Amylose Content and Grain Length of New Rice Transgressive Variants Derived from a Cross Between O. rufipogon and Malaysian Rice Cultivar MR219

Amylose content is one of the important grain quality properties of rice. A total of 10 new rice genotypes (BC2F7 generation) derived from a cross between O. rufipogon Griff. accession IRGC105491 and O. sativa subspecies indica cv. MR219 with high yield were evaluated for amylose content in three environments in Peninsular Malaysia. One of the parents, a popular high yielding Malaysian rice cultivar MR219 was used as a check. Based on the average amylose content across the environments, the genotype G13 showed significantly (p < 0.05) different amylose content (23.88 %) in comparison to other genotypes. Two genotypes G13 (25.7%) and G15 (25.6%) were higher than MR219 (25.1%) in terms of amylose content in Sungai Besar environment. There was a positive (r2=0.018) but no significant correlation between amylose content and grain length

Identification of lignin genes and regulatory sequences involved in secondary cell wall formation in Acacia auriculiformis and Acacia mangium via de novo transcriptome sequencing

<p>Abstract</p> <p>Background</p> <p><it>Acacia auriculiformis </it>× <it>Acacia mangium </it>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 <it>Acacia </it>hybrids. RNA-seq on short-read platforms is a rapid approach for obtaining comprehensive transcriptomic data and to discover informative sequence variants.</p> <p>Results</p> <p>We sequenced transcriptomes of <it>A. auriculiformis </it>and <it>A. mangium </it>from non-normalized cDNA libraries synthesized from pooled young stem and inner bark tissues using paired-end libraries and a single lane of an Illumina GAII machine. <it>De novo </it>assembly produced a total of 42,217 and 35,759 contigs with an average length of 496 bp and 498 bp for <it>A. auriculiformis </it>and <it>A. mangium </it>respectively. The assemblies of <it>A. auriculiformis </it>and <it>A. mangium </it>had a total length of 21,022,649 bp and 17,838,260 bp, respectively, with the largest contig 15,262 bp long. We detected all ten monolignol biosynthetic genes using Blastx and further analysis revealed 18 lignin isoforms for each species. We also identified five contigs homologous to R2R3-MYB proteins in other plant species that are involved in transcriptional regulation of secondary cell wall formation and lignin deposition. We searched the contigs against public microRNA database and predicted the stem-loop structures of six highly conserved microRNA families (miR319, miR396, miR160, miR172, miR162 and miR168) and one legume-specific family (miR2086). Three microRNA target genes were predicted to be involved in wood formation and flavonoid biosynthesis. By using the assemblies as a reference, we discovered 16,648 and 9,335 high quality putative Single Nucleotide Polymorphisms (SNPs) in the transcriptomes of <it>A. auriculiformis </it>and <it>A. mangium</it>, respectively, thus yielding useful markers for population genetics studies and marker-assisted selection.</p> <p>Conclusion</p> <p>We have produced the first comprehensive transcriptome-wide analysis in <it>A. auriculiformis </it>and <it>A. mangium </it>using <it>de novo </it>assembly techniques. Our high quality and comprehensive assemblies allowed the identification of many genes in the lignin biosynthesis and secondary cell wall formation in <it>Acacia </it>hybrids. Our results demonstrated that Next Generation Sequencing is a cost-effective method for gene discovery, identification of regulatory sequences, and informative markers in a non-model plant.</p

Effects of open- and self-pollination on fruit set and seed quality in Jatropha curcas L.

Investigation on different mating systems is necessary to improve fruit and seed production and seed quality in Jatropha curcas. In the present study, a total of 150 female flowers belonging to five accessions from Indonesia and Malaysia were screened for traits associated with fruit set and seed quality under open- and self-pollination. The study was conducted at Biodiesel Research Station, Universiti Kebangsaan Malaysia (UKM), Kuala Pilah from April to September 2015. The number of fruits per plant (NFP), number of seeds per plant (NSP) and number of seeds germinated (NSG) showed significant differences among the mating systems. Under open-pollination, the maximum mean values for NFP, NSP, NSG and number of seedlings surviving after three months (NSS) were 10, 29, 27 and 18, respectively. Conversely, self-pollination scored at 9, 26, 22 and 18 for NFP, NSP, NSG and NSS, respectively. Seed weight (SWt) showed significant differences among accessions whereas seed length (SLT) showed significant differences among the mating systems and accessions. UKMJC20 (Indonesia) showed the best performance in terms of NFP under both open- and self-pollination whereas UKMJC21 (Malaysia) showed the best performance in terms of SWt and SLT under both conditions. Two (UKMJC13 and UKMJC21) out of five accessions showed occurrence of apomixis

Genetic structure of glyphosate-resistant ( R ) and glyphosate-susceptible ( S ) populations of Eleusine indica (L.) Gaertn from Peninsular Malaysia

Glyphosate is the world’s most widely used herbicide, accounting for 11 % of worldwide herbicide sales (Powles et al., 1997). As a nonselective herbicide with no soil activity (Grossbard & Atkinson 1985), it is an ideal herbicide to control a broad range of weed species. In Malaysia, glyphosate is used to control various weed species growing in oil palm and rubber plantations. In some instances, multiple treatments have been carried out continuously for several years

Fine mapping of a grain weight quantitative trait locus, qGW6, using near isogenic lines derived from Oryza rufipogon IRGC105491 and Oryza sativa cultivar MR219

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

Comparative genetic diversity studies of Shorea curtisii (Dipterocarpaceae) an assessment using SSR and DAMD markers

Genetic diversity of Shorea curtisii from different age cohorts, namely, seedlings, saplings and adult trees were determined using six SSR loci and 33 DAMD loci. To quantify genetic diversity in S. curtisii we used standard genetic diversity measures for SSR data, and both phenotypic and genotypic methods with null-allele frequency corrected for deviation from Hardy-Weinberg equilibrium (HWE) with SSR markers for DAMD data. Results showed that the genetic diversity measured using DAMD genotypic method was lower than those derived from SSR data based on the same set of samples. This suggests that DAMD allele frequencies corrected from HWE deviation using fixation index derived from SSR data may be underestimated. The genetic distance matrix generated from SSR data was significantly correlated with DAMD genotype data (r = 0.990, p < 0.05), indicating a similar genetic structure of S. curtisii being depicted by both marker types among the age cohorts tested. The relationship between sample size and genetic diversity measures demonstrated a threshold level, i.e. n = 20 and n = 30 for seedlings and saplings respectively, and n = 15 and n = 20 for adult trees revealed by SSR and DAMD markers respectively. Genetic diversity measures dropped drastically below these levels. These results further imply that a highly heterogeneous population was observed in S. curtisii from each age cohort. Collectively, both SSR and DAMD markers have good genome coverage in the S. curtisii genome

Introgression of the QTL qSB11-1TT conferring sheath blight resistance in rice (Oryza sativa) into an elite variety, UKMRC 2, and evaluation of its backcross-derived plants

Introduction: Sheath blight (SB) is the most damaging fungal disease in rice caused by a soil-borne pathogenic fungus, Rhizoctonia solani Kuhn (R. solani). The disease resistance in rice is a complex quantitative trait controlled by a few major genes. UKMRC2 is a newly developed elite rice variety that possesses high yield potential but is susceptible to sheath blight disease indicating a huge risk of varietal promotion, mass cultivation, and large-scale adoption. The aim of our present study was the development of varietal resistance against R. solani in UKMRC2 to enhance its stability and durability in a wide range of environments and to validate the effects of an SB-resistance QTL on the new genetic background. Methods: In our study, we developed 290 BC1F1 backcross progenies from a cross between UKMRC2 and Tetep to introgress the QTL qSBR11-1TT into the UKMRC2 genetic background. Validation of the introgressed QTL region was performed via QTL analysis based on QTL-linked SSR marker genotyping and phenotyping against R. solani artificial field inoculation techniques. Results and Discussion: The QTL qSBR11-1TT was then authenticated with the results of LOD score (3.25) derived from composite interval mapping, percent phenotypic variance explained (14.6%), and additive effect (1.1) of the QTLs. The QTL region was accurately defined by a pair of flanking markers K39512 and RM7443 with a peak marker RM27360. We found that the presence of combination of alleles, RM224, RM27360 and K39512 demonstrate an improved resistance against the disease rather than any of the single allele. Thus, the presence of the QTL qSBR11-1TT has been validated and confirmed in the URMRC2 genetic background which reveals an opportunity to use the QTL linked with these resistance alleles opens an avenue to resume sheath blight resistance breeding in the future with marker-assisted selection program to boost up resistance in rice varieties

Efecto del uso de un secador solar tipo invernadero para la deshidratación de alfalfa (Medicago sativa l. var. zaino)

El objetivo del estudio fue determinar el efecto del uso de un secador solar tipo invernadero para la deshidratación de alfalfa (Medicago sativa L. var Zaino), las variables evaluadas fueron la humedad relativa y temperatura dentro y fuera del secador solar, los porcentajes de proteína bruta y materia seca parcial. El tamaño de partícula de la alfalfa fue reducido manualmente previo a su ingreso al secador solar donde permaneció durante 4 días para su estudio. Se le realizó a la muestra 2 exámenes bromatológicos completos, el primero antes de ser ingresada la muestra al secador y la segunda al salir de el. La temperatura, humedad relativa y el contenido de materia seca parcial de la muestra fueron evaluadas diariamente. El secador solar tipo invernadero a pesar de alcanzar en su interior niveles de temperatura y humedad mayores a los alcanzados fuera del mismo, no es capaz de producir alfalfa deshidratada, debido a los factores climáticos que afectaron el área de la ciudad de Guatemala, durante el período de evaluación