Wickneswari Ratnam

A transgressive brown rice mediates favourable glycaemic and insulin responses

BACKGROUND We evaluated glycaemic response of a brown rice variant (BR) developed by cross-breeding. Subjects (n = 9) consumed 50 g carbohydrate equivalents of BR, white rice (WR) and the polished brown rice (PR) in comparison to 50 g glucose reference (GLU) in a cross-over design. Plasma glucose and insulin at 0, 15, 45, 60, 90, 120 and 180 min were measured and incremental area under the curve (IAUC) and indices for glucose (GI) and insulin (II) calculated. RESULTS BR compared to PR or WR produced the lowest postprandial glycaemia (GI: 51 vs 79 vs 86) and insulinaemia (II: 39 vs 63 vs 68) irrespective of amylose content (19 vs 23 vs 26.5%). Only BR was significantly different from GLU for both plasma glucose (P = 0.012) and insulin (P = 0.013) as well as IAUC(glu) (P = 0.045) and IAUC(ins) (P = 0.031). Glycaemic and insulinaemic responses correlated positively (r = 0.550, P < 0.001). Linear trends for IAUC(glu) and IAUC(ins) indicated a greater secretion of insulin tied in with a greater glycaemic response for WR (r(2) = 0.848), moderate for PR (r(2) = 0.302) and weakest for BR (r(2) = 0.122). CONCLUSION The brown rice variant had the lowest GI and II values but these advantages were lost with polishing.

Impact of logging on genetic diversity in humid tropical forests.

Sustained management of natural forests depends on their ability to regenerate. Successful regeneration of forests accompanied by conservation of genetic diversity of its species is important for both short-term adaptation to environmental change and long-term impact on species and communities (Templeton 1995).

Genetic controls on starch amylose content in wheat and rice grains

Starch accumulates in plants as granules in chloroplasts of source organs such as leaves (transitory starch) or in amyloplasts of sink organs such as seeds, tubers and roots (storage starch). Starch is composed of two types of glucose polymers: the essentially linear polymer amylose and highly branched amylopectin. The amylose content of wheat and rice seeds is an important quality trait, affecting the nutritional and sensory quality of two of the world’s most important crops. In this review, we focus on the relationship between amylose biosynthesis and the structure, physical behaviour and functionality of wheat and rice grains. We briefly describe the structure and composition of starch and then in more detail describe what is known about the mechanism of amylose synthesis and how the amount of amylose in starch might be controlled. This more specifically includes analysis of GBSS alleles, the relationship between waxy allelic forms and amylose, and related quantitative trait loci. Finally, different methods for increasing or lowering amylose content are evaluated.

Evaluation and Bulked Segregant Analysis of Major Yield QTL qtl12.1 Introgressed into Indigenous Elite Line for Low Water Availability under Water Stress

Near isogenic lines carrying large-effect QTL (qtl12.1), which has a consistent influence on grain yield under upland drought stress conditions in a wide range of environments, were evaluated under water stress in the fields. The line which gave higher yield under drought was crossed with a local elite line, PMK3, and forwarded to F2:3 generation. Significant variation was found among the F2:3 lines for agronomic traits under water stress in the fields. Low to high broad sense heritability (H) for investigated traits was also found. Water stress indicators such as leaf rolling and leaf drying were negatively correlated with plant height, biomass and grain yield under stress. Bulked segregant analysis (BSA) was performed with the markers in the vicinity of qtl12.1, and RM27933 was found to be segregated perfectly well in individual components of drought resistant and drought susceptible bulks which were bulked based on yield under water stress among F2:3 lines. Hence, this simple and breeder friendly marker, RM27933, may be useful as a potentially valuable candidate marker for the transfer of the QTL qtl12.1 in the regional breeding program. Bioinformatic analysis of the DNA sequence of the qtl12.1 region was also done to identify and analyze positional candidate genes associated with this QTL and to ascertain the putative molecular basis of qtl12.1.

Mating system and seed variation of Acacia hybrid (A. mangium × A. auriculiformis)

The mating system and seed variation of Acacia hybrid (A. mangium × A. auriculiformis) were studied using allozymes and random amplified polymorphic DNA (RAPD) markers, respectively. Multi-locus outcrossing rate estimations indicated that the hybrid was predominantly outcrossed (mean±s.e. tm = 0.86±0.01). Seed variation was investigated using 35 polymorphic RAPD fragments. An analysis of molecular variance (AMOVA) revealed the highest genetic variation among seeds within a pod (66%–70%), followed by among pods within inflorescence (29%–37%), and the least variation among inflorescences within tree (<1%). In addition, two to four RAPD profiles could be detected among seeds within pod. Therefore, the results suggest that a maximum of four seeds per pod could be sampled for the establishment of a mapping population for further studies.

Cross-specific amplification of microsatellite DNA markers in Shorea platyclados

In the megadiverse forests of Southeast Asia, hundreds of timber species are economically important but the population genetics of only a few taxa are known. Cross-specific amplification of microsatellite loci among closely related taxa could enhance our ability to study and manage previously unstudied species. We successfully utilized STMS markers in Shorea platyclados, originally developed for Shorea curtisii. The six primer pairs we tried successfully produced PCR products of expected sizes. The number of alleles observed ranged from 10 to 14 and an average of 12 alleles were detected per locus. A high expected and observed heterozygosity was observed and it ranges from 0.718 to 0.827 among all populations across all six loci tested. Microsatellite DNA markers are highly polymorphic, co-dominant, reproducible, and amenable to high throughput genetic analyses. Overall, the cross-specific amplification of microsatellite loci appears to be complicated by numerous factors. While the approach may be effective for local management and conservation of poorly known species, the results must be carefully interpreted.

Molecular Characterization and Comparative Sequence Analysis of Defense-Related Gene, Oryza rufipogon Receptor-Like Protein Kinase 1

Many of the plant leucine rich repeat receptor-like kinases (LRR-RLKs) have been found to regulate signaling during plant defense processes. In this study, we selected and sequenced an LRR-RLK gene, designated as Oryza rufipogon receptor-like protein kinase 1 (OrufRPK1), located within yield QTL yld1.1 from the wild rice Oryza rufipogon (accession IRGC105491). A 2055 bp coding region and two exons were identified. Southern blotting determined OrufRPK1 to be a single copy gene. Sequence comparison with cultivated rice orthologs (OsI219RPK1, OsI9311RPK1 and OsJNipponRPK1, respectively derived from O. sativa ssp. indica cv. MR219, O. sativa ssp. indica cv. 9311 and O. sativa ssp. japonica cv. Nipponbare) revealed the presence of 12 single nucleotide polymorphisms (SNPs) with five non-synonymous substitutions, and 23 insertion/deletion sites. The biological role of the OrufRPK1 as a defense related LRR-RLK is proposed on the basis of cDNA sequence characterization, domain subfamily classification, structural prediction of extra cellular domains, cluster analysis and comparative gene expression.

The 172-kb genomic DNA region of the O. rufipogon yld1.1 locus: comparative sequence analysis with O. sativa ssp. japonica and O. sativa ssp. indica

Common wild rice (Oryza rufipogon) plays an important role by contributing to modern rice breeding. In this paper, we report the sequence and analysis of a 172-kb genomic DNA region of wild rice around the RM5 locus, which is associated with the yield QTL yld1.1. Comparative sequence analysis between orthologous RM5 regions from Oryza sativa ssp. japonica, O. sativa ssp. indica and O. rufipogon revealed a high level of conserved synteny in the content, homology, structure, orientation, and physical distance of all 14 predicted genes. Twelve of the putative genes were supported by matches to proteins with known function, whereas two were predicted by homology to rice and other plant expressed sequence tags or complementary DNAs. The remarkably high level of conservation found in coding, intronic and intergenic regions may indicate high evolutionary selection on the RM5 region. Although our analysis has not defined which gene(s) determine the yld1.1 phenotype, allelic variation and the insertion of transposable elements, among other nucleotide changes, represent potential variation responsible for the yield QTL. However, as suggested previously, two putative receptor-like protein kinase genes remain the key suspects for yld1.1.

Detecting mislabeling and identifying unique progeny in Acacia mapping population using SNP markers

Acacia hybrids offer a great potential for paper industry in Southeast Asia due to their fast growth and ability to grow on abandoned or marginal lands. Breeding Acacia hybrids with desirable traits can be achieved through marker assisted selection (MAS) breeding. To develop a MAS program requires development of linkage maps and QTL analysis. Two mapping populations were developed through interspecific hybridization for linkage mapping and QTL analysis. All seeds per pod were cultured initially to improve hybrid yield as quality and density of linkage mapping is affected by the size of the mapping population. Progenies from two mapping populations were field planted for phenotypic and genotypic evaluation at three locations in Malaysia, (1) Forest Research Institute Malaysia field station at Segamat, Johor, (2) Borneo Tree Seeds and Seedlings Supplies Sdn, Bhd. (BTS) field trial site at Bintulu, Sarawak, and (3) Asiaprima RCF field trial site at Lancang, Pahang. During field planting, mislabeling was reported at Segamat, Johor, and a similar problem was suspected for Bintulu, Sarawak. Early screening with two isozymes effectively selected hybrid progenies, and these hybrids were subsequently further confirmed by using species-specific SNPs. During field planting, clonal mislabeling was reported and later confirmed by using a small set of STMS markers. A large set of SNPs were also used to screen all ramets in both populations. A total of 65.36% mislabeled ramets were encountered in the wood density population and 60.34% in the fibre length mapping population. No interpopulation pollen contamination was detected because all ramets found their match within the same population in question. However, mislabeling was detected among ramets of the same population. Mislabeled individuals were identified and grouped as they originated from 93 pods for wood density and 53 pods for fibre length mapping populations. On average 2 meiotically unique seeds per pod (179 seeds/93 pods) for wood density and 3 meiotically unique seeds per pod (174 seeds/53 pods) for fibre length mapping population were found. A single step statistical method was used to evaluate the most informative set of SNPs that could subsequently be used for routine checks for mislabeling in multi-location field trials and for labelling superior clones to protect breeder’s rights. A preliminary set of SNPs with a high degree of informativeness was selected for the mislabeling analysis in conjunction with an assignment test. Two subsets were successfully identified, i.e., 51 SNPs for wood density and 64 SNPs for fibre length mapping populations to identify all mislabeled ramets which had been previously identified. Mislabeling seems to be a common problem due to the complexity involved in the production of mapping populations. Therefore, checking for mislabeling is imperative for breeding activities and for analyses such as linkage mapping in which a correlation between genotypic and phenotypic data is determined.

Transcriptome analysis of reproductive tissue differentiation in Jatropha curcas Linn.

Shoot and inflorescence are central physiological and developmental tissues of plants. Flowering is one of the most important agronomic traits for improvement of crop yield. To analyze the vegetative to reproductive tissue transition in Jatropha curcas, gene expression profiles were generated from shoot and inflorescence tissues. RNA isolated from both tissues was sequenced using the Ilumina HiSeq 2500 platform. Differential gene expression analysis identified key biological processes associated with vegetative to reproductive tissue transition. The present data for J. curcas may inform the design of breeding strategies particularly with respect to reproductive tissue transition. The raw data of this study has been deposited in the NCBIs Sequence Read Archive (SRA) database with the accession number SRP090662.