Mapping QTLs and candidate genes for iron and zinc concentrations in unpolished rice of Madhukar×Swarna RILs

Identifying QTLs/genes for iron and zinc in rice grains can help in biofortification programs. 168 F(7) RILs derived from Madhukar×Swarna were used to map QTLs for iron and zinc concentrations in unpolished rice grains. Iron ranged from 0.2 to 224ppm and zinc ranged from 0.4 to 104ppm. Genome wide mapping using 101 SSRs and 9 gene specific markers showed 5 QTLs on chromosomes 1, 3, 5, 7 and 12 significantly linked to iron, zinc or both. In all, 14 QTLs were identified for these two traits. QTLs for iron were co-located with QTLs for zinc on chromosomes 7 and 12. In all, ten candidate genes known for iron and zinc homeostasis underlie 12 of the 14 QTLs. Another 6 candidate genes were close to QTLs on chromosomes 3, 5 and 7. Thus the high priority candidate genes for high Fe and Zn in seeds are OsYSL1 and OsMTP1 for iron, OsARD2, OsIRT1, OsNAS1, OsNAS2 for zinc and OsNAS3, OsNRAMP1, Heavy metal ion transport and APRT for both iron and zinc together based on our genetic mapping studies as these genes strictly underlie QTLs. Several elite lines with high Fe, high Zn and both were identified.     

GABA transporters mediate glycine release from cerebellum nerve endings: roles of Ca(2+)channels, mitochondrial Na(+)/Ca(2+) exchangers, vesicular GABA/glycine transporters and anion channels

GABA transporters accumulate GABA to inactivate or reutilize it. Transporter-mediated GABA release can also occur. Recent findings indicate that GABA transporters can perform additional functions. We investigated how activation of GABA transporters can mediate release of glycine. Nerve endings purified from mouse cerebellum were prelabeled with [(3)H]glycine in presence of the glycine GlyT1 transporter inhibitor NFPS to label selectively GlyT2-bearing terminals. GABA was added under superfusion conditions and the mechanisms of the GABA-evoked [(3)H]glycine release were characterized. GABA stimulated [(3)H]glycine release in a concentration-dependent manner (EC(50) = 8.26 μM). The GABA-evoked release was insensitive to GABA(A) and GABA(B) receptor antagonists, but it was abolished by GABA transporter inhibitors. About 25% of the evoked release was dependent on external Ca(2+) entering the nerve terminals through VSCCs sensitive to ω-conotoxins. The external Ca(2+)-independent release involved mitochondrial Ca(2+), as it was prevented by the Na(+)/Ca(2+) exchanger inhibitor CGP37157. The GABA uptake-mediated increases in cytosolic Ca(2+) did not trigger exocytotic release because the [(3)H]glycine efflux was insensitive to clostridial toxins. Bafilomycin inhibited the evoked release likely because it reduced vesicular storage of [(3)H]glycine so that less [(3)H]glycine can become cytosolic when GABA taken up exchanges with [(3)H]glycine at the vesicular inhibitory amino acid transporters shared by the two amino acids. The GABA-evoked [(3)H]glycine efflux could be prevented by niflumic acid or NPPB indicating that the evoked release occurred essentially by permeation through anion channels. In conclusion, GABA uptake into GlyT2-bearing cerebellar nerve endings triggered glycine release which occurred essentially by permeation through Ca(2+)-dependent anion channels. Glial GABA release mediated by anion channels was proposed to underlie tonic inhibition in the cerebellum; the present results suggest that glycine release by neuronal anion channels also might contribute to tonic inhibition.     

Co-localisation of host plant resistance QTLs affecting the performance and feeding behaviour of the aphid Myzus persicae in the peach tree

The architecture and action of quantitative trait loci (QTL) contributing to plant resistance mechanisms against aphids, the largest group of phloem-feeding insects, are not well understood. Comparative mapping of several components of resistance to the green peach aphid (Myzus persicae) was undertaken in Prunus davidiana, a wild species related to peach. An interspecific F(1) population of Prunus persica var. Summergrand × P. davidiana clone P1908 was scored for resistance (aphid colony development and foliar damage) and 17 aphid feeding behaviour traits monitored by means of the electrical penetration graph technique. Seven resistance QTLs were detected, individually explaining 6.1-43.1% of the phenotypic variation. Consistency was shown over several trials. Nine QTLs affecting aphid feeding behaviour were identified. All resistance QTLs except one co-located with QTLs underlying aphid feeding behaviour. A P. davidiana resistance allele at the major QTL was associated with drastic reductions in phloem sap ingestion by aphids, suggesting a phloem-based resistance mechanism. Resistance was also positively correlated with aphid salivation into sieve elements, suggesting an insect response to restore the appropriate conditions for ingestion after phloem occlusion. No significant QTL was found for traits characterising aphid mouthpart activity in plant tissues other than phloem vessels. Two QTLs with effects on aphid feeding behaviour but without effect on resistance were identified. SSR markers linked to the main QTLs involved in resistance are of potential use in marker-assisted selection for aphid resistance. Linking our results with the recent sequencing of the peach genome may help clarify the physiological resistance mechanisms.     

中国灌木辣椒种质遗传多样性的SRAP和SSR分析

应用SRAP和SSR分子标记对8份辣椒种质进行了遗传多样性分析,结果表明,15对SRAP引物组合共扩增出321条带,平均每对引物扩增出21.40条,多态性位点比率为72.90%;18对SSR引物共扩增出109条带,平均每对引物扩增出6.06条,多态性位点比率为98.17%。与SRAP比较,SSR检测到的Shannon多样性指数(I)、观测等位基因数(Na)和有效等位基因数(Ne)等遗传多样性参数都较大,说明SSR有更高的多态性检测效率。基于SRAP的聚类与基于SSR的聚类之间存在极显著正相关,且都能将中国灌木辣椒种质与美洲灌木辣椒种质及一年生辣椒种质有效区分。     

东乡野生稻耐冷渐渗系的细胞学观察及SSR分析

以前期鉴定筛选的2个东乡野生稻强耐冷渐渗系(IL5243和IL5335)为试材,研究其减数分裂时期的染色体行为特征及外源基因的渗入分子证据。结果表明:(1)IL5243和IL5335中正常减数分裂的花粉母细胞分别达89.93%和90.22%,最终形成正常的成熟花粉粒,花粉离体萌发率分别为(83.03±2.82)%和(81.96±1.73)%,与受体亲本无显著性差异。(2)在减数分裂I中,2个耐冷渐渗系均观察到低频率异常染色体行为,如单价体、"8"字型二价体、多价体,以及后期I有少数花粉母细胞(3.95%～5.15%)存在落后染色体等,表明其染色体组之间发生了交换和重组;在粗线期,2个强耐冷渐渗系均观察到较高频率(IL5243和IL5335分别为27.0%和38.9%)的双核仁,而其双亲都是单核仁。(3)SSR标记和Structure分析进一步证实了栽培稻和野生稻染色体组间发生了交换重组,东乡野生稻部分DNA片段已渗入到强耐冷渐渗系中,这为水稻耐冷基因的挖掘与利用奠定了重要基础。     

马铃薯杂种F1的SSR鉴定

为选育抗黑痣病、高产优质的马铃薯新品种,选用引进品种‘大西洋’分别与‘陇薯6号’、‘陇薯7号’杂交,获得了杂种F1代,利用SSR标记技术对‘大西洋’与‘陇薯6号’的42个杂种F1、‘大西洋’与‘陇薯7号’的9个杂种F1单株进行了鉴定。从59对SSR引物中筛选出2对在亲本间存在差异、扩增稳定、条带清晰的引物S184和STM1049,用于‘大西洋’ב陇薯6号’杂种F1、‘大西洋’ב陇薯7号’杂种F1及其亲本的基因组DNA扩增。SSR带型分析显示,杂种F1的SSR带型呈双亲互补型、缺失型、父本型和母本型4类,依据带型特征鉴定出供试的51个马铃薯杂种F1单株均为真杂种,表明SSR分子标记技术用于马铃薯杂种真实性鉴定是可行的。该研究可为进一步开展马铃薯杂交后代目标性状优异株系选育提供依据。     

冀鲁豫花生育成品种的遗传多样性分析

以冀鲁豫三省不同地域的41个花生育成品种为材料,利用SSR分子标记结合田间表型鉴定、聚类分析等方法对其遗传多样性进行了研究。结果表明,21对SSR引物对41个花生育成品种进行了扫描,共检测到52个等位变异,每个位点2～4个,平均2.5个,Shannon信息指数变幅为0.21～1.40,平均为0.73,聚类分析显示在阈值为5.54可将供试品种分为3大类群7个亚类。不同品种9个农艺性状变异系数在13.16%～186.49%之间,基于农艺性状的聚类分析结果显示在阈值为5.48时可以将供试品种分为6大类群11个亚类,各大类群间品种的农艺性状表现各具特点。     

Towards an efficient computational mining approach to identify EST-SSR markers

Microsatellites are the markers of choice due to their high abundance reproducibility, degree of polymorphism and co-dominant nature. These are mainly used for studying the genetic variability in different species and Marker assisted selection. Expressed Sequence Tags (ESTs) serve as the main resource for Simple Sequence Repeats (SSRs). The computational approach for detecting SSRs and developing SSR markers from EST-SSRs is preferred over the conventional methods as it reduces time and cost to a great extent. The available EST sequence databases, various web interfaces and standalone tools provide the platform for an easy analysis of the EST sequences leading to the development of potential EST-SSR Markers. This paper is an overview of in silico approach to develop SSR Markers from the EST sequence using some of the most efficient tools that are available freely for academic purpose.     

铁皮石斛微卫星SSR设计与应用

通过Websat对来源于NCBI公共数据库的2 447条石斛属(Dendrobium)核苷酸序列进行简单重复序列SSR的搜索,剔除冗余序列后,找到124个SSR位点。利用primer3.0软件设计引物75对,并通过改良的方法提取铁皮石斛DNA作为模板,对铁皮石斛(Dendrobium officinaleKimuraetMigo)的SSR引物进行筛选,选出21对有较清晰且稳定的目标扩增产物的引物,对8个种源的铁皮石斛进行多态性分析和聚类分析,得到8个种源的铁皮石斛进行遗传多样性和亲缘关系。     

基于SSR标记的8个山荆子居群遗传多样性和遗传关系分析

采用10对SSR引物对8个山荆子[Malus baccata (L.) Borkh.]居群140个单株的基因组总DNA进行PCR扩增,并据此对8个居群的遗传多样性和遗传关系进行了分析.结果表明:用10对SSR引物共扩增出91条带,多态性条带百分率达100.00％.8个居群的遗传多样性参数差异较大,有效等位基因数为1.437 9～1.535 0,Nei's基因多样性指数为0.256 0～0.309 2,Shannon信息指数为0.376 7～0.459 2,多态性条带百分率为64.84％～85.71％.居群间的有效等位基因数为1.616 9,Nei's基因多样性指数为0.355 1,Shannon信息指数为0.528 5,均明显高于居群内;8个居群间的基因流为1.739 5,基因分化系数为0.223 3,显示居群间的基因交换较多.UPGMA聚类分析结果表明:在Nei's遗传距离0.148 6处,8个居群被分为3组,河北塞罕坝居群单独为一组,山西五台山居群和北京东灵山居群为一组,其余5个居群为一组.据此推测:山荆子起源于中国华北和东北地区,山西灵空山、黑龙江小兴安岭、吉林长白山和山西中条山居群可能是其遗传多样性的核心居群.