Genetic dissection of Al tolerance QTLs in the maize genome by high density SNP scan

Background

Aluminum (Al) toxicity is an important limitation to food security in tropical and subtropical regions. High Al saturation on acid soils limits root development, reducing water and nutrient uptake. In addition to naturally occurring acid soils, agricultural practices may decrease soil pH, leading to yield losses due to Al toxicity. Elucidating the genetic and molecular mechanisms underlying maize Al tolerance is expected to accelerate the development of Al-tolerant cultivars.

Results

Five genomic regions were significantly associated with Al tolerance, using 54,455 SNP markers in a recombinant inbred line population derived from Cateto Al237. Candidate genes co-localized with Al tolerance QTLs were further investigated. Near-isogenic lines (NILs) developed for ZmMATE2 were as Al-sensitive as the recurrent line, indicating that this candidate gene was not responsible for the Al tolerance QTL on chromosome 5, qALT5. However, ZmNrat1, a maize homolog to OsNrat1, which encodes an Al³⁺ specific transporter previously implicated in rice Al tolerance, was mapped at ~40 Mbp from qALT5. We demonstrate for the first time that ZmNrat1 is preferentially expressed in maize root tips and is up-regulated by Al, similarly to OsNrat1 in rice, suggesting a role of this gene in maize Al tolerance. The strongest-effect QTL was mapped on chromosome 6 (qALT6), within a 0.5 Mbp region where three copies of the Al tolerance gene, ZmMATE1, were found in tandem configuration. qALT6 was shown to increase Al tolerance in maize; the qALT6-NILs carrying three copies of ZmMATE1 exhibited a two-fold increase in Al tolerance, and higher expression of ZmMATE1 compared to the Al sensitive recurrent parent. Interestingly, a new source of Al tolerance via ZmMATE1 was identified in a Brazilian elite line that showed high expression of ZmMATE1 but carries a single copy of ZmMATE1.

Conclusions

High ZmMATE1 expression, controlled either by three copies of the target gene or by an unknown molecular mechanism, is responsible for Al tolerance mediated by qALT6. As Al tolerant alleles at qALT6 are rare in maize, marker-assisted introgression of this QTL is an important strategy to improve maize adaptation to acid soils worldwide.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-153) contains supplementary material, which is available to authorized users.     

A genetic variant in osteoprotegerin is associated with progression of joint destruction in rheumatoid arthritis

Introduction

Progression of joint destruction in rheumatoid arthritis (RA) is partly heritably; 45 to 58% of the variance in joint destruction is estimated to be explained by genetic factors. The binding of RANKL (Receptor Activator for Nuclear Factor κ B Ligand) to RANK results in the activation of TRAF6 (tumor necrosis factor (TNF) receptor associated factor-6), and osteoclast formation ultimately leading to enhanced bone resorption. This bone resorption is inhibited by osteoprotegerin (OPG) which prevents RANKL-RANK interactions. The OPG/RANK/RANKL/TRAF6 pathway plays an important role in bone remodeling. Therefore, we investigated whether genetic variants in OPG, RANK, RANKL and TRAF6 are associated with the rate of joint destruction in RA.

Methods

1,418 patients with 4,885 X-rays of hands and feet derived from four independent data-sets were studied. In each data-set the relative increase of the progression rate per year in the presence of a genotype was assessed. First, explorative analyses were performed on 600 RA-patients from Leiden. 109 SNPs, tagging OPG, RANK, RANKL and TRAF6, were tested. Single nucleotide polymorphisms (SNPs) significantly associated in phase-1 were genotyped in data-sets from Groningen (Netherlands), Sheffield (United Kingdom) and Lund (Switzerland). Data were summarized in an inverse weighted variance meta-analysis. Bonferonni correction for multiple testing was applied.

Results

We found that 33 SNPs were significantly associated with the rate of joint destruction in phase-1. In phase-2, six SNPs in OPG and four SNPs in RANK were associated with progression of joint destruction with P-value <0.05. In the meta-analyses of all four data-sets, RA-patients with the minor allele of OPG-rs1485305 expressed higher rates of joint destruction compared to patients without these risk variants (P = 2.35x10⁻⁴). This variant was also significant after Bonferroni correction.

Conclusions

These results indicate that a genetic variant in OPG is associated with a more severe rate of joint destruction in RA.     

An ultrasound based non-invasive method for the measurement of intrinsic foot kinematics during gait

Soft tissue artefact (STA) and marker placement variability are sources of error when measuring the intrinsic kinematics of the foot. This study aims to demonstrate a non-invasive, combined ultrasound and motion capture (US/MC) technique to directly measure foot skeletal motion. The novel approach is compared to a standard motion capture protocol. Fourteen participants underwent instrumented barefoot analysis of foot motion during gait. Markers were attached to foot allowing medial longitudinal arch angle and navicular height to be determined. For the US/MC technique, the navicular marker was replaced by an ultrasound transducer which was secured to the foot allowing the skeletal landmark to be imaged. Ultrasound cineloops showing the location of the navicular tuberosity during the walking trials were synchronised with motion capture measurements and markers mounted on the probe allowed the true position of the bony landmark to be determined throughout stance phase. Two discrete variables, minimum navicular height and maximum MLA angle, were compared between the standard and US/MC protocols. Significant differences between minimum navicular height (P=0.004, 95% CI (1.57, 6.54)) and maximum medial longitudinal arch angle (P=0.0034, 95% CI (13.8, 3.4)) were found between the measurement methods. The individual effects of STA and marker placement error were also assessed. US/MC is a non-invasive technique which may help to provide more accurate measurements of intrinsic foot kinematics.     

A Comparative Study of Leaf Breakdown of Three Native Tree Species in a Slowly‐Flowing Headwater Stream in the Colombian Andes

The dynamics of leaf breakdown in a headwater Colombian stream were evaluated for the native tree species Myrsine guianensis, Cupania latifolia and Nectandra lineatifolia using coarse and fine mesh litter bags. Ten bags of each species (five of each mesh size) were retrieved from the stream at 1, 8, 15, 30, 60 and 120 days. k values ranged from 0.0008 to 0.0058 day^–1 and density of macroinvertebrates from 35 to 55 individuals per leaf bag, peaking at day 8. Myrsine guianensis degraded more rapidly than the other species for both coarse and fine mesh bags. This species and Nectandra lineatifolia presented differences in k values between coarse and fine mesh bags, suggesting that macroinvertebrates influenced the decay rate. Despite the low densities of macroinvertebrates found, shredders represented 12.7% of individuals and 50 to 68% of the invertebrate biomass in bags, indicating that this functional feeding group was an important component of fauna associated with litter breakdown in this first order tropical stream. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

18S rRNA data indicate that Aschelminthes are polyphyletic in origin and consist of at least three distinct clades

The Aschelminthes is a collection of at least eight animal phyla, historically grouped together because the absence of a true body cavity was perceived as a pseudocoelom. Analyses of 18S rRNA sequences from six Aschelminth phyla (including four previously unpublished sequences) support polyphyly for the Aschelminthes. At least three distinct groups of Aschelminthes were detected: the Priapulida among the protostomes, the Rotifera-Acanthocephala as a sister group to the protostomes, and the Nematoda as a basal group to the triploblastic Eumetazoa.