Mapping QTLs for tolerance to salt stress at the early seedling stage in rice (Oryza sativa L.) using a newly identified donor ‘Madina Koyo’

Open Access Article; Published online: 13 Sep 2020Salt stress is a menace to rice production and a threat to food security worldwide. We evaluated 308 F4 families from Sahel 317/Madina Koyo for tolerance to salt stress at the early seedling stage. To better understand genomic regions controlling tolerance in the population, we genotyped the progenies and the two parents using single nucleotide polymorphism (SNP) markers and regressed the genotypic data on their phenotype to detect QTLs. An average reduction of 63.4% was observed for all fitness-related traits among the F4 families. A total of 46 progenies recorded an average salt injury score (SIS) between 1–3 and were rated as tolerant to salt stress at the early seedling stage. A high-density genetic map was constructed for the 12 rice chromosomes using 3698 SNP markers. Multiple interval mapping identified 13 QTLs for SIS, shoot length, shoot dry weight and root length on chromosomes 2, 3, 4, 6, 7, 10 and 12, with trait increasing alleles coming from both parents. Two (qSDW2 and qRL2.2) and three (qSL2, qRL2.1 and qSIS2) QTLs at different regions on chromosome 2 and another two on chromosome 7 (qSDW7 and qSL7) were tightly linked. These QTLs could facilitate breeding for salt tolerance at the early seedling stage as direct selection for one, would mean indirectly selecting for the other. Fine mapping of these novel QTLs in a different genetic background is necessary to confirm their stability and usefulness in breeding for tolerance to salinity in rice

White Paper: Shifting the goal post - from high impact journals to high impact data

The purpose of this white paper is to provide an overview of the ongoing initiatives at center level to respond to changing public expectations and to the challenge of improving the conduct of science by making research data widely available. We also attempt to provide a framework for implementing open access for research data to maximize CGIAR’s impact on development. The remainder of this paper proceeds as follows; firstly a summary of the diversity of research data produced by the centers is given, followed by an overview of the existing infrastructure for data management for each Center. Secondly, some of the limitations and barriers faced by the centers in their process to mainstream research data publishing are addressed. The paper concludes with recommendations for how these limitations and barriers can be tackled

Performance of testers with contrasting provitamin A content to evaluate provitamin A maize for resistance to Aspergillus flavus infection and aflatoxin production

Open Access JournalIn sub-Saharan Africa (SSA), millions of people depend on maize as a primary staple. However, maize consumers in SSA may be exposed to malnutrition due to vitamin A deficiency (VAD) and unsafe aflatoxin levels, which can lead to serious economic and public health problems. Provitamin A (PVA) biofortified maize has been developed to alleviate VAD and may have additional benefits such as reduced aflatoxin contamination. In this study, maize inbred testers with contrasting PVA content in grain were used to identify inbred lines with desirable combining ability for breeding to enhance their level of resistance to aflatoxin. Kernels of 120 PVA hybrids generated by crossing 60 PVA inbreds with varying levels of PVA (5.4 to 51.7 µg/g) and two testers (low and high PVA, 14.4 and 25.0 µg/g, respectively) were inoculated with a highly toxigenic strain of Aspergillus flavus. Aflatoxin had a negative genetic correlation with β-carotene (r = −0.29, p 0.5). Eight inbreds had combined significant negative GCA effects for aflatoxin accumulation and spore count with significant positive GCA effects for PVA. Five testcrosses had combined significant negative SCA effects for aflatoxin with significant positive SCA effects for PVA. The high PVA tester had significant negative GCA effects for aflatoxin, lutein, β-carotene, and PVA. The study identified lines that can be used as parents to develop superior hybrids with high PVA and reduced aflatoxin accumulation. Overall, the results point out the importance of testers in maize breeding programs to develop materials that can contribute to controlling aflatoxin contamination and reducing VAD

Validation of KASP-SNP markers in cassava germplasm for marker-assisted selection of increased carotenoid content and dry matter content

Open Access Journal; Published online: 12 Oct 2022Provitamin A biofortification and increased dry matter content are important breeding targets in cassava improvement programs worldwide. Biofortified varieties contribute to the alleviation of provitamin A deficiency, a leading cause of preventable blindness common among pre-school children and pregnant women in developing countries particularly Africa. Dry matter content is a major component of dry yield and thus underlies overall variety performance and acceptability by growers, processors, and consumers. Single nucleotide polymorphism (SNP) markers linked to these traits have recently been discovered through several genome-wide association studies but have not been deployed for routine marker-assisted selection (MAS). This is due to the lack of useful information on markers’ performances in diverse genetic backgrounds. To overcome this bottleneck, technical and biological validation of the loci associated with increased carotenoid content and dry matter content were carried out using populations independent of the marker discovery population. In the present study, seven previously identified markers for these traits were converted to a robust set of uniplex allele-specific polymerase chain reaction (PCR) assays and validated in two independent pre-breeding and breeding populations. These assays were efficient in discriminating marker genotypic classes and had an average call rate greater than 98%. A high correlation was observed between the predicted and observed carotenoid content as inferred by root yellowness intensity in the breeding (r = 0.92) and pre-breeding (r = 0.95) populations. On the other hand, dry matter content-markers had moderately low predictive accuracy in both populations (r< 0.40) due to the more quantitative nature of the trait. This work confirmed the markers’ effectiveness in multiple backgrounds, therefore, further strengthening their value in cassava biofortification to ensure nutritional security as well as dry matter content productivity. Our study provides a framework to guide future marker validation, thus leading to the more routine use of markers in MAS in cassava improvement programs

Emergence and spread of SARS-CoV-2 lineage B.1.620 with variant of concern-like mutations and deletions

Distinct SARS-CoV-2 lineages, discovered through various genomic surveillance initiatives, have emerged during the pandemic following unprecedented reductions in worldwide human mobility. We here describe a SARS-CoV-2 lineage - designated B.1.620 - discovered in Lithuania and carrying many mutations and deletions in the spike protein shared with widespread variants of concern (VOCs), including E484K, S477N and deletions HV69Delta, Y144Delta, and LLA241/243Delta. As well as documenting the suite of mutations this lineage carries, we also describe its potential to be resistant to neutralising antibodies, accompanying travel histories for a subset of European cases, evidence of local B.1.620 transmission in Europe with a focus on Lithuania, and significance of its prevalence in Central Africa owing to recent genome sequencing efforts there. We make a case for its likely Central African origin using advanced phylogeographic inference methodologies incorporating recorded travel histories of infected travellers

Correction: A Seroepidemiological Study of Serogroup A Meningococcal Infection in the African Meningitis Belt.

[This corrects the article DOI: 10.1371/journal.pone.0147928.]

Second asymptomatic carotid surgery trial (ACST-2): a randomised comparison of carotid artery stenting versus carotid endarterectomy

Background: Among asymptomatic patients with severe carotid artery stenosis but no recent stroke or transient cerebral ischaemia, either carotid artery stenting (CAS) or carotid endarterectomy (CEA) can restore patency and reduce long-term stroke risks. However, from recent national registry data, each option causes about 1% procedural risk of disabling stroke or death. Comparison of their long-term protective effects requires large-scale randomised evidence. Methods: ACST-2 is an international multicentre randomised trial of CAS versus CEA among asymptomatic patients with severe stenosis thought to require intervention, interpreted with all other relevant trials. Patients were eligible if they had severe unilateral or bilateral carotid artery stenosis and both doctor and patient agreed that a carotid procedure should be undertaken, but they were substantially uncertain which one to choose. Patients were randomly allocated to CAS or CEA and followed up at 1 month and then annually, for a mean 5 years. Procedural events were those within 30 days of the intervention. Intention-to-treat analyses are provided. Analyses including procedural hazards use tabular methods. Analyses and meta-analyses of non-procedural strokes use Kaplan-Meier and log-rank methods. The trial is registered with the ISRCTN registry, ISRCTN21144362. Findings: Between Jan 15, 2008, and Dec 31, 2020, 3625 patients in 130 centres were randomly allocated, 1811 to CAS and 1814 to CEA, with good compliance, good medical therapy and a mean 5 years of follow-up. Overall, 1% had disabling stroke or death procedurally (15 allocated to CAS and 18 to CEA) and 2% had non-disabling procedural stroke (48 allocated to CAS and 29 to CEA). Kaplan-Meier estimates of 5-year non-procedural stroke were 2·5% in each group for fatal or disabling stroke, and 5·3% with CAS versus 4·5% with CEA for any stroke (rate ratio [RR] 1·16, 95% CI 0·86–1·57; p=0·33). Combining RRs for any non-procedural stroke in all CAS versus CEA trials, the RR was similar in symptomatic and asymptomatic patients (overall RR 1·11, 95% CI 0·91–1·32; p=0·21). Interpretation: Serious complications are similarly uncommon after competent CAS and CEA, and the long-term effects of these two carotid artery procedures on fatal or disabling stroke are comparable. Funding: UK Medical Research Council and Health Technology Assessment Programme