Genome-wide association mapping for leaf tip necrosis and pseudo-black chaff in relation to durable rust resistance in wheat

The partial rust resistance genes Lr34 and Sr2 have been used extensively in wheat (Triticum aestivum L.) improvement, as they confer exceptional durability. Interestingly, the resistance of Lr34 is associated with the expression of leaf tip necrosis (LTN) and Sr2 with pseudo-black chaff (PBC). Genome-wide association mapping using CIMMYT’s stem rust resistance screening nursery (SRRSN) wheat lines was done to identify genotyping-bysequencing (GBS) markers linked to LTN and PBC. Phenotyping for these traits was done in Ithaca, New York (fall 2011); Njoro, Kenya (main and off-seasons, 2012), and Wellington, India (winter, 2013). Using the mixed linear model (MLM), 18 GBS markers were significantly associated with LTN. While some markers were linked to loci where the durable leaf rust resistance genes Lr34 (7DS), Lr46 (1BL), and Lr68 (7BL) were mapped, significant associations were also detected with other loci on 2BL, 5B, 3BS, 4BS, and 7BS. Twelve GBS markers linked to the Sr2 locus (3BS) and loci on 2DS, 4AL, and 7DS were significantly associated with PBC. This study provides insight into the complex genetic control of LTN and PBC. Further efforts to validate and study these loci might aid in determining the nature of their association with durable resistance.