Ribosomal DNA polymorphisms and the Oriental-Occidental genetic differentiation in cultivated barley

Summary A total of 289 accessions of cultivated barley were assayed for ribosomal DNA (rDNA) polymorphisms. These accessions comprised four independent samples: (1) 79 entries from China, (2) 59 accessions from Ethiopia, (3) 59 entries from Tibet and (4) 92 entries representing 36 barley growing countries of the world (referred to as world sample). In all, 17 rDNA phenotypes (genotypes) were observed, which were composed 10 alleles at two rDNA loci, Rrn1 and Rrn2. The world sample contained the largest number of phenotypes and alleles and also demonstrated the highest level of diversity. Ribosomal DNA phenotypes 104, 112 and 107, 112 occurred at high frequencies worldwide. Allele 112 was the predominant allele of Rrn1 in all four samples, and 104 and 107 were the two major alleles of Rrn2 worldwide. The distributions of rDNA genotypes and alleles demonstrated a clear differentiation of two distinct barley groups: an Oriental group represented by the samples from China and Tibet, which is characterized by allele 107 at the Rrn2 locus (rDNA phenotype 107, 112); and an Occidental group, represented by Ethiopian and world samples, which is comprised mostly of allele 104 at the Rrn2 locus (rDNA phenotype 104, 112). The results also raised new questions concerning the phylogeny and evolution of cultivated barley.     

Microgeographic edaphic differentiation in allozyme polymorphisms of wild barley (Hordeum spontaneum,Poaceae)

Allozymic variation in proteins encoded by 22 loci was analyzed electrophoretically in 278 individual plants of wild barley,Hordeum spontaneum, the progenitor of cultivated barley, in four 100 meter transects, in Israel, each equally subdivided into basalt and terra rossa soil types. Significant differentiation according to soil was found in 9 alleles. Our results suggest that allozyme polymorphisms in wild barley are at least partly adaptive, and differentiate by edaphic natural selection rather than by stochastic processes, and/or neutrality of allozymic variants.     

A DNA marker closely linked to the <Emphasis Type="Italic">vrs1</Emphasis> locus (row-type gene) indicates multiple origins of six-rowed cultivated barley (<Emphasis Type="Italic">Hordeum vulgare</Emphasis> L.)

The origin of six-rowed cultivated barley was studied using a DNA marker cMWG699 closely linked to the vrs1 locus. Restriction patterns of the PCR-amplified product of the cMWG699 locus were examined in 280 cultivated (Hordeum vulgare ssp. vulgare) and 183 wild (H. vulgare ssp. spontaneum) barleys. Nucleotide sequences of the PCR products were also examined in selected accessions. Six-rowed cultivated barleys were divided into two distinct groups, types I and II. Type I six-rowed cultivated barley was distributed widely while type II six-rowed cultivated barley was found only in the Mediterranean region. The type I sequence was also found in a wild barley accession from Turkmenistan whereas the type II sequence was also found in a two-rowed cultivated barley from North Africa and a wild barley from Morocco. These results suggested that the six-rowed type I and II barleys were derived from two-rowed type I and II barleys, respectively, by independent mutations at the vrs1 locus. Received: 3 November 2000 / Accepted: 17 April 2001     

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.     

Structure and inheritance of ribosomal DNA variants in cultivated and wild hop, Humulus lupulus L.

Genetic variation was assessed among cultivated and wild hop, Humulus lupulus, by restriction fragment length polymorphisms (RFLPs) of the ribosomal RNA genes (rDNA). Two rDNA length variants of 10.3 and 9.3 kbp represented by three phenotypes designated A, B and C were detected with XhoI. Restriction-site mapping showed that hop rDNA is structurally similar to those of most higher plants. A high level of homogeneity existed in rDNA repeat lengths among the diverse hop genotypes. Generally, phenotype A was predominant in wild and cultivated European and Asian genotypes; phenotype B in North American cultivars; while phenotype C was present only in native North American hop, providing a potential molecular marker for the identification of this germ plasm. The rDNA data provided genetic evidence for the separation of native and cultivated American genotypes and supports the hypothesis that North American hop cultivars are of hybrid origin from European and native American genotypes. The segregation of rDNA phenotypes in four F₁ families suggests that a single locus with two co-dominant alleles controls genetic variability for rDNA variants in hop.     

Genetic divergence of heat production within and between the wild progenitors of wheat and barley: evolutionary and agronomical implications

Summary We compared and contrasted calorimetrically heat production in seedlings incubated at 5°C and 24°C using genotypes from cold and warm Israeli populations of the wild progenitors of barley (Hordeum spontaneum) and wheat (Triticum dicoccoides). The wild barley sample comprised 14 accessions, 7 from cold localities and 7 from warm localities. The wild emmer wheat sample consisted of 12 accessions, 6 from a cold locality, and 6 from a warm locality. Our results indicated that (1) heat production was significantly higher in the two wild cereals at 5 °C than at 24 °C; (2) interspecifically, wild barley generates significantly more heat than wild wheat at both 5 °C and 24 °C; (3) intraspecifically, wild barley from warm environments generates significantly more heat than wild barley from cold ones, at 24 °C. We hypothesize that both the inter- and intraspecific differences in heat production evolved adaptively by natural selection in accordance with the niche-width genetic variation hypothesis. These differences presumably enhance biochemical processes, hence growth, thereby leading to the shorter annual cycle of barley compared to that of wheat, and may explain the wider range of the wild and cultivated gene pools of barley, as compared with those of wheat. We propose that a shortening of the growth period through utilizing heat production gene(s) is feasible by classical methods of breeding and/or modern biotechnology.     

Genetic Diversity Analysis of Tibetan Wild Barley Using SSR Markers

One hundred and six accessions of wild barley collected from Tibet, China, including 50 entries of the two-rowed wild barley Hordeum vulgare ssp. spontaneum (HS), 29 entries of the six-rowed wild barley Hordeum vulgare ssp. agriocrithon (HA), and 27 entries of the six-rowed wild barley Hordeum vulgare ssp. agriocrithon var. lagunculiforme (HL), were analyzed using 30 SSR markers selected from the seven barley linkage groups for studying genetic diversity and evolutionary relationship of the three subspecies of Tibetan wild barley to cultivated barley in China. Over the 30 genetic loci that were studied, 229 alleles were identified among the 106 accessions, of which 70 were common alleles. H. vulgare ssp. spontaneum possesses about thrice more private alleles (2.83 alleles/locus) than HS (0.93 alleles/locus), whereas almost no private alleles were detected in HL. The genetic diversity among-subspecies is much higher than that within-subspecies. Generally, the genetic diversity among the three subspecies is of the order HS > HL > HA. Phylogenetic analysis of the 106 accessions showed that all the accessions of HS and HA was clustered in their own groups, whereas the 27 accessions of HL were separated into two groups (14 entries with group HS and the rest with group HA). This indicated that HL was an intermediate form between HS and HA. Based on this study and previous works, we suggested that Chinese cultivated barley might evolve from HS via HL to HA.     

The Horn of Africa as a centre of barley diversification and a potential domestication site

According to a widely accepted theory on barley domestication, wild barley (Hordeum vulgare ssp. spontaneum) from the Fertile Crescent is the progenitor of all cultivated barley (H. vulgare ssp. vulgare). To determine whether barley has undergone one or more domestication events, barley accessions from three continents have been studied (a) using 38 nuclear SSR (nuSSRs) markers, (b) using five chloroplast SSR (cpSSR) markers yielding 5 polymorphic loci and (c) by detecting the differences in a 468 bp fragment from the non-coding region of chloroplast DNA. A clear separation was found between Eritrean/Ethiopian barley and barley from West Asia and North Africa (WANA) as well as from Europe. The data from chloroplast DNA clearly indicate that the wild barley (H. vulgare ssp. spontaneum) as it is found today in the “Fertile Crescent” might not be the progenitor of the barley cultivated in Eritrea (and Ethiopia). Consequently, an independent domestication might have taken place at the Horn of Africa. Jihad Orabi and Gunter Backes have contributed equally to this work.     

Haplotype diversity and population structure in cultivated and wild barley evaluated for Fusarium head blight responses

Fusarium head blight (FHB) is a threat to barley (Hordeum vulgare L.) production in many parts of the world. A number of barley accessions with partial resistance have been reported and used in mapping experiments to identify quantitative trait loci (QTL) associated with FHB resistance. Here, we present a set of barley germplasm that exhibits FHB resistance identified through screening a global collection of 23,255 wild (Hordeum vulgare ssp. spontaneum) and cultivated (Hordeum vulgare ssp. vulgare) accessions. Seventy-eight accessions were classified as resistant or moderately resistant. The collection of FHB resistant accessions consists of 5, 27, 46 of winter, wild and spring barley, respectively. The population structure and genetic relationships of the germplasm were investigated with 1,727 Diversity Array Technology (DArT) markers. Multiple clustering analyses suggest the presence of four subpopulations. Within cultivated barley, substructure is largely centered on spike morphology and growth habit. Analysis of molecular variance indicated highly significant genetic variance among clusters and within clusters, suggesting that the FHB resistant sources have broad genetic diversity. The haplotype diversity was characterized with DArT markers associated with the four FHB QTLs on chromosome 2H bin8, 10 and 13 and 6H bin7. In general, the wild barley accessions had distinct haplotypes from those of cultivated barley. The haplotype of the resistant source Chevron was the most prevalent in all four QTL regions, followed by those of the resistant sources Fredrickson and CIho4196. These resistant QTL haplotypes were rare in the susceptible cultivars and accessions grown in the upper Midwest USA. Some two- and six-rowed accessions were identified with high FHB resistance, but contained distinct haplotypes at FHB QTLs from known resistance sources. These germplasm warrant further genetic studies and possible incorporation into barley breeding programs.     

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.     

Phenotypic landscapes: phenological patterns in wild and cultivated barley

Phenotypic variation in natural populations is the outcome of the joint effects of environmentally induced adaptations and neutral processes on the genetic architecture of quantitative traits. In this study, we examined the role of adaptation in shaping wild barley phenotypic variation along different environmental gradients. Detailed phenotyping of 164 wild barley (Hordeum spontaneum) accessions from Israel (of the Barley1K collection) and 18 cultivated barley (H. vulgare) varieties was conducted in common garden field trials. Cluster analysis based on phenotypic data indicated that wild barley in this region can be differentiated into three ecotypes in accordance with their ecogeographical distribution: north, coast and desert. Population differentiation (Q_ST) for each trait was estimated using a hierarchical Bayesian model and compared to neutral differentiation (F_ST) based on 42 microsatellite markers. This analysis indicated that the three clusters diverged in morphological but not in reproductive characteristics. To address the issue of phenotypic variation along environmental gradients, climatic and soil gradients were compared with each of the measured traits given the geographical distance between sampling sites using a partial Mantel test. Flowering time and plant growth were found to be differentially correlated with climatic and soil characteristic gradients, respectively. The H. vulgare varieties were superior to the H. spontaneum accessions in yield components, yet resembled the Mediterranean types in vegetative characteristics and flowering time, which may indicate the geographical origin of domesticated barley.     

Genetic and Molecular Organization of Ribosomal DNA (Rdna) Variants in Wild and Cultivated Barley

Twenty rDNA spacer-length variants (slvs) have been identified in barley. These slvs form a ladder in which each variant (with one exception) differs from its immediate neighbors by a 115-bp subrepeat. The 20 slvs are organized in two families, one forming an eight-step ladder (slvs 100-107) in the nucleolus organizer region (NOR) of chromosome 7 and the other a 12-step ladder (slvs 108a-118) in the NOR of chromosome 6. The eight shorter slvs (100-107) segregate and serve as markers of eight alleles of Mendelian locus Rrn2 and the 12 longer slvs (108a-118) segregate and serve as markers of 12 alleles of Mendelian locus Rrn1. Most barley plants (90%) are homozygous for two alleles, including one from each the 100-107 and the 108a-118 series. Two types of departures from this typical pattern of molecular and genetic organization were identified, one featuring compound alleles marked by two slvs of Rrn1 or of Rrn2, and the other featuring presence in Rrn1 of alleles normally found in Rrn2, and vice versa. The individual and joint effects on adaptedness of the rDNA alleles are discussed. It was concluded that selection acting on specific genotypes plays a major role in molding the strikingly different allelic and genotypic frequency distributions seen in populations of wild and cultivated barley from different ecogeographical regions.     

应用微卫星标记研究西藏野生大麦的遗传多样性

以西藏不同地区的106份野生大麦为材料,其中包括50份野生二棱大麦（HS）,27份野生瓶形大麦（HL）和29份野生六棱大麦（HA）,用Liu等（1996）发表的SSR连锁图的每个连锁群的两个臂的不同位置上选取3～5个共30个SSR标记,研究了西藏3类野生大麦的遗传多样性。结果表明,这3类野生大麦在遗传组成及等位变异频率分布上存在着明显的遗传分化。在总样本中,共检测到229个等位变异,平均每个SSR位点检测到7．6个等位变异,其中70个为这3类野生大麦间共同的等位变异,等位变异数在这3类野生大麦间有明显的差异,亚种问的遗传多样性明显高于亚种内的遗传多样性。其遗传多样性大小顺序为HS〉HL〉HA。聚类分析表明,野生二棱大麦、野生六棱大麦分别聚在不同的两类,而野生瓶形大麦中各有约50％的材料分别聚在这两类。根据本研究及前人研究结果,我们认为中国栽培大麦是从野生二棱大麦经野生瓶形大麦向野生六棱大麦进化的。该结果支持了栽培大麦起源的“野生二棱大麦单系起源论”的观点。     

Variability of chloroplast DNA and nuclear ribosomal DNA in cassava (Manihot esculenta Crantz) and its wild relatives

Chloroplast DNA (cp) and nuclear ribosomal DNA (rDNA) variation was investigated in 45 accessions of cultivated and wild Manihot species. Ten independent mutations, 8 point mutations and 2 length mutations were identified, using eight restriction enzymes and 12 heterologous cpDNA probes from mungbean. Restriction fragment length polymorphism analysis defined nine distinct chloroplast types, three of which were found among the cultivated accessions and six among the wild species. Cladistic analysis of the cpDNA data using parsimony yielded a hypothetical phylogeny of lineages among the cpDNAs of cassava and its wild relatives that is congruent with morphological evolutionary differentiation in the genus. The results of our survey of cpDNA, together with rDNA restriction site change at the intergenic spacer region and rDNA repeat unit length variation (using rDNA cloned fragments from taro as probe), suggest that cassava might have arisen from the domestication of wild tuberous accessions of some Manihot species, followed by intensive selection. M. esculenta subspp flabellifolia is probably a wild progenitor. Introgressive hybridization with wild forms and pressures to adapt to the widely varying climates and topography in which cassava is found might have enhanced the crop's present day variability.     

A comparative analysis of genetic polymorphism in wild and cultivated barley from Tibet using isozyme and ribosomal DNA markers.

This study was conducted to address some of the issues concerning the possible significance of Tibet in the origin and evolution of cultivated barley. A total of 1757 barley accessions from Tibet, including 1496 entries of Hordeum vulgare ssp. vulgare (HV), 229 entries of the six-rowed wild barley H. vulgare ssp. agriocrithon (HA), and 32 entries of the two-rowed wild barley H. vulgare ssp. spontaneum (HS), were assayed for allozymes at four esterase loci. A subsample of 491 accessions was surveyed for spacer-length polymorphism at two ribosomal DNA loci. Genetic variation is extensive in these barley groups, and the amount of genetic diversity in cultivated barley of this region is comparable with that of cultivated barley worldwide. The level of genetic variation of HA is significantly lower than the other two barley groups, and there is also substantial heterogeneity in the level of polymorphism among different agrigeographical subregions. However, little genetic differentiation was detected among the three barley groups (HV, HA, and HS), as well as among different agrigeographical subregions. Comparison of the results from this and previous studies indicated a strong differentiation between Oriental and Occidental barley, thus favoring the hypothesis of a diphyletic origin of cultivated barley.     

Extraordinarily polymorphic ribosomal DNA in wild and cultivated rice.

A collection of 481 rice accessions was surveyed for ribosomal DNA (rDNA) intergenic spacer length polymorphism to assess the extent of genetic diversity in Chinese and Asian rice germplasm. The materials included 83 accessions of common wild rice, Oryza rufipogon, 75 of which were from China; 348 entries of cultivated rice (Oryza sativa), representing almost all the rice growing areas in China; and 50 cultivars from South and East Asia. A total of 42 spacer length variants (SLVs) were detected. The size differences between adjacent SLVs in the series were very heterogeneous, ranging from ca. 21 to 311 bp. The 42 SLVs formed 80 different rDNA phenotypic combinations. Wild rice displayed a much greater number of rDNA SLVs than cultivated rice, while cultivated rice showed a larger number of rDNA phenotypes. Indica and japonica groups of O. sativa contained about equal numbers of SLVs, but the SLV distribution was significantly differentiated: indica rice was preferentially associated with longer SLVs and japonica rice with shorter ones. The results may have significant implications regarding the origin and evolution of cultivated rice, as well as the inheritance and molecular evolution of rDNA intergenic spacers in rice. Key words : rDNA, Oryza rufipogon, Oryza sativa, germplasm diversity, evolution.     

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.     

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.     

Wild and cultivated barleys show similar affinities for mineral nitrogen

Summary The kinetics of net ammonium influx were very similar among several cultivars of barley (Hordeum vulgare) and several accessions of the wild taxa H.v. spontaneum and H. jubatum. For net nitrate influx, variation was greater among accessions than among species; accessions from warmer climates had faster rates than those from colder climates. These data indicate that domestication of barley has not reduced its affinity for mineral nitrogen.     

中国大麦叶绿体DNA和核糖体RNA基因限制性片段长度多型性

本文报道了我们对我国不同大麦区80份大麦品种叶绿体DNA和核糖体RNA基因限制性片段长度多型性的研究。结果表明:rDNA间隔序列长度存在丰富的多样性,80份材料中出现了8种长度变异炎型共组成8种表现型。长度变异类型及其表现型在地理分布上存在着明显的区域性。推测这种分布上的地区性与植物对环境的适应性有关。所用的两个叶绿体DNA克隆片段未检测到限制性片段长度多型性,说明栽培大麦叶绿体DNA变异程度低。