Efficiency of reduced primer selectivity and bulked DNA analysis for the rapid detection of AFLP† polymorphisms in a range of crop species

Two approaches to optimise AFLP fingerprinting forthe rapid detection of genetic polymorphisms, i.e.reduced primer selectivity and bulked DNA analysiswere examined. The efficiency of reduced primerselectivity to increase the detection frequency ofgenetic polymorphisms and to obtain more informativefingerprinting profiles was tested in six differentcrops. The number of selective nucleotides was reducedto six in onion, to five in barley, potato, lettuceand cabbage, and to four in flax. This allowed therapid identification of several primer pairs that wereable to discriminate between closely relatedgermplasm. Reproducibility tests on replicate DNAsamples indicated no major negative effects on thereliability of the fingerprinting profiles due to theuse of less selective primers, although for onionpurified DNA was needed to avoid irreproducibleresults. In barley, flax and onion, a less thanfourfold increase in the number of fragments wasobserved when primer pairs were reduced by oneselective nucleotide. This result was attributed todifferent tolerance levels for amplificationmismatches between primer pairs of differentselectivity.The efficiency of bulked DNA analysis to detectgenetic polymorphisms was investigated in differentmixtures of two barley DNA samples. AFLP's of varyingintensity could still be recovered when the two DNA'swere mixed in a 1:1 ratio. However, the frequency ofrecovered bands quickly dropped when in the mixturesthe presence of the DNA carrying the fragments wasdecreased below 50%.The usefulness of the two approaches is discussed inrelation to various aspects of genetic resourcesmanagement.     

Small‐scale cattle raising in East Java,Indonesia: A pathway out of poverty?

Despite its small area and intensively cropped landscape, East Java accounts for 30% of Indonesia's cattle population. About two million households draw on family labour to raise cattle in backyard sheds and small enclosures, largely for cash income. In this paper, we examine the opportunity for such small‐scale producers to benefit from Indonesia's economic transformation, given the rising urban demand for beef. The paper reports on a study in two contrasting sites in East Java – irrigated lowlands and rainfed uplands – to explore the constraints facing small‐scale cattle producers in these environments, the means by which they have adapted to these constraints (especially by going beyond the farm household to access feed supplies) and possible means to enhance their production systems and incomes. The findings suggest that such cattle production systems can provide a viable source of livelihood, even for resource‐poor households; hence, appropriately adapted cattle improvement programmes are a sensible component of a pro‐poor development strategy.     

Contents Volume 125 2002

Volume Contents

Contents Volume 125 2002     

与马铃薯晚疫病菌无毒基因Avr1连锁的AFLP标记

 以具有和不具有无毒基因Avr1表现型的马铃薯晚疫病菌株80029 (AVR1) 和88133 (avr1)以及其杂交F1代50个菌株群体为试材，限制性内切酶PstI和HhaI为酶切组合，采用荧光AFLP技术和混合分组分析法(BSA)，通过256对引物筛选得到了5个与Avr1连锁的候选AFLP标记并进行了菌株个体验证，遗传分析表明5个标记中有2个标记与Avr1连锁且在F1代中共分离，无交换重组发生。     

Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans

Coevolution of mammals and their gut microbiota has profoundly affected their radiation into myriad habitats. We used shotgun sequencing of microbial community DNA and targeted sequencing of bacterial 16S ribosomal RNA genes to gain an understanding of how microbial communities adapt to extremes of diet. We sampled fecal DNA from 33 mammalian species and 18 humans who kept detailed diet records, and we found that the adaptation of the microbiota to diet is similar across different mammalian lineages. Functional repertoires of microbiome genes, such as those encoding carbohydrate-active enzymes and proteases, can be predicted from bacterial species assemblages. These results illustrate the value of characterizing vertebrate gut microbiomes to understand host evolutionary histories at a supraorganismal level.     

Architecture of succinate dehydrogenase and reactive oxygen species generation

The structure of Escherichia coli succinate dehydrogenase (SQR), analogous to the mitochondrial respiratory complex II, has been determined, revealing the electron transport pathway from the electron donor, succinate, to the terminal electron acceptor, ubiquinone. It was found that the SQR redox centers are arranged in a manner that aids the prevention of reactive oxygen species (ROS) formation at the flavin adenine dinucleotide. This is likely to be the main reason SQR is expressed during aerobic respiration rather than the related enzyme fumarate reductase, which produces high levels of ROS. Furthermore, symptoms of genetic disorders associated with mitochondrial SQR mutations may be a result of ROS formation resulting from impaired electron transport in the enzyme.     

Serine-7 of the RNA polymerase II CTD is specifically required for snRNA gene expression

RNA polymerase II (Pol II) transcribes genes that encode proteins and noncoding small nuclear RNAs (snRNAs). The carboxyl-terminal repeat domain (CTD) of the largest subunit of mammalian RNA Pol II, comprising tandem repeats of the heptapeptide consensus Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7, is required for expression of both gene types. We show that mutation of serine-7 to alanine causes a specific defect in snRNA gene expression. We also present evidence that phosphorylation of serine-7 facilitates interaction with the snRNA gene-specific Integrator complex. These findings assign a biological function to this amino acid and highlight a gene type-specific requirement for a residue within the CTD heptapeptide, supporting the existence of a CTD code.