Genetic diversity analysis in sorghum germplasm as estimated by AFLP, SSR and morpho-agronomical markers

A comparison of the different methods of the estimation of genetic diversity is important to evaluate their utility as a tool in germplasm conservation and plant breeding. Amplified fragment length polymorphism (AFLP), microsatellites or SSR and morphological traits markers were used to evaluate 45 sorghum germplasm for genetic diversity assessment and discrimination power. The mean polymorphism information content (PIC) values were 0.65 (AFLPs) and 0.46 (SSRs). The average pairwise genetic distance estimates were 0.57 (morphological traits), 0.62 (AFLPs) and 0.60 (SSRs) markers data sets. The Shannon diversity index was higher for morphological traits (0.678) than AFLP (0.487) and SSR (0.539). The correlation coefficients obtained by the Mantel matrix correspondence test, which was used to compare the cophenetic matrices for the different markers, showed that estimated values of genetic relationship given for AFLP and SSR markers, as well as for morphological and SSR markers were significantly related (p <0.001). However, morphological and AFLP data showed non-significant correlation (p >0.05). Both data sets from AFLP and SSR allowed all accessions to be uniquely identified; two accessions could not be distinguished by the morphological data. In summary, AFLP and SSR markers proved to be efficient tools in assessing the genetic variability among sorghum genotypes. The patterns of variation appeared to be consistent for the three marker systems, and they can be used for designing breeding programmes, conservation of germplasm and management of sorghum genetic resources.     

Phylogenetics and taxonomic delimitation of the genus Guizotia (Asteraceae) based on sequences derived from various chloroplast DNA regions

Parsimony-based phylogenetic analyses of the genus Guizotia were undertaken based on DNA sequence data from the following chloroplast DNA (cpDNA) regions: trnT-trnL, trnL-trnF, trnY-rpoB, trnC-petN, psbM-trnD and rps16-trnQ intergenic spacers, trnL, rps16 and matK-5′trnK introns and matK gene. Out of the 26 primers used in this study, 14 were newly designed. The study was conducted to determine (1) the closest relative of Guizotia abyssinica, (2) the taxonomic status of some Guizotia taxa and (3) the subtribal placement of Guizotia in the tribe Heliantheae. The analyses of the sequence data showed that G. abyssinica, G. scabra ssp. scabra, G. scabra ssp. schimperi and G. villosa are phylogenetically closely related. However, G. scabra ssp. schimperi appeared as the most closely related taxon to G. abyssinica. Based on this phylogenetic analysis, we suggest that the two subspecies of G. scabra are better treated as separate species. The analysis also clearly demonstrated that “Chelelu” and “Ketcha” are distinct Guizotia species. The trnT-trnL and trnL-trnF intergenic spacer-based phylogenetic analysis of various subtribes of the tribe Heliantheae strongly supports the placement of the genus Guizotia within the subtribe Milleriinae.     

Seed colour loci, homoeology and linkage groups of the C genome chromosomes revealed in Brassica rapa-B. oleracea monosomic alien addition lines

Background and Aims

Brassica rapa and B. oleracea are the progenitors of oilseed rape B. napus. The addition of each chromosome of B. oleracea to the chromosome complement of B. rapa results in a series of monosomic alien addition lines (MAALs). Analysis of MAALs determines which B. oleracea chromosomes carry genes controlling specific phenotypic traits, such as seed colour. Yellow-seeded oilseed rape is a desirable breeding goal both for food and livestock feed end-uses that relate to oil, protein and fibre contents. The aims of this study included developing a missing MAAL to complement an available series, for studies on seed colour control, chromosome homoeology and assignment of linkage groups to B. oleracea chromosomes.

Methods

A new batch of B. rapa–B. oleracea aneuploids was produced to generate the missing MAAL. Seed colour and other plant morphological features relevant to differentiation of MAALs were recorded. For chromosome characterization, Snow''s carmine, fluorescence in situ hybridization (FISH) and genomic in situ hybridization (GISH) were used.

Key Results

The final MAAL was developed. Morphological traits that differentiated the MAALs comprised cotyledon number, leaf morphology, flower colour and seed colour. Seed colour was controlled by major genes on two B. oleracea chromosomes and minor genes on five other chromosomes of this species. Homoeologous pairing was largely between chromosomes with similar centromeric positions. FISH, GISH and a parallel microsatellite marker analysis defined the chromosomes in terms of their linkage groups.

Conclusions

A complete set of MAALs is now available for genetic, genomic, evolutionary and breeding perspectives. Defining chromosomes that carry specific genes, physical localization of DNA markers and access to established genetic linkage maps contribute to the integration of these approaches, manifested in the confirmed correspondence of linkage groups with specific chromosomes. Applications include marker-assisted selection and breeding for yellow seeds.     

Targeting Wnt/tenascin C-mediated cross talk between pancreatic cancer cells and stellate cells via activation of the metastasis suppressor NDRG1

A major barrier to successful pancreatic cancer (PC) treatment is the surrounding stroma, which secretes growth factors/cytokines that promote PC progression. Wnt and tenascin C (TnC) are key ligands secreted by stromal pancreatic stellate cells (PSCs) that then act on PC cells in a paracrine manner to activate the oncogenic β-catenin and YAP/TAZ signaling pathways. Therefore, therapies targeting oncogenic Wnt/TnC cross talk between PC cells and PSCs constitute a promising new therapeutic approach for PC treatment. The metastasis suppressor N-myc downstream-regulated gene-1 (NDRG1) inhibits tumor progression and metastasis in numerous cancers, including PC. We demonstrate herein that targeting NDRG1 using the clinically trialed anticancer agent di-2-pyridylketone-4-cyclohexyl-4-methyl-3-thiosemicarbazone (DpC) inhibited Wnt/TnC-mediated interactions between PC cells and the surrounding PSCs. Mechanistically, NDRG1 and DpC markedly inhibit secretion of Wnt3a and TnC by PSCs, while also attenuating Wnt/β-catenin and YAP/TAZ activation and downstream signaling in PC cells. This antioncogenic activity was mediated by direct inhibition of β-catenin and YAP/TAZ nuclear localization and by increasing the Wnt inhibitor, DKK1. Expression of NDRG1 also inhibited transforming growth factor (TGF)-β secretion by PC cells, a key mechanism by which PC cells activate PSCs. Using an in vivo orthotopic PC mouse model, we show DpC downregulated β-catenin, TnC, and YAP/TAZ, while potently increasing NDRG1 expression in PC tumors. We conclude that NDRG1 and DpC inhibit Wnt/TnC-mediated interactions between PC cells and PSCs. These results further illuminate the antioncogenic mechanism of NDRG1 and the potential of targeting this metastasis suppressor to overcome the oncogenic effects of the PC-PSC interaction.     

Genetic diversity in sorghum (Sorghum bicolor (L.) Moench) accessions of Zambia as revealed by simple sequence repeats (SSR)

Twenty seven accessions of sorghum conserved in the national gene bank of Zambia, representing two of the three agroecological regions of the country, were investigated using simple sequence repeats (SSR) markers in order to determine the extent and distribution of its genetic diversity. We used 10 microsatellite primer-pairs, which generated 2-9 alleles per locus and a total of 44 alleles across the 27 accessions. The observed heterozygosity (Ho(P) ) among the accessions ranged from 0 to 0.19 with an average of 0.04 whereas the average expected heterozygosity (He(P) ) among accessions was 0.07 in line with the fact that sorghum is predominately inbreeder. The analysis of molecular variance (AMOVA) revealed that 82% of the total genetic variation was attributable to the genetic variation among accessions (F(ST) = 0.824; p < 0.001) whereas the genetic variation within accessions accounted for 18% of the total genetic variation. AMOVA on sorghum accessions grouped based on four ethnic groups (Soli, Chikunda, Lozi and Tonga) associated with collection sites revealed a highly significant variation among groups (23%; p < 0.001). Although cluster analysis grouped most accessions according to their sites of collection, some accessions that originated from the same site were placed under different clusters. In addition to the extent and pattern of genetic diversity, consideration should also be given to other factors such as ecogeographic and ethnic differences when sampling sorghum genetic resources for rational and efficient conservation and utilization in the breeding program.     

Genome-wide association mapping of yield and yield components of spring wheat under contrasting moisture regimes

Key message

A stable QTL that may be used in marker-assisted selection in wheat breeding programs was detected for yield, yield components and drought tolerance-related traits in spring wheat association mapping panel.

Abstract

Genome-wide association mapping has become a widespread method of quantitative trait locus (QTL) identification for many crop plants including wheat (Triticum aestivum L.). Its benefit over traditional bi-parental mapping approaches depends on the extent of linkage disequilibrium in the mapping population. The objectives of this study were to determine linkage disequilibrium decay rate and population structure in a spring wheat association mapping panel (n = 285–294) and to identify markers associated with yield and yield components, morphological, phenological, and drought tolerance-related traits. The study was conducted under fully irrigated and rain-fed conditions at Greeley, CO, USA and Melkassa, Ethiopia in 2010 and 2011 (five total environments). Genotypic data were generated using diversity array technology markers. Linkage disequilibrium decay rate extended over a longer genetic distance for the D genome (6.8 cM) than for the A and B genomes (1.7 and 2.0 cM, respectively). Seven subpopulations were identified with population structure analysis. A stable QTL was detected for grain yield on chromosome 2DS both under irrigated and rain-fed conditions. A multi-trait region significant for yield and yield components was found on chromosome 5B. Grain yield QTL on chromosome 1BS co-localized with harvest index QTL. Vegetation indices shared QTL with harvest index on chromosome 1AL and 5A. After validation in relevant genetic backgrounds and environments, QTL detected in this study for yield, yield components and drought tolerance-related traits may be used in marker-assisted selection in wheat breeding programs.     

Differential CO2 effect on primary carbon metabolism of flag leaves in durum wheat (Triticum durum Desf.)

C sink/source balance and N assimilation have been identified as target processes conditioning crop responsiveness to elevated CO₂. However, little is known about phenology‐driven modifications of C and N primary metabolism at elevated CO₂ in cereals such as wheat. Here, we examined the differential effect of elevated CO₂ at two development stages (onset of flowering, onset of grain filling) in durum wheat (Triticum durum, var. Sula) using physiological measurements (photosynthesis, isotopes), metabolomics, proteomics and ¹⁵N labelling. Our results show that growth at elevated CO₂ was accompanied by photosynthetic acclimation through a lower internal (mesophyll) conductance but no significant effect on Rubisco content, maximal carboxylation or electron transfer. Growth at elevated CO₂ altered photosynthate export and tended to accelerate leaf N remobilization, which was visible for several proteins and amino acids, as well as lysine degradation metabolism. However, grain biomass produced at elevated CO₂ was larger and less N rich, suggesting that nitrogen use efficiency rather than photosynthesis is an important target for improvement, even in good CO₂‐responsive cultivars.     

Biocontrol of strawberry fruit infected by Botrytis cinerea: Effects on the microbial communities on fruit assessed by next‐generation sequencing

Fruit grey mould, caused by the fungus Botrytis cinerea, is known to be a harmful disease of strawberry at postharvest stage. However, effects of an application of biological control agents (BCAs) on strawberry fruit in terms of shift in the microbial community are still unknown. The present research aimed to investigate the effects of an application of BCAs on postharvest microbial populations present on strawberry fruits. Strawberry plants were sprayed with three kinds of BCA, RhizoVital 42 fl. (Bacillus amyloliquefaciens FZB42), Trianum‐P (Trichoderma harzianum T22) and Naturalis (Beauveria bassiana ATCC 74040), targeting Botrytis cinerea fungus. Control plots were composed of water and fungicide treatments. Microbial communities (bacteria and fungi) were analysed via next‐generation sequencing on an Illumina MiSeq. Analysis of 16S RNA and ITS rRNA sequences indicated that the BCAs application modified both bacterial and fungal community compositions and diversity. An application of two BCAs together had more effects on microbial community composition than a single application. These results suggest that BCAs can modify bacterial and fungal community composition and diversity on strawberry fruits, which may consequently improve the efficiency and establishment of these products on control of postharvest diseases of fruits, such as grey mould.     

Mapping potential wildlife habitats around Haro Abba Diko controlled hunting area,Western Ethiopia

Remote sensing and geographic information system technologies provide useful data to analyze and map potential wildlife habitats based on physical parameters collected from the field. HADCHA was established with a total area of 20,000 ha, while many more comparable potential wildlife habitats were left outside the area. This study aims to identify and map potential wildlife habitats around HADCHA. Data were collected using Landsat 5 thematic mapper and Sentinel‐2A satellite image, a digital elevation model with 30 m pixels downloaded from ASTER data, and existing GIS Shapefile layers. Thematic Mapper data were downloaded from USGS and processed with Erdas Imagine 2015 software. To evaluate potential wildlife habitat around HADCHA, habitat suitability parameters such as settlement, slope, water, and road buffer zones were used for habitat evaluation and mapping. Accordingly, 16,795 ha of potential wildlife habitats were identified and mapped on westwards of HADCHA. In the new PPWH, about 476.68 ha (2.84%) were moderately suitable, 14,119.17 ha (84.04%) suitable and 2,200.08 ha (13.10%) highly suitable but only 4.2 ha (0.02%) identified as unsuitable. Legal protection of the PPWH around HADCHA could increase the conservation of African buffalo, other mammals, and their habitats. While the mapped potential wildlife habitats had the potential to be parts of HADCHA, it was neglected and has not yet obtained conservation attention. The finding appeals for legal protection of the PPWH and expansion of HADCHA, which could maximize the conservation efforts taken to wild animals of the area. Neglecting this potential wildlife habitat for a long period of time exposed African buffalo and other large‐sized mammals to illegal hunting practices. Policymakers and conservationists shall revise and design the future action plan of HADCHA on how to expand the current‐controlled hunting area and maximize revenue generation from African buffalo and other potential trophy species of the area.     

Children with Moderate Acute Malnutrition with No Access to Supplementary Feeding Programmes Experience High Rates of Deterioration and No Improvement: Results from a Prospective Cohort Study in Rural Ethiopia

BackgroundChildren with moderate acute malnutrition (MAM) have an increased risk of mortality, infections and impaired physical and cognitive development compared to well-nourished children. In parts of Ethiopia not considered chronically food insecure there are no supplementary feeding programmes (SFPs) for treating MAM. The short-term outcomes of children who have MAM in such areas are not currently described, and there remains an urgent need for evidence-based policy recommendations.MethodsWe defined MAM as mid-upper arm circumference (MUAC) of ≥11.0cm and <12.5cm with no bilateral pitting oedema to include Ethiopian government and World Health Organisation cut-offs. We prospectively surveyed 884 children aged 6–59 months living with MAM in a rural area of Ethiopia not eligible for a supplementary feeding programme. Weekly home visits were made for seven months (28 weeks), covering the end of peak malnutrition through to the post-harvest period (the most food secure window), collecting anthropometric, socio-demographic and food security data.ResultsBy the end of the study follow up, 32.5% (287/884) remained with MAM, 9.3% (82/884) experienced at least one episode of SAM (MUAC <11cm and/or bilateral pitting oedema), and 0.9% (8/884) died. Only 54.2% of the children recovered with no episode of SAM by the end of the study. Of those who developed SAM half still had MAM at the end of the follow up period. The median (interquartile range) time to recovery was 9 (4–15) weeks. Children with the lowest MUAC at enrolment had a significantly higher risk of remaining with MAM and a lower chance of recovering.ConclusionsChildren with MAM during the post-harvest season in an area not eligible for SFP experience an extremely high incidence of SAM and a low recovery rate. Not having a targeted nutrition-specific intervention to address MAM in this context places children with MAM at excessive risk of adverse outcomes. Further preventive and curative approaches should urgently be considered.