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Biology subjects

Chin, J. H.

Publications and source records attributed to Chin, J. H..

4 recordsLinked to original sources

New rice varieties with improved phosphorus-efficiency for low-input smallholder rice production in Africa

Smallholder farmers in Sub-Saharan Africa frequently produce rice in marginal environments where low soil fertility and other biotic and abiotic stresses limit productivity. Rice varieties developed by centralized breeding under favorable conditions on research stations have often not been adopted by farmers in such marginal environments. Our objective was to develop modern rice varieties adapted to such low-input conditions through combining pre-breeding research with subsequent selection and variety testing directly in the target environment: smallholder farmers fields in Madagascar with phosphorus (P) fixing soils. Two breeding populations were developed for this purpose, one based on marker-assisted introgression of the Pup1 locus into IR64, the second using a donor (DJ123) for internal P utilization efficiency and external P acquisition efficiency. Selection within these populations was conducted in fields managed according to local farmers practice without mineral fertilizer addition. Selected breeding lines underwent government-supervised variety release testing including farmer participatory evaluations in four Malagasy regions between 18-1350 masl altitude, and two lines were released as varieties FyVary32 and VyVary85. Both had between 0.47-0.8 t ha-1 higher grain yield than parent IR64 and local check X265. Yield advantages were stable across a range from 2.1-5.5 t ha-1 (national average: 2.8 t ha-1). Higher yields were accompanied by superior root development and P uptake and by more efficient internal P utilization in FyVary85. Results show that decentralized breeding in marginal environments can produce varieties not only superior in lowest-yielding environments but across a broader range, clearly surpassing national average yields.

plant biology↗

Chromosome-level genome assembly of milk thistle (Silybum marianum (L.) Gaertn.)

Silybum marianum (L.) Gaertn., commonly known as milk thistle, is a medicinal plant belonging to the Asteraceae family. This plant has been recognized for its medicinal properties for over 2,000 years. However, the genome of this plant remains largely undiscovered, having no reference genome at a chromosomal level. Here, we assembled the chromosome-level genome of S. marianum, allowing for the annotation of 53,552 genes and the identification of transposable elements comprising 58% of the genome. The genome assembly from this study showed 99.1% completeness as determined by BUSCO assessment, while the previous assembly (ASM154182v1) showed 36.7%. Functional annotation of the predicted genes showed 50,329 genes (94% of total genes) with known protein functions in public databases. Comparative genome analysis among Asteraceae plants revealed a striking conservation of collinearity between S. marianum and C. cardunculus . The genomic information generated from this study will be a valuable resource for milk thistle breeding and for use by the larger research community.

genomics↗

Metagenomic Next-generation Sequencing of Cerebrospinal Fluid for the Diagnosis of Central Nervous System Infections: A Multicentre Prospective Study

BackgroundInfectious encephalitis and meningitis are often treated empirically without identification of the causative pathogen. Metagenomic next-generation sequencing (mNGS) is a high throughput technology that enables the detection of pathogens independent of prior clinical or laboratory information.\n\nMethodsThe present study was a multicentre prospective evaluation of mNGS of cerebrospinal fluid (CSF) for the diagnosis of suspected central nervous system infections.\n\nResultsA total of 276 patients were enrolled in this study between Jan 1, 2017 and Jan 1, 2018. Identification of an etiologic pathogen in CSF by mNGS was achieved in 101 patients (36.6%). mNGS detected 11 bacterial species, 7 viral species, 2 fungal species, and 2 parasitic species. The five leading positive detections were varicella-zoster virus (17), Mycobacterium tuberculosis (14), herpes simplex virus 1 (12), Epstein-Barr virus (12), and Cryptococcus neoformans (7). False positives occurred in 12 (4.3%) patients with bacterial infections known to be widespread in hospital environments. False negatives occurred in 16 (5.8%) patients and included bacterial, viral and fungal aetiologies.\n\nConclusionsmNGS of CSF is a powerful diagnostic method to identify the pathogen for many central nervous system infections.

genomics↗

Novel allelic variant of Lpa1 gene associated with a significant reduction in seed phytic acid content in rice (Oryza sativa L.)

In plants, myo-inositol-1,2,3,4,5,6-hexakisphosphate (InsP6), also known as phytic acid (PA), is a major component of organic phosphorus (P), and accounts for up to 85% of the total P in seeds. In rice (Oryza sativa L.), PA mainly accumulates in rice bran, and chelates mineral cations, resulting in mineral deficiencies among brown rice consumers. Therefore, considerable efforts have been focused on the development of low PA (LPA) rice cultivars. In this study, we performed genetic and molecular analyses of OsLpa1, a major PA biosynthesis gene, in Sanggol, a low PA mutant variety developed via chemical mutagenesis of Ilpum rice cultivar. Genetic segregation and sequencing analyses revealed that a recessive allele, lpa1-3, at the OsLpa1 locus (Os02g0819400) was responsible for a significant reduction in seed PA content in Sanggol. The lpa1-3 gene harboured a point mutation (C623T) in the fourth exon of the predicted coding region, resulting in threonine (Thr) to isoleucine (Ile) amino acid substitution at position 208 (Thr208Ile). Three-dimensional analysis of Lpa1 protein structure indicated that myo-inositol 3-monophosphate [Ins(3)P1] kinase binds to the active site of Lpa1, with ATP as a cofactor for catalysis. Furthermore, the presence of Thr208 in the loop adjacent to the entry site of the binding pocket suggests that Thr208Ile substitution is involved in regulating enzyme activity via phosphorylation. Therefore, we propose that Thr208Ile substitution in lpa1-3 reduces Lpa1 enzyme activity in Sanggol, resulting in reduced PA biosynthesis.

plant biology↗