Characterization of the chloroplast genome sequence of oil palm (Elaeis guineensis Jacq.).

Oil palm (Elaeis guineensis Jacq.) is an economically important crop, which is grown for oil production. To better understand the molecular basis of oil palm chloroplasts, we characterized the complete chloroplast (cp) genome sequence obtained from 454 pyrosequencing. The oil palm cp genome is 156,973 bp in length consisting of a large single-copy region of 85,192 bp flanked on each side by inverted repeats of 27,071 bp with a small single-copy region of 17,639 bp joining the repeats. The genome contains 112 unique genes: 79 protein-coding genes, 4 ribosomal RNA genes and 29 tRNA genes. By aligning the cp genome sequence with oil palm cDNA sequences, we observed 18 non-silent and 10 silent RNA editing events among 19 cp protein-coding genes. Creation of an initiation codon by RNA editing in rpl2 has been reported in several monocots and was also found in the oil palm cp genome. Fifty common chloroplast protein-coding genes from 33 plant taxa were used to construct ML and MP phylogenetic trees. Their topologies are similar and strongly support for the position of E. guineensis as the sister of closely related species Phoenix dactylifera in Arecaceae (palm families) of monocot subtrees.

The chloroplast genome sequence of mungbean (Vigna radiata) determined by high-throughput pyrosequencing: structural organization and phylogenetic relationships.

Mungbean is an economically important crop which is grown principally for its protein-rich dry seeds. However, genomic research of mungbean has lagged behind other species in the Fabaceae family. Here, we reported the complete chloroplast (cp) genome sequence of mungbean obtained by the 454 pyrosequencing technology. The mungbean cp genome is 151 271 bp in length which includes a pair of inverted repeats (IRs) of 26 474 bp separated by a small single-copy region of 17 427 bp and a large single-copy region of 80 896 bp. The genome contains 108 unique genes and 19 of these genes are duplicated in the IR. Of these, 75 are predicted protein-coding genes, 4 ribosomal RNA genes and 29 tRNA genes. Relative to other plant cp genomes, we observed two distinct rearrangements: a 50-kb inversion between accD/rps16 and rbcL/trnK-UUU, and a 78-kb rearrangement between trnH/rpl14 and rps19/rps8. We detected sequence length polymorphism in the cp homopolymeric regions at the intra- and inter-specific levels in the Vigna species. Phylogenetic analysis demonstrated a close relationship between Vigna and Phaseolus in the phaseolinae subtribe and provided a strong support for a monophyletic group of the eurosid I.

Molecular genetics of submergence tolerance in rice: QTL analysis of key traits.

Flash flooding of young rice plants is a common problem for rice farmers in south and south-east Asia. It severely reduces grain yield and increases the unpredictability of cropping. The inheritance and expression of traits associated with submergence stress tolerance at the seedling stage are physiologically and genetically complex. We exploited naturally occurring differences between certain rice lines in their tolerance to submergence and used quantitative trait loci (QTL) mapping to improve understanding of the genetic and physiological basis of submergence tolerance. Three rice populations, each derived from a single cross between two cultivars differing in their response to submergence, were used to identify QTL associated with plant survival and various linked traits. These included total shoot elongation under water, the extent of stimulation of shoot elongation caused by submergence, a visual submergence tolerance score, and leaf senescence under different field conditions, locations and years. Several major QTL determining plant survival, plant height, stimulation of shoot elongation, visual tolerance score and leaf senescence each mapped to the same locus on chromosome 9. These QTL were detected consistently in experiments across all years and in the genetic backgrounds of all three mapping populations. Secondary QTL influencing tolerance were also identified and located on chromosomes 1, 2, 5, 7, 10 and 11. These QTL were specific to particular traits, environments, or genetic backgrounds. All identified QTL contributed to increased submergence tolerance through their effects on decreased underwater shoot elongation or increased maintenance of chlorophyll levels, or on both. These findings establish the foundations of a marker-assisted scheme for introducing submergence tolerance into agriculturally desirable cultivars of rice.

Thai jasmine rice carrying QTLch9 (SubQTL) is submergence tolerant.

Submergence tolerance is an important agronomic trait for rice grown in South-East Asia, where flash flooding occurs frequently and unpredictably during the monsoons. Although mapping locations of one major and several minor quantitative trait loci (QTL) were known previously, improving submergence tolerance in agronomically desirable types of rice has not been achieved. KDML105 is jasmine rice widely grown in rain-fed lowland regions of Thailand. This cultivar is very intolerant of submergence stress. To improve submergence tolerance in this cultivar, three submergence-tolerant cultivars, FR13A, IR67819F2-CA-61 and IR49830-7-1-2-2, were cross-pollinated with KDML105. Transferring the major QTL for submergence tolerance was facilitated by four back-crossings to the recipient KDML105. Molecular markers tightly linked to the gene(s) involved were developed to facilitate molecular genotyping. We demonstrated that individuals of a BC4F3 line that retained a critical region on chromosome 9 transferred from tolerant lines were also tolerant of complete submergence while retaining all the agronomically desirable traits of KDML105. In addition, effects of secondary QTLch2 were detected statistically in back-cross progenies. Effects of secondary QTLch7 were not statistically significant. The close association between tightly linked markers of the tolerance locus on chromosome 9 and submergence tolerance in the field demonstrates the considerable promise of using these markers in lowland rice breeding programmes for selecting increased submergence tolerance.

Mapping of quantitative trait locus related to submergence tolerance in rice with aid of chromosome walking.

The major QTL for submergence tolerance was locate in the 5.9 cM interval between flanking RFLP markers. To narrow down this region, a physical map was constructed using YAC and BAC clones. A 400-kb YAC was identified in this region and later its end fragments were used to screen a rice BAC library. Through chromosome walking, 24 positive BAC clones formed two contigs around linked-RFLP markers, R1164 and RZ698. Using one YAC end, six BAC ends and three RFLP markers, a fine-scale map was constructed of the 6.8-cM interval of S10709-RZ698 on rice chromosome 9. The submergence tolerance and related trait were located in a small, well-defined region around BAC-end marker 180D1R and RFLP marker R1164. The physical-to-map distance ratio in this region is as small as 172.5 kb/cM, showing that this region is a hot spot for recombination in the rice genome.

Mapping of genes for cooking and eating qualities in Thai jasmine rice (KDML105).

Thai jasmine rice, KDML 105, is known as the best quality rice. It is known not only for its aroma but also for its good cooking and eating qualities. Amylose content (AC), gel consistency (GC) and gelatinization temperature (GT) are important traits determining rice quality. A population of recombinant inbred lines (RIL) derived from KDML105 x CT9993 cross was used to study the genetic control of AC, GC and GT traits. A total of 191 markers were used in the linkage map construction. The 1605.3 cM linkage map covering nearly the whole rice genome was used for QTL (define QTL) analysis. Four QTLs for AC were detected on chromosomes 3, 4, 6 and 7. These QTLs accounted for 80% of phenotypic variation explained (PVE) in AC. The presence of one major gene as well as several modifiers was responsible for the expression of the trait. Two QTLs on chromosome 6 and one on chromosome 7 were detected for GC, which accounts for 57% of PVE. A single gene of major effect along with modifier genes controls GC from this cross. The QTLs in the vicinity of waxy locus were major contributors in the expression of AC and GC. The finding that the position of QTLs for AC and GC were near each other may reflect tight linkage or pleiotropy. Three QTLs were detected, one on chromosome 2 and two on chromosome 6, which accounted for 67% of PVE in GT. Just like AC and GC, one major gene and modifier genes governed the variation in GT resulting from the KDML105 x CT9993 cross. Breeding for cooking and eating qualities will largely rely on the preferences of the end users.

Quantitative trait loci on barley (Hordeum vulgare L.) chromosome 7 associated with components of winterhardiness.

Quantitative trait loci (QTL) controlling traits associated with winterhardiness in barley (field survival, LT50, growth habit, and crown fructan content) were mapped to chromosome 7 in a population of 100 F1-derived doubled haploid lines. The largest QTL effects for all traits were detected in a 21% recombination interval on the long arm of chromosome 7. QTL in this region accounted for 37-68% of the variation for three measures of cold tolerance, 47% of the variation for growth habit, and 28% of the variation in crown fructan content. Trait association may be due to linkage rather than pleiotropy.

Sequence-tagged-site-facilitated PCR for barley genome mapping.

Speed, efficiency, and safety considerations have led many genome mapping projects to evaluate polymerase chain reaction (PCR) sequence amplification as an alternative to Southern blot analysis. However, the availability of informative primer sequences can be a limiting factor in PCR-based mapping. An alternative to random amplified polymorphism detection (RAPD) is the sequence-tagged-site (STS) approach. If informative primer sequences could be derived from known sequences, then current maps, which are based on both known function and anonymous clones, might be easily converted to maps utilizing PCR technology. In this paper, four pairs of primer sequences were obtained from published sequences, and four pairs were obtained by sequencing portions of DNA clones from genomic clones derived from a random genomic library used in the North American Barley Genome Mapping Project (NABGMP). These primers were used to screen for polymorphisms in the progeny of a winter x spring and a spring x spring barley cross. Two types of polymorphisms were distinguished using these primer sets: (1) insertion/deletion events that could be read directly from agarose gels, and (2) point mutation events. The latter were identified using polyacrylamide-gel electrophoresis of PCR products following digestion with restriction endonucleases (four-base cutters). To determine whether the PCR-based polymorphisms were allelic to polymorphisms identified by the clones from which the primer sequences derived, chromosomal assignments and (when possible) co-segregation analysis was performed.