Sustainable development in circular agriculture: An illustrative bee↺legume↺poultry example

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Genetic and molecular approaches to valorise protein and fibre in potato

On a global scale, potato is an important crop for both consumption and the starch industry. At present, the starch industry is keen to create economic value and to reduce its impact on the environment by valorising all resources in potatoes. One way to contribute towards this goal is to develop new potato varieties with elite traits, i.e. a high level of tuber protein content and a reduced level of fibre hydration. Improving these traits is however challenging due to their complex nature. Therefore, a better understanding of the genetics and biological processes underlying tuber protein content and fibre hydration are relevant. The objectives of this study were to shed light on the genetic and molecular architectures of tuber protein content and fibre hydration and to pinpoint key factors (i.e. biological processes, molecular structures, genes and alleles) that are involved in modulation of these traits. Chapter 1 provides a description of the potato crop and the starch industry. We present protein and fibre as key resources, where improvement of their quantity and quality will lead to a better valorisation of the potato crop. The principles of potato genetics, potato breeding and modern tools for trait improvement are described. In Chapter 2 we studied the genetics of tuber protein content in a panel of tetraploid potato varieties. We estimated a moderate level of trait heritability, identified marker-trait associations (QTLs), haplotypes and candidate genes. Our findings showed that alleles of StCDF1 were associated with tuber protein content. The results provide resources for genomics-enabled breeding. In Chapter 3 we performed a multi-allelic QTL analysis of tuber protein content in a large bi-parental population of tetraploid potato. We estimated a moderate level of trait heritability and identified QTLs. The alleles underlying the QTLs provided both positive and negative effects on the level of tuber protein content. Our results showed that tuber protein content is a complex trait in potato. In Chapter 4 we studied the overexpression effect of a putative nitrate transporter gene (StNPF1.11) on tuber protein content in potato. Overexpression of StNPF1.11 increased tuber protein content, leaf chlorophyll content and plant height of young potato plants. A pleiotropic effect on tuber dry matter content (a proxy for starch content), suggests that the nitrogen status may affect tuber starch accumulation in potato in vivo. In Chapter 5 we studied the role of pectic rhamnogalacturonan (RG-I) galactan side-chains on the water-binding capacity (WBC) of potato cell walls. Both in-vivo and in-vitro truncation of RG-I β-(1→4)-D-galactan side-chains altered the WBC, but with contrasting effects. Our results reinforce the view that RG-I galactan side-chains play a role in modulating the WBC of potato cell walls. In Chapter 6 the insights that were generated in the experimental chapters are evaluated and discussed in a broader context. Finally, implications and prospects for future research are presented

RG-I galactan side-chains are involved in the regulation of the water-binding capacity of potato cell walls

Potato cell walls (PCW) are a low value by-product from the potato starch industry. Valorisation of PCW is hindered by its high water-binding capacity (WBC). The composition of polysaccharides and interactions between these entities, play important roles in regulating the WBC in the cell wall matrix. Here, we show that in vivo exo-truncation of RG-I β-(1→4)-D-galactan side-chains decreased the WBC by 6–9%. In contrast, exo-truncation of these side-chains increased the WBC by 13% in vitro. We propose that degradation of RG-I galactan side-chains altered the WBC of PCW, due to cell wall remodelling and loosening that affected the porosity. Our findings reinforce the view that RG-I galactan side-chains play a role in modulating WBC, presumably by affecting polysaccharide architecture (spacing) and interactions in the matrix. Better understanding of structure-function relationships of pectin macromolecules is needed before cell wall by-products may be tailored to render added-value in food and biobased products.</p

Multi-allelic QTL analysis of protein content in a bi-parental population of cultivated tetraploid potato

Protein content is a key quality trait for the potato starch industry. The objective of this study was to identify allele-specific quantitative trait loci (QTLs) for tuber protein content in cultivated potato (Solanum tuberosum L.) at the tetraploid level. We analysed 496 full-sib F1 clones in a 3-year field trial to dissect the complex genetic architecture of soluble tuber protein content. Genotypic data from a 60K single nucleotide polymorphism (SNP) array was used for SNP dosage scoring, constructing homologue specific linkage maps and assembly of a dense integrated chromosomal linkage map. From the integrated map, probabilistic multi-locus identity-by-descent (IBD) haplotypes (alleles) were estimated and used to detect associations between the IBD haplotypes and the phenotypic trait values. Moderate levels of trait heritability were estimated between 40 and 74% that correspond with previous studies. Our contemporary naive analysis identified potential additive QTLs on chromosomes 2, 3, 5 (top arm) and 9 across the years. Moreover, cofactor QTL analysis identified two masked QTLs on chromosomes 1 and 5 (lower arm). The QTLs on chromosomes 2, 5 (lower arm) and 9 are reported here for the first time. The QTLs that we identified on chromosomes 1, 3 and 5 (top arm) show overlap with previous studies for protein content in potato. Collectively the naive QTLs explained 12 to 17% of the phenotypic variance. The underlying alleles of the QTLs provided both positive and negative effects on the phenotype. Our work uncovers the complex genetic architecture of this trait and describes potential breeding strategies for improvement. As protein has emerged as a high-value component from industrial potato starch production, the dissection of the genetic architecture and subsequent improvement of this trait by breeding has great economic and environmental relevance.</p

Overexpression of a putative nitrate transporter (StNPF1.11) increases plant height, leaf chlorophyll content and tuber protein content of young potato plants

Nitrate (NO3-) fertilisers are commonly used to improve the yield and quality of most non-legume crops such as potato (Solanum tuberosum L.). Root cells absorb nitrate from the soil using plasma membrane-bound transporters. In this study, we overexpressed a putative nitrate transporter from potato (StNPF1.11) to study its effect on the level of tuber protein content in potato. At 10 weeks after planting, overexpression of StNPF1.11 increased the mean level of protein content of all n = 23 transformants by 42% compared with the wild-type control. The level of chlorophyll content in leaves (from upper and lower plant parts) also increased for several individuals at 10 weeks. Tuber yield (fresh) was not structurally impaired; however, the mean tuber dry matter content of the transformants was reduced by 3-8% at 19 weeks. At 19 weeks, an overall increase in protein content was not clearly observed. Throughout plant development, half of the transformants were taller than the control. A basic understanding of the mechanisms that regulate plant nitrogen uptake, transport and utilisation, enable the development of tools to improve both crop nutrition and crop quality that are needed to enhance the viability and sustainability of future plant production systems.</p

Genome-wide association analysis in tetraploid potato reveals four QTLs for protein content

Valorisation of tuber protein is relevant for the potato starch industry to create added-value and reduce impact on the environment. Hence, protein content has emerged as a key quality trait for innovative potato breeders. In this study, we estimated trait heritability, explored the relationship between protein content and tuber under-water weight (UWW), inferred haplotypes underlying quantitative trait loci (QTLs) and pinpointed candidate genes. We used a panel of varieties (N = 277) that was genotyped using the SolSTW 20 K Infinium single-nucleotide polymorphism (SNP) marker array. Protein content data were collected from multiple environments and years. Our genome-wide association study (GWAS) identified QTLs on chromosomes 3, 5, 7 and 12. Alleles of StCDF1 (maturity) were associated with QTLs found on chromosome 5. The QTLs on chromosomes 7 and 12 are presented here for the first time, whereas those on chromosomes 3 and 5 co-localized with loci reported in earlier studies. The candidate genes underlying the QTLs proposed here are relevant for functional studies. This study provides resources for genomics-enabled breeding for protein content in potato

High-Resolution Amplified Fragment Length Polymorphism Typing of Lactococcus lactis Strains Enables Identification of Genetic Markers for Subspecies-Related Phenotypes▿

A high-resolution amplified fragment length polymorphism (AFLP) methodology was developed to achieve the delineation of closely related Lactococcus lactis strains. The differentiation depth of 24 enzyme-primer-nucleotide combinations was experimentally evaluated to maximize the number of polymorphisms. The resolution depth was confirmed by performing diversity analysis on 82 L. lactis strains, including both closely and distantly related strains with dairy and nondairy origins. Strains clustered into two main genomic lineages of L. lactis subsp. lactis and L. lactis subsp. cremoris type-strain-like genotypes and a third novel genomic lineage rooted from the L. lactis subsp. lactis genomic lineage. Cluster differentiation was highly correlated with small-subunit rRNA homology and multilocus sequence analysis (MLSA) studies. Additionally, the selected enzyme-primer combination generated L. lactis subsp. cremoris phenotype-specific fragments irrespective of the genotype. These phenotype-specific markers allowed the differentiation of L. lactis subsp. lactis phenotype from L. lactis subsp. cremoris phenotype strains within the same L. lactis subsp. cremoris type-strain-like genomic lineage, illustrating the potential of AFLP for the generation of phenotype-linked genetic markers

The validity of the DSM-IV diagnostic classification system of non-affective psychoses

Objective: The schizophrenia and other non-affective disorders categories listed in the DSM-IV, are currently under revision for the development of the fifth edition. The aim of the present study is to demonstrate the validity of these categories by investigating possible differences between diagnostic patient subgroups on various measures. Methods: 1064 patients with a diagnosis of non-affective psychosis (schizophrenia N = 731 (paranoid type 82%), schizoaffective N = 63, schizophreniform N = 120, psychosis not otherwise specified/brief psychotic disorder N = 150) participated in this study. Dependent variables were demographic and clinical characteristics, severity of psychopathology, premorbid and current functioning, and indicators of quality of life. Results: Within the diagnostic group of schizophrenia, no significant differences were observed between paranoid schizophrenia, disorganized, and undifferentiated schizophrenia. Patients with schizophrenia experienced more severe psychopathology and had poorer levels of current functioning compared to patients with psychosis not otherwise specified or brief psychotic disorder. Differences between schizophrenia and schizoaffective disorder were less clear. Conclusion: Our results do not support the validity of schizophrenia subtypes. Schizophrenia can be distinguished from brief psychotic disorder and psychotic disorder not otherwise specified. These findings may fuel the actual DSM-V discussion

Renal tract malformations: perspectives for nephrologists.

Contains fulltext : 71176.pdf (publisher's version ) (Closed access)Renal tract malformations are congenital anomalies of the kidneys and/or lower urinary tract. One challenging feature of these conditions is that they can present not only prenatally but also in childhood or adulthood. The most severe types of malformations, such as bilateral renal agenesis or dysplasia, although rare, lead to renal failure. With advances in dialysis and transplantation for young children, it is now possible to prevent the early death of at least some individuals with severe malformations. Other renal tract malformations, such as congenital pelviureteric junction obstruction and primary vesicoureteric reflux, are relatively common. Renal tract malformations are, collectively, the major cause of childhood end-stage renal disease. Their contribution to the number of adults on renal replacement therapy is less clear and has possibly been underestimated. Renal tract malformations can be familial, and specific mutations of genes involved in renal tract development can sometimes be found in affected individuals. These features provide information about the causes of malformations but also raise questions about whether to screen relatives. Whether prenatal decompression of obstructed renal tracts, or postnatal initiation of therapies such as prophylactic antibiotics or angiotensin blockade, improve long-term renal outcomes remains unclear