Race Ug99 of the fungus Puccinia graminis tritici that causes stem or black rust disease on wheat was first detected in Uganda in 1998. Seven races belonging to the Ug99 lineage are now known and have spread to various wheat-growing countries in the eastern African highlands, as well as Zimbabwe, South Africa, Sudan, Yemen, and Iran. Because of the susceptibility of 90% of the wheat varieties grown worldwide, the Ug99 group of races was recognized as a major threat to wheat production and food security. Its spread, either wind-mediated or human-aided, to other countries in Africa, Asia, and beyond is evident. Screening in Kenya and Ethiopia has identified a low frequency of resistant wheat varieties and breeding materials. Identification and transfer of new sources of race-specific resistance from various wheat relatives is underway to enhance the diversity of resistance. Although new Ug99-resistant varieties that yield more than current popular varieties are being released and promoted, major efforts are required to displace current Ug99 susceptible varieties with varieties that have diverse race-specific or durable resistance and mitigate the Ug99 threat.

Wheat is grown worldwide in diverse geographical regions, environments, and production systems. Although many diseases and pests are known to reduce grain yield potential and quality, the three rusts and powdery mildew fungi have historically caused major crop losses and continue to remain economically important despite the widespread use of host resistance and fungicides. The evolution and fast spread of virulent and more aggressive race lineages of rust fungi have only worsened the situation. Fusarium head blight, leaf spotting diseases, and, more recently, wheat blast (in South America and Bangladesh) have become diseases of major importance in recent years largely because of intensive production systems, the expansion of conservation agriculture, undesirable crop rotations, or increased dependency on fungicides. High genetic diversity for race-specific and quantitative resistance is known for most diseases; their selection through phenotyping reinforced with molecular strategies offers great promise in achieving more durable resistance and enhancing global wheat productivity.

Genomic selection (GS) is a promising approach exploiting molecular genetic markers to design novel breeding programs and to develop new markers-based models for genetic evaluation. In plant breeding it provides opportunities to increase genetic gain of complex traits per unit time and cost. The cost benefit balance was an important consideration for GS to work in crop plants. Availability of genome-wide high-throughput, cost effective and flexible markers, having low ascertainment bias, suitable for large population size as well for both model and non-model crop species with or without the reference genome sequence was the most important factor for its successful and effective implementation in crop species. These factors were the major limitations to marker systems viz., SSR and array-based, and was unimaginable before the availability of next-generation sequencing (NGS) technologies which have provided novel SNP genotyping platforms especially the genotyping by sequencing (GBS). These marker technologies have changed the entire scenario of marker applications and made the use of GS a routine work for crop improvement in both model and non-model crop species. The NGS based genotyping have increased genomic-estimated breeding value (GEBV) prediction accuracies over other established marker platform in cereals and other crop species, and made dream of GS true in crop breeding. But to harness the true benefits from GS, these marker technologies will be combined with high-throughput phenotyping (HTP) for achieving the valuable genetic gain from complex traits. Moreover, the continuous decline in sequencing cost will make the WGS feasible and cost effective for GS in near future. Till that time matures the targeted sequencing seems to be more cost-effective option for large scale marker discovery and GS, particularly in case of large and un-decoded genomes.

Wheat blast or ‘brusone’, caused by the ascomycetous fungus Magnaporthe oryzae B.C. Couch (synonym Pyricularia oryzae Cavara), was first identified in 1985 in Brazil. Magnaporthe oryzae is composed of a range of morphologically identical but genetically different host-specific pathotypes that are specialized for infecting rice (Oryza pathotype), wheat (Triticum pathotype - MoT), perennial and annual ryegrass (Lolium pathotype), foxtail millet (Setaria pathotype) and many other graminaceous hosts. Isolates from different hosts are genetically distinct, although cross infection occurs to some extent. Wheat blast has become a serious biotic constraint to wheat (Triticum aestivum L) production in parts of the warmer wheat growing areas of the Southern Cone region of South America causing yield losses of 10 to 100% in recent years (Duveiller et al. 2016). Wheat blast was observed for the first time outside of South America during the 2015-16 cropping season in the districts of Kushtia, Meherpur, Chuadanga, Jhe...