In the Southern Great Plains, wheat cultivars have been selected for a combination of outstanding yield and drought tolerance as a long-term breeding goal. To understand the underlying genetic mechanisms, this study aimed to dissect the quantitative trait loci (QTL) associated with yield components and kernel traits in two wheat cultivars `TAM 112' and `Duster' under both irrigated and dryland environments. A set of 182 recombined inbred lines (RIL) derived from the cross of TAM 112/Duster were planted in 13 diverse environments for evaluation of 18 yield and kernel related traits. High-density genetic linkage map was constructed using 5,081 single nucleotide polymorphisms (SNPs) from genotyping-by-sequencing (GBS). QTL mapping analysis detected 134 QTL regions on all 21 wheat chromosomes, including 30 pleiotropic QTL regions and 21 consistent QTL regions, with 10 QTL regions in common. Three major pleiotropic QTL on the short arms of chromosomes 2B (57.5 - 61.6 Mbps), 2D (37.1 - 38.7 Mbps), and 7D (66.0 - 69.2 Mbps) colocalized with genes Ppd-B1, Ppd-D1, and FT-D1, respectively. And four consistent QTL associated with kernel length (KLEN), thousand kernel weight (TKW), plot grain yield (YLD), and kernel spike-1 (KPS) (Qklen.tamu.1A.325, Qtkw.tamu.2B.137, Qyld.tamu.2D.3, and Qkps.tamu.6A.113) explained more than 5% of the phenotypic variation. QTL Qklen.tamu.1A.325 is a novel QTL with consistent effects under all tested environments. Marker haplotype analysis indicated the QTL combinations significantly increased yield and kernel traits. QTL and the linked markers identified in this study will facilitate future marker-assisted selection (MAS) for pyramiding the favorable alleles and QTL map-based cloning.

Adult plant resistance (APR) to wheat stem rust has been one of the approaches for resistance breeding since the evolution of the Ug99 race group and other races. This study was conducted to dissect and understand the genetic basis of APR to stem rust in spring wheat line ‘Copio’. A total of 176 recombinant inbred lines (RIL) from the cross of susceptible parent ‘Apav’ with Copio were phenotyped for stem rust resistance in six environments. Composite interval mapping (CIM) using 762 Genotyping-by-Sequencing (GBS) markers, identified 16 genomic regions conferring stem rust resistance. Assays with gene-linked molecular markers revealed that Copio carried known APR genes Sr2 and Lr46/Yr29/Sr58 in addition to the 2NS/2AS translocation that harbors race-specific genes Sr38, Lr37 and Yr17. Three QTL were mapped on chromosomes 2B, two QTL on chromosomes 3A, 3B, and 6A each, and one QTL on each of chromosomes 2A, 1B, 2D, 4B, 5D, 6D and 7A. The QTL QSr.umn.5D is potentially a new resistance gene and contributed to quantitative resistance in Copio. The RILs with allelic combinations of Sr2, Sr38, and Sr58 had 27-39% less stem rust coefficient of infection in all field environments compared to RILs with none of these genes and this gene combination was most effective in the US environments. We conclude that Copio carries several genes that provide both race-specific and non-race-specific resistance to diverse races of stem rust fungus and can be used by breeding programs in pyramiding other effective genes to develop durable resistance in wheat.

After decades of effective wheat stem rust control, due mainly to use of the Sr31 resistance gene in wheat, as of the early 2000s new virulent strains of the stem rust fungus, especially the Ug99 or the TTKSK races, are spreading and overcoming the resistance of commercial varieties worldwide, including the Sr24 and Sr36 resistance genes in Kenya. To address this, researchers are working to identify new resistance sources and to develop and release new high-yielding, resistant and adapted varieties. In this study we evaluated 707 advanced spring wheat lines and varieties for adult plant resistance (APR) to stem rust at the Njoro research station of the Kenya Agricultural & Livestock Research Organization, using a modified Cobb's scale, and for seedling resistance at the Cereal Disease Laboratory (CDL), University of Minnesota, using the 0-4 Stakman et al. (1962) scale. We found 101 lines that showed APR and, through molecular marker analysis, identified 18 lines carrying the stem rust resistance marker allele for the Sr25/Lr19 gene. Of these 18 lines, 11 were resistant to Ug99 at both the seedling and adult stages and 7 were susceptible at the seedling stage, showing infection type (IT) 3 to 4, and moderately susceptible at the adult plant stage. Another 20 lines were resistant at all stages of development, without Sr25/Lr19 marker allele indicated the possibility of carrying other genes for stem rust resistance. We shared the results with national program breeders and scientists in Pakistan to facilitate the use of resistant lines in crossing programs and enhance stem rust resistance in candidate wheat varieties. As a result number of lines resistant to Ug99/ and its variants (TTKSK, TTKST) have been identified and released as commercial varieties, including NR-397 (Pakistan-2013) and NR-356 (NARC-2011).

The spring wheat (Triticum aestivum L.) line 'Copio' has exhibited high level of adult plant resistance (APR) to the leaf rust (Puccinia triticina) pathogen in Mexico during field evaluations. To elucidate the genetic basis of leaf rust resistance in Copio, 176 F 4 -derived F 6 -recombinant inbred lines (RILs) from a cross of wheat lines 'Apav' and Copio were phenotyped in the field for two seasons in the United States and Mexico. A total of 762 genotyping-by-sequencing (GBS) single nucleotide polymorphic (SNP) markers were used to develop linkage maps. Composite interval mapping identified seven quantitative trait loci (QTL), all contributed by Copio. Three QTL on chromosome arms 1BL (QLr.umn-1B), 2AS (QLr.umn-2A), and 3BS (QLr.umn-3B) were consistently expressed across all four environments. The QTL on 1BL represents Lr46, which is a pleiotropic APR gene, while the QTL on 2AS is colocated to the Lr37 gene in the 2NS/2AS translocation fragment. The QTL on 3BS, mapped to the Sr2/Yr30/Lr27 genomic region, is more likely to be a unique locus conferring APR to leaf rust races because all phenotyping environments had Lr27 virulent pathotypes. Moreover, the functionality of Lr27 is complimented by Lr31 on chromosome 4BS, which is lacking in both parents. Marker haplotypes identified seven RILs carrying a combination of resistance alleles at all three loci. This combination reduced leaf rust coefficient of infection up to 52 and 36% in the Mexican and U.S. environments, respectively. This study reports the complex genetic mechanism of APR to leaf rust in Copio and its importance as a potential resistance source for gene pyramiding through recombination breeding.