Islands and streams: clusters and gene flow in wild barley populations from the Levant

The domestication of plants frequently results in a high level of genetic differentiation between domesticated plants and their wild progenitors. This process is counteracted by gene flow between wild and domesticated plants because they are usually able to inter‐mate and to exchange genes. We investigated the extent of gene flow between wild barley Hordeum spontaneum and cultivated barley Hordeum vulgare, and its effect on population structure in wild barley by analysing a collection of 896 wild barley accessions (Barley1K) from Israel and all available Israeli H. vulgare accessions from the Israeli gene bank. We compared the performance of simple sequence repeats (SSR) and single nucleotide polymorphisms (SNP) marker data genotyped over a core collection in estimating population parameters. Estimates of gene flow rates with SSR markers indicated a high level of introgression from cultivated barley into wild barley. After removing accessions from the wild barley sample that were recently admixed with cultivated barley, the inference of population structure improved significantly. Both SSR and SNP markers showed that the genetic population structure of wild barley in Israel corresponds to the three major ecogeographic regions: the coast, the Mediterranean north and the deserts in the Jordan valley and the South. Gene flow rates were estimated to be higher from north to south than in the opposite direction. As has been observed in other crop species, there is a significant exchange of alleles between the wild species and domesticated varieties that needs to be accounted for in the population genetic analysis of domestication.     

Hordein variation in the genus Hordeum as recognized by monoclonal antibodies.

The composition of the major storage protein, hordein, in wild barley species has been studied by using gel electrophoresis, Coomassie staining, and immunoblot assays. We have shown earlier that it is possible to obtain cross-reaction outside the cultivated barley, with monoclonal antibodies raised against hordeins from the barley cultivar Bomi. These antibodies have now been used to investigate the hordein composition in all species of the Hordeum genus. The results showed that polypeptides similar to the two major hordein groups of cultivated barley, the B- and C-hordeins, are produced in all wild Hordeum species, and that there are both similarities and differences between the two hordein groups. The similarities indicate a common evolutionary origin, while the distinction between B- and C-hordeins in the entire genus clearly shows that the divergence of their coding genes preceded the divergence of the Hordeum species. The presence of the same antigenic site in two different species indicates that they are evolutionarily related. Among the wild species, two rarely occurring sites were exclusively found in H. vulgare ssp. spontaneum and H. bulbosum, which confirms that they are the cultivated barley's closest relatives. Some of the antibodies also gave an extensive reaction pattern with H. murinum, which suggests a fairly close relationship to H. vulgare, though not as close as between H. vulgare and H. bulbosum.     

Invasion of <Emphasis Type="Italic">Rhynchosporium commune</Emphasis> onto wild barley in the Middle East

Rhynchosporium commune was recently introduced into the Middle East, presumably with the cultivated host barley (Hordeum vulgare). Middle Eastern populations of R. commune on cultivated barley and wild barley (H. spontaneum) were genetically undifferentiated and shared a high proportion of multilocus haplotypes. This suggests that there has been little selection for host specialization on H. spontaneum, a host population often used as a source of resistance genes introduced into its domesticated counterpart, H. vulgare. Low levels of pathogen genetic diversity on H. vulgare as well as on H. spontaneum, indicate that the pathogen was introduced recently into the Middle East, perhaps through immigration on infected cultivated barley seeds, and then invaded the wild barley population. Although it has not been documented, the introduction of the pathogen into the Middle East may have a negative influence on the biodiversity of native Hordeum species.     

Genotype peculiarities of crossability of cultivated sunflower with wild species and the use of embryo culture in interspecific hybridization

Peculiarities of the genotype effect of cultivated and wild sunflower species on crossability indices and in vitro hybrid embryonic development have been investigated. It was shown that selection of initial material can considerably influence seed-setting and in vitro embryonic development in the cross group of cultivated sunflower with annual and perennial wild species. The range of plant hybrids obtained through somatic embryogenesis and induction of adventitious shoots was higher in comparison with direct growth of embryos in in vitro culture.     

Reduced metaphase I associations between the short arms of homoeologous chromosomes in a <Emphasis Type="Italic">Hordeum vulgare </Emphasis>L. × <Emphasis Type="Italic">H. bulbosum</Emphasis> L. diploid hybrid influences the frequency of recombinant progeny

Hordeum vulgare (cultivated barley) × H. bulbosum (bulbous barley grass) hybrids have been used to obtain disease-resistant recombinant lines (RLs). The RLs contain chromatin transferred from the wild species mostly onto the long arms of recipient barley chromosomes. To determine whether differences in meiotic metaphase I (MI) associations between the long and short arms of homoeologous chromosomes can account for the preponderance of introgressions on the long arms, we carried out fluorescent in situ hybridisation on MI chromosome preparations obtained from pollen mother cells of a diploid interspecific hybrid. By using various probes, we established that MI associations between the long arms occurred more frequently than between the short arms for the five chromosomes tested.     

High capacity of plant regeneration from callus of interspecific hybrids with cultivated barley (Hordeum vulgare L.)

Callus was induced from hybrids between cultivated barley (Hordeum vulgare L. ssp. vulgare) and ten species of wild barley (Hordeum L.) as well as from one backcross line ((H. lechleri x H. vulgare) x H. vulgare). Successful callus induction and regeneration of plants were achieved from explants of young spikes on the barley medium J 25–8. The capacity for plant regeneration was dependent on the wild parental species. In particular, combinations with four related wild species, viz. H. jubatum, H. roshevitzii, H. lechleri, and H. procerum, regenerated high numbers of plants from calli.     

Accessing and exploiting genes of breeding value of distant relatives of crop Brassicas

The Brassicas are an important group of crops in India yielding edible oils and many vegetables. For improving cultivated Brassicas, the wild relatives are of considerable value. The Brassica group of seed oil and vegetables comprises six cultivated species, out of which three are diploids and three are digenomic tetraploids. Brassica juncea is the major seed oil crop in India which can be improved for several traits by incorporating genes from its distant relatives. The early work in India relating to genome manipulation consisted of synthesis of B. juncea by crossing B. campestris with B. nigra, experimental resynthesis of Brassica species and non-homologous pairing and genetic exchange at the interspecific level. The alloploid species B. napus and B. carinata have not been successful in India due to agrometereological limitations. However, synthetic forms of B. napus have been produced which have a desirable maturity period with good yield potential. Also, through non-homologous pairing, pod shatter resistant B. napus has been obtained, B. napus ordinarily suffers from pod shattering. Similarly, synthetic forms of B. carinata have been derived from reciprocal crosses between morphotypes of B. oleracea and B. nigra and also through protoplast fusion of B. nigra with B. oleracea. Molecular analysis has revealed that one of the somatic hybrids had a novel cytoplasmic combination which carried B. nigra mitochondrial and B. oleracea chloroplast genomes. A range of wild and weedy species related to crop Brassicas possess extensive genetic variability. Work for utilizing this variability included hybridization between wild and crop species, analysis of chromosome pairing and induction of alloploidy. Among Brassicas of interest to India, protoplast culture and regeneration has been successful in the case of B. oleracea, B. juncea, B. nigra and B. carinata (cultivated species) and Eruca sativa and Diplotaxis muralis (related wild species). Polyethylene glycol mediated protoplast fusion has been the most commonly used method in India for producing somatic hybrids involving Brassicas. The eight somatic hybrids produced and studied showed that in the majority of cases the fusions led to symmetric hybrids combining the complete genomes of the donor species. For developing suitable male sterile lines, B. juncea, B. campestris and B. napus nuclei have been combined with the cytoplasm of six wild species and stable male steriles have been developed. Protoplast fusion methodology has been used extensively for improving these CMS by manipulating cytoplasmic organelles, including production of new combinations of cp and mt.     

Identification of wild and cultivated Hordeum species using two-primer RAPD fragments

Random amplified polymorphic DNAs (RAPD) analysis has been adapted to assess the degree of RAPD polymorphism within the genus Hordeum to determine if this approach can distinguish wild and cultivated species. Nineteen wild and seven cultivated accessions were evaluated using 4 random 10-mer primers. The potential of the RAPD assay was further increased by combining two primers in a single polymerase chain reaction (PCR). RAPD fragments generated by two pairs of arbitrary 10-mer primers discriminated six wild species and one cultivated species by banding profiles. The size of the amplified DNA fragments ranged from 150 to 2300 base pairs. 33 %percent of the fragments were common to both wild and cultivated species; 67% were specific to either wild or cultivated species. The average difference in fragments was less within the species than among the species. By comparing RAPD fingerprints of wild and cultivated barley, markers were identified among the set of amplified DNA fragments which could be used to distinguish wild and cultivated Hordeum species. This revised version was published online in July 2006 with corrections to the Cover Date.     

Growth and fitness components of wild x cultivated Sorghum bicolor (Poaceae) hybrids in Nebraska

? Premise of the study: Gene flow from crops to wild relatives has received considerable attention since the advent of genetically modified crops. Numerous researchers have found wild-crop hybrids to be nearly as fit as their wild parents, which suggests that crop genes may persist in wild populations. Components of the ecological fitness of cultivated sorghum, its wild relative, shattercane, and their hybrids have not been studied. ? Methods: To assess the potential for gene introgression into shattercane, we crossed cultivated sorghum to a single inbred shattercane line to produce F(1) hybrids and measured growth and several components of ecological fitness in relation to both parents in Nebraska, USA. ? Key results: Germination of F(1) seeds was similar to that of its shattercane parent except at high temperatures, where it was as sensitive as the sorghum parent. The F(1) grew taller and produced more biomass than either parent, but the F(1) leaf area index was intermediate. Fecundity of the F(1) plant was similar to that of shattercane and much greater than that of cultivated sorghum. ? Conclusions: Considering all data, the ecological fitness of shattercane × cultivated sorghum F(1) hybrids may be equivalent to the wild shattercane parent, which suggests that crop genes that are either neutral or beneficial to shattercane would persist in populations within agroecosystems.     

Domestication, genomics and the future for banana

BACKGROUND: Cultivated bananas and plantains are giant herbaceous plants within the genus Musa. They are both sterile and parthenocarpic so the fruit develops without seed. The cultivated hybrids and species are mostly triploid (2n = 3x = 33; a few are diploid or tetraploid), and most have been propagated from mutants found in the wild. With a production of 100 million tons annually, banana is a staple food across the Asian, African and American tropics, with the 15 % that is exported being important to many economies. SCOPE: There are well over a thousand domesticated Musa cultivars and their genetic diversity is high, indicating multiple origins from different wild hybrids between two principle ancestral species. However, the difficulty of genetics and sterility of the crop has meant that the development of new varieties through hybridization, mutation or transformation was not very successful in the 20th century. Knowledge of structural and functional genomics and genes, reproductive physiology, cytogenetics, and comparative genomics with rice, Arabidopsis and other model species has increased our understanding of Musa and its diversity enormously. CONCLUSIONS: There are major challenges to banana production from virulent diseases, abiotic stresses and new demands for sustainability, quality, transport and yield. Within the genepool of cultivars and wild species there are genetic resistances to many stresses. Genomic approaches are now rapidly advancing in Musa and have the prospect of helping enable banana to maintain and increase its importance as a staple food and cash crop through integration of genetical, evolutionary and structural data, allowing targeted breeding, transformation and efficient use of Musa biodiversity in the future.     

Karyotype analysis of regenerated plants from callus cultures of interspecific hybrids of cultivated barley (Hordeum vulgare L.)

Summary The karyotype of 82 regenerated plants from callus cultures of interspecific hybrids between cultivated barley (Hordeum vulgare L.) and seven polyploid wild barley species was examined by C-banding or Feulgen staining. The karyotypic changes observed in 46 plants included aneuploidy, double haploidy, amphidiploidy, deletions, inversions, extra C-bands, and extra euchromatic segments. Apparently, chromosome 5, 6, and 7 of H. vulgare were more frequently exposed to elimination or structural change than the other chromosomes of this species. Irradiation of calli seemed to enhance the occurrence of karyotypic variants.     

Comparative assessment of genetic diversity in wild and primitive cultivated barley in a center of diversity

Wild barley (Hordeum spontaneum K.) and indigenous primitive varieties of cultivated barley (Hordeum vulgare L.), collected from 43 locations in four eastern Mediterranean countries, Jordan, Syria, Turkey and Greece, were electrophoretically assayed for genetic diversity at 16 isozyme loci. Contrary to a common impression, cultivated barley populations were found to maintain a level of diversity similar to that in its wild progenitor species. Apportionment of overall diversity in the region showed that in cultivated barley within-populations diversity was of higher magnitude than the between-populations component. Neighboring populations of wild and cultivated barleys showed high degree of genetic identity. Groups of 3 or 4 isozyme loci were analyzed to detect associations among loci. Multilocus associations of varying order were detected for all three groups chosen for the analysis. Some of the association terms differed between the two species in the region. Although there was no clear evidence for decrease in diversity attributable to the domestication of barley in the region, there was an indication of different multilocus organizations in the two closely related species.     

基于AFLP标记的中国西藏近缘野生大麦遗传多样性分析

选取7对引物组合, 构建了36份西藏近缘野生大麦和4份栽培大麦的AFLP指纹图谱, 共获得清晰可辨的条带227条, 其中多态性带194条, 占85.46％, 从DNA分子水平显示出所试材料遗传多样性较为丰富。计算得各样品间的遗传距离(欧氏距离)介于2.646~10.488之间, 应用离差平方和法对供试材料的AFLP数据结果进行聚类, 建立了40份大麦材料的AFLP树状图, 聚类结果将40份材料分为5类, 进一步揭示出供试材料间遗传背景的相似性和复杂性。结合Nei’s遗传一致性分析结果, 发现近缘六棱野生大麦较之近缘二棱野生与栽培大麦的亲缘关系更近, 支持栽培大麦是从野生二棱大麦起源, 而野生六棱大麦是进化过程中的过渡类型的大麦系统发生观点。     

Seminal roots of wild and cultivated barley differentially respond to osmotic stress in gene expression,suberization, and hydraulic conductivity

Wild barley, Hordeum vulgare spp. spontaneum, has a wider genetic diversity than its cultivated progeny, Hordeum vulgare spp. vulgare. Osmotic stress leads to a series of different responses in wild barley seminal roots, ranging from no changes in suberization to enhanced endodermal suberization of certain zones and the formation of a suberized exodermis, which was not observed in the modern cultivars studied so far. Further, as a response to osmotic stress, the hydraulic conductivity of roots was not affected in wild barley, but it was 2.5-fold reduced in cultivated barley. In both subspecies, osmotic adjustment by increasing proline concentration and decreasing osmotic potential in roots was observed. RNA-sequencing indicated that the regulation of suberin biosynthesis and water transport via aquaporins were different between wild and cultivated barley. These results indicate that wild barley uses different strategies to cope with osmotic stress compared with cultivated barley. Thus, it seems that wild barley is better adapted to cope with osmotic stress by maintaining a significantly higher hydraulic conductivity of roots during water deficit.     

On the origin and domestication history of Barley (Hordeum vulgare)

Remains of barley (Hordeum vulgare) grains found at archaeological sites in the Fertile Crescent indicate that about 10,000 years ago the crop was domesticated there from its wild relative Hordeum spontaneum. The domestication history of barley is revisited based on the assumptions that DNA markers effectively measure genetic distances and that wild populations are genetically different and they have not undergone significant change since domestication. The monophyletic nature of barley domestication is demonstrated based on allelic frequencies at 400 AFLP polymorphic loci studied in 317 wild and 57 cultivated lines. The wild populations from Israel-Jordan are molecularly more similar than are any others to the cultivated gene pool. The results provided support for the hypothesis that the Israel-Jordan area is the region in which barley was brought into culture. Moreover, the diagnostic allele I of the homeobox gene BKn-3, rarely but almost exclusively found in Israel H. spontaneum, is pervasive in western landraces and modern cultivated varieties. In landraces from the Himalayas and India, the BKn-3 allele IIIa prevails, indicating that an allelic substitution has taken place during the migration of barley from the Near East to South Asia. Thus, the Himalayas can be considered a region of domesticated barley diversification.     

The draft genome of a wild barley genotype reveals its enrichment in genes related to biotic and abiotic stresses compared to cultivated barley

Wild barley (Hordeum spontaneum) is the progenitor of cultivated barley (Hordeum vulgare) and provides a rich source of genetic variations for barley improvement. Currently, the genome sequences of wild barley and its differences with cultivated barley remain unclear. In this study, we report a high‐quality draft assembly of wild barley accession (AWCS276; henceforth named as WB1), which consists of 4.28 Gb genome and 36 395 high‐confidence protein‐coding genes. BUSCO analysis revealed that the assembly included full lengths of 95.3% of the 956 single‐copy plant genes, illustrating that the gene‐containing regions have been well assembled. By comparing with the genome of the cultivated genotype Morex, it is inferred that the WB1 genome contains more genes involved in resistance and tolerance to biotic and abiotic stresses. The presence of the numerous WB1‐specific genes indicates that, in addition to enhance allele diversity for genes already existing in the cultigen, exploiting the wild barley taxon in breeding should also allow the incorporation of novel genes. Furthermore, high levels of genetic variation in the pericentromeric regions were detected in chromosomes 3H and 5H between the wild and cultivated genotypes, which may be the results of domestication. This H. spontaneum draft genome assembly will help to accelerate wild barley research and be an invaluable resource for barley improvement and comparative genomics research.     

Fitness estimation through performance comparison of F1 hybrids with their parental species Oryza rufipogon and O. sativa

BACKGROUND AND AIMS: Introgression of crop genes into populations of wild relatives has important implications for germplasm conservation as well as for the persistence of novel transgenes in wild populations. Studies of hybrid fitness can be used to evaluate the potential for introgression to occur following episodes of interspecific hybridization. METHODS: This study estimated relative fitness of interspecific hybrids through performance comparison of F(1) hybrids with their parental species, a cultivated rice (Oryza sativa) Minghui-63 and perennial common wild rice (O. rufipogon) under the cultivation conditions. KEY RESULTS: Compared with their parents, the hybrids had the lowest values of seedling survival ability, pollen viability and seed production; intermediate values of seed germination, spikelet production and flag leaf areas; and the highest values of plant height, number of tillers and panicles. The hybrids performed poorly at the stage of sexual reproduction, although they had a slightly higher hybrid vigour at the vegetative growth stage and better tillering ability than their wild parent. There were no significant differences in composite fitness across the whole life-history between the hybrids and their wild parental species. CONCLUSIONS: Rice genes, including transgenes, might persist in wild rice populations through vegetative and sexual reproduction. Further studies are needed to examine whether the extent of gene flow from rice is sufficiently significant to influence genetic diversity in wild populations of O. rufipogon, a species that has become endangered in some regions of south-east Asia.     

Characterisation of progeny from backcrosses of triploid hybrids between Hordeum vulgare L. (2x) and H. bulbosum L (4x) to H. vulgare

Interspecific hybridisations between Hordeum vulgare L. (cultivated barley) and H. bulbosum L. (bulbous barley grass) have been carried out to transfer desirable traits, such as disease resistance, from the wild species into barley. In this paper we report the results of an extensive backcrossing programme of triploid hybrids (H. vulgare 2x x H. bulbosum 4x) to two cultivars of H. vulgare. Progenies were characterised cytologically and by restriction fragment length polymorphism analysis and comprised (1) haploid and diploid H. vulgare plants, (2) hybrids and aneuploids, (3) single and double monosomic substitutions of H. bulbosum chromosomes into H. vulgare and (4) chromosomal rearrangements and recombinants. Five out of the seven possible single monosomic chromosome substitutions have now been identified amongst backcross progeny and will be valuable for directed gene introgression and genome homoeology studies. The presence amongst progeny of 1 plant with an H. vulgare-H. bulbosum translocated chromosome and one recombinant indicates the value of fertile triploid hybrids for interspecific gene introgression.     

Polymorphic chloroplast simple sequence repeat primers for systematic and population studies in the genus Hordeum

In this study we report the development of primers to amplify polymorphic chloroplast simple sequence repeats in the genus Hordeum , which includes cultivated barley ( H. vulgare ssp. vulgare ) and its wild progenitor H. vulgare ssp. spontaneum . Polymorphic products were amplified in a wide range of Hordeum spp. and intraspecific variation was detected in both cultivated and wild barley. A decrease in cytoplasmic diversity was observed between sspp. spontaneum and vulgare as well as between ssp. vulgare landraces and cultivars, which is characteristic of domestication processes in many crop species. We also observed possible evidence for reticulate evolution of H. brachyantherum polyploids, with apparent multiple cytoplasmic introgressions during successive polyploidization events.     

野生稻与栽培稻及种间杂种F1叶表面亚显微结构的研究

用扫描电镜对原产中国的３种野生稻、２个栽培稻品种及栽培稻与野生稻间的杂种Ｆ１,就气孔频度、气孔器乳突、大瘤状乳突及本栓细胞乳突等叶片表面亚显微结构作了比较观察研究。结果显示这些性状具有种的特性,发现种间杂种的亚星微性状与两个亲本 特性及亲缘关系远近有关。