Genome-Wide Association Analysis for Resistance to Coniothyrium glycines Causing Red Leaf Blotch Disease in Soybean

Soybean is a high oil and protein-rich legume with several production constraints. Globally, several fungi, viruses, nematodes, and bacteria cause significant yield losses in soybean. Coniothyrium glycines (CG), the causal pathogen for red leaf blotch disease, is the least researched and causes severe damage to soybean. The identification of resistant soybean genotypes and mapping of genomic regions associated with resistance to CG is critical for developing improved cultivars for sustainable soybean production. This study used single nucleotide polymorphism (SNP) markers generated from a Diversity Arrays Technology (DArT) platform to conduct a genome-wide association (GWAS) analysis of resistance to CG using 279 soybean genotypes grown in three environments. A total of 6395 SNPs was used to perform the GWAS applying a multilocus model Fixed and random model Circulating Probability Unification (FarmCPU) with correction of the population structure and a statistical test p-value threshold of 5%. A total of 19 significant marker-trait associations for resistance to CG were identified on chromosomes 1, 5, 6, 9, 10, 12, 13, 15, 16, 17, 19, and 20. Approximately 113 putative genes associated with significant markers for resistance to red leaf blotch disease were identified across soybean genome. Positional candidate genes associated with significant SNP loci-encoding proteins involved in plant defense responses and that could be associated with soybean defenses against CG infection were identified. The results of this study provide valuable insight for further dissection of the genetic architecture of resistance to CG in soybean. They also highlight SNP variants and genes useful for genomics-informed selection decisions in the breeding process for improving resistance traits in soybean.

Phenotype based clustering, and diversity of common bean genotypes in seed iron concentration and cooking time

Common bean is the world's most important directly consumed legume food crop that is popular for calories, protein and micronutrients. It is a staple food in sub-Saharan Africa, and a significant source of iron for anemic people. However, several pests, soil and weather challenges still impede its production. Long cooking time, and high phytic acid and polyphenols that influence bioavailable iron also limit the health benefits. To inform population improvement strategies and selection decisions for resilient fast cooking and iron biofortified beans, the study determined diversity and population structure within 427 breeding lines, varieties, or landraces mostly from Alliance Uganda and Columbia. The genotypes were evaluated for days to flowering and physiological maturity, yield, seed iron (FESEED) and zinc (ZNSEED) and cooking time (COOKT). Data for all traits showed significant (P≤0.001) differences among the genotypes. Repeatability was moderate to high for most traits. Performance ranged from 52 to 87 ppm (FESEED), 23-38 ppm (ZNSEED), 36-361 minutes (COOKT), and 397-1299 kg/ha (yield). Minimal differences existed between the gene pools in the mean performance except in yield, where Mesoamerican beans were better by 117 kg/ha. The genotypes exhibited high genetic diversity and thus have a high potential for use in plant breeding. Improvement of FESEED and ZNSEED, COOKT and yield performance within some markets such as red and small white beans is possible. Hybridization across market classes especially for yellow beans is essential but this could be avoided by adding other elite lines to the population. Superior yielding and fast cooking, yellow and large white beans were specifically lacking. Adding Fe dense elite lines to the population is also recommended. The population was clustered into three groups that could be considered for specific breeding targets based on trait correlations.

Roles of Arbuscular Mycorrhizal Fungi on Soil Fertility: Contribution in the Improvement of Physical, Chemical, and Biological Properties of the Soil

Many of the world's soils are experiencing degradation at an alarming rate. Climate change and some agricultural management practices, such as tillage and excessive use of chemicals, have all contributed to the degradation of soil fertility. Arbuscular Mycorrhizal Fungi (AMFs) contribute to the improvement of soil fertility. Here, a short review focusing on the role of AMF in improving soil fertility is presented. The aim of this review was to explore the role of AMF in improving the chemical, physical, and biological properties of the soil. We highlight some beneficial effects of AMF on soil carbon sequestration, nutrient contents, microbial activities, and soil structure. AMF has a positive impact on the soil by producing organic acids and glomalin, which protect from soil erosion, chelate heavy metals, improve carbon sequestration, and stabilize soil macro-aggregation. AMF also recruits bacteria that produce alkaline phosphatase, a mineralization soil enzyme associated with organic phosphorus availability. Moreover, AMFs influence the composition, diversity, and activity of microbial communities in the soil through mechanisms of antagonism or cooperation. All of these AMF activities contribute to improve soil fertility. Knowledge gaps are identified and discussed in the context of future research in this review. This will help us better understand AMF, stimulate further research, and help in sustaining the soil fertility.

Arterial stiffness and age moderate the association between physical activity and global cognition in the older adults

Funding Acknowledgements

Type of funding sources: Public grant(s) – National budget only. Main funding source(s): The Merck Sharp & Dohme Corp Program of the Faculty of Medicine of the Université de Montréal The Canadian Institutes of Health Research (CIHR)

Background

The growing concern on the impact of higher arterial stiffness on cognitive decline in older adults, leads to the question of whether non-pharmacological interventions like physical activity should be introduced to correct or diminish the progression of arterial stiffness.

Purpose

The goal of this study is to elaborate a model for arterial stiffness as a moderator for the physical activity and global cognition relationship in function of age. 

Methods

One hundred ten healthy older adults aged 60 to 75 years old (46 men and 64 women) were examined for arterial stiffness (carotid-femoral Pulse Wave Velocity (cf-PWV)), global cognition (Montreal Cognitive Assessment and Mini Mental State Examination) and self-reported physical activity (PACED diary). The double moderation analysis used PROCESS macro for SPSS, where physical activity was included as the independent variable (X), global cognition as the dependent variable (Y), arterial stiffness as moderator 1 (W), and age moderator 2 (Z). This study used a cf-PWV cutoff of 8.5 m/s to identify micro-structural damage in the brain related to arterial stiffness.

Results

Results found that the arterial stiffness x age interaction moderated the effect of physical activity on global cognition (β = -.89, SE = .42, p = .037) (Model: R2 = .15, p = .018). Physical activity had a positive effect on cognition in younger-older adults (aged 60 to 68.5 years) with high arterial stiffness i.e. cf-PWV > 8.5 m/s (β = .57, SE = .222, p = .011, 95% CI .133 to 1.014), and in older-older adults (aged 68.6 to 75 years) with low arterial stiffness i.e. cf-PWV < 8.5 m/s (β = .49, SE = .190, p = .010, 95% CI = .116 to .869). 

Conclusions

These results support targeted physical activity interventions based on age and degree of arterial stiffness, furthering the notion that even daily life physical activity could play an important role in older adults’ cognitive performances.

Physical activity on global cognition Conditional effects of physical activity on global cognition Moderators cf-PWV Age Effect SE p CI < 8.5 m/s < 68.5 years .171 .245 .487 -.315 to .657 < 8.5 m/s > = 68.5 years .574 .222 .011* .133 to 1.014 > = 8.5 m/s < 68.5 years .492 .190 .010* .116 to .868 > = 8.5 m/s > = 68.5 years .002 .180 .990 -.355 to .359 Physical activity conditional effects on global cognition at determined values of arterial stiffness and age. SE: Standard Error, CI: Confidence Interval, cf-PWV: carotid-femoral Pulse Wave Velocity, *p-value<.05.

Factors Influencing Genomic Prediction Accuracies of Tropical Maize Resistance to Fall Armyworm and Weevils

Genomic selection (GS) can accelerate variety improvement when training set (TS) size and its relationship with the breeding set (BS) are optimized for prediction accuracies (PAs) of genomic prediction (GP) models. Sixteen GP algorithms were run on phenotypic best linear unbiased predictors (BLUPs) and estimators (BLUEs) of resistance to both fall armyworm (FAW) and maize weevil (MW) in a tropical maize panel. For MW resistance, 37% of the panel was the TS, and the BS was the remainder, whilst for FAW, random-based training sets (RBTS) and pedigree-based training sets (PBTSs) were designed. PAs achieved with BLUPs varied from 0.66 to 0.82 for MW-resistance traits, and for FAW resistance, 0.694 to 0.714 for RBTS of 37%, and 0.843 to 0.844 for RBTS of 85%, and these were at least two-fold those from BLUEs. For PBTS, FAW resistance PAs were generally higher than those for RBTS, except for one dataset. GP models generally showed similar PAs across individual traits whilst the TS designation was determinant, since a positive correlation (R = 0.92***) between TS size and PAs was observed for RBTS, and for the PBTS, it was negative (R = 0.44**). This study pioneered the use of GS for maize resistance to insect pests in sub-Saharan Africa.

Genome-wide association study identified candidate genes controlling continuous storage root formation and bulking in hexaploid sweetpotato

BACKGROUND

Continuous storage root formation and bulking (CSRFAB) in sweetpotato is an important trait from agronomic and biological perspectives. Information about the molecular mechanisms underlying CSRFAB traits is lacking.

RESULTS

Here, as a first step toward understanding the genetic basis of CSRFAB in sweetpotato, we performed a genome-wide association study (GWAS) using phenotypic data from four distinct developmental stages and 33,068 single nucleotide polymorphism (SNP) and insertion-deletion (indel) markers. Based on Bonferroni threshold (p-value < 5 × 10- 7), we identified 34 unique SNPs that were significantly associated with the complex trait of CSRFAB at 150 days after planting (DAP) and seven unique SNPs associated with discontinuous storage root formation and bulking (DCSRFAB) at 90 DAP. Importantly, most of the loci associated with these identified SNPs were located within genomic regions (using Ipomoea trifida reference genome) previously reported for quantitative trait loci (QTL) controlling similar traits. Based on these trait-associated SNPs, 12 and seven candidate genes were respectively annotated for CSRFAB and DCSRFAB traits. Congruent with the contrasting and inverse relationship between discontinuous and continuous storage root formation and bulking, a DCSRFAB-associated candidate gene regulates redox signaling, involved in auxin-mediated lateral root formation, while CSRFAB is enriched for genes controlling growth and senescence.

CONCLUSION

Candidate genes identified in this study have potential roles in cell wall remodeling, plant growth, senescence, stress, root development and redox signaling. These findings provide valuable insights into understanding the functional networks to develop strategies for sweetpotato yield improvement. The markers as well as candidate genes identified in this pioneering research for CSRFAB provide important genomic resources for sweetpotato and other root crops.

New sources of sorghum resistant genotypes to downy mildew disease in Uganda

Abstract. Kumi F, Badji A, Mwila N, Odong T, Ochwo-Ssemakula M, Tusiime G, Gibson P, Biruma M, Prom KL, Cuevas HE, Agbahoungba S, Rubaihayo P. 2019. New sources of sorghum resistant genotypes to downy mildew disease in Uganda. Biodiversitas 20: 3391-3397.  Sorghum downy mildew (SDM) disease is still prevalent in Uganda at varying levels of incidence and severity. In this study, a total of 100 sorghum genotypes, five (5) from (U.SA, India, and Sudan) and 95 genotypes from Uganda were evaluated for resistance to downy mildew and other agronomic traits during the second growing season of 2016 (August-December). The experiment was conducted in two locations at Makerere University Agricultural Research Institute at Kabanyolo (MUARIK) and Abi-Zonal Agricultural Research and Development Institute (Abi-ZARDI) research station at Arua. The experimental design used was 10 x 10 alpha lattice design with three replicates. Data were collected on plant disease incidence (PDI), plant disease severity (PDS), area under disease progress curve (AUDPC), days to 50% flowering, plant height, 1000 seed weight, and grain yield. Results for analysis of variance showed highly significant differences (P < 0.001) in genotypes, location, and AUDPC, yield and yield components. Disease incidence varied significantly (P < 0.001) between locations, and Arua recorded highest disease incidence and severity of 80.6 and 2.8, respectively. Results from correlation analysis showed a highly significant (P < 0.001) positive association of downy mildew disease incidence with AUDPC (0.835) which suggests that the severity of SDM disease increased with disease incidence, whiles significant (P < 0.001) negative correlation was recorded for days to 50 % flowering (-0.302), 1000 seed weight (-0.471), and grain yield (-0.585), suggesting that grain yield and yield component decreased significantly with increase in SDM incidence and severity. Two resistant (PI 656061 and PI 533831) and four moderately resistant (E 40, MAKSO 8, PI 655990 and Epuripur) genotypes were identified from this study. These genotypes were recommended for sorghum breeding program against downy mildew disease.

Recombination fraction and genetic linkage among key disease resistance genes (Co-42 /Phg-2 and Co-5/"P.ult") in common bean

Anthracnose (Colletotrichum lindemuthianum), Angular leaf spot (Pseudocercospora griseola) and Pythium root rot are important pathogens affecting common bean production in the tropics. A promising strategy to manage these diseases consists of combining several resistance (R) genes into one cultivar. The aim of the study was to determine genetic linkage between gene pairs, Co-4² /Phg-2, on bean-chromosome Pv08 and Co-5/"P.ult" on-chromosome Pv07, to increase the efficiency of dual selection of resistance genes for major bean diseases, with molecular markers. The level of recombination was determined by tracking molecular markers for both BC3F6 and F2 generations. Recombination fraction r, among gene pairs, the likelihood of linkage, L(r), and logarithm of odds (LOD) scores were computed using the statistical relationship of likelihood which assumes a binomial distribution. The SCAR marker pair SAB3/PYAA19 for the gene pair Co-5/"P.ult" exhibited moderate linkage (r = 32 cM with a high LOD score of 9.2) for BC₃F₆ population, but relatively stronger linkage for the F₂ population (r = 21 cM with a high LOD score of 18.7). However, the linkage among SCAR marker pair SH18/SN02, for the gene pair Co-4² /Phg-2 was incomplete for BC₃F₆ population (r = 47 cM with a low LOD score of 0.16) as well as F₂ population (r = 44 cM with a low LOD score of 0.7). Generally, the weak or incomplete genetic linkage between marker pairs studied showed that all the four genes mentioned earlier have to be tagged with a corresponding linked marker during selection. The approaches used in this study will contribute to two loci linkage mapping techniques in segregating plant populations.

Maize Combined Insect Resistance Genomic Regions and Their Co-localization With Cell Wall Constituents Revealed by Tissue-Specific QTL Meta-Analyses

Combinatorial insect attacks on maize leaves, stems, and kernels cause significant yield losses and mycotoxin contaminations. Several small effect quantitative trait loci (QTL) control maize resistance to stem borers and storage pests and are correlated with secondary metabolites. However, efficient use of QTL in molecular breeding requires a synthesis of the available resistance information. In this study, separate meta-analyses of QTL of maize response to stem borers and storage pests feeding on leaves, stems, and kernels along with maize cell wall constituents discovered in these tissues generated 24 leaf (LIR), 42 stem (SIR), and 20 kernel (KIR) insect resistance meta-QTL (MQTL) of a diverse genetic and geographical background. Most of these MQTL involved resistance to several insect species, therefore, generating a significant interest for multiple-insect resistance breeding. Some of the LIR MQTL such as LIR4, 17, and 22 involve resistance to European corn borer, sugarcane borer, and southwestern corn borer. Eleven out of the 42 SIR MQTL related to resistance to European corn borer and Mediterranean corn borer. There KIR MQTL, KIR3, 15, and 16 combined resistance to kernel damage by the maize weevil and the Mediterranean corn borer and could be used in breeding to reduce insect-related post-harvest grain yield loss and field to storage mycotoxin contamination. This meta-analysis corroborates the significant role played by cell wall constituents in maize resistance to insect since the majority of the MQTL contain QTL for members of the hydroxycinnamates group such as p-coumaric acid, ferulic acid, and other diferulates and derivates, and fiber components such as acid detergent fiber, neutral detergent fiber, and lignin. Stem insect resistance MQTL display several co-localization between fiber and hydroxycinnamate components corroborating the hypothesis of cross-linking between these components that provide mechanical resistance to insect attacks. Our results highlight the existence of combined-insect resistance genomic regions in maize and set the basis of multiple-pests resistance breeding.

Acute toxicity of locust insecticides to two indigenous invertebrates from Sahelian temporary ponds

During desert locust plagues large amounts of insecticides are used for control operations. Drift from these treatments and accidental overspraying may contaminate small surface waters such as temporary ponds. The present study describes methods for static acute toxicity tests with two abundant organisms that occur in temporary ponds in the African Sahel region: the fairy shrimp Streptocephalus sudanicus Daday (Branchiopoda, Anostraca, Streptocephalidae) and the backswimmer Anisops sardeus Herrich-Schåffer (Hemiptera, Notonectidae). The organisms were captured in the field and 48-h static toxicity tests were conducted in the laboratory. The assays were used to screen the toxicity of 11 formulated synthetic insecticides used in desert locust control and of spores of the mycopesticide Metarhizium anisopliae var. acridum. Most of the synthetic insecticides tested were highly toxic to both organisms (LC50 or EC50<1 mg/L). Exceptions were the toxicity of diflubenzuron to A. sardeus (moderately toxic: 1<LC50<10 mg/L), and that of fenitrothion (moderately toxic) and malathion (slightly toxic: 10<EC50<100 mg/L) to S. sudanicus. M. anisopliae var. acridum was moderately toxic to S. sudanicus and only slightly toxic to A. sardeus. EC50 values of the insecticides for S. sudanicus were not significantly correlated with L(E)C50 values for Daphnia magna collected from the literature. For A. sardeus a significant correlation with D. magna was found, but even in this data set the two species had widely differing sensitivities to some insecticides.

The Dielmo project: a longitudinal study of natural malaria infection and the mechanisms of protective immunity in a community living in a holoendemic area of Senegal

The Dielmo project, initiated in 1990, consisted of long-term investigations on host-parasite relationships and the mechanisms of protective immunity in the 247 residents of a Senegalese village in which malaria is holoendemic. Anopheles gambiae s.l. and An. funestus constituted more than 98% of 11,685 anophelines collected and were present all year round. Inoculation rates of Plasmodium falciparum, P. malariae, and P. ovale averaged respectively 0.51, 0.10, and 0.04 infective bites per person per night. During a four-month period of intensive parasitologic and clinical monitoring, Plasmodium falciparum, P. malariae, and P. ovale were observed in 72.0%, 21.1% and 6.0%, respectively, of the 8,539 thick smears examined. Individual longitudinal data revealed that 98.6% of the villagers harbored trophozoites of P. falciparum at least once during the period of the study. Infections by P. malariae and P. ovale were both observed in individuals of all age groups and their cumulative prevalences reached 50.5% and 40.3%, respectively. Malaria was responsible for 162 (60.9%) of 266 febrile episodes; 159 of these attacks were due to P. falciparum, three to P. ovale, and none to P. malariae. The incidence of malaria attacks was 40 times higher in children 0-4 years of age than in adults more than 40 years old. Our findings suggest that sterile immunity and clinical protection are never fully achieved in humans continuously exposed since birth to intense transmission.