Leaf rust and stripe rust are important foliar diseases of wheat worldwide. Leaf rust and stripe rust resistant introgression lines were developed by induced homoeologous chromosome pairing between wheat chromosome 5D and 5M(g) of Aegilops geniculata (U(g)M(g)). Characterization of rust resistant BC(2)F(5) and BC(3)F(6) homozygous progenies using genomic in situ hybridization with Aegilops comosa (M) DNA as probe identified three different types of introgressions; two cytologically visible and one invisible (termed cryptic alien introgression). All three types of introgression lines showed similar and complete resistance to the most prevalent pathotypes of leaf rust and stripe rust in Kansas (USA) and Punjab (India). Diagnostic polymorphisms between the alien segment and recipient parent were identified using physically mapped RFLP probes. Molecular mapping revealed that cryptic alien introgression conferring resistance to leaf rust and stripe rust comprised less than 5% of the 5DS arm and was designated T5DL.5DS-5M(g)S(0.95). Genetic mapping with an F(2)population of Wichita x T5DL.5DS-5M(g)S(0.95) demonstrated the monogenic and dominant inheritance of resistance to both diseases. Two diagnostic RFLP markers, previously mapped on chromosome arm 5DS, co-segregated with the rust resistance in the F(2) population. The unique map location of the resistant introgression on chromosome T5DL.5DS-5M(g)S(0.95) suggested that the leaf rust and stripe rust resistance genes were new and were designated Lr57 and Yr40. This is the first documentation of a successful transfer and characterization of cryptic alien introgression from Ae. geniculata conferring resistance to both leaf rust and stripe rust in wheat.

Cryo-electron microscopy (cryo-EM) maps usually show heterogeneous distributions of B-factors and electron density occupancies and are typically B-factor sharpened to improve their contrast and interpretability at high-resolutions. However, ‘over-sharpening’ due to the application of a single global B-factor can distort processed maps causing connected densities to appear broken and disconnected. This issue limits the interpretability of cryo-EM maps, i.e. ab initio modelling. In this work, we propose 1) approaches to enhance high-resolution features of cryo-EM maps, while preventing map distortions and 2) methods to obtain local B-factors and electron density occupancy maps. These algorithms have as common link the use of the spiral phase transformation and are called LocSpiral, LocBSharpen, LocBFactor and LocOccupancy. Our results, which include improved maps of recent SARS-CoV-2 structures, show that our methods can improve the interpretability and analysis of obtained reconstructions.

Aegilops tauschii, the D-genome progenitor of Triticum aestivum, encompasses huge diversity for various traits of potential economic importance such as yield, biotic and abiotic stress tolerance, quality and nutrition. In the present study, variation for grain size in Ae. tauschii germplasm was studied and its genetic basis dissected using genome-wide association study (GWAS). Grain length, width, and weight evaluated in 177 Ae. tauschii accessions over 3 years showed near normal distribution with 1.74-, 1.75-, and 2.82-fold variation, respectively. These lines were genetically characterized using genotyping-by-sequencing (GBS) protocol that produced 11,489 single nucleotide polymorphic (SNP) markers. Genetic diversity analysis revealed the presence of two distinct subgroups (designated as lineage 1 and 2) in Ae. tauschii. Based on GBS markers, the genetic similarity was calculated between the accessions and GWAS was conducted using 114 non-redundant accessions and 5,249 SNP markers. A total of 17 SNPs associated with grain size traits distributed over all the seven chromosomes were revealed with 6D, 5D, and 2D harboring most significant marker–trait associations. Some of the chromosomal regions such as 6D_66.4–71.1 cM, 1D_143.5–156.7 cM, and 2D_89.9–92.5 cM had associations with multiple traits. Candidate genes associated with cell division and differentiation were identified for some of the associated SNP markers. Further efforts to validate these loci will help to understand their role in determining grain size and allelic diversity in current germplasm and its effect on grain size upon transfer to bread wheat background.

Stripe rust, caused by Puccinia striiformis West. f.sp. tritici, is one of the most damaging diseases of wheat worldwide. Forty genes for stripe rust resistance have been catalogued so far, but the majority of them are not effective against emerging pathotypes. Triticum monococcum and T. boeoticum have excellent levels of resistance to rusts, but so far, no stripe rust resistance gene has been identified or transferred from these species. A set of 121 RILs generated from a cross involving T. monococcum (acc. pau14087) and T. boeoticum (acc. pau5088) was screened for 3 years against a mixture of pathotypes under field conditions. The parental accessions were susceptible to all the prevalent pathotypes at the seedling stage, but resistant at the adult plant stage. Genetic analysis of the RIL population revealed the presence of two genes for stripe rust resistance, with one gene each being contributed by each of the parental lines. A linkage map with 169 SSR and RFLP loci generated from a set of 93 RILs was used for mapping these resistance genes. Based on phenotypic data for 3 years and the pooled data, two QTLs, one each in T. monococcum acc. pau14087 and T. boeoticum acc. pau5088, were detected for resistance in the RIL population. The QTL in T. monococcum mapped on chromosome 2A in a 3.6 cM interval between Xwmc407 and Xwmc170, whereas the QTL from T. boeoticum mapped on 5A in 8.9 cM interval between Xbarc151 and Xcfd12 and these were designated as QYrtm.pau-2A and QYrtb.pau-5A, respectively. Based on field data for 3 years, their R2 values were 14 and 24%, respectively. T. monococcum acc. pau14087 and three resistant RILs were crossed to hexaploid wheat cvs WL711 and PBW343, using T. durum as a bridging species with the objective of transferring these genes into hexaploid wheat. The B genome of T. durum suppressed resistance in the F1 plants, but with subsequent backcrossing one resistance gene could be transferred from one of the RILs to the hexaploid wheat background. This gene was derived from T. boeoticum acc. pau5088 as indicated by co-introgression of T. boeoticum sequences linked to stripe rust resistance QTL, QYrtb.pau-5A. Homozygous resistant progenies with 40-42 chromosomes have been identified.

Genes transferred to crop plants from wild species are often associated with deleterious traits. Using molecular markers, we detected a cryptic introgression with a leaf rust resistance gene transferred from Aegilops triuncialis L. into common wheat (Triticum aestivum L.). One agronomically desirable rust‐resistant introgression line was selected and advanced to BC3F11 from a cross of hexaploid wheat and A. triuncialis In situ hybridization using A. triuncialis genomic DNA as a probe failed to detect the alien introgression. The translocation line was resistant to the most prevalent races of leaf rust in India and Kansas. Genetic mapping in a segregating F2:3 population showed that the rust resistance was monogenically inherited. Homeologous group 2 restriction fragment length polymorphism markers XksuF11, XksuH16, and Xbg123 showed diagnostically polymorphic alleles between the resistant and susceptible bulks. The alien transfer originated from homeologous chromosome recombination. The A. triuncialis‐specific alleles of XksuH16, XksuF11, Xbg123, and one simple sequence repeat marker Xcfd50 cosegregated with the rust resistance, suggesting that the wheat–A. triuncialis translocation occurred in the distal region of chromosome arm 2BL. This translocation was designated T2BS·2BL‐2tL(0.95). The unique source and map location of the introgression on chromosome 2B indicated that the leaf rust resistance gene is new and was designated Lr58