We identified 27 stable loci associated with agronomic traits in spring wheat using genome-wide association analysis, some of which confirmed previously reported studies. GWAS peaks identified in regions where no QTL for grain yield per se has been mapped to date, provide new opportunities for gene discovery and creation of new cultivars with desirable alleles for improving yield and yield stability in wheat. We undertook large-scale genetic analysis to determine marker-trait associations (MTAs) underlying agronomic and physiological performance in spring wheat using genome-wide association studies (GWAS). Field trials were conducted at seven sites in three countries (Sudan, Egypt, and Syria) over 2-3 years in each country. Twenty-five agronomic and physiological traits were measured on 188 wheat genotypes. After correcting for population structure and relatedness, a total of 245 MTAs distributed over 66 loci were associated with agronomic traits in individual and mean performance across environments respectively; some of which confirmed previously reported loci. Of these, 27 loci were significantly associated with days to heading, thousand kernel weight, grain yield, spike length, and leaf rolling for mean performance across environments. Despite strong QTL by environment interactions, eight of the loci on chromosomes 1A, 1D, 5A, 5D, 6B, 7A, and 7B had pleiotropic effects on days to heading and yield components (TKW, SM, and SNS). The winter-type alleles at the homoeologous VRN1 loci significantly increased days to heading and grain yield in optimal environments, but decreased grain yield in heat prone environments. Top 20 high-yielding genotypes, ranked by additive main effects and multiplicative interaction (AMMI), had low kinship relationship and possessed 4-5 favorable alleles for GY MTAs except two genotypes, Shadi-4 and Qafzah-11/Bashiq-1-2. This indicated different yield stability mechanisms due to potentially favorable rare alleles that are uncharacterized. Our results will enable wheat breeders to effectively introgress several desirable alleles into locally adapted germplasm in developing wheat varieties with high yield stability and enhanced heat tolerance.

Purpose This paper aims to review the current status of wheat production, farming systems, production constraints and wheat demand-supply chain analysis; the role of international and national breeding programs and their approaches in wheat genetic improvement including targeting mega environments, shuttle breeding, doubled haploids, marker-assisted selection and key location phenotyping; and future prospects and opportunities of wheat production in Sub Saharan Africa (SSA). Design/methodology/approach Relevant literature works have been used and cited accordingly. Findings Though traditionally wheat was not the leading staple crop in SSA, it is becoming an important food crop because of rapid population growth associated with increased urbanization and change in food preference for easy and fast food such as bread, biscuits, pasta, noodles and porridge. In 2013, total wheat consumption in SSA reached 25 million tons with import accounting for 17.5 million tons at a price of USD6 billion, while during the same period the region produces only 7.3 million tons on a total area of 2.9 million hectares. The low productivity (2t/ha) in the region is principally because of abiotic (drought and heat) and biotic (yellow rust, stem rust, septoria and fusarium) stresses which are increasing in intensity and frequency associated with climate change. Furthermore, increased cost of production, growing populations, increased rural-urban migration, low public and private investments, weak extension systems and policies, and low adoption rates of new technologies remain to be major challenges for wheat production in SSA. Wheat breeding in SSA is dominantly carried out by National Agricultural Research Systems, in partnership with the international research centers [International center for improvement of maize and wheat (CIMMYT) and International center for agricultural research in the dry areas (ICARDA)], to develop high yielding and widely adapted wheat genotypes with increased water-use efficiency, heat tolerance and resistance to major diseases and pests. Most of the cultivars grown in SSA are originated from the international research centers, CIMMYT and ICARDA. Practical implications This paper will help to promote available wheat technologies in SSA by creating awareness to wheat scientists, extension agents and policymakers. Originality/value This manuscript is an original review paper which has not been published in this form elsewhere.

The main goal of this study was to investigate the genetic basis of yield and grain quality traits in winter wheat genotypes using association mapping approach, and identify linked molecular markers for marker assisted selection. A total of 120 elite facultative/winter wheat genotypes were evaluated for yield, quality and other agronomic traits under rain-fed and irrigated conditions for two years (2011–2012) at the Tel Hadya station of ICARDA, Syria. The same genotypes were genotyped using 3,051 Diversity Array Technologies (DArT) markers, of which 1,586 were of known chromosome positions. The grain yield performance of the genotypes was highly significant both in rain-fed and irrigated sites. Average yield of the genotypes ranged from 2295 to 4038 kg/ha and 4268 to 7102 kg/ha under rain-fed and irrigated conditions, respectively. Protein content and alveograph strength (W) ranged from 13.6–16.1% and 217.6–375 Jx10-4, respectively. DArT markers wPt731910 (3B), wPt4680 (4A), wPt3509 (5A), wPt8183 (6B), and wPt0298 (2D) were significantly associated with yield under rain-fed conditions. Under irrigated condition, tPt4125 on chromosome 2B was significantly associated with yield explaining about 13% of the variation. Markers wPt2607 and wPt1482 on 5B were highly associated with protein content and alveograph strength explaining 16 and 14% of the variations, respectively. The elite genotypes have been distributed to many countries using ICARDA’s International system for potential direct release and/or use as parents after local adaptation trials by the NARSs of respective countries. The QTLs identified in this study are recommended to be used for marker assisted selection after through validation using bi-parental populations.

Identified DArT and SNP markers including a first reported QTL on 3AS, validated large effect APR on 3BS. The different genes can be used to incorporate stripe resistance in cultivated varieties. Stripe rust [yellow rust, caused by Puccinia striiformis f. sp. tritici (Pst)] is a serious disease in wheat (Triticum aestivum). This study employed genome-wide association mapping (GWAM) to identify markers linked to stripe rust resistance genes using Diversity Arrays Technology (DArT(®)) and single-nucleotide polymorphism (SNP) Infinium 9K assays in 200 ICARDA wheat genotypes, phenotyped for seedling and adult plant resistance in two sites over two growing seasons in Syria. Only 25.8 % of the genotypes showed resistance at seedling stage while about 33 and 44 % showed moderate resistance and resistance response, respectively. Mixed-linear model adjusted for false discovery rate at p < 0.05 identified 12 DArT and 29 SNP markers on chromosome arms 3AS, 3AL, 1AL, 2AL, 2BS, 2BL, 3BS, 3BL, 5BL, 6AL, and 7DS significantly linked to Pst resistance genes. Of these, the locus on 3AS has not been previously reported to confer resistance to stripe rust in wheat. The QTL on 3AS, 3AL, 1AL, 2AL, and 2BS were effective at seedling and adult plant growth stages while those on 3BS, 3BL, 5BL, 6AL and 7DS were effective at adult plant stage. The 3BS QTL was validated in Cham-6 × Cham-8 recombinant inbred line population; composite interval analysis identified a stripe resistance QTL flanked by the DArT marker, wPt-798970, contributed by Cham-6 parent which accounted for 31.2 % of the phenotypic variation. The DArT marker "wPt-798970" lies 1.6 cM away from the 3BS QTL detected within GWAM. Epistatic interactions were also investigated; only the QTL on 1AL, 3AS and 6AL exhibited interactions with other loci. These results suggest that GWAM can be an effective approach for identifying and improving resistance to stripe rust in wheat.

Heat stress decreases photosynthesis, pollen viability, and grain number and weight and hence lowers yield and quality of wheat (Triticum aestivum L.) by variable amounts among different cultivars and genotypes. The present study was performed to determine genetic variability of spring bread wheat genotypes for yield and other agronomic traits under heat‐stressed (Wad Medani, Sudan) and high‐yielding (Sids, Egypt) environments and to identify linked single nucleotide polymorphism (SNP) markers through association mapping. A heat association panel of 197 spring wheat genotypes from ICARDA was evaluated for yield and agronomic traits at Wad Medani and Sids stations for 2 yr (2014–2015). A total of 111 significant marker‐trait associations were detected. The wsnp_Ex_c12812_20324622 marker on chromosome 4A was significantly correlated with yield at both locations. At Wad Medani, wsnp_Ex_c2526_4715978 on chromosome 5A was significantly correlated with grain yield. Wheat genotypes carrying the cytosine base at the wsnp_Ex_c12812_20324622 and wsnp_Ex_c2526_4715978 markers outyielded the ones carrying the alternative bases by 15%, whereas genotypes carrying the cytosine base at only one of the two markers increased their yield by 7.9 to 10%, suggesting the importance of using these markers for marker‐assisted selection in breeding programs to increase yield under heat stress. The top 20 high‐yielding and heat‐tolerant genotypes identified in this study have been distributed to the national research systems of Central and West Asia and North Africa (CWANA) and sub‐Saharan Africa (SSA) for potential direct release and/or use as parents after local adaptation trials.