De novo assembly and characterization of the root transcriptome of Aegilops variabilis during an interaction with the cereal cyst nematode.

BACKGROUND: Aegilops variabilis No.1 is highly resistant to cereal cyst nematode (CCN). However, a lack of genomic information has restricted studies on CCN resistance genes in Ae. variabilis and has limited genetic applications in wheat breeding. RESULTS: Using RNA-Seq technology, we generated a root transcriptome at a sequencing depth of 4.69 gigabases of Ae. variabilis No. 1 from a pooled RNA sample. The sample contained equal amounts of RNA extracted from CCN-infected and untreated control plants at three time-points. Using the Trinity method, nearly 52,081,238 high-quality trimmed reads were assembled into a non-redundant set of 118,064 unigenes with an average length of 500 bp and an N50 of 599 bp. The total assembly was 59.09 Mb of unique transcriptome sequences with average read-depth coverage of 33.25×. In BLAST searches of our database against public databases, 66.46% (78,467) of the unigenes were annotated with gene descriptions, conserved protein domains, or gene ontology terms. Functional categorization further revealed 7,408 individual unigenes and three pathways related to plant stress resistance. CONCLUSIONS: We conducted high-resolution transcriptome profiling related to root development and the response to CCN infection in Ae. variabilis No.1. This research facilitates further studies on gene discovery and on the molecular mechanisms related to CCN resistance.

Starch granule-associated proteins of hull-less barley (Hordeum vulgare L.) from the Qinghai-Tibet Plateau in China.

BACKGROUND: The starch granule-associated proteins (SGAPs) are the minor components of the starch granules and a majority of them are believed to be starch biosynthetic enzymes. The Qinghai-Tibet Plateau in China, one of the centres of origin of cultivated barley, is abundant in hull-less barley resources which exhibit high polymorphism in SGAPs. RESULTS: The SGAPs of hull-less barley from Qinghai-Tibet Plateau were analysed by one-dimensional (1-D) SDS-PAGE, 2-D PAGE and ESI-Q-TOF MS/MS. In the 1-D SDS-PAGE gel, four proteins including a 80 kDa starch synthase, actin, actin 4 and ATP synthase ß-subunit were identified as novel SGAPs. A total of six different bands were identified as starch granule-bound starch synthase I (GBSSI) and the segregation of the novel GBSSI bands in F(1) and F(2) seeds derived from yf127 × yf70 was in accordance with Mendel's law. In the 2-D PAGE gel, 92 spots were identified as 42 protein species which could be classified into 15 functional groups. Thirteen protein species were identified as SGAPs for the first time and multiple spots were identified as GBSSI. CONCLUSION: This study revealed novel SGAPs in hull-less barley from the Qinghai-Tibet Plateau in China and these will be significant in further studies of starch biosynthesis in barley.

[Genetic analysis of contribution of low-molecular-weight glutenin subunits to dough strength in common wheat].

Locus-specific primers of low-molecular-weight glutenin subunit (LMW-GS) genes and gliadin bands tightly linked to LMW-GS genes were analyzed to evaluate the effect of LMW-GS genes on dough strength in common wheat (Triticum aestivum L.). Analysis of the F9 progeny from two crosses '99G45/Jing771' and 'Pm97034/J771' showed that the LMW-GS genes located at the Glu-B3 locus from the three parents had six Cysteine, but 'PB' (define) had a seven amino-acid deletion in the repetitive to 'GB' and 'JB' (define these abbreviations) and amino-acid substitution, two of which would be expected to cause changes in hydrophilicity.

[SGP polymorphism in cultivated naked barley from Qinghai-Tibet plateau in China and the relationship between SGPs and starch content].

Starch granule proteins (SGPs) are minor components bound with starch granule, which mutation may be related to starch properties. This study investigated the variation of SGPs in cultivated naked barley from Qinghai-Tibet Plateau in China for the first time, and the relationship between SGPs and starch content was preliminarily done. Ten major SGPs and 16 types of patterns were present in 66 cultivated naked varieties, indicating SGPs in cultivated naked barley from Qinghai-Tibet Plateau in China are polymorphic. SGPs in Tibet and Sichuan naked barley were greatly different and SGPs were specific to origin of site. Significance test analysis demonstrates SGPs described in this study except for SGP1 may be related with the variation of starch content in different naked barley.

Cloning and characterization of four B-hordein genes from Tibetan hull-less barley (Hordeum vulgare subsp. vulgare).

Four B-hordein genes, designated BH1-BH4, were cloned using PCR amplification from two hull-less barley cultivars, ZQ7239 and ZQ148, collected from Tibet. The results of sequencing indicated that BH1-BH4 contained complete open reading frames (ORFs). Comparison of their predicted polypeptide sequences with the published sequences suggested that they all share the same basic protein structure. Phylogenetic analysis indicated that the deduced amino-acid sequences of BH1-BH4 genes were more closely related to B-hordeins from cultivated barley (Hordeum vulgare L.) than to any other prolamins from wild barley and Aegilops tauschii. Comparison of the coding regions of BH1-BH4 genes showed that BH1 had a lower sequence identity to other previously published B-hordeins than the other three B-hordeins obtained in this study. BH1 was then cloned in a bacterial expression vector based on bacteriophage T7 RNA polymerase. The resulting plasmid produced a 28.15 kDa protein in Escherichia coli. The potential value of B-hordein genes in grain quality improvement of hull-less barley has been discussed.

Genetic variation and phylogenetic relationship analysis of Jatropha curcas L. inferred from nrDNA ITS sequences.

Genetic variation and phylogenetic relationships among 102 Jatropha curcas accessions from Asia, Africa, and the Americas were assessed using the internal transcribed spacer region of nuclear ribosomal DNA (nrDNA ITS). The average G+C content (65.04%) was considerably higher than the A+T (34.96%) content. The estimated genetic diversity revealed moderate genetic variation. The pairwise genetic divergences (GD) between haplotypes were evaluated and ranged from 0.000 to 0.017, suggesting a higher level of genetic differentiation in Mexican accessions than those of other regions. Phylogenetic relationships and intraspecific divergence were inferred by Bayesian inference (BI), maximum parsimony (MP), and median joining (MJ) network analysis and were generally resolved. The J. curcas accessions were consistently divided into three lineages, groups A, B, and C, which demonstrated distant geographical isolation and genetic divergence between American accessions and those from other regions. The MJ network analysis confirmed that Central America was the possible center of origin. The putative migration route suggested that J. curcas was distributed from Mexico or Brazil, via Cape Verde and then split into two routes. One route was dispersed to Spain, then migrated to China, eventually spreading to southeastern Asia, while the other route was dispersed to Africa, via Madagascar and migrated to China, later spreading to southeastern Asia.

[Chromosome analysis of Chongqing thermo-photo sensitive male sterile wheat].

Seed gliadin acid-polyacrylamide-gel-electrophoresis (APAGE) and chromosome C-banding techniques were used to identify chromosome constitution of Chongqing thermo-photo sensitive male sterile wheat. Results showed that 1BS of the male sterile lines was substituted by 1RS of rye. They were 1B/1R wheat with Triticum aestivum cytoplasm.

[Morphology, cytogenetics of intergeneric hybrid between Aegilops taucchii and Dasypyrum villosum].

"Aegilops tauschii x Dasypyrum villosum" F1 hybrids were obtained by the combination of hybridization and embryo culture in vitro. Chromosome pairing behavior in meiosis of the hybrid F1 was carried out. Results showed that in an average , 1.25 rod bivalents were observed in one PMC, meiotic configuration was 2n=14=11.49 I + 1.25 II (Xta=1.25) and most of PMCs possessed 1 approximately 5(rod) bivalens, indicating that the relatively high homeology was detected between the D genome of Ae. tauschii and the V genome of D. villosum. The morphological differences between F1 hybrids and their parents were significant. F1 plants were highly self-sterile, but partially self-fertile after treated by chromosome doubling technique.

Microsatellite analysis of genetic variation and population genetic differentiation in autotetraploid and diploid rice.

Genetic diversity and population genetic structure of autotetraploid and diploid populations of rice collected from Chengdu Institute of Biology, Chinese Academy of Sciences, were studied based on 36 microsatellite loci. Among 50 varieties, a moderate to high level of genetic diversity was observed at the population level, with the number of alleles per locus (Ae) ranging from 2 to 6 (mean 3.028) and polymorphism information content ranging from 0.04 to 0.76 (mean 0.366). The expected heterozygosity (He) varied from 0.04 to 0.76 (mean 0.370) and Shannon's index (I) from 0.098 to 1.613 (mean 0.649). The autotetraploid populations showed slightly higher levels of Ae, He, and I than the diploid populations. Rare alleles were observed at most of the simple sequence repeat loci in one or more of the 50 accessions, and a core fingerprint database of the autotetraploid and diploid rice was constructed. The F-statistics showed genetic variability mainly among autotetraploid populations rather than diploid populations (Fst = 0.066). Cluster analysis of the 50 accessions showed four major groups. Group I contained all of the autotetraploid and diploid indica maintainer lines and an autotetraploid and its original diploid indica male sterile lines. Group II contained only the original IR accessions. Group III was more diverse than either Group II or Group IV, comprising both autotetraploid and diploid indica restoring lines. Group IV included a japonica cluster of the autotetraploid and diploid rices. Furthermore, genetic differences at the single-locus and two-locus levels, as well as components due to allelic and gametic differentiation, were revealed between autotetraploid and diploid varieties. This analysis indicated that the gene pools of diploid and autotetraploid rice were somewhat dissimilar, as variation exists that distinguishes autotetraploid from diploid rices. Using this variation, we can breed new autotetraploid varieties with some important agricultural characters that were not found in the original diploid rice varieties.