Impact of CGIAR maize germplasm in Sub-Saharan Africa.

This study reports on the adoption and impacts of CGIAR-related maize varieties in 18 major maize-producing countries in sub-Saharan Africa (SSA) during 1995-2015. Of the 1345 maize varieties released during this timeframe, approximately 60% had a known CGIAR parentage. About 34% (9.5 million ha) of the total maize area in 2015 was cultivated with 'new' CGIAR-related maize varieties released between 1995 and 2015. In the same year, an additional 13% of the maize area was cultivated with 'old' CGIAR-related maize varieties released before 1995. The aggregate annual economic benefit of using new CGIAR-related maize germplasm for yield increase in SSA was estimated at US$1.1-1.6 billion in 2015, which we attributed equally to co-investments by CGIAR funders, public-sector national research and extension programs, and private sector partners. Given that the annual global investment in CGIAR maize breeding at its maximum was US$30 million, the benefit-cost ratios for the CGIAR investment and CGIAR-attributable portion of economic benefits varied from 12:1-17:1, under the assumption of a 5-year lag in the research investment to yield returns. The study also discusses the methodological challenges involved in large-scale impact assessments. Post-2015 CGIAR tropical maize breeding efforts have had a strong emphasis on stress tolerance.

Diversity analysis of 80,000 wheat accessions reveals consequences and opportunities of selection footprints.

Undomesticated wild species, crop wild relatives, and landraces represent sources of variation for wheat improvement to address challenges from climate change and the growing human population. Here, we study 56,342 domesticated hexaploid, 18,946 domesticated tetraploid and 3,903 crop wild relatives in a massive-scale genotyping and diversity analysis. Using DArTseqTM technology, we identify more than 300,000 high-quality SNPs and SilicoDArT markers and align them to three reference maps: the IWGSC RefSeq v1.0 genome assembly, the durum wheat genome assembly (cv. Svevo), and the DArT genetic map. On average, 72% of the markers are uniquely placed on these maps and 50% are linked to genes. The analysis reveals landraces with unexplored diversity and genetic footprints defined by regions under selection. This provides fertile ground to develop wheat varieties of the future by exploring specific gene or chromosome regions and identifying germplasm conserving allelic diversity missing in current breeding programs.

Genetic Analysis of Tropical Midaltitude- Adapted Maize Populations under Stress and Nonstress Conditions.

Maize (Zea mays L.) yield in sub-Saharan Africa (SSA) is low because of both abiotic and biotic constraints, and limited availability or use of improved seed in some areas. This study was conducted (i) to estimate combining ability and heterosis among seven stress-tolerant populations, and (ii) to assess diversity among the populations and the relationship between diversity and heterosis. Twenty-one hybrids developed from diallel crosses of seven populations, parents, and two checks were evaluated in 10 optimal and 11 stressed environments (drought, low N, and random stress) in Kenya, Ethiopia, Uganda, and Zimbabwe for 2 yr. Analysis II of Gardner and Eberhart showed that variety and heterosis were significant for grain yield (GY) under optimal and managed stress, and across environments. Heterosis accounted for most of the variation for GY among populations under optimal conditions (67%) and drought stress (53%), which suggested the importance of dominance in inheritance of GY under these conditions. Genetic distance (GD) among populations ranged from 0.328 to 0.477 (mean = 0.404). The correlation between GD and heterosis was low (r = 0.14-0.40) in all environments. The simple sequence repeat (SSR) marker-based and GY-based clustering of parental populations showed similar patterns, with three populations distinct from the rest, suggesting significant differentiation of allelic variation in these three populations. The SSR-based diversity and phenotypic analysis results should be useful in defining breeding strategies and maintaining heterotic patterns among these populations.

Molecular mapping across three populations reveals a QTL hotspot region on chromosome 3 for secondary traits associated with drought tolerance in tropical maize.

Identifying quantitative trait loci (QTL) of sizeable effects that are expressed in diverse genetic backgrounds across contrasting water regimes particularly for secondary traits can significantly complement the conventional drought tolerance breeding efforts. We evaluated three tropical maize biparental populations under water-stressed and well-watered regimes for drought-related morpho-physiological traits, such as anthesis-silking interval (ASI), ears per plant (EPP), stay-green (SG) and plant-to-ear height ratio (PEH). In general, drought stress reduced the genetic variance of grain yield (GY), while that of morpho-physiological traits remained stable or even increased under drought conditions. We detected consistent genomic regions across different genetic backgrounds that could be target regions for marker-assisted introgression for drought tolerance in maize. A total of 203 QTL for ASI, EPP, SG and PEH were identified under both the water regimes. Meta-QTL analysis across the three populations identified six constitutive genomic regions with a minimum of two overlapping traits. Clusters of QTL were observed on chromosomes 1.06, 3.06, 4.09, 5.05, 7.03 and 10.04/06. Interestingly, a ~8-Mb region delimited in 3.06 harboured QTL for most of the morpho-physiological traits considered in the current study. This region contained two important candidate genes viz., zmm16 (MADS-domain transcription factor) and psbs1 (photosystem II unit) that are responsible for reproductive organ development and photosynthate accumulation, respectively. The genomic regions identified in this study partially explained the association of secondary traits with GY. Flanking single nucleotide polymorphism markers reported herein may be useful in marker-assisted introgression of drought tolerance in tropical maize.

QTL mapping in three tropical maize populations reveals a set of constitutive and adaptive genomic regions for drought tolerance.

Despite numerous published reports of quantitative trait loci (QTL) for drought-related traits, practical applications of such QTL in maize improvement are scarce. Identifying QTL of sizeable effects that express more or less uniformly in diverse genetic backgrounds across contrasting water regimes could significantly complement conventional breeding efforts to improve drought tolerance. We evaluated three tropical bi-parental populations under water-stress (WS) and well-watered (WW) regimes in Mexico, Kenya and Zimbabwe to identify genomic regions responsible for grain yield (GY) and anthesis-silking interval (ASI) across multiple environments and diverse genetic backgrounds. Across the three populations, on average, drought stress reduced GY by more than 50 % and increased ASI by 3.2 days. We identified a total of 83 and 62 QTL through individual environment analyses for GY and ASI, respectively. In each population, most QTL consistently showed up in each water regime. Across the three populations, the phenotypic variance explained by various individual QTL ranged from 2.6 to 17.8 % for GY and 1.7 to 17.8 % for ASI under WS environments and from 5 to 19.5 % for GY under WW environments. Meta-QTL (mQTL) analysis across the three populations and multiple environments identified seven genomic regions for GY and one for ASI, of which six mQTL on chr.1, 4, 5 and 10 for GY were constitutively expressed across WS and WW environments. One mQTL on chr.7 for GY and one on chr.3 for ASI were found to be 'adaptive' to WS conditions. High throughput assays were developed for SNPs that delimit the physical intervals of these mQTL. At most of the QTL, almost equal number of favorable alleles was donated by either of the parents within each cross, thereby demonstrating the potential of drought tolerant × drought tolerant crosses to identify QTL under contrasting water regimes.

Prediction of genetic values of quantitative traits in plant breeding using pedigree and molecular markers.

The availability of dense molecular markers has made possible the use of genomic selection (GS) for plant breeding. However, the evaluation of models for GS in real plant populations is very limited. This article evaluates the performance of parametric and semiparametric models for GS using wheat (Triticum aestivum L.) and maize (Zea mays) data in which different traits were measured in several environmental conditions. The findings, based on extensive cross-validations, indicate that models including marker information had higher predictive ability than pedigree-based models. In the wheat data set, and relative to a pedigree model, gains in predictive ability due to inclusion of markers ranged from 7.7 to 35.7%. Correlation between observed and predictive values in the maize data set achieved values up to 0.79. Estimates of marker effects were different across environmental conditions, indicating that genotype × environment interaction is an important component of genetic variability. These results indicate that GS in plant breeding can be an effective strategy for selecting among lines whose phenotypes have yet to be observed.

Drought stress and tropical maize: QTL-by-environment interactions and stability of QTLs across environments for yield components and secondary traits.

A recombinant inbred line (RIL) population was evaluated in seven field experiments representing four environments: water stress at flowering (WS) and well-watered (WW) conditions in Mexico and Zimbabwe. The QTLs were identified for each trait in each individual experiment (single-experiment analysis) as well as per environment, per water regime across locations and across all experiments (joint analyses). For the six target traits (male flowering, anthesis-to-silking interval, grain yield, kernel number, 100-kernel fresh weight and plant height) 81, 57, 51 and 34 QTLs were identified in the four step-wise analyses, respectively. Despite high values of heritability, the phenotypic variance explained by QTLs was reduced, indicating epistatic interactions. About 80, 60 and 6% of the QTLs did not present significant QTL-by-environment interactions (QTL x E) in the joint analyses per environment, per water regime and across all experiments. The expression of QTLs was quite stable across years at a given location and across locations under the same water regime. However, the stability of QTLs decreased drastically when data were combined across water regimes, reflecting a different genetic basis of the target traits in the drought and well-watered trials. Several clusters of QTLs for different traits were identified by the joint analyses of the WW (chromosomes 1 and 8) and WS (chromosomes 1, 3 and 5) treatments and across water regimes (chromosome 1). Those regions are clear targets for future marker-assisted breeding, and our results confirm that the best approach to breeding for drought tolerance includes selection under water stress.

Workgroup report: public health strategies for reducing aflatoxin exposure in developing countries.

Consecutive outbreaks of acute aflatoxicosis in Kenya in 2004 and 2005 caused > 150 deaths. In response, the Centers for Disease Control and Prevention and the World Health Organization convened a workgroup of international experts and health officials in Geneva, Switzerland, in July 2005. After discussions concerning what is known about aflatoxins, the workgroup identified gaps in current knowledge about acute and chronic human health effects of aflatoxins, surveillance and food monitoring, analytic methods, and the efficacy of intervention strategies. The workgroup also identified public health strategies that could be integrated with current agricultural approaches to resolve gaps in current knowledge and ultimately reduce morbidity and mortality associated with the consumption of aflatoxin-contaminated food in the developing world. Four issues that warrant immediate attention were identified: a) quantify the human health impacts and the burden of disease due to aflatoxin exposure; b) compile an inventory, evaluate the efficacy, and disseminate results of ongoing intervention strategies; c) develop and augment the disease surveillance, food monitoring, laboratory, and public health response capacity of affected regions; and d) develop a response protocol that can be used in the event of an outbreak of acute aflatoxicosis. This report expands on the workgroup's discussions concerning aflatoxin in developing countries and summarizes the findings.