Analysis of >1000 single nucleotide polymorphisms in geographically matched samples of landrace and wild barley indicates secondary contact and chromosome-level differences in diversity around domestication genes.

Barley is a model species for the investigation of the evolution, adaptation and spread of the world's important crops. In this article, we describe the first application of an oligonucleotide pool assay single nucleotide polymorphism (SNP) platform to assess the evolution of barley in a portion of the Fertile Crescent, a key region in the development of farming. A large collection of >1000 genetically mapped, genome-wide SNPs was assayed in geographically matched landrace and wild barley accessions (N=448) from Jordan and Syria.

Berry polyphenols inhibit α-amylase in vitro: identifying active components in rowanberry and raspberry.

Polyphenol-rich extracts from a range of berries inhibited α-amylase in vitro, but the most effective were from raspberry and rowanberry (IC50 values of 21.0 and 4.5 μg/mL, respectively).

Plant influence on nitrification.

Modern agriculture has promoted the development of high-nitrification systems that are susceptible to major losses of nitrogen through leaching of nitrate and gaseous emissions of nitrogen oxide (NO and N2O), contributing to global warming and depletion of the ozone layer. Leakage of nitrogen from agricultural systems forces increased use of nitrogen fertilizers and causes water pollution and elevated costs of food production. Possible strategies for prevention of these processes involve various agricultural management approaches and use of synthetic inhibitors.

Patterns of genetic diversity and linkage disequilibrium in a highly structured Hordeum vulgare association-mapping population for the Mediterranean basin.

Population structure and genome-wide linkage disequilibrium (LD) were investigated in 192 Hordeum vulgare accessions providing a comprehensive coverage of past and present barley breeding in the Mediterranean basin, using 50 nuclear microsatellite and 1,130 DArT((R)) markers. Both clustering and principal coordinate analyses clearly sub-divided the sample into five distinct groups centred on key ancestors and regions of origin of the germplasm. For given genetic distances, large variation in LD values was observed, ranging from closely linked markers completely at equilibrium to marker pairs at 50 cM separation still showing significant LD.

Intronic noncoding RNAs and splicing.

The gene organization of small nucleolar RNAs (snoRNAs) and microRNAs (miRNAs) varies within and among different organisms. This diversity is reflected in the maturation pathways of these small noncoding RNAs (ncRNAs). The presence of noncoding RNAs in introns has implications for the biogenesis of both mature small RNAs and host mRNA.

Colon-available raspberry polyphenols exhibit anti-cancer effects on in vitro models of colon cancer.

Background: There is a probable association between consumption of fruit and vegetables and reduced risk of cancer, particularly cancer of the digestive tract. This anti-cancer activity has been attributed in part to anti-oxidants present in these foods. Raspberries in particular are a rich source of the anti-oxidant compounds, such as polyphenols, anthocyanins and ellagitannins.

A novel cleavage site within the potato leafroll virus P1 polyprotein.

To study the proteolytic processing of the potato leafroll virus replicase proteins, the multidomain P1 protein with a c-myc epitope tag attached at the N terminus was expressed in insect cells by using the baculovirus system. Western blotting showed that P1 was cleaved at a site upstream of the serine protease domain, in addition to the cleavage site downstream of the protease domain. Mutational analysis showed that the serine protease domain within P1 was responsible for this cleavage.

Barley stripe mosaic virus-encoded proteins triple-gene block 2 and gammab localize to chloroplasts in virus-infected monocot and dicot plants, revealing hitherto-unknown roles in virus replication.

Replication of Barley stripe mosaic virus (BSMV), genus Hordeivirus, is thought to be associated with vesicles in proplastids and chloroplasts, but the molecular details of the process and identity of virus proteins involved in establishing the virus replication complexes are unknown. In addition, BSMV encodes a triple-gene block of movement proteins (TGBs) that putatively share functional roles with their counterparts in other hordei-, pomo- and pecluviruses, but detailed information on the intracellular locations of the individual TGBs is lacking. Here, the subcellular localizations of BSMV-encoded proteins TGB2 and gammab fused to green or red fluorescent proteins were examined in epidermal cells of Nicotiana benthamiana and barley (Hordeum vulgare 'Black Hulless').

Rotting softly and stealthily.

The soft rot erwiniae, which are plant pathogens on potato and other crops world-wide, synthesize and secrete large quantities of plant cell wall degrading enzymes that are responsible for the soft rot phenotype, earning them the epithet 'brute force' pathogens. They have been distinguished from classic 'stealth' pathogens, such as Pseudomonas syringae, which possesses an extensive battery of Type III secreted effector proteins and phytotoxins to manipulate and suppress host defences. However, recent studies, including whole-genome sequencing, are revealing many components of stealth pathogenesis within the soft rot erwiniae (SRE), suggesting that 'stealth' and 'brute force' should not be regarded as mutually exclusive modes of pathogenesis.

Comparative analysis of population genetic structure in Athyrium distentifolium (Pteridophyta) using AFLPs and SSRs from anonymous and transcribed gene regions.

To examine the performance and information content of different marker systems, comparative assessment of population genetic diversity was undertaken in nine populations of Athyrium distentifolium using nine genomic and 10 expressed sequence tag (EST) microsatellite (SSR) loci, and 265 amplified fragment length polymorphism (AFLP) loci from two primer combinations. In range-wide comparisons (European vs. North American populations), the EST-SSR loci showed more reliable amplification and produced more easily scorable bands than genomic simple sequence repeats (SSRs).

Analysis of simple sequence repeats (SSRs) in wild barley from the Fertile Crescent: associations with ecology, geography and flowering time.

Wild barley, Hordeum spontaneum C. Koch, is the progenitor of cultivated barley, Hordeum vulgare. The centre of diversity is in the Fertile Crescent of the Near East, where wild barley grows in a wide range of conditions (temperature, water availability, day length, etc.

Incidence and Distribution of Raspberry bushy dwarf virus in Commercial Red Raspberry (Rubus idaeus) Crops in Scotland.

A survey was done in 1998 to determine whether Raspberry bushy dwarf virus (RBDV) was established in raspberry fruiting plantations in Scotland. Raspberry-producing holdings were selected according to geographical area and size. Samples (201), each comprising 60 shoots per stock, were obtained from 77 holdings and tested by enzyme-linked immunosorbent assay (ELISA).

A cysteine protease gene is expressed early in resistant potato interactions with Phytophthora infestans.

A potato cysteine protease (cyp) cDNA expressed at an early stage of an incompatible interaction with Phytophthora infestans was isolated. Both the nucleotide and deduced amino acid sequences are highly homologous to those of a tomato cysteine protease, CYP1. Striking protein similarity to all known cathepsins in animals, particularly cathepsin K, was also observed.

PCR analysis of oilseed rape cultivars (Brassica napus L. ssp. oleifera) using 5' -anchored simple sequence repeat (SSR) primers.

Primers complementary to simple sequence repeats (SSRs) and with variable three-base 'anchors' at their 5' end, were used in PCR analyses to compare pooled DNA samples from various Brassica napus and B. rapa cultivars. Amplification products were resolved on polyacrylamide gels and detected by silver-nitrate staining.