Junhua Peng

Domestication quantitative trait loci in Triticum dicoccoides, the progenitor of wheat

Wild emmer wheat, Triticum dicoccoides, is the progenitor of modern tetraploid and hexaploid cultivated wheats. Our objective was to map domestication-related quantitative trait loci (QTL) in T. dicoccoides. The studied traits include brittle rachis, heading date, plant height, grain size, yield, and yield components. Our mapping population was derived from a cross between T. dicoccoides and Triticum durum. Approximately 70 domestication QTL effects were detected, nonrandomly distributed among and along chromosomes. Seven domestication syndrome factors were proposed, each affecting 5–11 traits. We showed: (i) clustering and strong effects of some QTLs; (ii) remarkable genomic association of strong domestication-related QTLs with gene-rich regions; and (iii) unexpected predominance of QTL effects in the A genome. The A genome of wheat may have played a more important role than the B genome during domestication evolution. The cryptic beneficial alleles at specific QTLs derived from T. dicoccoides may contribute to wheat and cereal improvement.

Characterization of EST-derived microsatellites in the wheat genome and development of eSSR markers

EST-derived microsatellites or simple sequence repeats (eSSR) occur in expressed sequence tags (EST). Here we report characteristics of eSSRs in the wheat genome, construction of consensus chromosome bin maps of SSR-containing ESTs (SSRESTs), and development of eSSR markers for the 21 wheat chromosomes. A Perl script known as MISA was used to identify eSSRs in wheat ESTs available in the database http://wheat.pw.usda.gov/cgi-bin/ace/search/wEST). Among 492,832 ESTs from the database, 36,520 (7.41%) contained 43,598 eSSRs. This is equivalent to 1 eSSR per 5.46 kb EST sequence. About 60% of the eSSRs were trinucleotides, 19.7% were mononucleotide, 16.7% were dinucleotides, and the remaining ∼3% consisted of tetra-, penta-, and hexanucleotides. Among the identified eSSRs, (CCG/CGG)n is the most frequent (20.5%) followed by (A/T)n at 13.6%, (AAC/GTT)n at 11.7%, and (AG/CT)n at 8.7%. Among ESTs previously mapped to wheat chromosome bins, a total of 1,010 eSSR loci were derived from 341 SSRESTs. Consensus chromosome bin maps showing the chromosome locations of SSRESTs, SSR sequence motif, and cDNA library were constructed. A χ2 test indicated that the distribution pattern of eSSR loci was generally similar to that of the original mapped ESTs in the wheat genome. Forty-eight SSRESTs were converted into PCR-based eSSR markers, and 266 eSSR loci were mapped to specific chromosome arms using wheat cytogenetic stocks. The average polymorphism information content (0.45±0.16) of eSSR markers was lower than that reported for genomic SSRs (0.54±0.19), but higher than RFLPs (0.30±0.27). The eSSR markers were transferable among related Triticeae species, Triticum aestivum, T. durum, T. dicoccoides, Hordeum spontaneum, H. vulgare, and Secale cereale. The results confirm the presence of SSRs in expressed genes of wheat and demonstrate another application of ESTs in genomics research. eSSRs will be useful for gene tagging, gene cloning, and comparative genomics studies of cereal crops.

Microsatellite tagging of the stripe-rust resistance gene YrH52 derived from wild emmer wheat, Triticum dicoccoides, and suggestive negative crossover interference on chromosome 1B

Abstract Stripe rust caused by Puccinia striifomis West. is one of the most devastating diseases relating to wheat production. Wild emmer wheat, Triticum dicoccoides, the tetraploid progenitor of cultivated wheat, has proven to be a valuable source of novel stripe-rust resistance genes for wheat breeding. For example, T. dicoccoides accessions from Mt. Hermon, Israel, are uniformly and highly resistant to stripe-rust. The main objective of the present study is to map a stripe-rust resistance gene, derived from the unique Mt. Hermon population of wild emmer, using microsatellite markers. An F2 mapping population was established by crossing stripe-rust resistant T. dicoccoides accession H52 from Mt. Hermon with the Triticum durum cultivar Langdon. The stripe-rust resistance derived from accession H52 was found to be controlled by a single dominant gene which was temporarily designated as YrH52. Out of 120 microsatellite markers tested, 109 (91%) showed polymorphism between the parental lines. Among 79 segregating microsatellite loci generated from 56 microsatellite primer pairs, nine were linked to YrH52 with recombination frequencies of 0.02–0.35, and LOD scores of 3.56–54.22. A genetic map of chromosome 1B, consisting of ten microsatellite loci and the stripe-rust resistance gene YrH52, was constructed with a total map length of 101.5 cM. YrH52 is also closely linked to RFLP marker Nor1 with a map distance of 1.4 cM and a LOD value of 29.62. Apparent negative crossover interference was observed in chromosome 1B, especially in the region spanning the centromere. Negative crossover interference may be a common characteristic of gene-rich regions or gene clusters in specific chromosomes.

Synteny perturbations between wheat homoeologous chromosomes caused by locus duplications and deletions correlate with recombination rates

Loci detected by Southern blot hybridization of 3,977 expressed sequence tag unigenes were mapped into 159 chromosome bins delineated by breakpoints of a series of overlapping deletions. These data were used to assess synteny levels along homoeologous chromosomes of the wheat A, B, and D genomes, in relation to both bin position on the centromere-telomere axis and the gradient of recombination rates along chromosome arms. Synteny level decreased with the distance of a chromosome region from the centromere. It also decreased with an increase in recombination rates along the average chromosome arm. There were twice as many unique loci in the B genome than in the A and D genomes, and synteny levels between the B genome chromosomes and the A and D genome homoeologues were lower than those between the A and D genome homoeologues. These differences among the wheat genomes were attributed to differences in the mating systems of wheat diploid ancestors. Synteny perturbations were characterized in 31 paralogous sets of loci with perturbed synteny. Both insertions and deletions of loci were detected and both preferentially occurred in high recombination regions of chromosomes.

High-density molecular map of chromosome region harboring stripe-rust resistance genes YrH52 and Yr15 derived from wild emmer wheat, Triticum dicoccoides

Two stripe-rust resistance genes, YrH52 and Yr15, derived from the Israeli wild emmer wheat, Triticum dicoccoides, have been located on chromosome 1B. The main objectives of the present study were to increase marker density in the vicinity of YrH52 gene by means of AFLP, RAPD and microsatellite markers, to improve the map of another T. dicoccoides-derived stripe-rust resistance gene Yr15 using microsatellite markers, and to preliminarily discriminate these two genes. Additional 26 marker loci comprising 20 AFLPs, three RAPDs, and three microsatellites were found to be linked to YrH52 gene. An updated genetic map consisting of 45 marker loci, in the region of YrH52 gene, was constructed with a total map length of 107.7 cm. The mean interval length was 0.96 cm in the region Xgwm359b–P55M53b carrying YrH52 gene. YrH52 was bracketed by Xgwm413 (Nor1 and UBC212a) and Xgwm273a (Xgwm273d) with map distance of 1.3 and 2.7 cm from either side, respectively. Eight additional microsatellite markers were found to be linked with Yr15, and the linkage map of Yr15 gene was thus obviously improved. In the YrH52-mapping population, no crossover was detected in the interval UBC212a (Xgwm413)–Yr15–Nor1, and YrH52 was located distally outside this interval. It may suggest that YrH52 is different from Yr15 even though both of them are derived from T. dicoccoides and are mapped on chromosome 1BS. The large number of molecular makers revealed in the present study would be helpful for the marker-assisted introgression of the T. dicoccoides-derived YrH52 and Yr15 stripe-rust resistance genes into elite cultivars of wheat, and the high-density map would accelerate the map-based cloning of the two genes.

Three lignocellulose features that distinctively affect biomass enzymatic digestibility under NaOH and H2SO4 pretreatments in Miscanthus

In this study, total 80 typical Miscanthus accessions were examined with diverse lignocellulose features, including cellulose crystallinity (CrI), degree of polymerization (DP), and mole number (MN). Correlation analysis revealed that the crude cellulose CrI and MN, as well as crystalline cellulose DP, displayed significantly negative influence on biomass enzymatic digestibility under pretreatments with NaOH or H(2)SO(4) at three concentrations. By contrast, the comparative analysis of two Miscanthus samples with similar cellulose contents showed that crude cellulose DP and crystalline cellulose MN were positive factors on biomass saccharification, indicating cross effects among the cellulose levels and the three cellulose features. The results can provide insights into mechanism of the lignocellulose enzymatic digestion, and also suggest potential approaches for genetic engineering of bioenergy crops.

Phylogenetic analyses unravel the evolutionary history of NAC proteins in plants.

NAC (NAM/ATAF/CUC) proteins are one of the largest groups of transcription factors in plants. Although many NAC proteins based on Arabidopsis and rice genomes have been reported in a number of species, a complete survey and classification of all NAC genes in plant species from disparate evolutionary groups is lacking. In this study, we analyzed whole‐genome sequences from nine major lineages of land plants to unveil the relationships between these proteins. Our results show that there are fewer than 30 NAC proteins present in both mosses and lycophytes, whereas more than 100 were found in most of the angiosperms. Phylogenetic analyses suggest that NAC proteins consist of 21 subfamilies, most of which have highly conserved non‐NAC domain motifs. Six of these subfamilies existed in early‐diverged land plants, whereas the remainder diverged only within the angiosperms. We hypothesize that NAC proteins probably originated sometime more than 400 million years ago and expanded together with the differentiation of plants into organisms of increasing complexity possibly after the divergence of lycophytes from the other vascular plants.

Edaphic microsatellite DNA divergence in wild emmer wheat, Triticum dicoccoides, at a microsite: Tabigha, Israel

Abstract Twenty eight microsatellite markers were used to analyze genetic divergence in tandem dinucleotide repeated DNA regions between two edaphic subpopulations of Triticum dicoccoides growing on the contrasting terra rossa and basalt soilsfrom a microsite at Tabigha, north of the Sea of Galilee, Israel. The terra rossa soil niche was drier and more stressful than the basalt throughout the growing season (November to May). Significant microsatellite divergence in allele distribution, repeat length, genetic diversity, and linkage disequilibria were found between emmer wheat from the two soil types over two short transects of 100 m each. Soil-specific and -unique alleles and linkage disequilibria were observed in the terra rossa and basalt subpopulations. A permutation test showed that the effects of random genetic drift were very low for the significant genetic diversity at microsatellite loci between the two subpopulations, suggesting that an adaptive molecular pattern derived by edaphic selection may act upon variation of the microsatellites.

Genetic variation in Miscanthus × giganteus and the importance of estimating genetic distance thresholds for differentiating clones.

Miscanthus × giganteus (Mxg) is an important bioenergy feedstock crop, however, genetic diversity among legacy cultivars may be severely constrained. Only one introduction from Japan to Denmark of this sterile, triploid, vegetatively propagated crop was recorded in the 1930s. We sought to determine if the Mxg cultivars in North America were all synonyms, and if they were derived from the European introduction. We used 64 nuclear and five chloroplast simple sequence repeat (SSR) markers to estimate genetic similarity for 27 Mxg accessions from North America, and compared them with six accessions from Europe, including the species’ type‐specimen. A subset of accessions was also evaluated by restriction‐site associated DNA sequencing (RAD‐seq). In addition, we assessed the potential of new crosses to increase Mxg genetic diversity by comparing eight new triploid Mxg progeny grown from seed, along with samples of the parental species M. sacchariflorus and M. sinensis. Estimates of genotyping error rates were essential for distinguishing between experimental error and true genotypic differences among accessions. Given differences in estimated error rates and costs per marker for SSRs and RAD‐seq, the former is currently more cost‐effective for determining if two accessions are genetically identical. We concluded that all of the Mxg legacy cultivars were derived via vegetative propagation from a single genet. In contrast with the Mxg legacy cultivars, genetic similarity to the type‐specimen of eight new triploid Mxg progeny ranged from 0.46 to 0.56. Though genetic diversity among the Mxg legacy cultivars is critically low, new crosses can provide much‐needed variation to growers.

Genetic Diversity Revealed by Single Nucleotide Polymorphism Markers in a Worldwide Germplasm Collection of Durum Wheat

Evaluation of genetic diversity and genetic structure in crops has important implications for plant breeding programs and the conservation of genetic resources. Newly developed single nucleotide polymorphism (SNP) markers are effective in detecting genetic diversity. In the present study, a worldwide durum wheat collection consisting of 150 accessions was used. Genetic diversity and genetic structure were investigated using 946 polymorphic SNP markers covering the whole genome of tetraploid wheat. Genetic structure was greatly impacted by multiple factors, such as environmental conditions, breeding methods reflected by release periods of varieties, and gene flows via human activities. A loss of genetic diversity was observed from landraces and old cultivars to the modern cultivars released during periods of the Early Green Revolution, but an increase in cultivars released during the Post Green Revolution. Furthermore, a comparative analysis of genetic diversity among the 10 mega ecogeographical regions indicated that South America, North America, and Europe possessed the richest genetic variability, while the Middle East showed moderate levels of genetic diversity.