Combination of linkage and association mapping with genomic prediction to infer QTL regions associated with gray leaf spot and northern corn leaf blight resistance in tropical maize.

Among the diseases threatening maize production in Africa are gray leaf spot (GLS) caused by Cercospora zeina and northern corn leaf blight (NCLB) caused by Exserohilum turcicum. The two pathogens, which have high genetic diversity, reduce the photosynthesizing ability of susceptible genotypes and, hence, reduce the grain yield. To identify population-based quantitative trait loci (QTLs) for GLS and NCLB resistance, a biparental population of 230 lines derived from the tropical maize parents CML511 and CML546 and an association mapping panel of 239 tropical and sub-tropical inbred lines were phenotyped across multi-environments in western Kenya. Based on 1,264 high-quality polymorphic single-nucleotide polymorphisms (SNPs) in the biparental population, we identified 10 and 18 QTLs, which explained 64.2% and 64.9% of the total phenotypic variance for GLS and NCLB resistance, respectively. A major QTL for GLS, qGLS1_186 accounted for 15.2% of the phenotypic variance, while qNCLB3_50 explained the most phenotypic variance at 8.8% for NCLB resistance. Association mapping with 230,743 markers revealed 11 and 16 SNPs significantly associated with GLS and NCLB resistance, respectively. Several of the SNPs detected in the association panel were co-localized with QTLs identified in the biparental population, suggesting some consistent genomic regions across genetic backgrounds. These would be more relevant to use in field breeding to improve resistance to both diseases. Genomic prediction models trained on the biparental population data yielded average prediction accuracies of 0.66-0.75 for the disease traits when validated in the same population. Applying these prediction models to the association panel produced accuracies of 0.49 and 0.75 for GLS and NCLB, respectively. This research conducted in maize fields relevant to farmers in western Kenya has combined linkage and association mapping to identify new QTLs and confirm previous QTLs for GLS and NCLB resistance. Overall, our findings imply that genetic gain can be improved in maize breeding for resistance to multiple diseases including GLS and NCLB by using genomic selection.

Impact of the community healthcare plan and the free maternity services programme on maternal and child healthcare utilisation in rural Kenya: a dairy farmer population-based study.

BACKGROUND: Access to and utilisation of quality maternal and child healthcare services is generally recognized as the best way to reduce maternal and child mortality. OBJECTIVES: We evaluated whether the introduction of a voluntary family health insurance programme, combined with quality improvement of healthcare facilities [The Community Health Plan (TCHP)], and the introduction of free access to delivery services in all public facilities [Free Maternity Services programme (FMS)] increased antenatal care utilisation and use of facility deliveries among pregnant women in rural Kenya. METHODS: TCHP was introduced in 2011, whilst the FMS programme was launched in 2013. To measure the impact of TCHP, percentage points (PP) changes in antenatal care utilisation and facility deliveries from the pre-TCHP to the post-TCHP period between the TCHP programme area and a control area were compared in multivariable difference-in-differences analysis. To measure the impact of the FMS programme, PP changes in antenatal care utilisation and facility deliveries from the pre-FMS to the post-FMS period in the pooled TCHP programme and control areas was assessed in multivariable logistic regression analysis. Data was collected through household surveys in 2011 and 2104. Households (n=549) were randomly selected from the member lists of 2 dairy companies, and all full-term pregnancies in the 3.5 years preceding the baseline and follow-up survey among women aged 15-49 at the time of pregnancy were eligible for this study (n=295). RESULTS: Because only 4.1% of eligible women were insured through TCHP during pregnancy, any increase in utilisation attributable to the TCHP programme could only have come about as a result of the quality improvements in TCHP facilities. Antenatal care utilisation significantly increased after TCHP was introduced (14.4 PP; 95% CI: 4.5-24.3; P=0.004), whereas no effect was observed of the programme on facility deliveries (8.8 PP; 95% CI: -14.1 to +31.7; P=0.450). Facility deliveries significantly increased after the introduction of the FMS programme (27.9 PP; 95% CI: 11.8-44.1; P=0.001), but antenatal care utilisation did not change significantly (4.0 PP; 95% CI: -0.6 to +8.5; P=0.088). CONCLUSION: Access to the FMS programme increased facility deliveries substantially and may contribute to improved maternal and new-born health and survival if the quality of delivery services is sustained or further improved. Despite low up-take, TCHP had a positive effect on antenatal care utilisation among uninsured women by improving the quality of existing healthcare facilities. An alignment of the two programmes could potentially lead to optimal results. FUNDING: The study was funded by the Health Insurance Fund (http://www.hifund.org/), through a grant from the Dutch Ministry of Foreign Affairs.

Combining ability and testcross performance of drought-tolerant maize inbred lines under stress and non-stress environments in Kenya.

Drought and poor soil fertility are among the major abiotic stresses affecting maize productivity in sub-Saharan Africa. Maize breeding efforts at the International Maize and Wheat Improvement Center (CIMMYT) have focused on incorporating drought stress tolerance and nitrogen-use efficiency (NUE) into tropical maize germplasm. The objectives of this study were to estimate the general combining ability (GCA) and specific combining ability (SCA) of selected maize inbred lines under drought stress (DS), low-nitrogen (LN) and optimum moisture and nitrogen (optimum) conditions, and to assess the yield potential and stability of experimental hybrids under these management conditions. Forty-nine experimental three-way cross hybrids, generated from a 7 × 7 line by tester crosses, and six commercial checks were evaluated across 11 optimum, DS and LN sites in Kenya in 2014 using an alpha lattice design with two replicates per entry at each site. DS reduced both grain yield (GY) and plant height (PH), while anthesis-silking interval (ASI) increased under both DS and LN. Hybrids 'L4/T2' and 'L4/T1' were found to be superior and stable, while inbreds 'L4' and 'L6' were good combiners for GY and other secondary traits across sites. Additive variance played a greater role for most traits under the three management conditions, suggesting that further progress in the improvement of these traits should be possible. GY under optimum conditions was positively correlated with GY under both DS and LN conditions, but GY under DS and LN was not correlated. Our results suggest the feasibility for simultaneous improvement in grain yield performance of genotypes under optimum, DS and LN conditions.

Genetic analysis of tropical maize inbred lines for resistance to maize lethal necrosis disease.

Maize lethal necrosis (MLN) disease is a recent outbreak in eastern Africa and has emerged as a significant threat to maize production in the region. The disease is caused by the co-infection of Maize chlorotic mottle virus and any member of potyviridae family. A total of 28 maize inbred lines with varying levels of tolerance to MLN were crossed in a half-diallel mating design, and the resulting 340 F1 crosses and four commercial checks were evaluated under MLN artificial inoculation at Naivasha, Kenya in 2015 and 2016 using an alpha lattice design with two replications. The objectives of the study were to (i) investigate the magnitude of general combining ability variance (σGCA 2) and specific combining ability variance (σSCA 2) and their interaction with years; (ii) evaluate the efficiencies of GCA based prediction and hybrid performance by means of a cross-validation procedure; (iii) estimate trait correlations in the hybrids; and (iv) identify the MLN tolerant single cross hybrids to be used as female parents for three-way cross hybrids. Results of the combined analysis of variance revealed that both GCA and SCA effects were significant (P < 0.05) for all traits except for ear rot. For MLN scores at early and late stages, GCA effects were 2.5-3.5 times higher than SCA effects indicating that additive gene action is more important than non-additive gene action. The GCA based prediction efficiency for MLN resistance and grain yield accounted for 67-90% of the variations in the hybrid performance suggesting that GCA-based prediction can be proposed to predict MLN resistance and grain yield prior to field evaluation. Three parents, CKDHL120918, CML550, and CKLTI0227 with significant GCA effects for GY (0.61-1.21; P < 0.05) were the most resistant to MLN. Hybrids "CKLTI0227 × CML550", "CKDHL120918 × CKLTI0138", and "CKDHL120918 × CKLTI0136" ranked among the best performing hybrids with grain yield of 6.0-6.6 t/ha compared with mean yield of commercial check hybrids (0.6 t/ha). The MLN tolerant inbred lines and single cross hybrids identified in this study could be used to improve MLN tolerance in both public and private sector maize breeding programs in eastern Africa.