择为主要影响因素,同时受到其他因素的影响。结合高表达优越密码子和高频密码子确定GUU、GUA、UCU、AGU、CCU、ACU、GGU、GCU、CAA、AAA、UGU、AGA和AUU等13个密码子为最优密码子。     

锥栗基因组SSR开发及农家品种的遗传多样性分析

本文对锥栗SSR富集文库进行Illumina MiSeq高通量测序,利用生物信息学对得到的序列进行SSR特征分析,开发锥栗基因组SSR并对农家品种进行了遗传多样性分析。在2051475条序列中,总共搜索到2117345个SSR,以复合形式存在的SSR数量为640155个。二核苷酸为重复单元的SSR数量最多,占总数的73.22%,之后依次为三核苷酸(12.61%)、单核苷酸(12.56%)、四核苷酸(1.33%),单碱基重复、二碱基重复和三碱基重复的优势重复单元分别为:A/T、AC/GT、AAG/CTT。对SSR的长度多态性进行了评价。以8个农家品种为材料,在100对基因组SSR引物中筛选出多态性和特异性较好的引物10对。对25个锥栗农家品种进行了遗传多样性分析观测等位基因和期望杂合度分别为6.3和0.705,有效等位基因数为3.628,Shannon信息指数为1.441,表明锥栗农家品种具有较高的遗传多样性水平。     

Asia1型口蹄疫病毒基因组的测序分析

对中国口蹄疫病毒Asia1/JS/2005毒株的全基因组进行了分段扩增并测序。结果表明,该毒株的基因组全长为8 174 nt,其中 5’UTR 为1 092 nt;ORF为6 990 nt;3’UTR为92 nt。利用DNAstar软件对该毒株和Asia1型其他24毒株基因组序列进行同源性分析表明,该毒株的非结构蛋白和5’UTR比较保守。研究还发现了可能与生物学功能相关的新的保守和变异区域。系统树分析表明Asia1/JS/2005, Asia1/1/YZ/2006,Asia1/WHN/2006,Asia1/HN/2006和Asia1/YS/2005属于同一分支,表明这些毒株间有着紧密的遗传关系,其中与其亲缘关系最为密切的是Asia1/YS/2005。     

RNAi的研究进展(英文)

RNAi是由与靶基因同源的内源或外源双链RNA(doublestrandedRNA,dsRNA)所引发的一种在动植物中普遍存在的基因沉默现象。它最早在植物体中被发现,现在已发展成为一种生物技术,并成为了后基因时代的重要研究手段。对RNAi技术在生物基础、医学、药学、植物学等领域的研究成果进行了综述。     

基因表达系列分析技术在植物基因表达分析中的应用

 基因表达系列分析技术 (SAGE)是一种以测序为基础 ,采用数字化分析手段 ,在转录物水平上研究细胞或组织基因表达模式的有效工具。该技术不仅能够全面地分析特定组织或细胞表达的基因 ,获得这些基因表达丰度的数量信息 ,还可比较不同组织、不同时空条件下基因表达的差异 ,从而发现新基因。SAGE技术在植物方面的应用相对较少 ,但进展很快。本文着重介绍了SAGE在植物基因表达分析中的应用 ,分析SAGE所存在的问题、改进方法及发展前景     

小麦基因组AFLP反应体系的建立

利用小麦抗叶锈近等基因系研究了小麦基因组AFLP反应体系,建立了适于小麦基因组的AFLP反应体系:40μL酶切体系中采用7.5UPstⅠ和5UMseⅠ37℃3h,65℃3h双酶切0.1～0.2μgDNA,然后加入10μL接头、T4连接酶混合液,16℃连接过夜;吸取未稀释的酶切连接液4μL,加入75ng预扩增引物,10mmol/LdNTP,1.5UTaq酶,1×buffer,加PCR水至40μL进行预扩,将预扩产物稀释20倍,吸取5μL,加入40ng选择性引物,1.25UTaq酶,7.5mmol/LdNTP,2%去离子甲酰胺,1×buffer,加PCR水至25μL进行选择性扩增。本研究为小麦抗叶锈基因的分子标记克隆及抗病育种的辅助选择提供有力的工具。