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The identification of haplotypes influencing traits of agronomic interest, with well-defined effects across environments, is of key importance to develop varieties adapted to their context of use. It requires advanced crossing schemes, multi-environment characterization and relevant statistical tools. Here we present a sorghum multi-reference back-cross nested association mapping (BCNAM) population composed of 3901 lines produced by crossing 24 diverse parents to three elite parents from West and Central Africa (WCA-BCNAM). The population was characterized in environments contrasting for photoperiod, rainfall, temperature, and soil fertility. To analyse this multi-parental and multi-environment design, we developed a new methodology for QTL detection and parental effect estimation. In addition, envirotyping data were mobilized to determine the influence of specific environmental covariables on the genetic effects, which allowed spatial projections of the QTL effects. We mobilized this strategy to analyse the genetic architecture of flowering time and plant height, which represent key adaptation mechanisms in environments like West Africa. Our results allowed a better characterisation of well-known genomic regions influencing flowering time concerning their response to photoperiod with Ma6 and Ma1 being photoperiod sensitive and candidate gene Elf3 being insensitive. We also accessed a better understanding of plant height genetic determinism with the combined effects of phenology dependent (Ma6) and independent (qHT7.1 and Dw3) genomic regions. Therefore, we argue that the WCA-BCNAM constitutes a key genetic resource to feed breeding programs in relevant elite parental lines and develop climate-smart varieties.

DNA-based methodology employing quantitative polymerase chain reaction (qPCR) has been successfully used to examine the incidence of genetically modified (GM) maize in Mali. This study aims to ascertain whether screening elements could also be used to detect GM maize. Fourteen maize varieties and one unknown dark color seeded variety from Mali were tested. DNA was extracted from three seeds of each variety. Three screening elements were used for qPCR amplification, the 35s promoter of the Cauliflower mosaic virus (CaMV), the nopaline synthase (NOS terminator) from Agrobacterium tumefaciens and the 35s promoter from the Figwort mosaic virus (FMV). The 14 varieties were negative for P35s CaMV (forward) and T-NOS (reverse) markers. In contrast, the unknown dark color seeded variety was positive with 94 bp PCR product. While, no DNA fragments were amplified using the FMV as the screening element. These data were supported by Ct values in which the 14 varieties had values above 50; whereas, the unknown variety showed values of 24.5 for P-35s-CaMV and 30 for the T-NOS. The study demonstrates the ability in detecting GM maize using screening elements and the usefulness of our laboratory in training and reinforcing regional concern about GMO circulation. Key words: Genetically modified organism (GMO) detection, quantitative polymerase chain reaction (qPCR), capacity building, maize, Mali.

Local landrace and breeding germplasm is a useful source of genetic diversity for regional and global crop improvement initiatives. Sorghum (Sorghum bicolorL. Moench) in West Africa has diversified across a mosaic of cultures and end-uses, and along steep precipitation and photoperiod gradients. To facilitate germplasm utilization, a West African sorghum association panel (WASAP) of 756 accessions from national breeding programs of Niger, Mali, Senegal, and Togo was assembled and characterized. Genotyping-by-sequencing was used to generate 159,101 high-quality biallelic SNPs, with 43% in intergenic regions and 13% in genic regions. High genetic diversity was observed within the WASAP (π = 0.00045), only slightly less than in a global diversity panel (π = 0.00055). Linkage disequilibrium decayed to background level (r2< 0.1) by ~50 kb in the WASAP. Genome-wide diversity was structured both by botanical type, and by populations within botanical type, with eight ancestral populations identified. Most populations were distributed across multiple countries, suggesting several potential common gene pools across the national programs. Genome-wide association studies of days to flowering and plant height revealed eight and three significant quantitative trait loci (QTL), respectively, with major height QTL at canonical height lociDw3andSbHT7.1. Colocalization of two of eight major flowering time QTL with flowering genes previously described in US germplasm (Ma6andSbCN8) suggests that photoperiodic flowering in WA sorghum is conditioned by both known and novel genes. This genomic resource provides a foundation for genomics-enabled breeding of climate-resilient varieties in West Africa.

Developing drought resistant cereal crops continues to be a major challenge in the climate change scenario. Sorghum is a C4 crop and its yield levels are highly affected by terminal drought stress under rainfed conditions. Efficient screening methods coupled with high throughput phenotyping techniques are required for breeding climate resilient crops. Plant adaptation to drought stress is manifested by several modifications at morphological, anatomical, physiological levels. Several mechanisms including osmotic adjustments, stay green, leaf rolling, waxyness on stem, root morphology and its architecture, transpiration efficiency, secretion of soluble solutes are known to play important role in bringing drought tolerance. Several breeding methods have been proposed and a single method may not hold good for all the crop species. Recombination, mutation and molecular breeding methods are mainly used for breeding drought resistant plants. At molecular level, several QTL's governing pre- and post flowering drought tolerance have been identified in cereals and specifically in sorghum. At genome level, genes involved in proline metabolism, transmembrane ion transporter, abscisic acid metabolism, etc., are known to be upregulated under water deficit conditions. Recent studies on transcriptome analysis showed that genes which are expressed in sensitive plants are related to stress responses and oxy reduction reactions. Recently high throughput phenotyping tools have been developed to associate drought responsive traits to genomic regions governing quantitative traits. In this review, detailed mechanisms and breeding approaches related to drought stress in cereals and specifically in sorghum are discussed.

AGAP; International audience; In West Africa Sudano-Sahelian zone, sorghum sensitivity to photoperiod is a major trait for flowering adjustment toward the end of the rainy season. This trait ensures that conditions for crop development are optimal. Improving the understanding of the genetic control of flowering time in sorghum is thus an important step toward breeding climate resilient varieties for meeting the challenge of climate smart agriculture. In the wake of green revolution, most sorghum breeders eliminated photoperiod sensitivity to develop early maturing varieties. The evidence is now that simultaneous improvement of production, yield stability and grain quality requires the development of photoperiod-sensitive varieties. A segregating sorghum population derived from a cross between two photoperiod sensitive elite parents was evaluated in three different locations and five environments. CERES crop model was applied to decompose the flowering time of each genotype into basic vegetative phase, critical photoperiod and photoperiod sensitivity. Phenology and model derived variables were used for genetic analysis. The three model parameters were controlled by specific genomic regions. A major QTL affecting critical photoperiod was identified, whereas only independent minor QTLs were found for basic vegetative phase and photoperiod sensitivity. Candidate gene analysis in the major QTL region allowed us to propose a candidate gene (ELF3) involved in the circadian clock as a key regulator of flowering time in photoperiod-sensitive sorghum. Our findings provide critical information supporting the development of photoperiod-sensitive genotypes specifically adapted to climate variability encountered in Sudano-Sahelian zone.

Mali is a Sahelian country with a large climatic contrast from North to South. The current climatic and production evolutionary study is focused on the six major agro-climatic cereal production zones ranging from Kayes (400 mm) to Sikasso (>1000 mm) of rainfalls. Climatic data are rainfall records, daily maximum and minimum temperatures from 60 years of the six major synoptic weather observation stations. Data were analyzed on comparing average decades of the two normal periods of 30 years (1951-1980) and (1981-2010). Annual agronomic production data for millet, sorghum, maize and rice are derived from Mali's agricultural statistics base from 1984 to 2013. Main climatic results analyses indicate that climate change resulted in a decrease of 100 mm isohyets between the 2 periods of 30 years. The structure of the rainy season was little changed between these two periods since the average start of the season was delayed by 6 days and the average end date of the season became earlier by 4 days. Maximum temperatures increased significantly from + 0.44°C to + 1.53°C and minimum temperatures significantly increased from + 1.05°C to + 1.93°C in varying way depending on the sites. Statistics of major agronomic food crop production in Mali from 1984 to 2013 indicate an average increase of 985 to 4492 thousand tones, or 22% increase per year. There is a positive upward in saw tooth trend in Malian production from 1984 to 2013. This positive trend is the result of a combination of agricultural extension, agronomic research application and the management of small farmer holder in the Sahel. This evolution needs better study for drawing necessary right conclusions.

International audience; One of the most frequently consumed sorghum food in Mali is a thick porridge, known as to. Many grain traits contribute to its firmness and color, which are the most important qualities for consumers. These traits are related to chemical composition, physical properties, but also grain size, shape, glume adherence and color, pericarp thickness, or the presence of a testa. Quantitative trait loci for to consistency, to color, 16 grain traits, as well as day to flowering and grain yield, were investigated in two elite breeding populations, involved in a marker assisted selection program. A total of 51 and 71 QTLs were detected for P114 and P118, respectively. Several QTLs with high R-2 corresponded to major genes segregating in the populations such as the Z gene for pericarp thickness, the B2 and B1 genes for testa presence, the P gene for anthocyanin, and a QTL for flowering time. Many QTLs with moderate effect were detected for grain attributes associated to to quality, without showing antagonism between grain quality and yield. The results of this study will contribute to producing new varieties combining grain productivity and grain quality favorable alleles, through the use of marker assisted selection.

Sorghum retains a crucial role in Sub-Saharan Africa for food and in the future feed. Unfortunately, the movement of sorghum technology onto farmers' fields in Sub-Saharan Africa has been slow in spite of substantial research since the great African drought of 1968-1973. What is necessary to get African sorghum yields and profitability up?After reviewing the situation of sorghum in the world, the USA, and Sub-Saharan Africa from 2007 to 2017 the results and the lessons of a twelve-year program in the Sahel of West Africa to introduce new sorghum technology and marketing strategies are the focus of the rest of the paper. In Mali, the program identified new technologies that were extended into a large number of farmers' associations. The Mali program then collaborated with two other agencies to scale up this pilot program. The pilot project demonstrated that yields with moderate fertilization, new varieties, and improved agronomic practices could be increased 50 to 100% and prices increased 30 to 50%. The 2012 military coup and then invasion of Al Queda from the north shut down both the pilot and the scaling up activities as the US government banned collaboration with Malian government agencies after the coup. The pilots were continued in Niger and Burkina Faso through 2014 and then with a Gates Foundation grant from 2014 to 2016. The pilot program in Mali responded to two of the three Second Generation problems identified. But more significantly the pilot project identified the lack of funds for responding to Second Generation problems as a major constraint for implementing a technology-marketing program in a low-income country.

International audience; The thickness of grain pericarp, the outer layer of the kernel, is an important breeding criterion for sorghum. This cereal is mainly used through traditional processing in family-based food systems in many regions of the world. We investigated in this study how pericarp thickness could be predicted by Near Infrared Reflectance Spectroscopy (NIRS), a fast and non-destructive measurement method that is commonly used to measure physico-chemical parameters of sorghum grains, and how this trait also influences the prediction of those parameters. We showed that, using a classification approach, it was possible to discriminate thick from thin pericarp whole grain samples with a good accuracy and that the proportion of thin and thick grains in mixed samples could also be predicted. In addition, pericarp thickness had a significant effect on the calibration performance for other grain parameters indicating that the pericarp can distort spectral information of whole grain samples. As a practical consequence, we suggest to develop separate whole grain calibration models for thin and thick pericarp samples, combined with a two-steps prediction approach to improve the accuracy of whole grain NIRS calibrations for grain quality parameters in sorghum.

Sorghum (Sorghum bicolor (L). Moench) is an important staple food crop produced essentially under rained conditions in Mali. To preserve and exploit sorghum genetic diversity, germplasm collection was undertaken in 1978 across Mali. During this germplasm evaluation in 1982, a particular guinea sorghum cultivar from Chegue village in north western Mali, recorded as CSM63, was identified for its earliness and photoperiod insensitivity. This cultivar was unfortunately segregating not only for a testa presence, which is detrimental to To color and nutritional quality, but also for flowering time and plant height. Field screening coupled with the potassium hydroxide and bleach (KOH: B) tests were performed to eliminate testa while maintaining CSM63 agronomic values. Overall objectives were to trace history of CSM63 native population, screen for testa absence and define its favorable cropping zone. Field experiments were conducted at the Cinzana Agronomic Research Station (SRAC) while laboratory tests for testa absence and cooking quality were conducted at Sotuba Food Technology Laboratory (LTA) in Mali. Two thousand (2000) plants from original CSM63 population were grown in a complete isolation from other sorghum varieties to select 288 panicles for testa absence. For yield trial, a completely randomized block design was used with 3 replications. After series of selfing, a pure new line (CSM63-18-1AF) was identified without a testa with similar maturity, grain yield, better To color and nutritional values than the original CSM63. The new line was named CSM63E and its cropping zones were delimited beyond its center of origin. CSM63E was released for large scale production by Institut d'Economie Rurale (IER) and registered in National and West African Countries Regional Sorghum Catalogs. The adopted line is named Jakunbe (prevent drought) in Bambara language) by farmers. Jakunbe is the number one certified sorghum seed produced in Mali in 2016 in term of quantity. Cropping both Jakunbe and late maturing varieties beyond isohyets 700 mm exposes farmers to yield losses caused by non-proper environment.

Maize is produced in varying environment dictating yield performance and stability in Mali. To validate yield and stability performance, 78 hybrids and 2 checks were tested across eight environments at six sites in Mali during the rainy season of 2011. Two planting dates were used in Sotuba and Siramana locations to create additional environments. The hybrids were evaluated in Randomized Complete Block Design with two replications for one year. The objectives were (1) to study the nature and the magnitude of the genotype x environment interaction and (2) the grain yield stability within and across environments. Sotuba 1, Sotuba 2, Kebila and Kafara were high yielding environments characterized by better performance and very high yield. Siramana 1, Siramana 2, Tamala, and Koulikoro were low yielding environments which was determined with GGE biplot analysis. Nine hybrids were stable across the high yielding environments. Across the low yielding sites, twenty two hybrids exhibited stable performance. Seven Inbred lines showed positive GCA in high yielding environments indicating a predominance of additive gene action. The best SCAs were obtained with P43SRC9FS100‐1‐ 1‐8/V481‐73, CML442/87036 and (KU1403x1368)/CML505. The hybrid with the best SCA value P43SRC9FS100‐1‐1‐ 8/V481‐73 was from parents exhibiting the highest GCA values.

Recurrent drought is one of the major constraints to maize production in West Africa. It can be devastating if it occurs for a long period, especially during flowering. Hybrid maize varieties that are tolerant to drought are not available. Therefore, many farmers in Mali have not yet adopted hybrid maize varieties. In this study, maize inbreds and hybrids were evaluated for their tolerance to drought and the gene effects conditioning performance under both drought and no drought conditions were studied to identify hybrids tolerant to drought stress that could be released. The association of inbred root characteristics and tolerance to drought was also evaluated. Hybrids generated from crosses between thirteen inbred lines were evaluated for drought tolerance. Seventy-eight hybrids and two checks were evaluated under water stress and non-water stress conditions across four environments during the off-season of 2010. The seventy-eight hybrids were obtained from a diallel cross of thirteen parents. The test sites included: Farako (10°50’00’’ North 6°51’0’’ West), Sotuba (12°39’47’’North 7°54’50’’ West) and Yanfolila (11°11’0’’ North 8°9’0’’). Two planting dates were used to create two different environments at Farako. The experiment consisted of a split-plot with water regime as the main plot and hybrids as the sub plots. The water regime consisted of a well watered plot where irrigation was supplied through-out the plant cycle and a drought imposed plot where irrigation was stopped 40 days after planting for 20 days. The sub-plots consisted of the 78 hybrids and checks arranged in an alpha lattice with two replications. Water stress increased anthesissilking interval resulting in reduced grain yield. Hybrid V841-73/9071 had the lowest grain yield reduction (35.3%) due to water stress, followed by CML 505/1368 (41.9%). Line 9071 has good root weight and good root number under stress while line1368exhibited good root number, good root length and good root weight under stress. The following Genotypes9071/CML442; CML442/TZ COMP3-C2-S2, 87036/CML442, CML505/1368, V481-73/CML442, C11O5/9071, J-16-1/TZ COMP3-C2-S2 and CML444/87036 performed well under both well watered and water stress conditions. The inbreds 9071 and CML442 exhibited the highest frequency of appearance as parents among the best hybrids both under well watered and water stress conditions demonstrating their superior SCA with some of the other parental inbreds studied here.