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Thinopyrum distichum (Thunb.) Á. Löve (2n = 4x = 28; J1dJ1dJ2dJ2d) inhabits harsh, dry saline coastal dunes. Its adaptive genes can be of value to cultivated cereals; therefore, single‐chromosome additions were previously developed in hexaploid triticale (×Triticosecale Wittm. ex A. Camus) and common wheat (Triticum aestivum L.); however, their homoeology to triticale and wheat chromosomes remained largely unknown. Here we used genotyping‐by‐sequencing (GBS) to supplement conventional markers and determine the synteny of the Th. distichum addition chromosomes. Twenty‐seven triticale lines with single Th. distichum addition chromosomes were analyzed. Genotyping‐by‐sequencing yielded 2.75 million unique sequences that included 134,506 Th. distichum‐specific tags absent in the wheat, durum wheat [Triticum turgidum L. subsp. Durum (Desf.) van Slageren], ×Triticosecale spp., and rye (Secale cereale L.) controls. The Th. distichum‐specific tags were then sorted into 125,262 informative, single‐pair tags (from one homoeologous group) and 9,244 uninformative, multi‐group tags associated with more than one homoeologous group. Presence–absence patterns produced by the single‐pair tags suggested the presence of 11 different Th. distichum addition chromosomes whose associated sequence tags were then aligned to the Th. elongatum (Host) D. R. Dewey and Chinese Spring (CS) genomic databases to reveal their homoeology. Five prominent translocations were detected among the 11 Th. distichum addition chromosomes and three chromosomes appeared to be extensively restructured. The extra chromosomes in 10 additions to common wheat represented five different Th. distichum chromosomes that were also represented in the triticale set. The 11 distinct Th. distichum addition chromosomes constitute a useful genetic resource for continued dissection of the Th. distichum genomes. [ABSTRACT FROM AUTHOR]

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 homoeolocus (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. [ABSTRACT FROM AUTHOR]

Durum wheat has the tendency of accumulating more cadmium (Cd), a biotoxic heavy metal, in seeds than other commonly grown cereals, thus posing a serious food safety/public health concern. This could have serious negative impact on the national pasta industry and the international export market of durum wheat. The phenotyping for selecting low Cd lines is expensive and time consuming. The use of markers could be a more sustainable approach for selecting lines with low Cd levels. Here, a RIL population developed from a cross between Grenora (high Cd) × Haurani (low Cd) and two association mapping panels consisting of advanced breeding lines from the North Dakota durum wheat breeding program were used to identify QTL and associated markers for Cd. A major QTL, with Haurani contributing low Cd uptake allele and explaining 54.3 % phenotypic variation, was detected on chromosome 5BL. Association mapping using 2010 collection validated the results of linkage mapping and identified major QTL on 5BL. The 2009 collection, showed the presence of a major QTL on chromosome 2B. The SNP marker associated with major QTL on 5BL was converted to user friendly KASPar assay. The major QTL and associated KASPar marker were further validated using another RIL population developed from a cross of Strongfield (low Cd) and Alkabo (high Cd). The development of suitable marker assay, associated with major Cd uptake QTL, would help the selection for low Cd accumulating lines, minimizing the costly phenotypic evaluation for this important trait. [ABSTRACT FROM AUTHOR]

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 6 AL. 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 6 AS telomere. The Ae. sharonensis chromatin that remains in each line includes a homoeolocus of the wheat marker locus Xdupw217 (on 6 BS) 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. [ABSTRACT FROM AUTHOR]

Interspecific hybridization can be considered an accelerator of evolution, otherwise a slow process, solely dependent on mutation and recombination. Upon interspecific hybridization, several novel interactions between nuclear and cytoplasmic genomes emerge which provide additional sources of diversity. The magnitude and essence of intergenomic interactions between nuclear and cytoplasmic genomes remain unknown due to the direction of many crosses. This study was conducted to address the role of nuclear-cytoplasmic interactions as a source of variation upon hybridization. Wheat ( Triticum aestivum) alloplasmic lines carrying the cytoplasm of Aegilops mutica along with an integrated approach utilizing comparative quantitative trait locus (QTL) and epigenome analysis were used to dissect this interaction. The results indicate that cytoplasmic genomes can modify the magnitude of QTL controlling certain physiological traits such as dry matter weight. Furthermore, methylation profiling analysis detected eight polymorphic regions affected by the cytoplasm type. In general, these results indicate that novel nuclear-cytoplasmic interactions can potentially trigger an epigenetic modification cascade in nuclear genes which eventually change the genetic network controlling physiological traits. These modified genetic networks can serve as new sources of variation to accelerate the evolutionary process. Furthermore, this variation can synthetically be produced by breeders in their programs to develop epigenomic-segregating lines. [ABSTRACT FROM AUTHOR]

Key message: 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. Abstract: 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·6S ·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. [ABSTRACT FROM AUTHOR]

A population of 186 recombinant inbred lines of bread wheat (Superhead#2/Roshan) was evaluated to identify quantitative trait loci (QTL) for yield and yield components under normal (2 ds m) and salt-stress (10-12 ds m) conditions. A genetic map was constructed with 451 markers, including, 23 simple sequences repeats (SSRs) and 428 diversity arrays technology markers (DArTs). The main-effect QTL were identified by composite interval mapping (CIM) analysis using QTL Cartographer v2.5 and Qgene v4.3.2 and a mixed-model-based composite interval mapping (MCIM) method using QTLNetwork v2.1. A total of 98 significant QTL were detected at two testing locations on 20 chromosomes. Of these, only 40 QTL were detected by at least two of these software programs. A total of 24 QTL on ten chromosomes were identified for grain yield, most of which had a minor effect, contributing less than 10 % of the total phenotypic variation. Two grain-yield QTL intervals were detected on 1A and 3B, which contributed 11.02 % and 10.3 % to the total phenotypic variation, respectively. Roshan alleles were associated with an increase in grain yield under stress conditions on 1A, 2B, 3B, 6B, 1D, 2D. Among the 20 chromosomes, chromosome 3B with 27 QTL and two distinctive cluster regions was the most important. SSR markers gwm282, gwm247, gwm566, and gwm33 were tightly linked to QTL for the same or different traits under normal, stress or both conditions, and accounted for about 17 %, 43 %, 43 % and 20 % of the total phenotypic variation, respectively. These markers are suitable for marker-assisted selection to improve grain yield under normal and salt-stress conditions. [ABSTRACT FROM AUTHOR]

For the first time, this study has described the characterization of 25 novel polymorphic microsatellite loci from a repeat-enriched genomic library of V. arctostaphylos using a modified FIASCO method. Polymorphism of each locus was assessed in 64 individuals of the Vaccinium. The average allele number of the microsatellites, observed (H) and expected (H) heterozygosities were 5.88, 0.85 and 0.67 per locus, respectively. The polymorphic information content (PIC) value and inbreeding coefficient (F) ranged from 0.26 to 0.87 and −0.72 to 0.03, respectively. Ten of the twenty-five loci showed significant departures from Hardy-Weinberg equilibrium. These microsatellite loci could be useful to study genetic diversity and population structure of V.arctostaphylos. [ABSTRACT FROM AUTHOR]

Pomegranate (Punica granatum L.) has been cultivated from ancient times for its economic, ornamental and medicinal properties globally. Here, we report the isolation and characterization of 12 polymorphic microsatellite markers from a repeat-enriched genomic library of Punica granatum L. The genetic diversity of these loci was assessed in 60 genotypes of Punica granatum L. All loci were variable: the number of polymorphic alleles per locus ranged from two to five (average 2.9). The observed and expected heterozygosities ranged from 0.15 to 0.87 and 0.29 to 0.65, respectively. The polymorphic information content ranged from 0.26 to 0.61 (average: 0.43). To the best of our knowledge, this is the first time that polymorphic microsatellite markers have been reported for P. granatum L. These new markers should allow studies of the population structure and genetic diversity of pomegranate to be performed in the future. [ABSTRACT FROM AUTHOR]

Iran is one of the two major centres of Pistacia diversity and the main producer of pistachios in the world. About 282 Iranian pistachio genotypes (Pistacia spp.), together with 22 foreign cultivars (P. vera), were genotyped using 10 simple sequence repeat (SSR) markers to analyse the genetic diversity and relationships among Pistacia species and cultivars. The results revealed that the genetic diversity within P. atlantica subsp. kurdica was considerably lower than in P. vera or P. khinjuk. Principal coordinate analysis revealed a clear separation between the different Pistacia spices, as well as between the Iranian and foreign cultivars. AMOVA analysis showed that the variation between the species, between different populations, and within populations accounted for 41, 9, and 50% of the total variation, respectively. The results demonstrated that the study of genetic diversity and relationships among Pistacia species and cultivars using SSR markers provides important information for the collection and conservation of pistachio germplasm. In addition, the Iranian cultivars had a broader genetic background than that of the foreign cultivars. Thus, they are very important for genetic conservation and the planning of future breeding programmes. We also determined the different levels of genetic diversity that exist between and within the species and populations and showed that gene flow occurs between the Iranian cultivars and wild-type P. vera populations. The study provides practical information that policy-makers and scientists can apply to the conservation and sustainable use of all the species studied. [ABSTRACT FROM AUTHOR]