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Lodging reduces grain yield in cereal crops. The height, diameter and strength of stem are crucial for lodging resistance, grain yield, and photosynthate transport in barley. Understanding the genetic basis of stem benefits barley breeding. Here, we evaluated 13 stem related traits after 28 days of heading in a barley DH population in two consecutive years. Significant phenotypic correlations between lodging index (LI) and other stem traits were observed. Three mapping methods using the experimental data and the BLUP data, detected 27 stable and major QTLs, and 22 QTL clustered regions. Many QTLs were consistent with previously reported traits for grain filling rate, internodes, panicle and lodging resistance. Further, candidate genes were predicted for stable and major QTLs and were associated with plant development and adverse stress in the transition from vegetative stage to reproductive stage. This study provided potential genetic basis and new information for exploring barley stem morphology, and laid a foundation for map-based cloning and further fine mapping of these QTLs.

Wheat contains the largest number of miR396 family with 17 miR396 in Poaceae. MiR396 regulatory network underlying wheat grain development has not comprehensively been explored. Our results showed that precursor miR396 family in Poaceae exhibited not only conservativeness but also diversification especially in wheat. Five haplotypes were detected in Poaceae species, while 4 haplotypes in wheat with Hap-4 (miR396a) and Hap-5 (miR396n) unique to wheat. GO enrichment analysis of target genes showed that the first 20 enrichment functions of miR396a and miR396n are completely different from each other, and also completely different from miR396(b-g), miR396(h-m), and miR396(o-q). Functional annotation on the 18 target genes shared by miR396(b-g), miR396(h-m), and miR396(o-q) found that 11 of the 18 target genes are growth-regulating factor (GRF) genes. Our results indicated that, during the grain filling stage of wheat, miR396 is involved in the development of grains by regulating the expression of GRF genes (GRF1, GRF6, and GRF9). Although the enrichment function of miR396(b-g), miR396(h-m), and miR396(o-q) is the same, the gene functional networks they formed differ greatly. Our results indicated that polyploidization enriches not only the diversity of miR396 family and its target genes but also gene functional networks in wheat. These results laid foundation for further elucidating function of miR396 gene family underlying wheat grain development.

To understand the molecular and physiological mechanism underlying the heat stress in maize, transcriptional and physiological response to heat stress in the heat-resistant Huangzaosi (HZS) and heat-sensitive Lv-9-Kuan (L9K) inbred lines at seedling stage were analyzed and compared at seedling stage. Our results indicated that MDA content of the two inbred lines increased significantly under heat stress; the values of MDA in L9K was significantly higher than that in HZS. The level of SOD, CAT, and POD enzyme activities in HZS was higher than those in L9K for both the heat-treated group and controls. The values of Fv/Fm, qP, and ФPSII reduced by heat stress in L9K were higher than the respective values in HZS. RNA-seq data showed that heat stress induced more heat stress-related genes in HZS (257 heat stress-related genes) than in L9K (224 heat stress-related genes). GO and KEGG enrichment analyses indicated that HZS and L9K changed their physiological and biochemical mechanisms in response to heat stress through different molecular mechanisms. Weighted Gene Co-expression Network Analysis showed that HZS might obtain stronger heat resistance than L9K through a unique transcriptional regulatory network. Our findings provide insights into the molecular networks that mediate the tolerance of maize heat stress and also help us to mine key heat stress-related genes.

More methylation changes occur in late interval than in early interval of wheat seed development with protein and the starch synthesis-related pathway enriched in the later stages. Wheat seed development is a critical process to determining wheat yield and quality, which is controlled by genetics, epigenetics and environments. The N6-methyladenosine (m

Seed size is one of the vital traits determining seed appearance, quality, and yield. Untangling the genetic mechanisms regulating soybean 100-seed weight (100-SW), seed length and seed width across environments may provide a theoretical basis for improving seed yield. However, there are few reports related to QTL mapping of 100-SW across multiple ecological regions. In this study, 21 loci associated with seed size traits were identified using a genome-wide association of 5361 single nucleotide polymorphisms (SNPs) across three ecoregions in China, which could explain 8.12%–14.25% of the phenotypic variance respectively. A new locus, named as SW9-1 on chromosome 9 that explained 10.05%–10.93% of the seed weight variance was found significantly related to seed size traits, and was not previously reported. The selection effect analysis showed that SW9-1 locus has a relatively high phenotypic effect (13.67) on 100-SW, with a greater contribution by the accessions with bigger seeds (3.69) than the accessions with small seeds (1.66). Increases in seed weight were accompanied by increases in the frequency of SW9-1T allele, with >90% of the bred varieties with a 100-SW >30 g carrying SW9-1T. Analysis of SW9-1 allelic variation in additional soybean accessions showed that SW9-1T allele accounting for 13.83% of the wild accessions, while in 46.55% and 51.57% of the landraces and bred accessions, respectively, this results indicating that the SW9-1 locus has been subjected to artificial selection during the early stages of soybean breeding, especially the utilization of SW9-1T in edamame for big seed. These results suggest that SW9-1 is a novel and reliable locus associated with seed size traits, and might have an important implication for increasing soybean seed weight in molecular design breeding. Cloning this locus in future may provide new insights into the genetic mechanisms underlying soybean seed size traits. Keywords: Soybean [Glycine max (L.) Merr.], Seed size/weight, SW9-1, Molecular breeding

Barley, Hordeum vulgare L., was first domesticated at about 8000 BCE. Throughout the domestication process, selection in the wild species resulted in the loss of seed shattering, minimization of se...

Background Elytrigia lolioides (Kar. et Kir.) Nevski, which is a perennial, cross-pollinating wheatgrass that is distributed in Russia and Kazakhstan, is classified into Elytrigia, Elymus, and Lophopyrum genera by taxonomists on the basis of different taxonomic classification systems. However, the genomic constitution of E. lolioides is still unknown. To identify the genome constitution and evolution of E. lolioides, we used single-copy nuclear genes acetyl-CoA carboxylase (Acc1) and elongation factor G (EF-G), multi-copy nuclear gene internal transcribed space (ITS), chloroplast gene trnL-F together with fluorescence and genomic in situ hybridization. Results Despite the widespread homogenization of ITS sequences, two distinct lineages (genera Pseudoroegneria and Hordeum) were identified. Acc1 and EF-G sequences suggested that in addition to Pseudoroegneria and Hordeum, unknown genome was the third potential donor of E. lolioides. Data from chloroplast DNA showed that Pseudoroegneria is the maternal donor of E. lolioides. Data from specific FISH marker for St genome indicated that E. lolioides has two sets of St genomes. Both genomic in situ hybridization (GISH) and fluorescence in situ hybridization (FISH) results confirmed the presence of Hordeum genome in this species. When E genome was used as the probe, no signal was found in 42 chromosomes. The E-like copy of Acc1 sequences was detected in E. lolioides possibly due to the introgression from E genome species. One of the H chromosomes in the accession W6–26586 from Kazakhstan did not hybridize H genome signals but had St genome signals on the pericentromeric regions in the two-color GISH. Conclusions Phylogenetic and in situ hybridization indicated the presence of two sets of Pseudoroegneria and one set of Hordeum genome in E. lolioides. The genome formula of E. lolioides was designed as StStStStHH. E. lolioides may have originated through the hybridization between tetraploid Elymus (StH) and diploid Pseudoroegneria species. E and unknown genomes may participate in the speciation of E. lolioides through introgression. According to the genome classification system, E. lolioides should be transferred into Elymus L. and renamed as Elymus lolioidus (Kar. er Kir.) Meld.

The evolutionary mechanism where autopolyploid tolerate abiotic stresses better than its diploid ancestor is poorly known. Large-scale gene-expression changes were not observed in synthetic autopolyploids compared to their respective diploids. However, natural autopolyploids with longer evolutionary periods might have experienced major changes that resulted in greater adaptation of autopolyploids, which might contribute to gene expression in natural autopolyploid differently from that in synthetic autopolyploid, and explain why genome doubling can help plants develop a stronger ability to adapt to various environmental stresses. However, information on this is still lacking. Here, diploid and autotetraploid sea barley tolerance to drought stress were analyzed. Our data showed that autotetraploids showed higher tolerance to drought stress than diploids. The results of GO enrichment and KEGG pathway enrichment showed that diploid and tetraploid would alter their physiological and biochemical process, even morphology to respond to drought stress via different molecular mechanism. Genome duplication resulted in more differentially expressed drought-related genes and higher expression level of those genes in autopolyploid than in diploid, 186 drought-related genes with 97 genes up-regulated in comparison of DiH826Dr_vs_DiH826Ck, while 297 drought-related genes with 126 up-regulated in TetraH832Dr_vs_TetraH832Ck. Among these drought-related genes, 81 of them were specific significantly expressed in DiH826Dr_vs_DiH826Ck, 192 genes were specific significantly expressed in TetraH832Dr_vs_TetraH832Ck. Although our results indicated that the autopolyploid does not seem to undergo major changes of gene expression over long periods (2.84%) and under drought stress, more DEGs and more up-regulated DEGs between autotetraploid and diploid were observed than those in the CK. Furthermore, genome duplication also resulted in gain or loss of drought-related genes, which might offer potential for autopolyploid to survive better under drought environment.

Background Barley is one of the earliest domesticated crops and regarded as one of the founder of Neolithic transition in the Near East Fertile Crescent. Domestication process of cultivated barley (especially east-Asian cultivated barley) has been under debate because of the controversial origin centers of barley, which caused by widely dispersal of wild barley. What’s more, no comprehensive study regarding alteration in metabolism during domestication has been delineated in barley so far. Results Transcriptomic and non-targeted metabolic analyses were performed for two wild barley populations (wild barley of Near East Fertile Crescent (Wb-NE), and wild barley of Tibetan Plateau (Wb-T)), and one cultivated barley population (cultivated barley of China (Cb-C)), the results revealed two stages of the domestication process of Cb-C, first from Wb-NE to Wb-T, and then from Wb-T to Cb-C. The Wb-T played an important intermediate role in the domestication from Wb-NE to Cb-C, and had made more genetic contribution than Wb-NE to Cb-C. Meanwhile, we found continuous gene flow, a large number of selective genes and metabolites during domestication. Divergent metabolites of alkaloids and phenylpropanoids were specific targeted in stages from Wb-NE to Wb-T and from Wb-T to Cb-C, respectively. The key missense SNPs in genes HORVU6Hr1G027650 and HORVU4Hr1G072150 might be related to the divergence of metabolites of alkaloids and phenylpropanoids during domestication. Conclusions Our results revealed that two stages of the domestication process of Cb-C, and distinct sets of metabolites were targeted by selection during the evolution from wild barley of the Near East Fertile Crescent to Tibetan wild barley to cultivated barley of China. Our findings not only provided genetic and metabolic insights into domestication process of barley but also highlighted the power of combining omics data for trait dissection.

Triticum aestivum xylanase inhibitor (TaXI) gene plays an important role in plant defense. Recently, TaXI–III inhibitor has been shown to play a dual role in wheat resistance to Fusarium graminearum infection. Thus, identifying the members of the TaXI gene family and clarifying its role in wheat resistance to stresses are essential for wheat resistance breeding. However, to date, no comprehensive research on TaXIs in wheat (Triticum aestivum L.) has been conducted. In this study, a total of 277 TaXI genes, including six genes that we cloned, were identified from the recently released wheat genome database (IWGSC RefSeq v1.1), which were unevenly located on 21 chromosomes of wheat. Phylogenetic analysis divided these genes into six subfamilies, all the six genes we cloned belonged to XI-2 subfamily. The exon/intron structure of most TaXI genes and the conserved motifs of proteins in the same subfamily are similar. The TaXI gene family contains 92 homologous gene pairs or clusters, 63 and 193 genes were identified as tandem replication and segmentally duplicated genes, respectively. Analysis of the cis-acting elements in the promoter of TaXI genes showed that they are involved in wheat growth, hormone-mediated signal transduction, and response to biotic and abiotic stresses. RNA-seq data analysis revealed that TaXI genes exhibited expression preference or specificity in different organs and developmental stages, as well as in diverse stress responses, which can be regulated or induced by a variety of plant hormones and stresses. In addition, the qRT-PCR data and heterologous expression analysis of six TaXI genes revealed that the genes of XI-2 subfamily have double inhibitory effect on GH11 xylanase of F. graminearum, suggesting their potential important roles in wheat resistance to F. graminearum infection. The outcomes of this study not only enhance our understanding of the TaXI gene family in wheat, but also help us to screen more candidate genes for further exploring resistance mechanism in wheat.

BackgroundUlmus lamellosa(one of the ancient species ofUlmus) is an endemic and endangered plant that has undergone climatic oscillations and geographical changes. The elucidation of its demographic history and genetic differentiation is critical for understanding the evolutionary process and ecological adaption to forests in Northern China.ResultsPolymorphic haplotypes were detected in most populations ofU. lamellosavia DNA sequencing. All haplotypes were divided into three phylogeographic clades fundamentally corresponding to their geographical distribution, namely THM (Taihang Mountains), YM (Yinshan Mountains), and YSM (Yanshan Mountains) groups. The YSM group, which is regarded as ancestral, possessed higher genetic diversity and significant genetic variability in contrast to the YSM and YM groups. Meanwhile, the divergence time of intraspecies haplotypes occurred during the Miocene-Pliocene, which was associated with major Tertiary geological and/or climatic events. Different degrees of gene exchanges were identified between the three groups. During glaciation, the YSM and THM regions might have served as refugia forU. lamellosa. Based on ITS data, range expansion was not expected through evolutionary processes, except for the THM group. A series of mountain uplifts (e.g., Yanshan Mountains and Taihang Mountains) following the Miocene-Pliocene, and subsequently quaternary climatic oscillations in Northern China, further promoted divergence betweenU. lamellosapopulations.ConclusionsGeographical topology and climate change in Northern China played a critical role in establishing the current phylogeographic structural patterns ofU. lamellosa. These results provide important data and clues that facilitate the demographic study of tree species in Northern China.

In common wheat, stem strength is one of the key factors for lodging resistance, which is influenced by lignin content. Cinnamyl alcohol dehydrogenase (CAD) is a vital enzyme in the pathway of lignin biosynthesis. Cloning and marker development of the CAD gene could be helpful for lodging resistance breeding. In this study, the full-length genomic DNA sequence of CAD gene in wheat was cloned by using homologous strategy. A marker 5-f2r2 was developed based on CAD sequence and used to genotype 258 wheat lines. Four haplotype combinations of CAD genes were identified in 258 wheat lines. Correction analyses among the CAD gene expression, CAD activity, and stem strength indicated significant positive correlation between CAD gene expression and CAD activity, between wheat CAD activity and wheat stem strength. The haplotype combination B is significantly associated with the lower enzyme activity and weak stem strength, which was supported by the level of CAD gene expression. The CAD activity and stem strength of wheat could be distinguished to some extent using this pair of specific primer 5-f2r2 designed in this study, indicating that the sequence targeted site (STS) marker 5-f2r2 could be used in marker assistant selection (MAS) breeding.

Several studies have shown that autopolyploid can tolerate abiotic stresses better than its diploid ancestor. However, the underlying molecular mechanism is poorly known. microRNAs (miRNAs) are small RNAs that regulate the target gene expression post-transcriptionally and play a critical role in the response to abiotic stresses. Duplication of the whole genome can result in the expansion of miRNA families, and the innovative miRNA-target interaction is important for adaptive responses to various environments. We identified new microRNAs induced by genome duplication, that are also associated with stress response and the distinctive microRNA networks in tetraploid and diploid Hordeum bulbosum using high-throughput sequencing. Physiological results showed that autotetraploid Hordeum bulbosum tolerated salt stress better than its diploid. Comparison of miRNAs expression between diploid and tetraploid check (CK) and salt stress revealed that five miRNAs affected by genome doubling were also involved in salt stress response. Of these, miR528b-3p was only detected in the tetraploid, and downregulated under salt stress relative to that in tetraploid CK. Moreover, through target prediction, it was found that miR528b-3p was not only involved in DNA replication and repair but also participated in salt stress response. Finally, by analyzing all the differentially expressed microRNAs and their targets, we also discovered distinguished microRNAs-target regulatory networks in diploid and tetraploid, respectively. Overall, the results demonstrated the critical role of microRNAs in autopolyploid to have better tolerance salt stress.

In Hordeum vulgare, nine differentially expressed novel miRNAs were induced by colchicine. Five novel miRNA in colchicine solution showed the opposite expression patterns as those in water. Colchicine is a commonly used agent for plant chromosome set doubling. MicroRNA-mediated responses to colchicine treatment in plants have not been characterized. Here, we characterized new microRNAs induced by colchicine treatment in Hordeum vulgare using high-throughput sequencing. Our results showed that 39 differentially expressed miRNAs were affected by water treatment, including 34 novel miRNAs and 5 known miRNAs; 42 miRNAs, including 37 novel miRNAs and 5 known miRNAs, were synergistically affected by colchicine and water, and 9 differentially expressed novel miRNAs were induced by colchicine. The novel_mir69, novel_mir57, novel_mir75, novel_mir38, and novel_mir56 in colchicine treatment showed the opposite expression patterns as those in water. By analyzing these 9 differentially expressed novel miRNAs and their targets, we found that novel_mir69, novel_mir56 and novel_mir25 co-target the genes involving the DNA repair pathway. Based on our results, microRNA-target regulation network under colchicine treatment was proposed, which involves actin, cell cycle regulation, cell wall synthesis, and the regulation of oxidative stress. Overall, the results demonstrated the critical role of microRNAs mediated responses to colchicine treatment in plants.

Grain size and weight are crucial components of barley yield and quality and are the target characteristics of domestication and modern breeding. Despite this, little is known about the genetic and molecular mechanisms of grain size and weight in barley. Here, we evaluated nine traits determining grain size and weight, including thousand grain weight (Tgw), grain length (Gl), grain width (Gw), grain length-width ratio (Lwr), grain area (Ga), grain perimeter (Gp), grain diameter (Gd), grain roundness (Gr), and factor form density (Ffd), in a double haploid (DH) population for three consecutive years. Using five mapping methods, we successfully identified 60 reliable QTLs and 27 hotspot regions that distributed on all chromosomes except 6H which controls the nine traits of grain size and weight. Moreover, we also identified 164 barley orthologs of 112 grain size/weight genes from rice, maize, wheat and 38 barley genes that affect grain yield. A total of 45 barley genes or orthologs were identified as potential candidate genes for barley grain size and weight, including 12, 20, 9, and 4 genes or orthologs for barley, rice, maize, and wheat, respectively. Importantly, 20 of them were located in the 14 QTL hotspot regions on chromosome 1H, 2H, 3H, 5H, and 7H, which controls barley grain size and weight. These results indicated that grain size/weight genes of other cereal species might have the same or similar functions in barley. Our findings provide new insights into the understanding of the genetic basis of grain size and weight in barley, and new information to facilitate high-yield breeding in barley. The function of these potential candidate genes identified in this study are worth exploring and studying in detail.

Recent molecular phylogenetic studies on Elymus have added to our understanding of the origination of Elymus species. However, evolutionary dynamics and speciation of most species in Elymus are unclear. Molecular phylogeny has demonstrated that reticulate evolution has occurred extensively in the genus, as an example, the largest subunit of RNA polymerase II (rpb2) and phosphoenolpyruvate carboxylase (pepC) data revealed two versions of the St genome, St1 and St2 contributing to speciation of E. caninus. Phylogenetic analyses of E. pendulinus uncovered additional genome-level complexity. Our data indicated that both chloroplast and nuclear gene introgression have occurred in the evolutionary process of E. pendulinus. Non-donor species genomes have been detected in several Elymus species, such as in allohexaploid E. repens (StStStStHH), a Taeniatherum-like (Ta genome in Triticeae) GBSSI sequence, Bromus- (Bromeae) and Panicum-like (Paniceae) ITS sequences have been detected. The chloroplast DNA data indicated that Pseudoroegneria is the maternal genome donor to Elymus species, but whether different Elymus species originated from different St donors remains an open question. The origin of the Y genome in Elymus is puzzling. It is clear that the Y genome is distinct from the St genome, but unclear on the relationships of Y to other genomes in Triticeae. Introgressive hybridization may be an important factor complicating the evolutionary history of the species in Elymus. The extent of introgression and its role in creating diversity in Elymus species should be the objective of further investigations.

Bread wheat (AABBDD) originated from the diploid progenitor Triticum urartu (AA), a relative of Aegilops speltoides (BB), and Ae. tauschii (DD). The DREB1 transcriptional factor plays key regulatory role in low-temperature tolerance. The modern breeding strategies resulted in serious decrease of the agricultural biodiversity, which led to a loss of elite genes underlying abiotic stress tolerance in crops. However, knowledge of this gene's natural diversity is largely unknown in the genome donor species of wheat. We characterized the dehydration response element binding protein 1 (DREB1) gene-diversity pattern in Ae. speltoides, Ae. tauschii, T. monococcum and T. urartu. The highest nucleotide diversity value was detected in Ae. speltoides, followed by Ae. tauschii and T. monococcum. The lowest nucleotide diversity value was observed in T. urartu. Nucleotide diversity and haplotype data might suggest no reduction of nucleotide diversity during T. monococcum domestication. Alignment of the 68 DREB1 sequences found a large-size (70 bp) insertion/deletion in the accession PI486264 of Ae. speltoides, which was different from the copy of sequences from other accessions of Ae. speltoides, suggesting a likely existence of two different ancestral Ae. speltoides forms. Implication of sequences variation of Ae. speltoides on origination of B genome in wheat was discussed.

Waterlogging is a main stress factor during the late growing stage of winter wheat (Triticum aestivum L.) in the southern Huanghuai and Yangtze Valley regions of China. The effects of nitrogen spraying on post-anthesis of winter wheat under waterlogging stress were studied in continuous growing seasons from 2009 to 2011. The results showed that waterlogging after the anthesis stage significantly reduced root respiratory activity, leaf greenness (SPAD reading), photosynthetic rate (Pn), stomatal conductance (Gs) and transpiration rate (Tr) by averages of 11.09, 10.75, 15.18, 8.97 and 8.82 %, respectively, increased intercellular CO2 concentration (Ci) by 9.74 % and decreased grain number per spike, 1,000-grain weight and grain yield by 8.07, 12.68 and 20.11 %, respectively. Nitrogen spraying significantly improved root respiratory activity, leaf greenness (SPAD reading), photosynthetic rate (Pn), stomatal conductance (Gs) and transpiration rate (Tr) by 4.96, 7.35, 7.01, 5.09 and 5.09 %, respectively, reduced intercellular CO2 concentration (Ci) by 9.74 % and increased grain number per spike, 1,000-grain weight and grain yield by 4.71, 6.45 and 11.48 %, respectively. However, neither nitrogen spraying nor waterlogging had significant effects on spike number. There was significant interaction between waterlogging and nitrogen spraying. Our results suggest that nitrogen spraying is an effective way to alleviate the negative effects of waterlogging stress after anthesis stage in winter wheat.

A long-period duration of seed dormancy helps to reduce pre-harvest sprouting (PHS) damage in common wheat when a long period of rainfall or high humidity occurs. Identification of genes or loci underlying seed dormancy duration is of high importance for investigating genetic mechanism of PHS tolerance of wheat. In the present study, the germination index (GI) of different mapping populations at 5 days (GI5), 15 days (GI15), and 30 days (GI30) after harvest (DAH) was recorded during the 2011–2012, 2012–2013, 2013–2014, and 2014–2015 cropping seasons. Field sprouting (FS) values were also determined in 2012–2013 and 2014–2015 cropping seasons. Association analysis was performed in 260 wheat varieties and advanced lines differing in seed dormancy (SD) using 557 SSR and 14 gene-specific markers for PHS/SD-related genes. The result indicated that a total of 47 loci were significantly (P

Thousand-grain weight (TGW) of wheat (Triticum aestivum L.) contributes significantly to grain yield. In the present study, a candidate gene associated with TGW was identified through specific-locus amplified fragment sequencing (SLAF-seq) of DNA bulks of recombinant inbred lines (RIL) derived from the cross between Jing 411 and Hongmangchun 21. The gene was located on chromosome 7A, designated as TaTGW-7A with a complete genome sequence and an open reading frame (ORF). A single nucleotide polymorphism (SNP) was present in the first exon between two alleles at TaTGW-7A locus, resulting in a Val to Ala substitution, corresponding to a change from higher to lower TGW. Cleaved amplified polymorphic sequence (CAPS) (TGW7A) and InDel (TG9) markers were developed to discriminate the two alleles TaTGW-7Aa and TaTGW-7Ab for higher and lower TGW, respectively. A major QTL co-segregating with TaTGW-7A explained 21.7–27.1% of phenotypic variance for TGW in the RIL population across five environments. The association of TaTGW-7A with TGW was further validated in a natural population and Chinese mini-core collections. Quantitative real-time PCR revealed higher transcript levels of TaTGW-7Aa than those of TaTGW-7Ab during grain development. High frequencies of the superior allele TaTGW-7Aa for higher TGW in Chinese mini-core collections (65.0%) and 501 wheat varieties (86.0%) indicated a strong and positive selection of this allele in wheat breeding. The molecular markers TGW7A and TG9 can be used for improvement of TGW in breeding programs.

Brassica rapa L. is an important vegetable and oilseed crop. Cytoplasmic diversity of 36 B. rapa accessions was analyzed using the mitochondria-specific markers. Twelve representative materials including five additional Brassica species and one Eruca sativa Mill. were used as references. A modified multiplex PCR amplification using four pairs of primers was performed to test the mitochondrial types (mitotypes) of the tested materials. Ten accessions were detected with Cam-I mitotype which could amplify 500 and 800 bp bands, twenty-two accessions with Cam-II mitotype which could amplify 500, 800 and 906 bp bands, one accession with Pol mitotype. Interestingly, three B. rapa accessions were revealed with nap mitotype, two of them were local landraces in northern Shaanxi, the third one was a variety from Gansu province which was developed using one local landrace from Northern Shaanxi as female parent. The considerable cytoplasmic diversity in B. rapa provides useful information on studying the possible origin and evolution of B. rapa accessions, and conservation of the germplasm.

In the rice genome, insertions and eliminations of transposable elements have generated numerous transposon insertion polymorphisms (TIPs). Common wild rice (O. rufipogon Griff.), the ancestor of Asian cultivated rice (O. sativa L.), carries abundant genetic variations. To find subspecies-specific (SS) markers that can distinguish O. sativa ssp. indica and ssp. japonica, some long terminal repeat (LTR) sequences (sc1-14) of AA genome-specific RIRE retrotransposon were isolated from O. rufipogon genome. Sequences sc1 and sc12 were successfully utilized to develop the SS marker system based on retrotransposon inserted position polymorphisms. Twenty-two SS markers (ssi1-9, ssj1-13) were developed, where ssi1-9 are the indica-specific types, and ssj1-13 the japonica-specific types. The average accuracy of these markers in distinguishing the two subspecies is over 85%. SS marker ssj-10 can distinguish the two subspecies at 100% accuracy. Principal component analysis (PCA) showed that these markers could successfully distinguish indica from japonica varieties, regardless of their geographical origin.

Molecular diversity of 40 accessions of Tibetan wild barley (TB), 10 Syrian (SY), 72 North American (NA), 36 European (EU), 9 South American (SA) and 8 Australian (AU) varieties were characterized using multiple microsatellite loci. The 42 SSR primers amplified 278 alleles across the 175 barley accessions tested in the present study. The average gene diversity for the whole sample was 0.3387 whereas the mean value for the each population was as follows: TB = 0.3286, SY = 0.2474, EU = 0.299, AU = 0.2867, NA = 0.3138, SA = 0.2536. Clustering analysis based on Nei’s original genetic distance showed that the EU and NA barley populations were grouped together. The TB population was well separated from the other 5 barley populations. Associations between microsatellite markers and 14 quantitative traits were also investigated. Significant associations were found for 18 microsatellite marker loci. The number of marker loci associated with each trait ranged from one (stem diameter, filled grains per plant, grain weight per plant, length of main spike and awn length) to seven (plant height). The percentage of the total variation explained by each marker ranged from 4.59% (HVM2 associated with plant height) to 17.48% (Bmac90 associated with density of main spike). This study provides candidate markers for further QTL mapping of these traits and for marker-assisted selection.

Heterosis has been exploited in many crops and made a significant contribution to the world food supply. Genetic distance (GD) is one of valuable criteria for selecting parents in hybrid breeding. The objectives of this study were to estimate GD between a novel photoperiod-thermo sensitive male sterile wheat line 337S and several common cultivars using simple sequence repeat (SSR) markers, and to evaluate the relationship of GD and heterosis. The line 337S, as a maternal parent, was crossed with 16 common wheat varieties to produce 16 hybrids. Eight agronomic traits were investigated for the parents and F1 hybrids. Mid-parent heterosis (MPH) and specific combining ability (SCA) were calculated. GD and cluster analysis were performed among the 17 parents. The correlations of GD with F1 performance, MPH and SCA were analyzed. The results showed that GD estimates among the 17 parents averaged 0.42 with a range from 0.26 to 0.57, and the averaged GD between 337S and the 16 parental cultivars was 0.44. Cluster analysis separated the 17 parents into three main groups. SSR markers were useful in analyzing genetic divergences among the 17 parental lines. However, GD based on SSR markers poorly correlated with F1 performance, MPH and SCA. Thus, GD revealed by SSR markers can not provide a reliable prediction in practical wheat hybrid breeding.

Although there have been several studies on the maternal genome donor of StStYY Elymus species, due to either the lack of inclusion of all the Triticeae diploid species or limited number of StY species used in the previous studies, it is necessary to investigate the origin of the maternal genome of the StStYY Elymus species with comprehensive samples of Triticeae diploid species. In this study we analyzed 18 tetraploid StStYY Elymus species along with 27 diploid Triticeae species using chloroplast gene encoding ribosomal protein S16 (rps16) in an attempt to identify the maternal genome donor of StStYY Elymus species. The rps16 data indicates that Pseudoroegneria is the maternal genome donor of StStYY Elymus species. A close relationship of the chloroplast of Thinopyrum and Dasypyrum with the St genome is found which leaves the possibility that Thinopyrum and Dasypyrum may have contributed to the chloroplast genome in StStYY species. We also analyzed the cpDNA phylogeny for the monogenomic genera. Psathyrostachys juncea is at the base of the Triticeae tree, while the rest of the Triticeae species forms a well supported clade with a 91% bootstrap value. Triticum monococcum, Secale cereale, Heteranthelium piliferum and all the Aegilops species form a clade. A very similar chloroplast genome between Agropyron and Eremopyrum is detected. Our rps16 data supports the placement of Henrardia within the Triticeae in a Henrardia + Eremopyrum clade.

High embryogenesis capacity of soybean (Glycine max (L.) Merr.) in vitro possessed potential for effective genetic engineering and tissue culture. The objects of this study were to identify quantitative trait loci (QTL) underlying embryogenesis traits and to identify genotypes with higher somatic embryogenesis capacity. A mapping population, consisting of 126 F(5:6) recombinant inbred lines, was advanced by single-seed-descent from cross between Peking (higher primary and secondary embryogenesis) and Keburi (lower primary and secondary embryogenesis). This population was evaluated for primary embryogenesis capacity from immature embryo cultures by measuring the frequency of somatic embryogenesis (FSE), the somatic embryo number per explant (EPE) and the efficiency of somatic embryogenesis (ESE). A total of 89 simple sequence repeat markers were used to construct a genetic linkage map. Six QTL were associated with somatic embryogenesis. Two QTL for FSE were found, QFSE-1 (Satt307) and QFSE-2 (Satt286), and both were located on linkage group C2 that explained 45.21 and 25.97% of the phenotypic variation, respectively. Four QTL for EPE (QEPE-1 on MLG H, QEPE-2 on MLG G and QEPE-3 on MLG G) were found, which explained 7.11, 7.56 and 6.12% of phenotypic variation, respectively. One QTL for ESE, QESE-1 (Satt427), was found on linkage group G that explained 6.99% of the phenotypic variation. QEPE-2 and QESE-1 were located in the similar region of MLG G. These QTL provide potential for marker assistant selection of genotypes with higher embryogenesis.

Trigrain wheat normally produces up to three gynoecia in a single floret and forms three close-set grains. The gene conferring the multi grain phenotype was earlier designated Mg, the multiple gynoecia gene. Different genetic patterns controlling this trait have been reported. In the present work we studied the inheritance of the three grains trait and identified simple sequence repeats (SSR) markers linked to the Mg gene. Segregation analysis in the cross IGDB-TW (trigrain wheat)/Chinese Spring confirmed that a single dominant gene controlled the three grains trait. An allelism test showed that the same gene controlled the trigrain trait in line Trigrain-Yin 1. A total of 339 microsatellite markers were tested for polymorphism by bulked segregation analysis (BSA) in an F2 population. Six microsatellite markers, Xcfd233, Xgdm6, Xgdm87, Xgwm311, Xgwm349 and Xgwm539, on chromosome 2DL, were linked to Mg. Using the CS 2D deletion lines, Mg gene was localized to the distal region of chromosome 2DL. The microsatellite markers identified in this study have the potential for further mapping and map-based cloning of the gene.Key words: Simple sequence repeats, physical mapping, trigrain wheat

The relationship between the floral morphology, especially the heterostyly, and the pollination ability in Epimedium sagittatum was investigated. Three distinct kinds of flowers were observed in this species: (1) about 54% of the flowers had pistils that were of equal length or shorter than the stamens (PESS); (2) in 23.5% of the flowers, the pistils were longer than the stamens (PLS), and; (3) in 22.5% of the flowers, the styles were positioned axially away from the anthers (SAA). No significant difference in fruit setting rate was observed between PLS and SAA flowers, but PESS flowers set less fruits than the other two. A breeding experiment indicated that the species was self-incompatible, and revealed that the presence of PLS and SAA could increase outcrossing and fruit set. A field experiment showed that open-pollinated flowers of E. sagittatum produced significantly less fruits than an artificial xenogamy experiment. This may be because most of the flowers in natural populations have pistils and anthers of the same length (PESS). The principal visitors and effective pollinators are Bombus sp1 and Bombus sp2. Attractant experiments indicated that the fruit set of flowers whose spurs were removed was significantly lower than that of flowers whose stamens were removed, suggesting that the spurs of the flowers could strongly increase the pollinator visitation and fruit set. The results therefore showed that floral morphology could significantly affect fruit set in E. sagittatum.

It is well known that Elymus arose through hybridization between representatives of different genera and several different polyhaplomic genomes have been described. Cytogenetically, five basic genomes (St, H, Y, P and W) in different combinations have been found in the genus. The vast majority of species are tetraploids and they are characterized by having the StY genome or the StH genome. It is not known where the Y genome originated, although it is a common in Elymus from Central and East Asia. It has been hypothesized from isozymic and cytological studies of Elymus species that the Old and New World taxa may be of separate origin of the H genome in the StH genome species. Data from single copy of nuclear gene RPB2 indicated that the Eurasian and American StH genome species have independent alloploid origins with different Hgenome donors. This hypothesis is needed to be tested by using more molecular data. Sequences from single copy of nuclear genes (RPB2, β-amylase gene and EF-G) indicated that StY genome species is allopolyploid origin. This paper presents a briefly review on current status of molecular evolution and origin of tetraploid Elymus species.

The supernumerary spikelet character of bread wheat (Triticum aestivum L.) is an abnormal spike with extra spikelet per spike. Supernumerary spikelet line 51885 was derived from the cross between octoploid Triticale and common wheat Fei 5056. The number of spikelet is over 30, and supernumerary spikelet is genetically stable. The inheritance of supernumerary spikelets in the line 51885 was genetically analyzed by crossed with seven commercial cultivars of normal head type. The results indicated that supernumerary spikelet in the line 51885 was controlled by two dominant genes which shows complementary function. Transgressive segregation for increasing the number of spikelet were observed in the four crosses, suggesting the possibility of the presence of minor effect gene(s) or modification gene(s) affecting the expression of the supernumerary spikelet in addition to the two major dominant genes. The relatively simple inheritance, feature of dominance plus the stability of expression of supernumerary spikelet in the line 51885 indicate that line 51885 could be easily incorporated in high yield breeding program in common wheat.

Random amplified polymorphic DNA (RAPD) and simple sequence repeat (SSR) markers were used to estimate the genetic relationships among 101 soybean cultivars developed in north-eastern China. Fifty-three fragments of the 100 RAPD markers and 35 SSR markers tested were polymorphic across the 101 soybean cultivars. Similarity values among these soybean cultivars ranged from 45.2% to 100% for RAPD data, and ranged from 36.1% to 100% for SSR data. The similarity matrices for SSR data and RAPD data were moderately correlated (r = 0.31, P 2200. Four RAPD markers and eight SSR markers were significantly associated with the maturity ratings of soybean.

The genus Dipteronia Oliv. endemic to central and southern China consists of two species, D. sinensis Oliv. and D. dyerana Henry, both of them are rare and endangered. In the present study, genetic variation in 17 populations of D. sinensis and four populations of D. dyerana was estimated using ten polymorphic chloroplast microsatellite loci (cpSSR). Forty-nine chloroplast haplotypes were identified from 204 individuals analyzed. Thirty-nine haplotypes were found in D. sinensis, while ten in D. dyerana. No haplotype was shared between the species. AMOVA analysis revealed that the majority of the genetic variation was partitioned among populations within D. sinensis (FST = 0.7980) and D. dyerana (FST = 0.654). Cluster analysis grouped the 21 populations into two groups according to their species delimitation. The populations of D. sinensis were further divided into two subgroups corresponding to their geographical distributions. Correlation analysis revealed significant correlation between geographical distance and genetic distance of these populations (r = 0.326, p < 0.01 for D. sinensis vs. r = 0.777, p < 0.05 for D. dyerana). Genetic structure of these populations and a calculated pollen-to-seed flow ratio of (3.2:1 vs. 0.6:1) within the species suggested that little gene flow has occurred among the populations over an extended period. Thus, it implies that the genus Dipteronia might have experienced a genetic bottleneck and limited expansion during its evolutionary history.

In rice, the TGW6 gene determines grain weight and encodes a protein with indole-3-acetic acid (IAA)-glucose hydrolase activity. Its homolog in wheat, TaTGW6, is considered as a candidate gene related to grain development. To amplify this gene, we designed primers based on a homologous conserved domain of the rice TGW6 gene. Sequence analysis indicated that TaTGW6 comprises only one exon, with 1656 bp in total and an open reading frame of 1035 bp. Three alleles at TaTGW6 locus detected by the primer pair TG23 were designated as TaTGW6-a, TaTGW6-b and TaTGW6-c, respectively. Compared with TaTGW6-a, TaTGW6-b had a 6-bp InDel at the position 170 downstream of initiation codon, and TaTGW6-c was a null mutant. Both TaTGW6-b and TaTGW6-c could significantly increase grain size and weight other than TaTGW6-a; however, the former two alleles showed a low frequency distribution in modern varieties. TaTGW6 was located on chromosome 4AL using a recombinant inbred line population and a set of Chinese Spring nullisomic-tetrasomic lines. It was linked to the SSR locus Xbarc1047 with a genetic distance of 6.62 cM and explained 15.8–21.0 % of phenotypic variation of grain weight in four environments. Association analysis using a natural population and Chinese wheat mini-core collections additionally validated the relationship of TaTGW6 with grain weight; the gene could explain 7.7–12.4 % of phenotypic variation in three environments. Quantitative real-time PCR revealed that TaTGW6-b showed relatively lower expression than TaTGW6-a in immature grain at 20 and 30 days post-anthesis and in mature grain. The low expression of TaTGW6 generally associated with low IAA content, but with high grain weight. The novel functional marker, designated as TG23, can be used for marker-assisted selection to improve grain weight in wheat and also provides insights into the regulatory mechanism underlying grain weight.

Elymus trachycaulus complex species are known for their morphological variability, but little is known about their genetic basis. The phylogenetic relationships among the E. trachycaulus complex, and their systematic relation to other species in Triticeae remain unknown. Nucleotide diversity of ribulose-1,5 bisphosphate-carboxylase (rbcL) gene in E. trachycaulus complex species and several other Triticeae was first characterized and compared. A primary conclusion of the present study is that nucleotide diversity for rbcL gene in E. trachycaulus species was detected with the estimates of nucleotide diversity θ = 0.00039 and π = 0.00043. The estimate of nucleotide diversity in rbcL gene for species with different genome constitution here ranged from 0.00099 (π) and 0.00099 (θ) for the species with Ns genome to 0.00226 (π) and 0.00291 (θ) for the species with St genome. The phylogenetic relationships of these species were assessed using these rbcL sequences. A total of 47 variable positions including 19 parsimony-informative sites were detected among 24 accessions of 18 species/subspecies. The species with St, H/I and Ns genomes well separated from each other, and formed a three distinct clades with higher bootstrap values support for both Parsimony and NJ analyses. The St genome containing species is sister group of H/I genome containing species. Our result confirms that Pseudoroegneria is the maternal genome donor to these Elymus species studied here, regardless of their distribution. Elymus trachycaulus complex are more related to each other than to E. glaucescens, E. patagonicus, and E. solandri. This study suggested that Elymus species with StH genomes may form from multiple closely related sets of donors.

The origin, evolution, and distribution of cultivated barley provides powerful insights into the historic origin and early spread of agrarian culture. Here, population-based genetic diversity and phylogenetic analyses were performed to determine the evolution and origin of barley and how domestication and subsequent introgression have affected the genetic diversity and changes in cultivated barley on a worldwide scale. A set of worldwide cultivated and wild barleys from Asia and Tibet of China were analyzed using the sequences for NAM-1 gene and gene-associated traits-grain protein content (GPC). Our results showed Tibetan wild barley distinctly diverged from Near Eastern barley, and confirmed that Tibet is one of the origin and domestication centers for cultivated barley, and in turn supported a polyphyletic origin of domesticated barley. Comparison of haplotype composition among geographic regions revealed gene flow between Eastern and Western barley populations, suggesting that the Silk Road might have played a crucial role in the spread of genes. The GPC in the 118 cultivated and 93 wild barley accessions ranged from 6.73 to 12.35% with a mean of 9.43%. Overall, wild barley had higher averaged GPC (10.44%) than cultivated barley. Two unique haplotypes (Hap2 and Hap7) caused by a base mutations (at position 544) in the coding region of the NAM-1 gene might have a significant impact on the GPC. Single nucleotide polymorphisms and haplotypes of NAM-1 associated with GPC in barley could provide a useful method for screening GPC in barley germplasm. The Tibetan wild accessions with lower GPC could be useful for malt barley breeding.

The genetic diversity and relationships among 63 rapeseed accessions, including 34 Chinese, 22 Czech, 2 Swedish, 2 German, one French and 2 Canadian accessions, were evaluated by nine agronomically important characters in the field at Yangling, Shaanxi, China. Significant differences between Chinese and European group in plant height, setting position of the first primary branch, number of siliques of the terminal raceme, thousand seed weight and seed yield per plant were detected. There were significant variations in nine agronomic characters among the tested rapeseed accessions. Ward’s minimum variance cluster analysis based on Mahalanobis distances on the raw data of nine agronomic characters clearly separated the European accessions from the Chinese ones. However, the Chinese accessions with erucic acid free and/or low glucosinolates could not be separated from those Chinese accessions with both high erucic acid and glucosinolates. In general, cluster analysis of the 63 accessions based on the selected agronomic characters was consistent with known pedigree information and geographic origin, as well as the previous RAPD results of these accessions. The European rapeseed could be important germplasm resources for enriching the genetic background of Chinese rapeseed, and vice versa.

A sulphonylurea herbicide, tribenuron-methyl, methyl 2-[[[[(4-methoxy-6-methyl-1,3,5-triazin-2-yl) methylamino] carbonyl] amino] sulphonyl] benzoate, was used to induce male sterility in rapeseed. Application of 0.2 [mu]g tribenuron-methyl per plant at the bolting stage with the longest floral bud 0.2 [mu]g per plant) did have some significant impact on rapeseed, including stunting, fading leaves and petals, reduction in the size of floral parts and a shortened duration of flowering. The percentage of hybrid seeds from '84004' treated with 0.2 [mu]g [multiplication] 2 tribenuron-methyl per plant and pollinated by a male parent 'Huaye' was 92.7%, which met the hybridity requirement in China. The results suggest that tribenuron-methyl could be used as an efficient chemical hybridizing agent.

Species of the E. trachycaulus complex species are known for their morphological variability, but little is known about their genetic basis. The delimitation of taxa within the complex has been controversial and difficult. E. trachycaulus is predominantly self-pollinating, and lacks clear morphological boundaries between it and E. alaskanus. Another controversial taxonomic issue of E. trachycaulus is the relationships of this complex species to non-North American E. caninus. The objectives of this study were to examine genetic diversity and the systematic relationships among the species of the E. trachycaulus complex and their relationships with E. caninus, E. alaskanus and E. mutabilis. Random amplified polymorphic DNA method was used to study 35 accessions of E. trachycaulus complex and other Elymus species. Higher genetic variation was detected within species of E. trachycaulus complex. Eurasian accessions are as variable as the North American ones. Both UPGMA and NJ analyses did not show clearly separation among species of the E. trachycaulus complex. No clear association between geographic origin and genetic grouping among these species was found. Eurasian E. trachycaulus probably originated from multiple North American populations.

Random amplified polymorphic DNA (RAPD) markers were used to determine the levels and pattern of molecular variation in four populations of Elymus trachycaulus, and to estimate genetic similarity among different populations of E. trachycaulus from British Columbia and the Northwest Territories and one population of Elymus alaskanus from the Northwest Territories. Based on 124 RAPD bands (loci), mean percent polymorphic loci for E. trachycaulus (PP) was 67.4% (a range 41.2% to 86.3%), and mean gene diversity (He) for E. trachycaulus species was 0.23 (range 0.18 to 0.27). The total genetic diversity was 0.32. Differentiation among populations was 31% (FST = 0.31) with most of the genetic variation found within populations (69%). This pattern of genetic variation was different from that reported for inbred species in general.

Variation at seven microsatellite loci was investigated in three local E. alaskanus populations from Norway and microsatellite variation was compared with allozyme variation. The percentage of polymorphic loci was 81%, the mean number of alleles per polymorphic locus was 5.7 and expected heterozygosity was 0.37. An F-statistic analysis revealed an overall 48% deficit of heterozygotes over Hardy-Weinberg expectations. Gene diversity is mainly explained by the within population component. The averaged between population differentiation coefficient, Fst, over 7 loci is only 0.13, which accounts for only 13% of the whole diversity and was contrary to allozyme analysis. The mean genetic distance between populations was 0.12. However, a χ2 -test showed that allele frequencies were different (p < 0.05) among the populations at 5 of the 7 loci. In comparison with the genetic variation detected by allozymes, microsatellite loci showed higher levels of genetic variation. Microsatellite analysis revealed that population H10576 possesses the lowest genetic variation among the tested three populations, which concur with allozyme analysis. The dendrogram generated by microsatellites agreed very well with allozymic data. Our results suggest that natural selection may be an important factor in shaping the genetic diversity in these three local E. alaskanus populations. Possible explanations for deficit heterozygosity and incongruence between microsatellites and allozymes are discussed.

Genetic diversity in a natural Elymus caninus population from Denmark was assessed using isozyme and microsatellite markers. A total of 119 individuals from 46 maternal plants were assayed. Microsatellite loci are shown to display higher levels of variation than isozyme loci. The mean number of alleles per locus was 1.04 for isozymes and 1.38 for microsatellites. The percentage of polymorphic loci for isozymes and microsatellites was 4.7% and 23.6% across the maternal plant, respectively. The genetic diversity at population level was 0.1 for isozymes, and 0.63 for microsatellites. The mean genetic diversity at maternal plant level was 0.027 for isozyme loci and 0.117 for microsatellite loci. The average of total allozyme diversity (HT) was 0.22. The average of total microsatellite diversity was 0.56. Isozyme and microsatellite variation showed the same pattern of differentiation between maternal plants. More than 75% total genetic diversity was found among maternal plants. About 25% total genetic diversity was detected within maternal plants. Ten (22.7%) maternal plants produced heterozygous offspring at allozyme loci, and 30 (68.2%) maternal plants gave heterozygous offspring at microsatellite loci. Both types of markers revealed a relatively high genetic diversity in this population.

To study the magnitude and nature of genetic variation in E. fibrosus, the levels and distribution of allozyme and RAPD variations were investigated in populations collected from Finland and Russia. The results obtained from the allozyme and RAPD studies were compared to each other in 10 of the populations. The allozyme analysis showed that 6 of 12 presumed loci (50%) were polymorphic within the species, while the mean number of polymorphic loci within populations was 4.8%. The mean number of allele per locus for the species was 1.5 and 1.05 across the populations. Genetic diversity at the species level was low (Hes = 0.025), and the mean population genetic diversity was even lower (Hep = 0.007). Both these values were much lower than the average for other Elymus and self-fertilising species. The largest proportion of the total allozyme diversity was found among, rather than within the populations (GST = 0.70). The allozyme genetic distances between the populations did not reflect geographic distances. Cluster and principal coordinates analyses revealed the same allozyme relationship patterns among the populations. A comparison of allozyme and RAPD variation in 10 of the populations showed differences in the amount of genetic variation. The RAPD analysis revealed higher levels of variation (Ap = 1.19, Pp = 20.3 and Hep = 0.09) than the allozyme one) Ap = 1.06, Pp = 5.8 and Hep = 0.008). For both markers, the largest proportion of the total gene diversity was found among the populations studied (Gst = 0.63 for RAPDs and Gst = 0.65 for allozyme). In contrast to the allozyme analysis, the RAPD based genetic distances did reflect geographic distances. The cluster and principal coordinates analyses showed different grouping of populations for each data set. There was a positive, but not significant, correlation (r = 0.41) between the genetic distance matrices resulting from these markers. Regional comparison revealed that the Finnish populations had a higher diversity than the Russian ones. Generally, this study indicates that E. fibrosus contains low genetic variation in its populations. The results are discussed in the context of conservation of the species.

The importance of wild barley from Qinghai-Tibet Plateau in the origin and domestication of cultivated barley has long been underestimated. Population-based phylogenetic analyses were performed to study the origin and genetic diversity of Chinese domesticated barley, and address the possibility that the Tibetan region in China was an independent center of barley domestication. Wild barley (Hordeum vulgare ssp. spontaneum) populations from Southwest Asia, Central Asia, and Tibet along with domesticated barley from China were analyzed using two nuclear genes. Our results showed that Tibetan wild barley distinctly diverged from Southwest Asian (Near East) wild barley, that Central Asian wild barley is related to Southwest Asian wild barley, and that Chinese domesticated barley shares the same haplotypes with Tibetan wild barley. Phylogenetic analysis showed a close relationship between Chinese domesticated barley and the Tibetan wild barley, suggesting that Tibetan wild barley was the ancestor of Chinese domesticated barley. Our results favor the polyphyletic origin for cultivated barley.

Hybridization and introgression represent important means for the transfer and/or de novo origination of traits and play an important role in facilitating speciation and plant breeding. Two sets of introgression lines in Brassica napus L. were previously established by its intertribal hybridizations with two wild species and long-term selection. In this study, the methods of amplified fragment length polymorphisms (AFLP), sequence-specific amplification polymorphism (SSAP) and methylation-sensitive amplified polymorphism (MSAP) were used to determine their genomic change, retrotransposon mobilization and cytosine methylation alteration in these lines. The genomic change revealed by the loss or gain of AFLP bands occurred for ∼10% of the total bands amplified in the two sets of introgressions, while no bands specific for wild species were detected. The new and absent SSAP bands appeared for 9 out of 11 retrotransposons analyzed, with low frequency of new bands and their total percentage of about 5% in both sets. MSAP analysis indicated that methylation changes were common in these lines (33.4-39.8%) and the hypermethylation was more frequent than hypomethylation. Our results suggested that certain extents of genetic and epigenetic alterations were induced by hybridization and alien DNA introgression. The cryptic mechanism of these changes and potential application of these lines in breeding were also discussed.

Origin and evolution of tetraploid Elymus fibrosus (Schrenk) Tzvelev were characterized using low-copy nuclear gene Rpb2 (the second largest subunit of RNA polymerase II), and chloroplast region trnL–trnF (spacer between the tRNA Leu (UAA) gene and the tRNA-Phe (GAA) gene). Ten accessions of E. fibrosus along with 19 Elymus species with StH genomic constitution and diploid species in the tribe Triticeae were analyzed. Chloroplast trnL–trnF sequence data suggested that Pseudoroegneria (St genome) was the maternal donor of E. fibrosus. Rpb2 data confirmed the presence of StH genomes in E. fibrosus, and suggested that St and H genomes in E. fibrosus each is more likely originated from single gene pool. Single origin of E. fibrosus might be one of the reasons causing genetic diversity in E. fibrosus lower than those in E. caninus and E. trachycaulus, which have similar ecological preferences and breeding systems with E. fibrosus, and each was originated from multiple sources. Convergent evolution of St and H copy Rpb2 sequences in some accessions of E. fibrosus might have occurred during the evolutionary history of this allotetraploid.

Numerous hybrid and polypoid species are found within the Triticeae. It has been suggested that the H subgenome of allopolyploid Elymus (wheatgrass) species originated from diploid Hordeum (barley) species, but the role of hybridization between polyploid Elymus and Hordeum has not been studied. It is not clear whether gene flow across polyploid Hordeum and Elymus species has occurred following polyploid speciation. Answering these questions will provide new insights into the formation of these polyploid species, and the potential role of gene flow among polyploid species during polyploid evolution. In order to address these questions, disrupted meiotic cDNA1 (DMC1) data from the allopolyploid StH Elymus are analyzed together with diploid and polyploid Hordeum species. Phylogenetic analysis revealed that the H copies of DMC1 sequence in some Elymus are very close to the H copies of DMC1 sequence in some polyploid Hordeum species, indicating either that the H genome in theses Elymus and polyploid Hordeum species originated from same diploid donor or that gene flow has occurred among them. Our analysis also suggested that the H genomes in Elymus species originated from limited gene pool, while H genomes in Hordeum polyploids have originated from broad gene pools. Nucleotide diversity (π) of the DMC1 sequences on H genome from polyploid species (π = 0.02083 in Elymus, π = 0.01680 in polyploid Hordeum) is higher than that in diploid Hordeum (π = 0.01488). The estimates of Tajima's D were significantly departure from the equilibrium neutral model at this locus in diploid Hordeum species (P