Spot blotch (SB) disease caused by the hemibiotrophic pathogen Bipolaris sorokiniana inflicting major losses to the wheat grown in warm and highly humid areas of the Indian subcontinent, including Bangladesh, necessitates identification of QTLs stably expressing in Indian subcontinent conditions. Thus, two RIL mapping populations, i.e., WC (WUYA × CIANO T79) and KC (KATH × CIANO T79), were phenotyped at Dinajpur, Bangladesh for three consecutive years (2013-2015) and genotyped on a DArTseq genotyping by sequencing (GBS) platform at CIMMYT, Mexico. In both populations, quantitative inheritance along with transgressive segregation for SB resistance was identified. The identified QTLs were mostly minor and were detected on 10 chromosomes, i.e., 1A, 1B, 2A, 2B, 2D, 4B, 4D, 5A, 5D, and 7B. The phenotypic variation explained by the identified QTLs ranged from 2.3–15.0%, whereby QTLs on 4B (13.7%) and 5D (15.0%) were the largest in effect. The identified QTLs upon stacking showed an additive effect in lowering the SB score in both populations. The probable presence of newly identified Sb4 and durable resistance gene Lr46 in the identified QTL regions indicates the importance of these genes in breeding for SB resistance in Bangladesh and the whole of South Asia.

Wheat blast (WB) disease, since its first identification in Bangladesh in 2016, is now an established serious threat to wheat production in South Asia. There is a need for sound knowledge about resistance sources and associated genomic regions to assist breeding programs. Hence, a panel of genotypes from India and Bangladesh was evaluated for wheat blast resistance and a genome-wide association study (GWAS) was performed. Disease evaluation was done during five crop seasons—at precision phenotyping platform (PPPs) for wheat blast disease at Jashore (2018–19), Quirusillas (2018–19 and 2019–20) and Okinawa (2019 and 2020). Single nucleotide polymorphisms (SNP) across the genome were obtained using DArTseq genotyping-by-sequencing platform, and in total 5713 filtered markers were used. GWAS revealed 40 significant markers associated with WB resistance, of which 33 (82.5%) were in the 2NS/2AS chromosome segment and one each on seven chromosomes (3B, 3D, 4A, 5A, 5D, 6A and 6B). The 2NS markers contributed significantly in most of the environments, explaining an average of 33.4% of the phenotypic variation. Overall, 22.4% of the germplasm carried 2NS/2AS segment. So far, 2NS translocation is the only effective WB resistance source being used in the breeding programs of South Asia. Nevertheless, the identification of non-2NS/2AS genomic regions for WB resistance provides a hope to broaden and diversify resistance for this disease in years to come.

While the three rusts are the most predominant wheat diseases in the global scale, various other diseases dominate in different geographical regions. In this chapter, some major non-rust diseases of wheat with global and/or regional economic importance are addressed, including three spike diseases (Fusarium head blight, wheat blast, and Karnal bunt), four leaf spotting diseases (tan spot, Septoria nodorum blotch, spot blotch, and Septoria tritici blotch), and several root diseases.

Identifying gene interactions and markers associated with physiological traits, especially at later stages of grain filling, can help develop effective breeding methodology in wheat crop. Six generations (P1, P2, F1, F2, BC1P1 and BC1P2) of four different spring wheat crosses (drought-responsive x drought susceptible) and F3 generation of a single cross, i.e., MACS6272 x UP2828 were phenotyped and genotyped to decipher gene action and associated markers. Ample variation in canopy temperature depression (CTD - 2.6 - 5.6°C), chlorophyll content by SPAD (39.6 - 51.3), relative water content (RWC - 51.5 - 75.4 %), grain filling period (GFP - 61.1 - 80.1 days), 100 seed weight (3.7 - 5.5 grams), harvest index (HI - 25.8 - 46.2 %), biological yield (BY - 35.5 - 89.8 grams) and grain yield (GY - 13.4 - 36.5 grams) per plant were observed in six generations. GY positively correlated with CTD, SPAD, 100SW, BY and HI (0.08* - 0.85**). BY had the maximum direct (0.82) and indirect effect via other traits on GY. Significant non-additive epistatic interactions (j & l) and duplicate gene action were found for most traits except GFP and 100SW. Seven different SSR markers associated with CTD, SPAD, NDVI, RWC, 100SW, and explained phenotypic variation (PVE) ranging from 10.1% to 18.4%, with marker Xcfd35 explaining highest PVE for RWC. The identified candidate genes (in silico) belonged to transmembrane proteins (Xcfd32, Xcfd50), nucleic acid binding domains (Xbarc124, Xgwm484) and having enzymatic activity (Xcfd35, Xwmc47, Xwmc728) important for abiotic stress tolerance. Complex inheritance deciphered by six generations indicated delaying the selection to later stages of segregation so that useful transgressive segregants can be selected for improving grain yields in wheat.