Genomic regions associated with leaf rust and end-use quality traits in hexaploid wheat

Abstract

The goal of wheat breeding programs is to develop elite germplasm with attributes desired by producers, millers, bakers, and consumers. Successful wheat cultivars and hybrids are high yielding and possess acceptable end-use quality and effective levels of disease resistance. Advancements in molecular breeding technology have allowed identification of genetic architecture controlling these traits. The following work describes genetic mapping of quantitative trait loci (QTL) associated with end-use quality, leaf rust resistance, and expression of leaf tip necrosis (LTN). In the first study we investigated the haplotypes introgressed from both Ae. tauschii ssp. strangulata and Ae. tauschii ssp. tauschii and their association with end-use quality traits in common bread wheat (Triticum aestivum L.). We developed 351 introgression lines from six hexaploid winter wheat parents and 21 Ae. tauschii accessions and collected phenotypic data on all introgression lines from field trials grown in Kansas between 2018 and 2020. Haplotype-trait associations were detected for lactic acid-sodium dodecyl sulfate solvent retention capacity (LA-SDS SRC) on chromosomes 3DS and 6DS, for protein quality score on chromosomes 1DS, 1DL, and 6DL, and for grain protein concentration on chromosome 6DL. Two introgressed haplotypes were unique to Ae. tauschii and were associated with increases in LA-SDS SRC. These detected haplotypes contain potentially novel alleles for improving end-use quality in common wheat. The second study used a biparental population to identify QTL associated with adult plant resistance (APR) to leaf rust. A doubled haploid (DH) population consisting of 159 lines was developed from a cross between cultivars ’Everest’ and ’WB-Cedar’. The DH population and parents were scored for leaf rust reaction at the seedling stage and adult plant stage using artificial inoculation in the greenhouse, and at Castroville, TX under natural inoculum. Nine QTL were detected on chromosomes 1BL, 2AS, 2AL, 2BS, 3BL, 4DL, 5AL, 7BL, and 7DS. WB-Cedar was confirmed to carry the APR race non-specific gene Lr34 while the slow rusting APR gene Lr68 was shown to be present in Everest. Everest also contributed QLr.ksu-2AL, a potential all-stage resistance (ASR) locus, observed at both seedling and adult plant stages. In a third study, a greenhouse experiment was performed to phenotype LTN traits on the Everest by WB-Cedar DH population. Five QTL associated with LTN were detected on chromosomes 1D, 2A, 4D, 5A, and 7D. The QTL on 2A was previously associated with an all-stage resistance (ASR) gene for leaf rust. Ltn1/Lr34 (7D) contributed the greatest effect on LTN expression, whereas no evidence for any association was detected in the region containing Ltn4/Lr68 (7B). The results of these studies impart important insights into the genetic basis of end-use quality and leaf rust resistance in elite cultivars adapted to the Great Plains. The associated loci described provide a base for further exploration and development of diagnostic markers to facilitate breeding for improved germplasm.