Spot blotch (SB), caused by Bipolaris sorokiniana, is a devastating disease of wheat globally, especially in South Asia and South America. Understanding the genetics of resistance to SB is important for developing breeding strategies to improve resistance. A panel of 301 genotypes from Afghanistan was phenotyped over two crop seasons using a mixture of virulent B. sorokiniana isolates and genotyped using DArTSeq to obtain genome‐wide markers. Fifty genotypes (16.6%) showed disease scores less than the resistant control. Principal component analysis using the genotypic data clustered the genotypes into five different groups. Among models used for genome‐wide association mapping, the multilocus mixed model, and fixed and random model circulating probability unification algorithms were most effective in identifying significant marker‐trait associations (MTA). Twenty‐five MTAs at p ≤ .001 were identified on chromosomes 1A, 1B, 1D, 2B, 2D, 3A, 3B, 4A, 5A, 5B, 6A, 7A, and 7D, indicating the quantitative nature of resistance to SB. Phenotypic variation explained by these markers ranged from 2.0% to 17.7%, and genomic regions on the chromosomes 1D, 2D, 3A, 3B, 4A, 5A, and 5B coincided with loci identified in previous studies. Three single nucleotide polymorphism (SNP) markers on chromosomes 1B (SNP 1113207) and 5A (SNPs 5411867 and 998276) were significant in both crop seasons as well as in the combined analysis across seasons. Marker 5411867 is close to Vrn‐A1, shown to be associated with SB in previous studies. Furthermore, among known SB resistance genes, Sb2 on chromosome 5B was predicted to be significant in this panel.

Karnal bunt disease of wheat, caused by the fungus Neovossia indica, is one of the most important challenges to the grain industry as it affects the grain quality and also restricts the international movement of infected grain. It is a seed-, soil- and airborne disease with limited effect of chemical control. Currently, this disease is contained through the deployment of host resistance but further improvement is limited as only a few genotypes have been found to carry partial resistance. To identify genomic regions responsible for resistance in a set of 339 wheat accessions, genome-wide association study (GWAS) was undertaken using the DArTSeq® technology, in which 18 genomic regions for Karnal bunt resistance were identified, explaining 5–20% of the phenotypic variation. The identified quantitative trait loci (QTL) on chromosome 2BL showed consistently significant effects across all four experiments, whereas another QTL on 5BL was significant in three experiments. Additional QTLs were mapped on chromosomes 1DL, 2DL, 4AL, 5AS, 6BL, 6BS, 7BS and 7DL that have not been mapped previously, and on chromosomes 4B, 5AL, 5BL and 6BS, which have been reported in previous studies. Germplasm with less than 1% Karnal bunt infection have been identified and can be used for resistance breeding. The SNP markers linked to the genomic regions conferring resistance to Karnal bunt could be used to improve Karnal bunt resistance through marker-assisted selection.

Wheat (Triticum aestivum L.) is an essential food security crop in Afghanistan. To determine the contribution of wheat breeding to increasing productivity, we analyzed data obtained from 192 trials conducted over 11 locations from 2002–2003 to 2015–2016. Using this data, we estimated annual genetic gains for grain yield, days to heading and plant height over the 14‐yr period. We used best linear unbiased estimates to measure genetic gains across CIMMYT Elite Spring Wheat Yield Trials per se and for the top 5 and top 10% performing genotypes relative to checks. Mean realized genetic gain for grain yield was 115 kg ha–1 yr−1, whereas the top 10 genotypes achieved annual yield gains of 123 kg ha–1. The continually replaced local check s also contributed an annual genetic gain for yield of 107 kg ha–1. The associated adaptive traits days to heading and plant height varied in their response over time with the top 10 yielding genotypes having a 1.82 d annual reduction in heading date while plant height increased by 0.77 cm yr−1 for the same set of genotypes. Results show that continual breeding improvements confer yield gains, contributing to increasing Afghan wheat productivity. This has wider relevance for demonstrating the value of continued investment in public sector plant breeding supporting wheat production and food security in Central Asia.

The production and availability of food underpins societal stability. In Afghanistan, wheat is the major arable agricultural crop and source of dietary energy. The withdrawal of NATO allies and partner countries from Afghanistan presents numerous well-documented societal and political challenges and has impacts on immediate and longer-term food security. Conflict-impacted irrigation infrastructure coupled with growing climate instability have also contributed markedly to reductions in current food, and specifically wheat, production. Here, we review the status of Afghan wheat improvement and propose a research agenda to support the regeneration of Afghanistan's wheat and agricultural sector.