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Fulltext Expression of a key gene involved in the biosynthetic pathway of vitamin E in red pericarp and white rice grains

Fasahat, P., Abdullah, A., Muhammad, K., Wickneswari, R.

International Food Research Journal, 2013;20(6):3395-3401.
MyJurnal

Tocochromanols (tocopherols and tocotrienols) unitedly known as vitamin E, are the necessary antioxidant components of both human and animal diets. There is a considerable interest in plants with increased or customized vitamin E content, due to their potential health benefits. To quantify the tocochromanol content and determine the expression of a key tocotrienol biosynthesis gene among a set of contrasting red pericarp and light brown rice genotypes of advanced breeding lines together with their parents; expression pattern of homogentisate geranylgeranyl transferase (HGGT), the key gene was studied by semi-quantitative RT-PCR in milky and matured grain stages. Vitamin E analysis was carried out by high performance liquid chromatography (HPLC). The chloroform-methanolic extracts prepared from red pericarp and light brown rice advanced breeding lines showed significant differences for vitamin E content. Averaged across all samples, the content of γ-tocotrienol > α-tocopherol > α-tocotrienol > γ-tocopherol > δ-tocotrienol, and total E vitamin content ranged from 10.30 to 31.65 µg/g. Genotype G37 (red pericarp) was found to have higher expression than G7 (light brown) and G33 (red pericarp) at both grain development stages but lower than both parents whereas their transcript levels were comparatively lower in mature grain, which indicates their possible regulation by plant growth stage. HPLC results of γ-tocotrienol content supported gene expression results with the exception of the recurrent parent MR219.
Fulltext New red rice transgressive variants with high antioxidant capacity

Fasahat, P., Wickneswari, R., Abdullah, A., Musa, K.H., Muhammad, K.

International Food Research Journal, 2013;20(3):1497-1501.
MyJurnal

Red coloured rice, has been shown to contain high levels of bioactive properties. The aim of this study was to quantify the major antioxidant compounds in the whole grain of two new red rice transgressive variants together with their parents which was determined by the oxygen radical absorbance capacity (ORAC) method, measured in methanol extract. A Thailand commercial red rice was used as a control. Although, the ORAC values for some red rice samples were similar, they were higher than light brown rice control, MR219. The antioxidant capacity was also evaluated by ferric-reducing antioxidant power assay. FRAP result was well correlated with ORAC (r = 0.94).
Fulltext Identification of introgressed alien chromosome segments associated with grain quality in Oryza rufipogon x MR219 advanced breeding lines using SSR markers

Fasahat P, Muhammad K, Abdullah A, Wickneswari R

Genet. Mol. Res., 2012;11(3):3534-46.
PMID: 23079848 DOI: 10.4238/2012.September.26.10

A limited backcross procedure was utilized to introgress genes associated with grain quality traits from Oryza rufipogon (Accession No. IRGC 105491), a wild rice from Malaysia, to the cultivated rice O. sativa cv. MR219, a popular high yielding Malaysian rice cultivar. A set of 10 BC(2)F(7) progenies were selected based on the field performance and phenotypic appearance in BC(2)F(5) and BC(2)F(6) generations, which initially started with 266 progenies in the BC(2)F(2) generation. These 10 advanced breeding lines are similar to each other but differ in several important grain quality traits, which can be traced to O. rufipogon introgressions. Phenotyping and genotyping of BC(2)F(7) variants were considered for QTL analysis. The introgressed lines did not show any significant changes compared to the recurrent parent MR219 for the traits grain density and milled rice percentage. All 10 progenies showed significantly higher head rice percentages (70-88%) than the recurrent parent MR219. Variants G13 and G15 had higher amylose contents than MR219. All variants were analyzed using polymorphic SSR markers. Of the 34 SSR markers, only 18 showed introgression from O. rufipogon for chromosomes 1, 2, 3, 5, 6, 8, 10, and 11. Graphical genotypes were prepared for each variant, and association between the introgression regions and the traits that increased grain quality was visualized. Based on marker trait association, some of the QTLs are stable across environments and genetic backgrounds and could be used universally.
Fulltext Characterization of microRNAs expressed during secondary wall biosynthesis in Acacia mangium

Ong SS, Wickneswari R

PLoS One, 2012;7(11):e49662.
PMID: 23251324 DOI: 10.1371/journal.pone.0049662

MicroRNAs (miRNAs) play critical regulatory roles by acting as sequence specific guide during secondary wall formation in woody and non-woody species. Although thousands of plant miRNAs have been sequenced, there is no comprehensive view of miRNA mediated gene regulatory network to provide profound biological insights into the regulation of xylem development. Herein, we report the involvement of six highly conserved amg-miRNA families (amg-miR166, amg-miR172, amg-miR168, amg-miR159, amg-miR394, and amg-miR156) as the potential regulatory sequences of secondary cell wall biosynthesis. Within this highly conserved amg-miRNA family, only amg-miR166 exhibited strong differences in expression between phloem and xylem tissue. The functional characterization of amg-miR166 targets in various tissues revealed three groups of HD-ZIP III: ATHB8, ATHB15, and REVOLUTA which play pivotal roles in xylem development. Although these three groups vary in their functions, -psRNA target analysis indicated that miRNA target sequences of the nine different members of HD-ZIP III are always conserved. We found that precursor structures of amg-miR166 undergo exhaustive sequence variation even within members of the same family. Gene expression analysis showed three key lignin pathway genes: C4H, CAD, and CCoAOMT were upregulated in compression wood where a cascade of miRNAs was downregulated. This study offers a comprehensive analysis on the involvement of highly conserved miRNAs implicated in the secondary wall formation of woody plants.
Genetic diversity of oil palm (Elaeis guineensis Jacq.) germplasm collections from Africa: implications for improvement and conservation of genetic resources

Hayati A, Wickneswari R, Maizura I, Rajanaidu N

Theor Appl Genet, 2004 May;108(7):1274-84.
PMID: 14676949

A total of 723 accessions of oil palm ( Elaeis guineensis Jacq.) from 26 populations representing ten countries in Africa and one Deli dura family were screened for allelic variation at seven enzyme loci from six enzyme systems using starch gel electrophoresis. On average, 54.5% of the loci were polymorphic (0.99 criterion). The average and effective number of alleles per locus was 1.80 and 1.35, respectively. Mean expected heterozygosity was 0.184, with values ranging from 0.109 (population 8, Senegal) to 0.261 (population 29, Cameroon). The genetic differentiation among populations was high (F(ST)=0.301), indicating high genetic divergence. The calculation of F(ST) by geographic zones revealed that the high F(ST) was largely due to F(ST) among populations in West Africa, suggesting diversifying selection in this region. The mean genetic distance across populations was 0.113. The lowest genetic distance (D) was observed between population 5 from Tanzania and population 7 from the Democratic Republic of the Congo (0.000) and the highest was found between population 4 from Madagascar and population 13 from Sierra Leone (0.568). The total gene flow across oil palm populations was low, with an Nm of 0.576, enhancing genetic structuring, as evident from the high F(ST) values. UPGMA cluster analysis revealed three main clusters; the western outlying populations from Senegal and Sierra Leone were in one cluster but separated into two distinct sub-clusters; the eastern outlying populations from Madagascar were in one cluster; the populations from Angola, Cameroon, The Democratic Republic of the Congo, Ghana, Tanzania, Nigeria and Guinea were in one cluster. The Deli dura family seems to be closely related to population 6 from Guinea. Oil palm populations with high genetic diversity-i.e. all of the populations from Nigeria, Cameroon and Sierra Leone, population 6 of Guinea, population 1 of Madagascar and population 2 of Senegal should be used in improvement programmes, whereas for conservation purposes, oil palm populations with high allelic diversity (A(e)), which include populations 22 and 29 from Cameroon, populations 39 and 45 from Nigeria, population 6 from Guinea, populations 5 and 13 from Sierra Leone and population 1 from Madagascar should be selected for capturing as much genetic variation as possible.
Fulltext Expression profile of small RNAs in Acacia mangium secondary xylem tissue with contrasting lignin content - potential regulatory sequences in monolignol biosynthetic pathway

Ong SS, Wickneswari R

BMC Genomics, 2011 Nov 30;12 Suppl 3(Suppl 3):S13.
PMID: 22369296 DOI: 10.1186/1471-2164-12-S3-S13

BACKGROUND: Lignin, after cellulose, is the second most abundant biopolymer accounting for approximately 15-35% of the dry weight of wood. As an important component during wood formation, lignin is indispensable for plant structure and defense. However, it is an undesirable component in the pulp and paper industry. Removal of lignin from cellulose is costly and environmentally hazardous process. Tremendous efforts have been devoted to understand the role of enzymes and genes in controlling the amount and composition of lignin to be deposited in the cell wall. However, studies on the impact of downregulation and overexpression of monolignol biosynthesis genes in model species on lignin content, plant fitness and viability have been inconsistent. Recently, non-coding RNAs have been discovered to play an important role in regulating the entire monolignol biosynthesis pathway. As small RNAs have critical functions in various biological process during wood formation, small RNA profiling is an important tool for the identification of complete set of differentially expressed small RNAs between low lignin and high lignin secondary xylem.
RESULTS: In line with this, we have generated two small RNAs libraries from samples with contrasting lignin content using Illumina GAII sequencer. About 10 million sequence reads were obtained in secondary xylem of Am48 with high lignin content (41%) and a corresponding 14 million sequence reads were obtained in secondary xylem of Am54 with low lignin content (21%). Our results suggested that A. mangium small RNAs are composed of a set of 12 highly conserved miRNAs families found in plant miRNAs database, 82 novel miRNAs and a large proportion of non-conserved small RNAs with low expression levels. The predicted target genes of those differentially expressed conserved and non-conserved miRNAs include transcription factors associated with regulation of the lignin biosynthetic pathway genes. Some of these small RNAs play an important role in epigenetic silencing. Differential expression of the small RNAs between secondary xylem tissues with contrasting lignin content suggests that a cascade of miRNAs play an interconnected role in regulating the lignin biosynthetic pathway in Acacia species.
CONCLUSIONS: Our study critically demonstrated the roles of small RNAs during secondary wall formation. Comparison of the expression pattern of small RNAs between secondary xylem tissues with contrasting lignin content strongly indicated that small RNAs play a key regulatory role during lignin biosynthesis. Our analyses suggest an evolutionary mechanism for miRNA targets on the basis of the length of their 5' and 3' UTRs and their cellular roles. The results obtained can be used to better understand the roles of small RNAs during lignin biosynthesis and for the development of gene constructs for silencing of specific genes involved in monolignol biosynthesis with minimal effect on plant fitness and viability. For the first time, small RNAs were proven to play an important regulatory role during lignin biosynthesis in A. mangium.
Fulltext Identification of floral genes for sex determination in Calamus palustris Griff. by using suppression subtractive hybridization

Ng CY, Wickneswari R, Choong CY

Genet. Mol. Res., 2014;13(3):6037-49.
PMID: 25117361 DOI: 10.4238/2014.August.7.18

Calamus palustris Griff. is an economically important dioecious rattan species in Southeast Asia. However, dioecy and onset of flowering at 3-4 years old render uncertainties in desired female:male seedling ratios to establish a productive seed orchard for this rattan species. We constructed a subtractive library for male floral tissue to understand the genetic mechanism for gender determination in C. palustris. The subtractive library produced 1536 clones with 1419 clones of high quality. Reverse Northern screening showed 313 clones with differential expression, and sequence analyses clustered them into 205 unigenes, including 32 contigs and 173 singletons. The subtractive library was further validated with reverse transcription-quantitative polymerase chain reaction analysis. Homology identification classified the unigenes into 12 putative functional proteins with 83% unigenes showing significant match to proteins in databases. Functional annotations of these unigenes revealed genes involved in male flower development, including MADS-box genes, pollen-related genes, phytohormones for flower development, and male flower organ development. Our results showed that the male floral genes may play a vital role in sex determination in C. palustris. The identified genes can be exploited to understand the molecular basis of sex determination in C. palustris.
Fulltext Identification of lignin genes and regulatory sequences involved in secondary cell wall formation in Acacia auriculiformis and Acacia mangium via de novo transcriptome sequencing

Wong MM, Cannon CH, Wickneswari R

BMC Genomics, 2011;12:342.
PMID: 21729267 DOI: 10.1186/1471-2164-12-342

Acacia auriculiformis × Acacia mangium hybrids are commercially important trees for the timber and pulp industry in Southeast Asia. Increasing pulp yield while reducing pulping costs are major objectives of tree breeding programs. The general monolignol biosynthesis and secondary cell wall formation pathways are well-characterized but genes in these pathways are poorly characterized in Acacia hybrids. RNA-seq on short-read platforms is a rapid approach for obtaining comprehensive transcriptomic data and to discover informative sequence variants.
Phylogeny of Hopea (Dipterocarpaceae) inferred from chloroplast DNA and nuclear PgiC sequences

Choong CY, Wickneswari R, Norwati M, Abbott RJ

Mol Phylogenet Evol, 2008 Sep;48(3):1238-43.
PMID: 18280183 DOI: 10.1016/j.ympev.2008.01.004
Fulltext Development of high-throughput SNP-based genotyping in Acacia auriculiformis x A. mangium hybrids using short-read transcriptome data

Wong MM, Cannon CH, Wickneswari R

BMC Genomics, 2012;13:726.
PMID: 23265623 DOI: 10.1186/1471-2164-13-726

Next Generation Sequencing has provided comprehensive, affordable and high-throughput DNA sequences for Single Nucleotide Polymorphism (SNP) discovery in Acacia auriculiformis and Acacia mangium. Like other non-model species, SNP detection and genotyping in Acacia are challenging due to lack of genome sequences. The main objective of this study is to develop the first high-throughput SNP genotyping assay for linkage map construction of A. auriculiformis x A. mangium hybrids.
Fulltext Incorporating Drought and Submergence Tolerance QTL in Rice (Oryza sativa L.)-The Effects under Reproductive Stage Drought and Vegetative Stage Submergence Stresses

Mohd Ikmal A, Noraziyah AAS, Wickneswari R

Plants (Basel), 2021 Jan 24;10(2).
PMID: 33498963 DOI: 10.3390/plants10020225

Drought and submergence have been the major constraint in rice production. The present study was conducted to develop high-yielding rice lines with tolerance to drought and submergence by introgressing Sub1 into a rice line with drought yield QTL (qDTY; QTL = quantitative trait loci) viz. qDTY3.1 and qDTY12.1 using marker-assisted breeding. We report here the effect of different combinations of Sub1 and qDTY on morpho-physiological, agronomical traits and yield under reproductive stage drought stress (RS) and non-stress (NS) conditions. Lines with outstanding performance in RS and NS trials were also evaluated in vegetative stage submergence stress (VS) trial to assess the tolerance level. The QTL class analysis revealed Sub1 + qDTY3.1 as the best QTL combination affecting the measured traits in RS trial followed by Sub1 + qDTY12.1. The effects of single Sub1, qDTY3.1 and qDTY12.1 were not as superior as when the QTLs are combined, suggesting the positive interaction of Sub1 and qDTY. Best performing lines selected from the RS and NS trials recorded yield advantage up to 4453.69 kg ha-1 and 6954 kg ha-1 over the parents, respectively. The lines were also found having great tolerance to submergence ranging from 80% to 100%, contributed by a lower percentage of shoot elongation and reduction of chlorophyll content after 14 days of VS. These lines could provide yield sustainability to farmers in regions impacted with drought and submergence while serving as important genetic materials for future breeding programs.
Fulltext Green synthesis and characterization of UKMRC-8 rice husk-derived mesoporous silica nanoparticle for agricultural application

Dorairaj D, Govender N, Zakaria S, Wickneswari R

Sci Rep, 2022 Nov 23;12(1):20162.
PMID: 36424408 DOI: 10.1038/s41598-022-24484-z

Agriculture plays a crucial role in safeguarding food security, more so as the world population increases gradually. A productive agricultural system is supported by seed, soil, fertiliser and good management practices. Food productivity directly correlates to the generation of solid wastes and utilization of agrochemicals, both of which negatively impact the environment. The rice and paddy industry significantly adds to the growing menace of waste management. In low and middle-income countries, rice husk (RH) is an underutilized agro-waste discarded in landfills or burned in-situ. RH holds enormous potential in the development of value-added nanomaterials for agricultural applications. In this study, a simple and inexpensive sol-gel method is described to extract mesoporous silica nanoparticles (MSNs) from UKMRC8 RH using the bottom-up approach. RHs treated with hydrochloric acid were calcinated to obtain rice husk ash (RHA) with high silica purity (> 98% wt), as determined by the X-ray fluorescence analysis (XRF). Calcination at 650 °C for four hours in a box furnace yielded RHA that was devoid of metal impurities and organic matter. The X-ray diffraction pattern showed a broad peak at 2θ≈20-22 °C and was free from any other sharp peaks, indicating the amorphous property of the RHA. Scanning electron micrographs (SEM) showed clusters of spherically shaped uniform aggregates of silica nanoparticles (NPs) while transmission electron microscopy analysis indicated an average particle size of
Nucleotide variability in the 5-enolpyruvylshikimate-3-phosphate synthase gene from Eleusine indica (L.) Gaertn

Chong JL, Wickneswari R, Ismail BS, Salmijah S

Pak J Biol Sci, 2008 Feb 01;11(3):476-9.
PMID: 18817177

This study reports the results of the partial DNA sequence analysis of the 5-enolpyruvyl-shikimate-3-phosphate synthase (EPSPS) gene in glyphosate-resistant (R) and glyphosate-susceptible (S) biotypes of Eleusine indica (L.) Gaertn from Peninsular Malaysia. Sequencing results revealed point mutation at nucleotide position 875 in the R biotypes of Bidor, Chaah and Temerloh. In the Chaah R population, substitution of cytosine (C) to adenine (A) resulted in the change of threonine (Thr106) to proline (Pro106) and from C to thymidine (T) in the Bidor R population, leading to serine (Ser106) from Pro106. As for the Temerloh R, C was substituted by T resulting in the change of Pro106 to Ser106. A new mutation previously undetected in the Temerloh R was revealed with C being substituted with A, resulting in the change of Pro106 to Thr106 indicating multiple founding events rather than to the spread of a single resistant allele. There was no point mutation recorded at nucleotide position 875 previously demonstrated to play a pivotal role in conferring glyphosate resistance to E. indica for the Lenggeng, Kuala Selangor, Melaka R populations. Thus, there may be another resistance mechanism yet undiscovered in the resistant Lenggeng, Kuala Selangor and Melaka populations.
Fulltext Fine mapping of a grain weight quantitative trait locus, qGW6, using near isogenic lines derived from Oryza rufipogon IRGC105491 and Oryza sativa cultivar MR219

Ngu MS, Thomson MJ, Bhuiyan MA, Ho C, Wickneswari R

Genet. Mol. Res., 2014;13(4):9477-88.
PMID: 25501158 DOI: 10.4238/2014.November.11.13

Grain weight is a major component of rice grain yield and is controlled by quantitative trait loci. Previously, a rice grain weight quantitative trait locus (qGW6) was detected near marker RM587 on chromosome 6 in a backcross population (BC2F2) derived from a cross between Oryza rufipogon IRGC105491 and O. sativa cv. MR219. Using a BC2F5 population, qGW6 was validated and mapped to a region of 4.8 cM (1.2 Mb) in the interval between RM508 and RM588. Fine mapping using a series of BC4F3 near isogenic lines further narrowed the interval containing qGW6 to 88 kb between markers RM19268 and RM19271.1. According to the Duncan multiple range test, 8 BC4F4 near isogenic lines had significantly higher 100-grain weight (4.8 to 7.5% over MR219) than their recurrent parent, MR219 (P < 0.05). According to the rice genome automated annotation database, there are 20 predicted genes in the 88-kb target region, and 9 of them have known functions. Among the genes with known functions in the target region, in silico gene expression analysis showed that 9 were differentially expressed during the seed development stage(s) from gene expression series GSE6893; however, only 3 of them have known functions. These candidates provide targets for further characterization of qGW6, which will assist in understanding the genetic control of grain weight in rice.
Fulltext Identification of four functionally important microRNA families with contrasting differential expression profiles between drought-tolerant and susceptible rice leaf at vegetative stage

Cheah BH, Nadarajah K, Divate MD, Wickneswari R

BMC Genomics, 2015;16:692.
PMID: 26369665 DOI: 10.1186/s12864-015-1851-3

Developing drought-tolerant rice varieties with higher yield under water stressed conditions provides a viable solution to serious yield-reduction impact of drought. Understanding the molecular regulation of this polygenic trait is crucial for the eventual success of rice molecular breeding programmes. microRNAs have received tremendous attention recently due to its importance in negative regulation. In plants, apart from regulating developmental and physiological processes, microRNAs have also been associated with different biotic and abiotic stresses. Hence here we chose to analyze the differential expression profiles of microRNAs in three drought treated rice varieties: Vandana (drought-tolerant), Aday Sel (drought-tolerant) and IR64 (drought-susceptible) in greenhouse conditions via high-throughput sequencing.
Fulltext Evaluating Crossbred Red Rice Variants for Postprandial Glucometabolic Responses: A Comparison with Commercial Varieties

Se CH, Chuah KA, Mishra A, Wickneswari R, Karupaiah T

Nutrients, 2016 May 20;8(5).
PMID: 27213446 DOI: 10.3390/nu8050308

Consumption of white rice predisposes some Asian populations to increased risk of type 2 diabetes. We compared the postprandial glucometabolic responses to three newly-developed crossbred red rice variants (UKMRC9, UKMRC10, UKMRC11) against three selected commercial rice types (Thai red, Basmati white, Jasmine white) using 50-g carbohydrate equivalents provided to 12 normoglycaemic adults in a crossover design. Venous blood was drawn fasted and postprandially for three hours. Glycaemic (GI) and insulin (II) indices, incremental areas-under-the-curves for glucose and insulin (IAUCins), indices of insulin sensitivity and secretion, lactate and peptide hormones (motilin, neuropeptide-Y, orexin-A) were analyzed. The lowest to highest trends for GI and II were similar i.e., UKMRC9 < Basmati < Thai red < UKMRC10 < UKMRC11 < Jasmine. Postprandial insulinaemia and IAUCins of only UKMRC9 were significantly the lowest compared to Jasmine. Crude protein and fiber content correlated negatively with the GI values of the test rice. Although peptide hormones were not associated with GI and II characteristics of test rice, early and late phases of prandial neuropeptide-Y changes were negatively correlated with postprandial insulinaemia. This study indicated that only UKMRC9 among the new rice crossbreeds could serve as an alternative cereal option to improve diet quality of Asians with its lowest glycaemic and insulinaemic burden.
Fulltext Identification of functionally important microRNAs from rice inflorescence at heading stage of a qDTY4.1-QTL bearing Near Isogenic Line under drought conditions

Cheah BH, Jadhao S, Vasudevan M, Wickneswari R, Nadarajah K

PLoS One, 2017;12(10):e0186382.
PMID: 29045473 DOI: 10.1371/journal.pone.0186382

A cross between IR64 (high-yielding but drought-susceptible) and Aday Sel (drought-tolerant) rice cultivars yielded a stable line with enhanced grain yield under drought screening field trials at International Rice Research Institute. The major effect qDTY4.1 drought tolerance and yield QTL was detected in the IR77298-14-1-2-10 Backcrossed Inbred Line (BIL) and its IR87705-7-15-B Near Isogenic Line (NIL) with 93.9% genetic similarity to IR64. Although rice yield is extremely susceptible to water stress at reproductive stage, currently, there is only one report on the detection of drought-responsive microRNAs in inflorescence tissue of a Japonica rice line. In this study, more drought-responsive microRNAs were identified in the inflorescence tissues of IR64, IR77298-14-1-2-10 and IR87705-7-15-B via next-generation sequencing. Among the 32 families of inflorescence-specific non-conserved microRNAs that were identified, 22 families were up-regulated in IR87705-7-15-B. Overall 9 conserved and 34 non-conserved microRNA families were found as drought-responsive in rice inflorescence with 5 conserved and 30 non-conserved families induced in the IR87705-7-15-B. The observation of more drought-responsive non-conserved microRNAs may imply their prominence over conserved microRNAs in drought response mechanisms of rice inflorescence. Gene Ontology annotation analysis on the target genes of drought-responsive microRNAs identified in IR87705-7-15-B revealed over-representation of biological processes including development, signalling and response to stimulus. Particularly, four inflorescence-specific microRNAs viz. osa-miR5485, osa-miR5487, osa-miR5492 and osa-miR5517, and two non-inflorescence specific microRNAs viz. osa-miR169d and osa-miR169f.2 target genes that are involved in flower or embryonic development. Among them, osa-miR169d, osa-miR5492 and osa-miR5517 are related to flowering time control. It is also worth mentioning that osa-miR2118 and osa-miR2275, which are implicated in the biosynthesis of rice inflorescence-specific small interfering RNAs, were induced in IR87705-7-15-B but repressed in IR77298-14-1-2-10. Further, gene search within qDTY4.1 QTL region had identified multiple copies of NBS-LRR resistance genes (potential target of osa-miR2118), subtilisins and genes implicated in stomatal movement, ABA metabolism and cuticular wax biosynthesis.
Fulltext A gene co-expression network model identifies yield-related vicinity networks in Jatropha curcas shoot system

Govender N, Senan S, Mohamed-Hussein ZA, Wickneswari R

Sci Rep, 2018 Jun 15;8(1):9211.
PMID: 29907786 DOI: 10.1038/s41598-018-27493-z

The plant shoot system consists of reproductive organs such as inflorescences, buds and fruits, and the vegetative leaves and stems. In this study, the reproductive part of the Jatropha curcas shoot system, which includes the aerial shoots, shoots bearing the inflorescence and inflorescence were investigated in regard to gene-to-gene interactions underpinning yield-related biological processes. An RNA-seq based sequencing of shoot tissues performed on an Illumina HiSeq. 2500 platform generated 18 transcriptomes. Using the reference genome-based mapping approach, a total of 64 361 genes was identified in all samples and the data was annotated against the non-redundant database by the BLAST2GO Pro. Suite. After removing the outlier genes and samples, a total of 12 734 genes across 17 samples were subjected to gene co-expression network construction using petal, an R library. A gene co-expression network model built with scale-free and small-world properties extracted four vicinity networks (VNs) with putative involvement in yield-related biological processes as follow; heat stress tolerance, floral and shoot meristem differentiation, biosynthesis of chlorophyll molecules and laticifers, cell wall metabolism and epigenetic regulations. Our VNs revealed putative key players that could be adapted in breeding strategies for J. curcas shoot system improvements.
Association between QTLs and morphological traits toward sheath blight resistance in rice (Oryza sativa L.)

Hossain MK, Jena KK, Bhuiyan MA, Wickneswari R

Breed Sci, 2016 Sep;66(4):613-626.
PMID: 27795687

Sheath blight is considered the most significant disease of rice and causes enormous yield losses over the world. Breeding for resistant varieties is the only viable option to combat the disease efficiently. Seventeen diverged rice genotypes along with 17 QTL-linked SSR markers were evaluated under greenhouse conditions. Pearson's correlation showed only the flag leaf angle had a significant correlation with sheath blight resistance under greenhouse screening. Multivariate analysis based on UPGMA clustering and principal component analysis (PCA) indicated that the flag leaf angle, flag leaf length, and plant compactness were significantly associated with the following SSR marker alleles: RM209 (116,130), RM202 (176), RM224 (126), RM257 (156), RM426 (175), and RM6971 (196), which are linked to the SB QTLs: QRlh11, qSBR11-3, qSBR11-1, qSBR9-1, qShB3-2, and qSB-9. A Mantel test suggested a weak relationship between the observed phenotypes and allelic variation patterns, implying the independent nature of morphological and molecular variations. Teqing and Tetep were found to be the most resistant cultivars. IR65482-4-136-2-2, MR219-4, and MR264 showed improved resistance potentials. These results suggest that the morphological traits and QTLs which have been found to associate with sheath blight resistance are a good choice to enhance resistance through pyramiding either 2 QTLs or QTLs and traits in susceptible rice cultivars.
Fulltext Isolation and characterization of CCoAOMT in interspecific hybrid of Acacia auriculiformis x Acacia mangium--a key gene in lignin biosynthesis

Pang SL, Ong SS, Lee HH, Zamri Z, Kandasamy KI, Choong CY, et al.

Genet. Mol. Res., 2014;13(3):7217-38.
PMID: 25222227 DOI: 10.4238/2014.September.5.7

This study was directed at the understanding of the function of CCoAOMT isolated from Acacia auriculiformis x Acacia mangium. Full length cDNA of the Acacia hybrid CCoAOMT (AhCCoAOMT) was 1024-bp long, containing 750-bp coding regions, with one major open reading frame of 249 amino acids. On the other hand, full length genomic sequence of the CCoAOMT (AhgflCCoAOMT) was 2548 bp long, containing three introns and four exons with a 5' untranslated region (5'UTR) of 391 bp in length. The 5'UTR of the characterized CCoAOMT gene contains various regulatory elements. Southern analysis revealed that the Acacia hybrid has more than three copies of the CCoAOMT gene. Real-time PCR showed that this gene was expressed in root, inner bark, leaf, flower and seed pod of the Acacia hybrid. Downregulation of the homologous CCoAOMT gene in tobacco by antisense (AS) and intron-containing hairpin (IHP) constructs containing partial AhCCoAOMT led to reduction in lignin content. Expression of the CCoAOMT in AS line (pART-HAS78-03) and IHP line (pART-HIHP78-06) was reduced respectively by 37 and 75% compared to the control, resulting in a decrease in the estimated lignin content by 24 and 56%, respectively. AhCCoAOMT was found to have altered not only S and G units but also total lignin content, which is of economic value to the pulp industry. Subsequent polymorphism analysis of this gene across eight different genetic backgrounds each of A. mangium and A. auriculiformis revealed 47 single nucleotide polymorphisms (SNPs) in A. auriculiformis CCoAOMT and 30 SNPs in A. mangium CCoAOMT.

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