Unlocking Allelic Diversity for Sustainable Development of Salinity Stress Tolerance in Rice

Rice is a major cereal crop, negatively impacted by soil-salinity, both in terms of plant growth as well as productivity. Salinity tolerant rice varieties have been developed using conventional breeding approaches, however, there has been limited success which is primarily due to the complexity of the trait, low yield, variable salt stress response and availability of genetic resources. Furthermore, the narrow genetic base is a hindrance for further improvement of the rice varieties. Therefore, there is a greater need to screen available donor germplasm in rice for salinity tolerance related genes and traits. In this regard, genomics based techniques are useful for exploring new gene resources and QTLs. In rice, the vast allelic diversity existing in the wild and cultivated germplasm needs to be explored for improving salt tolerance. In the present review, we provide an overview of the allelic diversity in the Quantitative Trait Loci (QTLs) like Saltol, qGR6.2, qSE3 and RNC4 as well as genes like OsHKT1;1, SKC1 (OsHKT1;5/HKT8) and OsSTL1 (salt tolerance level 1 gene) related to salt tolerance in rice. We have also discussed approaches for developing salt-tolerant cultivars by utilizing the effective QTLs or genes/alleles in rice.     

Non-invasive genetic sampling and individual identification

Individual identification via non-invasive sampling is of prime importance in conservation genetics and in behavioural ecology. This approach allows for genetics studies of wild animals without having to catch them, or even to observe them. The material used as a source of DNA is usually faeces, shed hairs, or shed feathers. It has been recendy shown that this material may lead to genotyping errors, mainly due to allelic dropout. In addition to these technical errors, there are problems with accurately estimating the probability of identity (PI, or the probability of two individuals having identical genotypes) because of the presence of close relatives in natural populations. As a consequence, before initiating an extensive study involving non-invasive sampling, we strongly suggest conducting a pilot study to assess both the technical difficulties and the PI for the genetic markers to be used. This pilot study could be carried out in three steps: (i) estimation of the PI using preliminary genetic data; (ii) simulations taking into account the PI and choosing the technical error rate mat is sufficiently low for assessing the scientific question; (iii) polymerase chain reaction (PCR) experiments to check if it is technically possible to achieve this error rate.     

青海藏族HLA II类基因多态性的研究

用PCR-RFLP的技术进一步研究了青海藏族HLA-DPB1的多态性。在19个HLA-DPB1 的等位基因中,共检出18个等位基因。其中,*0501的频率最高（AF=38.0%）;其次为*0201（AF=20.0%）;未检出*1601。在HLA-DPB1各等位基因的分布上,藏族与中国南方汉族、中国北方汉族等无明显差异,而与高加索人及尼格罗人的差异则较为显著。综合隶属于三大人种11个群体中的HLA-DQA1、-DQB1和-DPB1基因座各等位基因的分布频率,用UPGMA方法构建了分子系统树, 实验结果进一步证实汉藏同源说。 Abstract:Following the study of the polymorphism of the HLA-DQA1and -DQB1in Tibetans of Qinghai Province, the polymorphism of the HLA-DPB1was investigated by the same technique―PCR-RFLP. Among the 19 detectable alleles of HLA-DPB1gene, 18 alleles were detected. The allele *0501 was the most frequent one (AF=38.0%); the allele *0201 (AF=20.0%）was the second one; and *1601 was not found by this technique. Compared with that of Southern Han and Northern Han nationality in China, the distribution of the alleles showed little difference; while compared with that of the Caucasoid and Negroid, it showed significant difference. The result of this report confirmed once more that the Tibetan and Han nationalities came from the same ancestors. Based on the allele frequencies of the three loci within HLAclass II region-HLA-DQA1、-DQB1and -DPB1from 11 groups among three main races in the world, a molecular phylogenetic tree was constructed with the method UPGMA.     

Mapping and genome organization of microsatellite sequences in rice (Oryza sativa L.)

In order to enhance the resolution of an existing genetic map of rice, and to obtain a comprehensive picture of marker utility and genomic distribution of microsatellites in this important grain species, rice DNA sequences containing simple sequence repeats (SSRs) were extracted from several small-insert genomic libraries and from the database. One hundred and eighty eight new microsatellite markers were developed and evaluated for allelic diversity. The new simple sequence length polymorphisms (SSLPs) were incorporated into the existing map previously containing 124 SSR loci. The 312 microsatellite markers reported here provide whole-genome coverage with an average density of one SSLP per 6 cM. In this study, 26 SSLP markers were identified in published sequences of known genes, 65 were developed based on partial cDNA sequences available in GenBank, and 97 were isolated from genomic libraries. Microsatellite markers with different SSR motifs are relatively uniformly distributed along rice chromosomes regardless of whether they were derived from genomic clones or cDNA sequences. However, the distribution of polymorphism detected by these markers varies between different regions of the genome. Received: 5 May 1999 / Accepted: 16 August 1999     

中国小麦微核心种质资源Psy基因的等位变异

根据已发表的麦族植物体Psy基因序列的保守区设计引物PsyO2,克隆小麦Psy基因（片段）。结果表明,PsyO2引物的扩增产物出现2种带型：196bp和233bp,序列分析表明两条特异条带涵盖了小麦Psy基因第2外显子全部序列,相差的37bp为Psy基因第2内含子中的一段插入序列,可反映不同黄色素含量（YPC）,属小麦风,,基因的等位变异。验证试验表明,248份小麦微核心种质中有153份材料（占样品数的65．7％）扩增出196bp条带,群体内YPC均值7．314mg kg^-1,属高YPC范畴;另有95份材料（占样品总数的38．3％）扩增出233bp条带,群体内YPE均值为5．207mg kg^-1,属低YPC范畴,方差分析表明二者YPC差异达1％极显著水平差异,说明上述37bp的插入序列是导致小麦品种间YPC产生差异的原因之一,因此该引物扩增的Psy基因对小麦YPC具有显著影响,引物PsyO2是对小麦YPC进行分子鉴定的重要标记。     

Analysis of Polymorphic Residues Reveals Distinct Enzymatic and Cytotoxic Activities of the Streptococcus pyogenes NAD+ Glycohydrolase

The Streptococcus pyogenes NAD⁺ glycohydrolase (SPN) is secreted from the bacterial cell and translocated into the host cell cytosol where it contributes to cell death. Recent studies suggest that SPN is evolving and has diverged into NAD⁺ glycohydrolase-inactive variants that correlate with tissue tropism. However, the role of SPN in both cytotoxicity and niche selection are unknown. To gain insight into the forces driving the adaptation of SPN, a detailed comparison of representative glycohydrolase activity-proficient and -deficient variants was conducted. Of a total 454 amino acids, the activity-deficient variants differed at only nine highly conserved positions. Exchanging residues between variants revealed that no one single residue could account for the inability of the deficient variants to cleave the glycosidic bond of β-NAD⁺ into nicotinamide and ADP-ribose; rather, reciprocal changes at 3 specific residues were required to both abolish activity of the proficient version and restore full activity to the deficient variant. Changing any combination of 1 or 2 residues resulted in intermediate activity. However, a change to any 1 residue resulted in a significant decrease in enzyme efficiency. A similar pattern involving multiple residues was observed for comparison with a second highly conserved activity-deficient variant class. Remarkably, despite differences in glycohydrolase activity, all versions of SPN were equally cytotoxic to cultured epithelial cells. These data indicate that the glycohydrolase activity of SPN may not be the only contribution the toxin has to the pathogenesis of S. pyogenes and that both versions of SPN play an important role during infection.     

Using DNA from non-invasive samples to identify individuals and census populations: an evidential approach tolerant of genotyping errors

DNA extracted from hair or faeces shows increasing promise for censusing populations whose individuals are difficult to locate. To date, the main problem with this approach has been that genotyping errors are common. If these errors are not identified, counting genotypes is likely to overestimate the number of individuals in a population. Here, we describe an algorithm that uses maximum likelihood estimates of genotyping error rates to calculate the evidence that samples came from the same individual. We test this algorithm with a hypothetical model of genotyping error and show that this algorithm works well with substantial rates of genotyping error and reasonable amounts of data. Additional work is necessary to develop statistical models of error in empirical data.     

gemini: software for testing the effects of genotyping errors and multitubes approach for individual identification

Improvements in the determination of individual genotypes from samples with low DNA quantity and quality are of prime importance in molecular ecology and conservation for reliable genetic individual identification (molecular tagging using microsatllites loci). Thus, errors (e.g. allelic dropout and false allele) appearing during samples genotyping must be monitored and eliminated as far as possible. The multitubes approach is a very effective but a costly and time‐consuming solution. In this paper, we present a simulation software that allows evaluation of the effect of genotyping errors on genetic identification of individuals and the effectiveness of a multitubes approach to correct these errors.     

Allele mining in crops: Prospects and potentials

Enormous sequence information is available in public databases as a result of sequencing of diverse crop genomes. It is important to use this genomic information for the identification and isolation of novel and superior alleles of agronomically important genes from crop gene pools to suitably deploy for the development of improved cultivars. Allele mining is a promising approach to dissect naturally occurring allelic variation at candidate genes controlling key agronomic traits which has potential applications in crop improvement programs. It helps in tracing the evolution of alleles, identification of new haplotypes and development of allele-specific markers for use in marker-assisted selection. Realizing the immense potential of allele mining, concerted allele mining efforts are underway in many international crop research institutes. This review examines the concepts, approaches and applications of allele mining along with the challenges associated while emphasizing the need for more refined ‘mining’ strategies for accelerating the process of allele discovery and its utilization in molecular breeding.     

种群微卫星DNA分析中样本量对各种遗传多样性度量指标的影响

我们以中国飞蝗种群的微卫星遗传分析数据为例 ,评估了取样对种群遗传多样性指标的影响 ,结果显示 :样本大小与所观测到的每位点等位基因数、平均等位基因数及基因丰富度指数均呈显著正相关 ,而与期望杂合度无显著相关 ;微卫星位点多态性的高低直接影响所观测到的种群基因丰富度及其检测所需的样本量 ;对大多数种群遗传和分子生态学研究而言 ,30 - 5 0个个体是微卫星DNA分析所需要的最小样本量。基因丰富度经过稀疏法或多次随机抽样法校正后 ,可适用于瓶颈效应等种群历史数量变动的检测。另外 ,在研究中 ,还应避免采集时间的不同及样本的性比构成所可能造成的对种群遗传结构的影响