A compensating, recombined Lr59 translocation with greatly reduced alien chromatin was identified. Microsatellite locus Xdupw217 occurs within the remaining segment and can be used as a co-dominant marker for Lr59. In earlier studies, leaf rust (caused by Puccinia triticina Eriks.) resistance gene Lr59 was transferred from Aegilops peregrina (Hackel) Maire et Weiler to chromosome arm 1AL of common wheat (Triticum aestivum L.). The resistance gene was then genetically mapped on the translocated chromosome segment following homoeologous pairing induction. Eight recombinants that retained the least alien chromatin apparently resulted from crossover within a terminal region of the translocation that was structurally different from 1AL. These recombinants could not be differentiated by size, and it was not clear whether they were compensating in nature. The present study determined that the distal part of the original translocation has group 6 chromosome homoeology and a 6BS telomere (with the constitution of the full translocation chromosome being 1AS·1L(P)·6S(P) ·6BS). During the allosyndetic pairing induction experiment to map and shorten the full size translocation, a low frequency of quadrivalents involving 1A, the 1A translocation, and two 6B chromosomes was likely formed. Crossover within such quadrivalents apparently produced comparatively small compensating alien chromatin inserts within the 6BS satellite region on chromosome 6B of seven of the eight recombinants. It appears that the Gli-B2 storage protein locus on 6BS has not been affected by the recombination events, and the translocations are therefore not expected to affect baking quality. Simple sequence repeat marker results showed that Lr59-151 is the shortest recombinant, and it will therefore be used in breeding. Marker DUPW217 detects a homoeo-allele within the remaining alien chromatin that can be used for marker-assisted selection of Lr59.

Assembly of a training population (TP) is an important component of effective genomic selection-based breeding programs. In this study, we examined the power of diverse germplasm assembled from two cassava (Manihot esculenta Crantz) breeding programs in Tanzania at different breeding stages to predict traits and discover quantitative trait loci (QTL). This is the first genomic selection and genome-wide association study (GWAS) on Tanzanian cassava data. We detected QTL associated with cassava mosaic disease (CMD) resistance on chromosomes 12 and 16; QTL conferring resistance to cassava brown streak disease (CBSD) on chromosomes 9 and 11; and QTL on chromosomes 2, 3, 8, and 10 associated with resistance to CBSD for root necrosis. We detected a QTL on chromosome 4 and two QTL on chromosome 12 conferring dual resistance to CMD and CBSD. The use of clones in the same stage to construct TPs provided higher trait prediction accuracy than TPs with a mixture of clones from multiple breeding stages. Moreover, clones in the early Abbreviations: AYTKIB, advanced yield trial at Kibaha; BLUPs, best linear unbiased predictors; CBSD, cassava brown streak disease; CBSDRS, cassava brown streak disease root necrosis severity;

In an attempt to transfer the Lr56/Yr38 resistance loci from Aegilops sharonensis to wheat, a 6A‐6Ssh chromosome translocation was produced. It involves essentially the entire chromosome 6Ssh with a small terminal segment of 6AL. Induced homoeologous recombination of the translocated chromosome with 6A produced numerous recombinants including three recombined chromosomes carrying Lr56 that could not be precisely mapped for lack of suitable markers. This study aimed to determine the chromosomal locations of the translocation breakpoints in these three recombinants using various DNA markers as well as physical and genetic mapping. The three recombinants Lr56‐39, ‐157 and ‐175 carry small segments of Ae. sharonensis chromatin distally to the Xgpw4329 and IWA5416 loci near the 6AS telomere. The Ae. sharonensis chromatin that remains in each line includes a homoeolocus of the wheat marker locus Xdupw217 (on 6BS) and its characteristic amplification product can be used as a dominant marker for the presence of Lr56. Of the three recombined chromosomes, Lr56‐157 retained the least alien chromatin and appears to be the best candidate for use in wheat breeding.

Durumwheat [Triticum turgidum L. ssp. durum (Desf.)] production is constrained by fungal diseases including stripe rust caused by Puccinia striiformis Westend. f. sp. tritici Erikss. (Pst). Continuous mining of germplasm for the discovery and deployment of stripe rust resistance (Yr) genes is needed to counter the impact of this disease. In this study, we evaluated a worldwide collection of 432 durum wheat accessions to seven U.S. Pst races that carry diverse virulence and avirulence combinations on wheat Yr genes. We found that 47–82% of the durum wheat accessions were susceptible to each of the tested Pst races. A total of 32 accessions were resistant to all seven races. Genome‐wide association studies (GWAS) using over 97,000 single‐nucleotide polymorphism markers generated from genotyping‐by‐sequencing of 364 accessions identified 56 quantitative trait loci (QTL) associated with all‐stage stripe rust resistance located on all 14 durum wheat chromosomes. Six of these QTL were associated with resistance to 2–4 Pst races, and none were associated with resistance to all seven races. The remaining 50 QTL were race specific. Eighteen of the 56 identified QTL had relatively large effects against at least one of the races. A map‐based comparison of the discovered QTL in this study with previously published Yr genes and QTL showed that 29 were previously identified, whereas the remaining 27 QTL appeared to be novel. This study reports effective sources of stripe rust resistance to contemporary races in the United States and shows that this durum wheat collection is abundant in novel resistance loci that can be transferred into adapted durum cultivars.

The Lr19 translocation continues to provide broad resistance to Puccinia triticina in many parts of the world and can be particularly useful in resistance gene pyramids. Previously, an associated gene for yellow endosperm pigmentation precluded its use in many countries, and as a result, allosyndetic recombinants and mutants lacking the pigmentation genes have been developed. Such a primary white endosperm recombinant (Lr19‐149) and four secondary recombinants (Lr19‐149–252, −299, −462, and −478) were obtained in earlier studies. This study characterized the translocations making use of fluorescence genomic in situ hybridization (FGISH), simple sequence repeat (SSR), sequence tagged site (STS), and single nucleotide polymorphism (SNP) markers. The recombined segments were shown to be intercalary inserts of different size and were mapped to the most distal 7BL deletion bin. In addition to a previously reported duplication that involves the Wsp‐1 locus, primary recombinant −149 also has a deletion of the PSY‐1 containing region. These apparently small aberrations have been retained in three of the secondary recombinants that resulted from single, proximal crossovers. The fourth secondary recombinant (−478) resulted from a distal crossover that apparently restored a normal wheat telomeric region with single copies of the Wsp‐B1 and PSY‐B1 loci and appears to be the most useful.

Cassava has been found to carry high levels of recessive deleterious mutations and it is known to suffer from inbreeding depression. Breeders therefore consider specific approaches to decrease cassava’s genetic load. Using self fertilization to unmask deleterious recessive alleles and therefore accelerate their purging is one possibility. Before implementation of this approach we sought to understand better its consequences through simulation. Founder populations with high directional dominance were simulated using a natural selection forward simulator. The founder population was then subjected to five generations of genomic selection in schemes that did or did not include a generation of phenotypic selection on selfed progeny. We found that genomic selection was less effective under the directional dominance model than under the additive models that have commonly been used in simulations. While selection did increase favorable allele frequencies, increased inbreeding during selection caused decreased gain in genotypic values under the directional dominance. While purging selection on selfed individuals was effective in the first breeding cycle, it was not effective in later cycles, an effect we attributed to the fact that the generation of selfing decreased the relatedness of the genomic prediction training population from selection candidates. That decreased relatedness caused genomic prediction accuracy to be lower in schemes incorporating selfing. We found that selection on individuals partially inbred by one generation of selfing did increase mean genetic value of the partially inbred population, but that this gain was accompanied by a relatively small increase in favorable allele frequencies such that improvement in the outbred population was lower than might have been intuited.

Development of durum wheat (Triticum turgidum L.) × Thinopyrum hybrids as a new salt‐tolerant crop was first attempted in England. These hybrids (here called b‐tritipyrums) were based on the diploid grass Th. bessarabicum (Savul. & Rayss) Á Löve . Although salt tolerant, b‐tritipyrums (AABBJbJb) had poor agrotype, brittle rachis, and poor threshability, which impeded their continued development. In this study, we have developed alternative hexaploid hybrids (d‐tritipyrums) containing a single, rearranged J genome from Th. distichum (Thunb.) Á Löve (a segmental autotetraploid; J1dJ1dJ2dJ2d). Four first generation d‐tritipyrums with genomes AABBJJ were selected from segregating generations of crosses among primary and secondary durum wheat × Th. distichum amphiploids. The J genome in each appears to consist of seven rearranged Thinopyrum chromosomes, with each individual chromosome having been derived from either of the J1d or J2d genomes and altered through recombination with its homoeologue. A lineage with seedling salt tolerance, nonbrittle rachis, and moderately good threshability was then crossed with common wheat (Triticum aestivum L.) × Th. distichum secondary amphiploids to broaden J‐genome variability. Despite close homoeology, the J1d and J2d genomes appear to be highly diverse and second‐generation hexaploids and near‐hexaploids exhibited a rich diversity of Thinopyrum‐derived traits. Continued breeding for productivity in marginal soils can further the development of d‐tritipyrums to constitute an intermediate, well‐adapted germplasm. It will then be possible to compare it more effectively to wheat for the analysis and transfer of key physiological trait genes from the J genomes.

Leaf rust resistance gene Lr62 was transferred from Aegilops neglecta Req. ex Bertol. to chromosome 6A of common wheat (Triticum aestivum L.) in 2008. After homoeologous chromosome pairing induction, smaller translocations that retained Lr62 were derived from it. This study compared the original translocation and the four apparently shortest recombinants to determine which would be the best suited for breeding. The translocations were analyzed using chromosome 6A and 6B simple sequence repeat (SSR) markers and genomic in situ hybridization. Recombined translocations 133, 135, and 136 were found to occur at the 6AS telomere. In addition to the wheat Xdupw217aest SSR locus on chromosome arm 6BS, the three recombinants also expressed an Ae. neglecta–derived homoeo‐locus (Xdupw217negl) that could be used to detect the presence of the Ae. neglecta chromosomal segment. The Lr62‐129 translocation was relocated to 6BS in an allosyndetic recombination event that replaced the Xdupw217aest locus with Xdupw217negl. Lr62‐129 retained the least Ae. neglecta chromatin and is therefore recommended for use in wheat breeding.