Glenda Willems

Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines

Although pioneered by human geneticists as a potential solution to the challenging problem of finding the genetic basis of common human diseases, genome-wide association (GWA) studies have, owing to advances in genotyping and sequencing technology, become an obvious general approach for studying the genetics of natural variation and traits of agricultural importance. They are particularly useful when inbred lines are available, because once these lines have been genotyped they can be phenotyped multiple times, making it possible (as well as extremely cost effective) to study many different traits in many different environments, while replicating the phenotypic measurements to reduce environmental noise. Here we demonstrate the power of this approach by carrying out a GWA study of 107 phenotypes in Arabidopsis thaliana, a widely distributed, predominantly self-fertilizing model plant known to harbour considerable genetic variation for many adaptively important traits. Our results are dramatically different from those of human GWA studies, in that we identify many common alleles of major effect, but they are also, in many cases, harder to interpret because confounding by complex genetics and population structure make it difficult to distinguish true associations from false. However, a-priori candidates are significantly over-represented among these associations as well, making many of them excellent candidates for follow-up experiments. Our study demonstrates the feasibility of GWA studies in A. thaliana and suggests that the approach will be appropriate for many other organisms.

A Major Quantitative Trait Locus for Cadmium Tolerance in Arabidopsis halleri Colocalizes with HMA4, a Gene Encoding a Heavy Metal ATPase

Cadmium (Cd) tolerance seems to be a constitutive species-level trait in Arabidopsis halleri sp. halleri. Therefore, an interspecific cross was made between A. halleri and its closest nontolerant interfertile relative, Arabidopsis lyrata sp. petraea, and a first-generation backcross population (BC1) was used to map quantitative trait loci (QTL) for Cd tolerance. Three QTL were identified, which explained 43%, 24%, and 16% of the phenotypic variation in the mapping population. Heavy metal transporting ATPases4 (HMA4), encoding a predicted heavy metal ATPase, colocalized with the peak of the major QTL Cdtol-1 and was consequently further studied. HMA4 transcripts levels were higher in the roots and the shoots of A. halleri than in A. lyrata sp. petraea. Furthermore, HMA4 was also more highly expressed in all BC1 genotypes harboring the HMA4 A. halleri allele at the QTL Cdtol-1, independently of the presence of an A. halleri allele at the two other QTL. Overexpression of AhHMA4 in yeast (Saccharomyces cerevisiae) supported a role of HMA4 in zinc (Zn) and Cd transport by reducing the Cd and Zn contents of the yeast cells. In epidermal tobacco (Nicotiana tabacum) cells, AhHMA4:green fluorescent protein was clearly localized in the plasma membrane. Taken together, all available data point to the elevated expression of HMA4 P1B-type ATPase as an efficient mechanism for improving Cd/Zn tolerance in plants under conditions of Cd/Zn excess by maintaining low cellular Cd2+ and Zn2+ concentrations in the cytoplasm.

The Genetic Basis of Zinc Tolerance in the Metallophyte Arabidopsis halleri ssp. halleri (Brassicaceae): An Analysis of Quantitative Trait Loci

The species Arabidopsis halleri, an emerging model for the study of heavy metal tolerance and accumulation in plants, has evolved a high level of constitutive zinc tolerance. Mapping of quantitative trait loci (QTL) was used to investigate the genetic architecture of zinc tolerance in this species. A first-generation backcross progeny of A. halleri ssp. halleri from a highly contaminated industrial site and its nontolerant relative A. lyrata ssp. petraea was produced and used for QTL mapping of zinc tolerance. A genetic map covering most of the A. halleri genome was constructed using 85 markers. Among these markers, 65 were anchored in A. thaliana and revealed high synteny with other Arabidopsis genomes. Three QTL of comparable magnitude on three different linkage groups were identified. At all QTL positions zinc tolerance was enhanced by A. halleri alleles, indicating directional selection for higher zinc tolerance in this species. The two-LOD support intervals associated with these QTL cover 24, 4, and 13 cM. The importance of each of these three regions is emphasized by their colocalization with HMA4, MTP1-A, and MTP1-B, respectively, three genes well known to be involved in metal homeostasis and tolerance in plants.

Stimulating effect of gastrin on cell proliferation kinetics in canine fundic mucosa.

The effects of porcine gastrin and histamine on deoxyribonucleic acid synthesis and on mitotic activity in the fundic glands were explored in dogs. Fundic mucosal specimens were labeled in vitro with H 3 -thymidine and autoradiographs were prepared. Twelve hours after administration of gastrin, at doses corresponding to a maximal acid secretion, the labeling index in the mucosa was abruptly increased, whereas mitotic index rose only from the 20th hr. Such a sequence of kinetic features clearly indicated that cell proliferation was stimulated. By contrast, no significant variations of the proliferative parameters were observed after maximal stimulation of acid secretion with histamine. This confirms the hypothesis that gastrin exerts a trophic action on the fundic mucosa.

Methicillin-resistant Staphylococcus aureus ST398 in swine farm personnel, Belgium

We assessed methicillin-resistant Staphylococcus aureus (MRSA) in persons on 49 swine farms in Belgium. Surveys showed that 48 (37.8%) persons carried MRSA ST398 and 1 (0.8%) had concurrent skin infection. Risk factors for carriage were MRSA carriage by pigs, regular contact with pigs and companion animals, and use of protective clothing.

Colonic mucosal atrophy induced by a liquid elemental diet in rats

The weight, the total crypt cell population, and the proliferation parameters of the colon were estimated in rats during a 4-week administration of a liquid elemental diet (Vivonex® standard). Both mitotic and DNA synthesis activity were decreased (P<0.01) in the colonic mucosa during the administration of the diet. The weight of the colon was electively decreased (P<0.01) from the first week of the treatment. After four weeks, a 75% decrease in the cell population of mucosal glands was observed. This showed that considerable atrophy of the colonic mucosa occurred under the effect of feeding the elemental diet. This atrophy was probably mediated by a reduction in the proliferative activity of the stem cells in the mucosal glands.

Cell population kinetics of zymogen and parietal cells in the stomach of mice.

SummaryWith autoradiography after labelling with tritiated thymidine, the kinetics of zymogen and parietal cells were studied in the gastric mucosa of mice. After one intraperitoneal injection of the DNA precursor, zymogen cells in the DNA synthesis phase were clearly identified on autoradiograms, whereas no parietal cells were seen to synthesize DNA.In another group of mice, multiple injections were used in order to obtain a greater number of labelled cells. Following the latter procedure, analysis of grain count distributions over labelled zymogen cells and of labelling indices allowed detection of two subsequent zymogen cell divisions within an interval of approximately two months. This indicates that the cell turnover of zymogen cells is at least partly assured by their own mitotic activity.By contrast, parietal cells showed no evidence of cell division, but appeared to be derived through differentiation from other cells in the neck area of the gland. Analysis of spatial distribution of the labelled parietal cells in the glandular tube indicated that, in time, most newly formed parietal cells undergo a slow migration directed downwards to the bottom of the fundic glands.These results clearly show that the zymogen and the parietal cell population of the fundic glands have a different kinetic behaviour.

Quantitative trait loci analysis of mineral element concentrations in an Arabidopsis halleri × Arabidopsis lyrata petraea F2 progeny grown on cadmium-contaminated soil.

SUMMARY This study describes the quantitative trait locus (QTL) analysis of cadmium (Cd), zinc (Zn), iron (Fe), potassium (K), magnesium (Mg) and calcium (Ca) accumulation in the pseudometallophyte Arabidopsis halleri under conditions of Cd excess using an interspecific A. halleri x Arabidopsis lyrata F(2) population. *Our data provide evidence for the implication of one major QTL in Cd hyperaccumulation in A. halleri, and suggests that Cd tolerance and accumulation are not independent in A. halleri. Moreover, the major loci responsible for Zn hyperaccumulation in the absence of Cd appear to be the same when Cd is present at high concentrations. *More than twofold higher Fe concentrations were measured in A. halleri shoots than in A. lyrata, suggesting a different regulation of Fe accumulation in the hyperaccumulator. *With the exception of Ca, the accumulation of Cd was significantly correlated with the accumulation of all elements measured in the F(2) progeny, suggesting pleiotropic gene action. However, QTL analysis identified pleiotropic QTLs only for Cd, Zn and Fe. Mg accumulation was negatively correlated with Cd accumulation, as well as with dry shoot biomass, suggesting that it might indicate cellular damage.

Prevalence and Antimicrobial Susceptibility of Methicillin-Resistant Staphylococcus aureus Among Pigs in Belgium

The prevalence, distribution, and antimicrobial susceptibility of methicillin-resistant Staphylococcus aureus (MRSA) in Belgian pig farms has been investigated. To that end, nasal samples were collected from 1,500 pigs on 50 farms randomly selected over Belgium. Both closed (breeding or farrow-to-finish) and open (fattening) farms were included. Within closed farms different age groups were investigated. A total number of 663 (44%) pigs belonging to 34 (68%) farms carried MRSA. According to their management practice, MRSA was detected on 94% of the open farms and 56% of the closed farms. Focusing on the in-herd prevalence among fattening pigs for both management systems, a significantly higher rate was found in open farms (72%) compared to closed farms (26%). Within the closed farms, piglets (41%) showed a higher MRSA prevalence than sows (26%) and fattening pigs (26%). All strains tested were ST398 and showed mainly spa-type t011, as commonly found on pig herds in Europe. Less dominating spa-types were t034, t567, and t2970. The MRSA strains carried two SCCmec-types, type IVa or V. All 643 MRSA strains were resistant to tetracycline and additional resistances to trimethoprim (97%), lincosamides (73%), macrolides (56%), aminoglycosides (48%), and fluoroquinolones (32%) were found. Multiresistance (defined as resistance to four or more non-β-lactam antimicrobial classes) was found in 63% of the tested strains. In conclusion, a high prevalence of MRSA was found in Belgian pig farms, with the highest prevalence in open farms. In accordance with other European countries, age-related and management-related differences in MRSA prevalence were observed that should be considered when control strategies are outlined.

Cell Renewal in the Gastric Mucosa

The mechanisms controlling cell division in the stomach are still unknown. Among the procedures available for determining kinetic parameters in the mucosa, autoradiographic methods with 3H-thymidine are the most widely used. As yet, they have allowed observation of two basic control factors in the gastric mucosa: A tissue specific inhibitory substance of mitotic activity called ‘gastric chalone’ and a stimulating hormone released after food ingestion, which is most probably gastrin. Other possible factors are now to be further investigated.