Rapid evolutionary divergence of an invasive weed from its crop ancestor and evidence for local diversification

Feral rye is an invasive North American weed that evolved from domesticated rye in the last century. In order to determine how this weed diverged from its cultivated ancestor and whether it has evolved regional differences across its new range in the western United States, we planted both feral rye from different regions and its progenitor in three common garden sites spanning the North-South axis of that range (eastern Washington, northern California, and southern California, respectively). We measured seedling emergence, survival, vegetative growth, flowering phenology, and reproductive output concurrently across sites over a single growing season. All traits were found to be genetically based. All feral populations were typically shattering contrasting with domesticated rye's typically non-shattering seed head. They also flowered later, tillered more, grew shorter, and produced smaller seeds in at least one population. Near the center and proposed origin of its introduced range, all feral rye populations produced significantly more seed than cultivars. Northern feral populations flowered later than southern populations and cultivars. Shifts were not symmetrical: southern populations performed well at all sites. But northern populations showed more evidence of local adaptation, faring poorly in southern California. Clearly, feral rye has evolved from its cultivated progenitor by more than just acquiring shattering. Furthermore, it has diverged regionally, although not all populations are fully locally adapted. Notably, feral rye populations exhibited a greater range of phenotypes than rye cultivars, suggesting that its evolution is not simply due to selection acting on existing variation within individual cultivars.     

On the origin of cultivated rye

The origin of cultivated rye has been studied, taking into consideration evidence from various fields. Based on morphological resemblances and cytogenetic affinities, cultivated rye is included in Secale cereale L. emend. Sencer, which also includes annual wild and weedy ryes. Wild populations of 5. cereale , which have evolved from Secale montanum Guss. emend. Sencer, invaded wheat and barley fields during the early days of cultivation and gave rise to weedy ryes with varying degrees of rachis brittleness. Cultivated rye was selected from weedy ryes for non-brittle rachis and bigger caryopsis both unconsciously and consciously by man. The geographic origin of cultivated rye is postulated for the Büyük Ari Dai (Mt. Ararat) and Lake Van area in eastern Turkey. It spread from this area as a weed in wheat and barley fields towards the north, east and west and imposed itself as a secondary crop under conditions unfavourable for wheat and barley. It thus became a crop in its own right in several places independently, in addition to it being known by the people living in the Caucasus and Transcaucasus from very early agricultural times.     

Crop seed spillage along roads: a factor of uncertainty in the containment of GMO

Feral populations of crop species along roadsides contribute to the uncertainty regarding the containment of genetically modified (GM) crops, as the feral populations could promote the persistence of transgenes outside of cultivated fields. Roadside populations of several common crop species are known to occur far from arable fields, and the dispersal pathways that promote their recruitment in road verges are unclear. Human-aided dispersal, in particular adhesive dispersal by vehicles, has been suggested as a possible vector, but this has not yet been proven experimentally. We sampled the seed rain from vehicles inside two motorway tunnels in an urban environment to reveal the contribution of crop species to seeds unintentionally dispersed by traffic beyond agricultural production areas. Three species of arable crops, wheat Triticum aestivum , rye Secale cereale and oilseed rape Brassica napus , were among the most frequent species deposited by vehicles inside the motorway tunnels. Each of the three species was clearly more predominant in one direction of traffic. While seeds of Triticum aestivum and Secale cereale were primarily transported into the city, Brassica napus was significantly more abundant in samples from lanes leading out of the city. Seed sources in the local surroundings of the tunnels were virtually nonexistent, and the high magnitude of seed deposition combined with high seed weights suggests a dispersal mechanism different from other species in the sample, at least for Triticum aestivum and Secale cereale . This provides evidence that spillage during transport is a major driver for long-distance dispersal of crops. Our results suggest that seed dispersal by vehicles is the major driver in the recruitment of roadside populations of arable crops, providing a possible escape route for GM crops. Risk management should thus aim at curbing transport losses of GM crops.     

Isoenzymes of aspartate aminotransferase in perennial and annual rye and their hybrids.

Aspartate aminotransferase patterns were screened in a collection of rye genotypes that included 24 accessions of wild perennial rye (Secale montanum Guss.), 6 accessions of cultivated perennial Derzhavin and Tsitsin rye (Secale cereale x S. montanum), 15 accessions of winter and spring rye cultivars (S. cereale L.), and 9 accessions of perennial and annual rye genotypes bred from S. montanum ssp. kuprijanovii, Derzhavin rye, and winter rye for their resistance to fungal diseases. Aspartate aminotransferase is coded for by four loci. The data fit the model where AAT 1/4 is coded by Aat 1 and Aat 4, two duplicate loci, with null and two active alleles for each locus, alleles 1 and 3 for locus Aat 1 and alleles 2 and 4 for locus Aat 4; dimeric AAT 1/4 enzyme molecules are the products of both intralocus and interloci complementation. Allele 1 of Aat 1 was the most prominent in the isoenzyme patterns of the rye species. Alleles null and 2 of Aat 4 were twice as frequent in the perennial rye accessions, including Derzhavin and Tsitsin rye, than in winter and spring rye. In contrast, allele 4 of Aat 4 was characteristic of S. cereale. Within the screened collection, locus Aat 2 was monomorphic. Among three alleles of Aat 3, allele 2 dominated isoenzyme profiles of both rye species, whereas the other two alleles were species-specific: allele 1 was characteristic of S. montanum and allele 3 was found only in S. cereale. Key words : rye, Secale cereale, Secale derzhavinii, Secale montanum, aspartate aminotransferase, isoenzymes, perennial habit, polymorphism.     

Discrimination of Repetitive Sequences Polymorphism in Secale cereale by Genomic In Situ Hybridization-Banding

Genomic in situ hybridization banding (GISH-banding), a technique slightly modified from conventional GISH, was used to probe the Chinese native rye (Secale cereale L.) DNA, and enabled us to visualize the Individual rye chromosomes and create a universal reference karyotype of the S. cereale chromosome 1R to 7R. The GISH-banding approach used in the present study was able to discriminate S. cereale chromosomes or segments in the wheat (Triticum aeativum L.) background, including the Triticale, wheat-rye addition and translocation lines. Moreover, the GISH-banding pattern of S.cereale subsp. Afghanicum chromosomes was consistent with that of Chinese native rye cv. Jingzhou rye; whereas the GISH-banding pattem of Secale vavilovli was different from that of S. cereale, indicating that GISH-banding can be used to study evolutionary polymorphism in species or subspecies of Secale. In addition, the production and application of GISH-banding to the study of adenine-thymine-riched heterochromatin is discussed.     

Cold pretreatment to enhance green plant regeneration from rye anther culture

Cold pretreatment of detached tillers of rye, Secale cereale, was tested under two light regimes. The ryes included two spring and two winter cultivars. Significant increases in green plant regeneration were recorded in each experiment when cold pretreatments of two to four weeks were applied. Dim light during the stress period improved green plant regeneration for two of the four cultivars tested. The highest regeneration rate, 30.6 green plants per 100 plated anthers, was reached following three weeks at +4 °C under dim light, for spring rye Jo02. Starvation stress applied to plated anthers in mannitol medium suppressed anther response. This revised version was published online in June 2006 with corrections to the Cover Date.     

Phylogenetic relationships of the genus Secale based on the characterisation of rDNA ITS sequences

 Sequence analysis of the internal transcribed spacer of the 18S-5.8S-26S rDNA (ITS-1) region was performed in order to analyse the phylogenetic relationships of eleven taxa of cultivated and wild rye species. The ITS regions were amplified using designed primers. At least ten positive clones of each taxonomic unit were sequenced and compared. Two different ITS sequences were found in three taxa: Secale sylvestre Host, Secale strictum ssp. kuprijanovii Grossh. and Secale strictum ssp. africanum Stapf. Secale sylvestre Host was the species that showed the greatest number of comparative differences in the sequences, and was the most distant of all the taxonomic units analysed. A certain degree of variation was found among all four subspecies of S. strictum analysed. S. strictum Presl ssp. strictum was most closely related to S. strictum ssp. africanum Stapf and S. strictum ssp. kuprijanovii Grossh to S. strictum ssp. anatolicum (Boiss.) Hammer. S. vavilovii showed similarities with this group of subspecies and with the S. cereale group. No differences were found between the weed forms of S. cereale and cultivated rye. Received March 8, 2002; accepted May 31, 2002 Published online: November 20, 2002 Address of the authors: Alfredo De Bustos, Nicolás Jouve (e-mail: nicolas.jouve@uah.es), Department of Cell Biology and Genetics, University of Alcalá, E-28871 Alcalá de Henares (Madrid), Spain.     

Genetic analysis of the short-stem populations of rye (Secale cereale L.) for the plant height trait

The process and results of genetic analysis of the short-stem rye populations (Secale cereale L.) for the trait "plant height" are described. The analysis has been performed with the joint scaling test using data of estimation of the parental and hybrid populations developed in the cyclic reciprocal crosses between four initial populations. Monogenic, digenic, and trigenic differences between parental rye populations for two genes of incomplete dominance and one multiallelic gene with additive allelic interaction were determined.     

黑麦基因组特异DNA片段的分离与SCAR标记的建立

以2个栽培黑麦、2个野生黑麦和4个普通小麦为材料,从200条10碱基RAPD随机引物中筛选出1条引物H11。H11在小麦中有1条低拷贝扩增,而在黑麦中却有极高拷贝的扩增。对H11在黑麦中的高拷贝片段进行克隆、测序,得其全长679 bp,记作OPH11679。根据OPH11679设计特异PCR引物H11-F和H11-R,对小麦族其它物种和含黑麦染色质的物种进行验证,结果发现仅含黑麦染色质的物种能扩增出长为643 bp的片段(命名为pScH643),这表明该片段为黑麦所特有。用H11-F和H11-R对1套中国春-Imperial黑麦附加系等进行扩增,结果显示pScH643片段分布在黑麦整套染色体上,这一结果在小麦-黑麦异源材料的分析中得到进一步验证。即表明pScH643片段可作为SCAR标记用于含黑麦染色质材料的检测。     

The history of rye cultivation in Europe

During recent years finds from several prehistoric and medieval periods have thrown new light on the history of the spread of rye. It is now proven that wild rye is indigenous to Anatolia and was already domesticated there by the early Neolithic at the beginning of agriculture. Secale migrated to Central Europe as a weed among other cereals, and single grains of weed rye have been recorded there since the early Neolithic. The number of finds increased during the Bronze Age and Iron Age, and the status of rye changed from weed to crop plant, probably in the course of the early Iron Age. This acculturation of Secale cereale in central and eastern Europe was obviously independent of the earlier one in Anatolia. The first stages towards deliberate cultivation happened unintentionally through harvesting close to the ground, so that the rye was permanently represented in the seed corn. From this point rye was able to take advantage of its competitive strength on poor soils and in areas with unfavourable climate. The start of rye as a crop in its own right during the pre-Roman Iron Age and Roman period presumably took place independently in different areas. The expansion of intensive rye cultivation occurred in the Middle Ages. However, new finds from north-west Germany, which are presented here, show that in this area rye has been cultivated as a main crop on poor soils since the Roman period. In two maps all rye finds up to 1000 A.D. are shown, which after critical consideration can be regarded as cultivated rye.     

Evolutionary trends of microsatellites during the speciation process and phylogenetic relationships within the genus Secale

Eleven weedy or wild species or subspecies of the genus Secale L. were compared with a set of cultivated rye accessions, based on inter-simple sequence repeat (ISSR) markers to analyze their phylogenetic relationships. A total of 846 bands were amplified from reactions using 12 screening primers, including 79 loci with a mean of 10.1 alleles per locus. The number of amplified bands for each primer ranged from 12 to 134, with a mean of 70.5 amplified bands per primer. The presence and distribution of amplified bands in different accessions demonstrate that a rapid evolutionary trend of microsatellite repeats occurred during the speciation process from the perennial wild form to annual cultivated rye. In addition, variation, amplification, and deletion of microsatellites in genomes revealed phylogenetic relationships in the genus Secale. Analysis of the presence, number, and distribution of amplified bands in genomes, as well as the comparison with genetic similarity (GS) indices based on ISSR, indicate that Secale strictum subsp. africanum (Stapf) Hammer, Secale strictum anatolicum (Boiss.) Hammer, Secale sylvestre Host, and Secale strictum subsp. strictum (C. Presl) Hammer emerged in succession from a common ancestor of Secale following geographic separation and genetic differentiation. The annual weedy rye evolved from S. strictum subsp. strictum, which was domesticated as present-day cultivated rye. Data from ISSR analyses separated all investigated accessions of the genus Secale into three distinct groups. These results support the division of the genus Secale into three species: the annual wild species S. sylvestre; the perennial wild species S. strictum, including several differential subspecies forms such as strictum, africanum, and anatolicum; and S. cereale, including cultivated and weedy rye as subspecies forms.     

Determining the plasmotypic structure of rye populations by SCAR markers

In rye (Secale cereale L.), 2 types of cytoplasmic male sterility are known: Pampa type (CMS-P) and Vavilovii type (CMS-V). As an alternative method to the conventional plasmotype-genotype interaction test, for identification of the cytoplasm type, the use of sequence-characterised amplified region (SCAR) markers was validated in this study. In over 2600 individual rye plants, representing 26 populations originating from Poland (18 cultivars), Iran (5 populations of primitive rye), and South America (3 populations), the cytoplasm type was determined by using a set of 3 SCAR markers. For about 10% of these individuals, the plasmotype-genotype interaction test was performed in parallel. The results of both tests were fully consistent. In the majority of the Polish populations, CMS-V was present, and only 4 populations contained CMS-P. Primitive Iranian populations contained predominantly normal cytoplasm, and only occasionally CMS-P was identified in them. South American populations displayed a mixture of normal cytoplasm, CMS-P and CMS-V. This work validates the use of SCAR markers as a reliable and quick method to determine the plasmotypic diversity of rye populations on a large scale.     

Resistance to Ergot in Self-incompatible Germplasm Resources of Winter Rye

The poor progress in breeding for resistance to ergot ( Claviceps purpurea [Fr.] Tul.) in rye ( Secale cereale L.) is attributed to the lack of appreciable genotypic variation for this trait. The present study was, therefore, undertaken to evaluate 52 indigenous and exotic genetic resources and 13 open-pollinated cultivars for ergot resistance. These 65 self-incompatible populations were evaluated in four environments with each entry plot surrounded by wheat plots on four sides. Inoculation with a pathogen mixture was done thrice during flowering and harvesting was done early by hand. Resistance traits were ergot incidence and severity. Logit-transformed data were subjected to analyses of variance. The lowest disease severity in any environment was 0.18%, and that was still higher than the official threshold of 0.1% for feed. In the pooled analysis across environments, significant genotypic differences as well as genotype × environment interaction were present. The correlation between ergot severity and pollen shedding was not significant indicating that genotypic differences were not affected by pollen shedding. Broad-sense heritability ( h ² ) estimates were moderate (0.54–0.65). 'Halo', an old German cultivar, and the genetic resources 'Schmidt-Roggen' and 'Dukat', had low ergot severity (Halo having the lowest severity) as well as low disease incidence. The results document a significant, but moderate genotypic variance for ergot resistance among self-incompatible rye that can be exploited to breed ergot-resistant rye.     

中国春及其ph2b突变体与秦岭黑麦杂种胚胎发育的比较研究

对普通小麦中国春(CS)及其突变体(CSph2b)与秦岭黑麦远缘杂交的受精过程及其杂种早期胚胎发育进行了研究.结果显示,大部分秦岭黑麦花粉能在CS及CSph2b小麦柱头上萌发,花粉管可顺利伸入花柱和胚囊;CS和CSph2b已授粉子房中,分别有80.12%和84.80%完成双受精过程而形成正常胚及胚乳,也有小部分仅有卵核受精或极核受精而只形成胚或胚乳,两者总受精率分别为86.74%和88.89%,成胚率分别为83.73%和87.14%.表明中国春及其突变体CSph2b与秦岭黑麦的可杂交性都很高,并且CSph2b略高于CS.     

Polymorphism of the storage proteins in Portuguese rye (Secale cereale L.) populations

Currently, due to the abandonment of traditional agricultural practices and the decline of rye production in Portugal, there is a need to assess the genetic diversity of rye in order to preserve its biodiversity. Furthermore, a greater knowledge of rye secalins is important for rye bread-making quality and other crop breeding purposes. The genetic variation and diversity of storage proteins were estimated for fourteen populations of rye (Secale cereale L.) sampled in northern Portugal. The work showed the high genetic diversity within the Portuguese rye gene-pool as an important source for plant breeding and emphasized the necessity of an integrated resources genetic program to allow a more efficient management and conservation of these resources. The rye populations were compared with 'Picasso' and 'Marder' varieties. Several alleles were identified by the single electrophoretic mobility patterns. We studied a set of 1600 rye seeds, including regional populations and varieties, having observed a total of 24, 5, 21 and 47 alleles for HMW, 75k γ-, 40k γ- and ω-secalins, respectively. The coefficient of similarity within populations is presented using cluster representation. The mean value of genetic variation indices (H) for rye storage proteins was very high in regional populations, ranging from 0.67 to 0.78, while in the varieties ranged from 0.57 to 0.58. Knowledge of the diversity of secalins will increase our understanding of the quality differences between rye varieties, especially considering the relative small number of rye cultivars grown around the world.     

Origins of weedy rice revealed by polymorphisms of chloroplast DNA sequences and nuclear microsatellites

Conspecific weeds that permanently infest worldwide agroecosystems are evolved from their crop species. These weeds cause substantial problems for crop production by competing for resources in agricultural fields. Weedy rice represents such a conspecific weed infesting rice ecosystems, and causing tremendous rice yield losses owing to its strong competitiveness and abundant genetic diversity, likely resulted from its complex origins. Here, we report the use of chloroplast DNA (cpDNA) fingerprints to determine whether weedy rice is evolved from its wild (exo‐feral) or cultivated (endo‐feral) rice progenitor as the maternal donor in recent hybridization events. In addition, we also applied nuclear simple sequence repeat (SSR) markers to confirm the exo‐feral or endo‐feral origins of weedy rice accessions determined by the cpDNA fingerprints. We found that the studied weedy rice accessions evolved either from their wild or cultivated rice progenitor, as the maternal donor, based on the cpDNA network and structure analyses. Combined analyses of cpDNA and nuclear SSR markers indicated that a much greater proportion of weedy rice accessions had the endo‐feral origin. In addition, results from the genetic structure of nuclear SSR markers indicated that weedy rice accessions from the endo‐feral pathway are distinctly associated with either indica or japonica rice cultivars, suggesting their complex origins through crop–weed introgression. The complex pathways of origin and evolution could greatly promote genetic diversity of weedy rice. Therefore, innovative methods should be developed for effective weedy rice control.     

Microdissection and Recovery of 1R Chromosome in Rye ( Secale cereale )

The technique of mieromanipulaion has been used to establish a system of single chromosome mierodissection. According to the standard karyotype of rye ( Secale cereale L. ), 1R chromosome carrying disease-resistant gene has been identified, microdissected and transferred into Ep-pendorf tube using mieromanipulator. The results showed that IR chromosome in cells pretreated with α-bromonaphthalene could be identified quickly and the efficiency of microdissection was greatly improved when the technique of wall degradation and hypotonic treatment was applied.     

二甲基亚砜对黑麦根尖分生组织细胞超显微结构的影响

黑麦根尖在原位用二甲垫亚砜(DMSO)处理之后,电子显微镜下观察发现根尖分生组织区细胞的细胞核和细胞质内也出现类似微丝的微纤丝结构。与我们以前在经DMSO处理过的黑麦小孢子母细胞核中所看到的微纤丝结构一样,根尖分生组织区细胞中微纤丝结构直径也约为6—9 nm,许多根微纤丝平行地排列在一起构成微纤丝束,本研究提示DMSO对于植物的体细胞和小孢子母细胞具有相同的生物学效应。也提示黑麦根尖分生组织细胞和小孢子母细胞的核基质可能具有相似的组成。     

Assessment of Genetic Diversity in <Emphasis Type="Italic">Secale cereale</Emphasis> Based on SSR Markers

The primary aim of this study was to estimate genetic diversity among Secale cereale L. accessions using 22 previously published simple sequence repeat (SSR) markers. The plant material included 367 rye accessions comprising historical and contemporary cultivars, cultivated materials, landraces, and breeding strains from the Polish breeding company Danko. The studied accessions represented a wide geographical diversity. Several methods were employed to analyze genetic diversity among the Secale cereale L. accessions and to determine population structure: principal coordinate analysis (PCoA), neighbor-joining (NJ), and Bayesian clustering. We also defined a core collection of 25 rye accessions representing over 93 % of SSR alleles. The results of these analyses showed that accessions from the rye gene bank are clearly divergent in comparison with materials received directly from European breeding companies. Our findings suggest also that the genetic pool of current rye cultivars is becoming narrower during breeding processes. The selected panel of SSR markers performed well in detection of genetic diversity patterns and can be recommended for future germplasm characterization studies in rye.