Using cross-country datasets for association mapping in Arachis hypogaea L.

Groundnut (Arachis hypogaea L.) is one of the most important climate-resilient oil crops in sub-Saharan Africa. There is a significant yield gap for groundnut in Africa because of poor soil fertility, low agricultural inputs, biotic and abiotic stresses.

"Something Like That": Awareness and Acceptability of HIV PrEP and PEP Among Kenyan Adolescents.

Background: Adolescents account for 15% of new HIV cases in Kenya. HIV pre-exposure prophylaxis (PrEP) and post-exposure prophylaxis (PEP) are highly effective prevention tools, but uptake is low among adolescents, particularly in resource-limited settings. We assessed awareness and acceptability of PrEP and PEP among Kenyan adolescents.

Genome-wide association study and expression of candidate genes for Fe and Zn concentration in sorghum grains.

Sorghum germplasm showed grain Fe and Zn genetic variability, but a few varieties were biofortified with these minerals. This work contributes to narrowing this gap. Fe and Zn concentrations along with 55,068 high-quality GBS SNP data from 140 sorghum accessions were used in this study.

Validation of sorghum quality control (QC) markers across African breeding lines.

Sorghum [Sorghum bicolor (L.) Moench] is a cereal crop of critical importance in the semi-arid tropics, particularly in Africa where it is second only to maize (Zea mays L.) by area of cultivation.

Meta-transcriptomic identification of groundnut RNA viruses in western Kenya and the novel detection of groundnut as a host for Cauliflower mosaic virus.

Background: Groundnut (Arachis hypogaea L.) is the 13th most important global crop grown throughout the tropical and subtropical regions of the world. One of the major constraints to groundnut production is viruses, which are also the most economically important and most abundant pathogens among cultivated legumes.

Brief Report: HIV Pre-Exposure Prophylaxis Awareness and Use Among Adolescents in Kenya.

Background: HIV pre-exposure prophylaxis (PrEP) is an effective prevention tool; however, use among adolescents is thought to be low. To determine the unmet need and opportunity to expand use, we assessed awareness, prior use, and willingness to take PrEP among Kenyan adolescents.

Methods: The Maneno Yetu study recruited a community-based sample of adolescents aged 15-19 years (N = 3061) in Kisumu for a survey using respondent-driven sampling.

Genomic and phenotypic characterization of finger millet indicates a complex diversification history.

Advances in sequencing technologies mean that insights into crop diversification can now be explored in crops beyond major staples. We use a genome assembly of finger millet, an allotetraploid orphan crop, to analyze DArTseq single nucleotide polymorphisms (SNPs) at the whole and sub-genome level. A set of 8778 SNPs and 13 agronomic traits was used to characterize a diverse panel of 423 landraces from Africa and Asia.

Plant genome resequencing and population genomics: Current status and future prospects.

Advances in DNA sequencing technology have sparked a genomics revolution, driving breakthroughs in plant genetics and crop breeding. Recently, the focus has shifted from cataloging genetic diversity in plants to exploring their functional significance and delivering beneficial alleles for crop improvement. This transformation has been facilitated by the increasing adoption of whole-genome resequencing.

HIV Infection Among Adolescents Residing in Urban Informal Settlements of Kenya.

Adolescents comprise approximately 15% of new HIV infections in Kenya. Impoverished living conditions in informal settlements place residents at high risk for HIV infection. We assessed factors associated with HIV infection among adolescents residing in urban informal settlements in Kisumu.

Genome analyses reveal population structure and a purple stigma color gene candidate in finger millet.

Finger millet is a key food security crop widely grown in eastern Africa, India and Nepal. Long considered a 'poor man's crop', finger millet has regained attention over the past decade for its climate resilience and the nutritional qualities of its grain. To bring finger millet breeding into the 21 century, here we present the assembly and annotation of a chromosome-scale reference genome.

Exploring the sorghum race level diversity utilizing 272 sorghum accessions genomic resources.

Due to evolutionary divergence, sorghum race populations exhibit significant genetic and morphological variation. A -based sorghum race sequence comparison identified the conserved s of all 272 accessions from sorghum and the race-specific genetic signatures identified the gene variability in 10,321 genes (PAVs). To understand sorghum race structure, diversity and domestication, a deep learning-based variant calling approach was employed in a set of genotypic data derived from a diverse panel of 272 sorghum accessions.

Genome-wide association studies reveal novel loci for resistance to groundnut rosette disease in the African core groundnut collection.

We identified markers associated with GRD resistance after screening an Africa-wide core collection across three seasons in Uganda Groundnut is cultivated in several African countries where it is a major source of food, feed and income. One of the major constraints to groundnut production in Africa is groundnut rosette disease (GRD), which is caused by a complex of three agents: groundnut rosette assistor luteovirus, groundnut rosette umbravirus and its satellite RNA. Despite several years of breeding for GRD resistance, the genetics of the disease is not fully understood.

Climate change challenges, plant science solutions.

Climate change is a defining challenge of the 21st century, and this decade is a critical time for action to mitigate the worst effects on human populations and ecosystems. Plant science can play an important role in developing crops with enhanced resilience to harsh conditions (e.g.

Mechanisms of pre-attachment Striga resistance in sorghum through genome-wide association studies.

Witchweeds (Striga spp.) greatly limit production of Africa's most staple crops. These parasitic plants use strigolactones (SLs)-chemical germination stimulants, emitted from host's roots to germinate, and locate their hosts for invasion.

A high-density linkage map of finger millet provides QTL for blast resistance and other agronomic traits.

Finger millet [Eleusine coracana (L.) Gaertn.] is a critical subsistence crop in eastern Africa and southern Asia but has few genomic resources and modern breeding programs.

"We Don't Fear HIV. We Just Fear Walking around Pregnant.": A Qualitative Analysis of Adolescent Sexuality and Pregnancy Stigma in Informal Settlements in Kisumu, Kenya.

In Kenya, adolescent pregnancy rates are high, contraception utilization is low, and adolescent sexuality is stigmatized. We describe how perceptions of sexuality and pregnancy stigma influence decision-making among adolescents in the informal settlements of Kisumu. We used purposive sampling to recruit 120 adolescent boys and girls aged 15-19 for focus group discussions.

GWAS provides biological insights into mechanisms of the parasitic plant (Striga) resistance in sorghum.

Background: Sorghum yields in sub-Saharan Africa (SSA) are greatly reduced by parasitic plants of the genus Striga (witchweed). Vast global sorghum genetic diversity collections, as well as the availability of modern sequencing technologies, can be potentially harnessed to effectively manage the parasite.

Results: We used laboratory assays - rhizotrons to screen a global sorghum diversity panel to identify new sources of resistance to Striga; determine mechanisms of resistance, and elucidate genetic loci underlying the resistance using genome-wide association studies (GWAS).

Genotypic Variation in Cultivated and Wild Sorghum Genotypes in Response to Infestation.

is the most important parasitic weed in sub-Saharan Africa and remains one of the most devastating biotic factors affecting sorghum production in the western regions of Kenya. Farmers have traditionally managed using cultural methods, but the most effective and practical solution to poor smallholder farmers is to develop -resistant varieties. This study was undertaken with the aim of identifying new sources of resistance to in comparison with the conventional sources as standard checks.

Sorghum Pan-Genome Explores the Functional Utility for Genomic-Assisted Breeding to Accelerate the Genetic Gain.

Sorghum ( L.) is a staple food crops in the arid and rainfed production ecologies. Sorghum plays a critical role in resilient farming and is projected as a smart crop to overcome the food and nutritional insecurity in the developing world.

Modeling Illustrates That Genomic Selection Provides New Opportunities for Intercrop Breeding.

Intercrop breeding programs using genomic selection can produce faster genetic gain than intercrop breeding programs using phenotypic selection. Intercropping is an agricultural practice in which two or more component crops are grown together. It can lead to enhanced soil structure and fertility, improved weed suppression, and better control of pests and diseases.

Genetics and breeding for climate change in Orphan crops.

Climate change is rapidly changing how we live, what we eat and produce, the crops we breed and the target traits. Previously underutilized orphan crops that are climate resilient are receiving much attention from the crops research community, as they are often the only crops left in the field after periods of extreme weather conditions. There are several orphan crops with incredible resilience to biotic and abiotic stresses.

Genomic resources in plant breeding for sustainable agriculture.

Climate change during the last 40 years has had a serious impact on agriculture and threatens global food and nutritional security. From over half a million plant species, cereals and legumes are the most important for food and nutritional security. Although systematic plant breeding has a relatively short history, conventional breeding coupled with advances in technology and crop management strategies has increased crop yields by 56 % globally between 1965-85, referred to as the Green Revolution.