Deciphering the complex nature of bolting time regulation in <Emphasis Type="Italic">Beta vulgaris</Emphasis>

Key message

Only few genetic loci are sufficient to increase the variation of bolting time in Beta vulgaris dramatically, regarding vernalization requirement, seasonal bolting time and reproduction type.

Abstract

Beta species show a wide variation of bolting time regarding the year of first reproduction, seasonal bolting time and the number of reproduction cycles. To elucidate the genetics of bolting time control, we used three F₃ mapping populations that were produced by crossing a semelparous, annual sugar beet with iteroparous, vernalization-requiring wild beet genotypes. The semelparous plants died after reproduction, whereas iteroparous plants reproduced at least twice. All populations segregated for vernalization requirement, seasonal bolting time and the number of reproduction cycles. We found that vernalization requirement co-segregated with the bolting locus B on chromosome 2 and was inherited independently from semel- or iteroparous reproduction. Furthermore, we found that seasonal bolting time is a highly heritable trait (h ² > 0.84), which is primarily controlled by two major QTL located on chromosome 4 and 9. Late bolting alleles of both loci act in a partially recessive manner and were identified in both iteroparous pollinators. We observed an additive interaction of both loci for bolting delay. The QTL region on chromosome 4 encompasses the floral promoter gene BvFT2, whereas the QTL on chromosome 9 co-localizes with the BR ₁ locus, which controls post-winter bolting resistance. Our findings are applicable for marker-assisted sugar beet breeding regarding early bolting to accelerate generation cycles and late bolting to develop bolting-resistant spring and winter beets. Unexpectedly, one population segregated also for dwarf growth that was found to be controlled by a single locus on chromosome 9.

     

The effect of <Emphasis Type="Italic">INDEHISCENT</Emphasis> point mutations on silique shatter resistance in oilseed rape (<Emphasis Type="Italic">Brassica napus</Emphasis>)

Key message

This study elucidates the influence of indehiscent mutations on rapeseed silique shatter resistance. A phenotype with enlarged replum-valve joint area and altered cell dimensions in the dehiscence zone is described.

Abstract

Silique shattering is a major factor reducing the yield stability of oilseed rape (Brassica napus). Attempts to improve shatter resistance often include the use of mutations in target genes identified from Arabidopsis (Arabidopsis thaliana). A variety of phenotyping methods assessing the level of shatter resistance were previously described. However, a comparative and comprehensive evaluation of the methods has not yet been undertaken. We verified the increase of shatter resistance in indehiscent double knock-down mutants obtained by TILLING with a systematic approach comparing three independent phenotyping methods. A positive correlation of silique length and shatter resistance was observed and accounted for in the analyses. Microscopic studies ruled out the influence of different lignification patterns. Instead, we propose a model to explain increased shattering resistance of indehiscent rapeseed mutants by altered cell shapes and sizes within the contact surfaces of replum and valves.

     

Whole‐transcriptome analysis reveals genetic factors underlying flowering time regulation in rapeseed (Brassica napus L.)

Rapeseed (Brassica napus L.), one of the most important sources of vegetable oil and protein‐rich meals worldwide, is adapted to different geographical regions by modification of flowering time. Rapeseed cultivars have different day length and vernalization requirements, which categorize them into winter, spring, and semiwinter ecotypes. To gain a deeper insight into genetic factors controlling floral transition in B. napus, we performed RNA sequencing (RNA‐seq) in the semiwinter doubled haploid line, Ningyou7, at different developmental stages and temperature regimes. The expression profiles of more than 54,000 gene models were compared between different treatments and developmental stages, and the differentially expressed genes were considered as targets for association analysis and genetic mapping to confirm their role in floral transition. Consequently, 36 genes with association to flowering time, seed yield, or both were identified. We found novel indications for neofunctionalization in homologs of known flowering time regulators like VIN3 and FUL. Our study proved the potential of RNA‐seq along with association analysis and genetic mapping to identify candidate genes for floral transition in rapeseed. The candidate genes identified in this study could be subjected to genetic modification or targeted mutagenesis and genotype building to breed rapeseed adapted to certain environments.     

Surface reconstruction of torsos with and without scoliosis

Visible surface asymmetries such as uneven shoulders, waist and hips, shoulder height differences and a shoulder blade prominence are often the most troublesome features associated with adolescent scoliosis. Treatment considerations are influenced by the severity and changes over time of these asymmetries. Outcomes are judged on how well the asymmetries are improved towards a normal trunk shape. In this paper, a deformable self organizing feature map (SOFM) is used as a geometric surface reconstruction tool to model the torso surface of subjects with and without scoliosis. The proposed parameterization technique provides a means of quantifying the surface asymmetries and assessing the changes due to either natural history or the effects of treatment. For evaluation 10 control subjects without scoliosis and 10 adolescents with scoliosis were scanned and their torsos were reconstructed. This preliminary study demonstrates that in around 5 min a torso scan with 60,000 data points can be transformed into a 2562 nodes mesh using SOFM. The accuracy of the final mesh is around 1.40 mm on average. The high accuracy and speed of this technique, makes it well suitable to be used in a clinical setting to assess surface features of subjects with scoliosis.     

An APETALA1 ortholog affects plant architecture and seed yield component in oilseed rape (Brassica napus L.)

Exploring the natural occurring genetic variation of the wild barley genepool has become a major target of barley crop breeding programmes aiming to increase crop productivity and sustainability in global climate change scenarios. However this diversity remains unexploited and effective approaches are required to investigate the benefits that unadapted genomes could bring to crop improved resilience. In the present study, a set of Recombinant Chromosome Substitution Lines (RCSLs) derived from an elite barley cultivar ‘Harrington’ as the recurrent parent, and a wild barley accession from the Fertile Crescent ‘Caesarea 26–24’, as the donor parent (Matus et al. Genome 46:1010–23, 2003) have been utilised in field and controlled conditions to examine the contribution of wild barley genome as a source of novel allelic variation for the cultivated barley genepool. Twenty-eight RCSLs which were selected to represent the entire genome of the wild barley accession, were genotyped using the 9 K iSelect SNP markers (Comadran et al. Nat Genet 44:1388–92, 2012) and phenotyped for a range of morphological, developmental and agronomic traits in 2 years using a rain-out shelter with four replicates and three water treatments. Data were analysed for marker traits associations using a mixed model approach. We identified lines that differ significantly from the elite parent for both qualitative and quantitative traits across growing seasons and water regimes. The detailed genotypic characterisation of the lines for over 1800 polymorphic SNP markers and the design of a mixed model analysis identified chromosomal regions associated with yield related traits where the wild barley allele had a positive response increasing grain weight and size. In addition, variation for qualitative characters, such as the presence of cuticle waxes on the developing spikes, was associated with the wild barley introgressions. Despite the coarse location of the QTLs, interesting candidate genes for the major marker-trait associations were identified using the recently released barley genome assembly. This study has highlighted the role of exotic germplasm to contribute novel allelic variation by using an optimised experimental approach focused on an exotic genetic library. The results obtained constitute a step forward to the development of more tolerant and resilient varieties.     

Serum concentrations of MCP-1 and IL-6 in combination predict the presence of coronary artery disease and mortality in subjects undergoing coronary angiography

The UBA–UBX domain-containing proteins can interact with ubiquitinated substrates and p97 during endoplasmic reticulum-associated degradation (ERAD). Here, we found that the expressions of all UBA–UBX genes p47, SAKS1, UBXD8, FAF1, and UBXD7 were elevated upon ER stress, albeit with different levels. Of which p47, SAKS1, and UBXD8 are ‘immediate’ respondents whereas FAF1 and UBXD7 were ‘late’ respondents to ER stress. Interestingly, the expression of specific UBA–UBX genes were altered in cells stably expressing three different ERAD substrates such as α-TCR, α1-antitrypsin, and δCD3. We first found that p47 and UBXD8 expression levels were increased in α-TCR and α1-antitrypsin stable cell lines, respectively, whereas SAKS1 expression level was reduced in all the three ERAD substrates tested. Of note, we also found p47 promotes, whereas SASK1 delays the degradation of a single ERAD substrate, α-TCR. Additionally, we found that SAKS1 selectively inhibits the degradation of ERAD substrates without affecting cytosolic proteasomal substrates. Taken together, our results identified that UBA–UBX proteins possess substrate selectivity and opposite role of two different UBA–UBX proteins in the degradation of a single ERAD substrate.     

Genome-wide association study of shank length and diameter at different developmental stages in chicken F2 resource population

In order to find SNPs and genes affecting shank traits, we performed a GWAS in a chicken F2 population of eight half-sib families from five hatches derived from reciprocal crosses between an Arian fast-growing line and an Urmia indigenous slow-growing chicken. A total of 308 birds were genotyped using a 60K chicken SNP chip. Shank traits including shank length and diameter were measured weekly from birth to 12 weeks of age. A generalized linear model and a compressed mixed linear model (CMLM) were applied to achieve the significant regions. The value of the average genomic inflation factor (λ statistic) of the CMLM model (0.99) indicated that the CMLM was more effective than the generalized linear model in controlling the population structure. The genes surrounding significant SNPs and their biological functions were identified from NCBI, Ensembl and UniProt databases. The results indicated that 12 SNPs at 12 different ages passed the LD-adjusted 5% Bonferroni significant threshold. Two SNPs were significant for shank length and nine SNPs were significant for shank diameter. The significant SNPs were located near to or inside 11 candidate genes. The results showed that a number of significant SNPs in the middle ages were higher than the rest. The MXRA8 gene was related to the significant SNP at week 1 that promotes proliferation of growth plate chondrocytes. A unique SNP of Gga_rs16689511 located on chicken Z chromosome within the LOC101747628 gene was related to shank length at three different ages of birds (weeks 8, 9 and 11). The significant SNPs for shank diameter were found at weeks 4 and 7 (four and five SNPs respectively). The identifications of SNPs and genes here could contribute to a better understanding of the genetic control of shank traits in chicken.