Biology subjects

Raman, H.

Publications and source records attributed to Raman, H..

7 recordsLinked to original sources

bioRxiv2025

De Novo Genome Assembly and Characterization of Plant Growth-Promoting Rhizobacteria isolated from field grown Canola Plants

Plant growth-promoting rhizobacteria have the potential to reduce reliance on synthetic fertilizers. Yet the rhizosphere microbiome of canola (Brassica napus) remains understudied despite the crops global significance. In this study, we isolated and characterized 12 bacterial strains from canola roots, to better understand the diversity and potential agricultural benefits of the canola microbiome. Using a combination of long- and short-read whole-genome sequencing, we generated high-quality genome assemblies of all 12 bacterial species. Genomic analysis revealed genes linked to nitrogen fixation, phosphorus solubilization and phytohormone production, suggesting these bacterial strains may play beneficial roles in plant growth and resilience. Growth assays showed that most isolates proliferated in the presence of canola root exudates, indicating their adaptation to the rhizosphere. Several strains also exhibited nitrogen fixation traits, including growth in nitrogen-deficient media and ammonium production, yet bacterial inoculation did not significantly enhance early seedling development under nitrogen-limited conditions. Our findings expand the current knowledge of the diversity and functional potential of the canola microbiome and highlight promising bacterial candidates for development as biofertilizers or biocontrol agents, with implications for improving soil health and canola productivity.

microbiology↗

bioRxiv2024

Genome-wide association study elucidates the genetic architecture of manganese tolerance in Brassica napus

Brassica napus (canola) is a significant contributor to the worlds oil production and is cultivated across continents, yet acidic soils with Al3+ and Mn2+ toxicities limit its production. The genetic determinants underlying acidic soil tolerance in canola are unknown and require to be uncovered for canola breeding and production. Here, through comprehensive phenotyping, whole genome resequencing, and genome-wide association analysis, we identified three QTLs for tolerance to Mn2+ toxicity on chromosomes A09, C03, and C09. Allelism tests between four tolerance sources confirmed that at least one locus on A09 controls Mn2+ tolerance in B. napus. Integrated analysis of genomic and expression QTL and Mn2+ tolerance data reveals that BnMTP8.A09, in conjunction with BnMATE.C03, BnMTP8.C04 and BnMTP8.C08, play a central role in conferring Mn2+ tolerance in B. napus. Gene expression analysis revealed a high correlation (R2 = 0.74) between Mn2+ tolerance and the BnMTP8.A09 expression. Yeast complementation assays show that BnMTP8.A09 can complement manganese-hypersensitive yeast mutant strain PMR1{Delta} and restore Mn2+ tolerance to wild-type levels. Inductively coupled plasma mass spectrometry revealed that Mn2+ tolerant accessions accumulate less Mn in the shoots compared to Mn2+ sensitives, suggesting that the BnMTP8.A09 transporter likely sequesters Mn2+ into the tonoplast. Taken together, our research unveils the genetic architecture of Mn2+ tolerance and identifies BnMTP8.A09 as a major gene imparting tolerance to Mn2+ toxicity in B. napus.

plant biology↗

bioRxiv2021

Multi-environment QTL analysis delineates a major locus associated with homoeologous exchanges for water-use efficiency and seed yield in allopolyploid Brassica napus

O_LICanola varieties exhibit discernible variation in drought avoidance and drought escape traits, suggesting its adaptation to water-deficit environments. However, the underlying mechanisms are poorly understood. C_LIO_LIA doubled haploid (DH) population was analysed to identify QTL associated with water use efficiency (WUE) related traits. Based on the resequenced parental genome data, we developed sequence-capture based markers for fine mapping. mRNA-Seq was performed to determine the expression of candidate genes underlying QTL for carbon isotope discrimination ({Delta}13C). C_LIO_LIQTL contributing to main and QTL x Environment interaction effects for {Delta}13C and for agronomic WUE were identified. One multi-trait QTL for {Delta}13C, days to flower, plant height and seed yield was identified on chromosome A09, in the vicinity of ERECTA. Interestingly, this QTL region was overlapped with a homoeologous exchange event (HE), suggesting its association with the major QTL. Transcriptome analysis revealed several differentially expressed genes between parental lines, including in HE regions. C_LIO_LIThis study provides insights into the complexity of WUE related genes in the context of canola adaptation to water-deficit conditions. Our results suggest that alleles for high {Delta}13C contribute positively to canola yield. Genetic and genomic resources developed herein could be utilised to make genetic gains for improving canola WUE. C_LI

plant biology↗

bioRxiv2020

QTL mapping reveals genomic regions for yield based on incremental tolerance index to drought stress and related agronomic traits in canola

Drought stress especially at the reproductive stage is a major limiting factor that compromises the productivity and profitability of canola in many regions of the world. Improved genetics for drought tolerance would enable the identification and development of resilient varieties, resulting in increased canola production. The main objective of this study was to dissect the genetic basis of seed yield under water-limited conditions in canola. A doubled haploid population derived from a cross between two Australian parental lines, RP04 and Ag-Outback, was evaluated to identify the genetic variation in fractional normalised deviation vegetative index (NDVI), above ground shoot biomass accumulation, flowering time, and plasticity in seed yield under irrigated and rainfed field conditions in two consecutive years. An irrigation treatment was applied at the 50% flowering stage and an incremental drought tolerance index (DTI) was estimated for seed yield. By utilising a genetic linkage map based on 18,851 genome-wide DArTseq markers, we identified 25 genomic regions significantly associated with different traits (LOD [≥] 3), accounting for 5.5 to 22.3% of the genotypic variance. Three significant genomic regions on chromosome A06, A10 and C04 were associated with DTI for seed yield. Some of the QTL were localised in the close proximity of candidates genes involved in traits contributing to drought escape and drought avoidance mechanisms, including FLOWERING LOCUS T (FT) and FLOWERING LOCUS C (FLC). Trait-marker associations identified herein can be validated across diverse environments, and the sequence based markers may be used in a marker assisted selection breeding strategy to enhance drought tolerance in canola breeding germplasm.

plant biology↗

bioRxiv2019

An epigenetic LTR-retrotransposon insertion in the upstream region of BnSHP1.A9 controls quantitative pod shattering resistance in Brassica napus

Seed loss resulting from pod shattering is a major problem in oilseed rape (Brassica napus L.) production worldwide. However, the molecular mechanisms underlying pod shatter resistance are not well understood. Here we show that the pod shatter resistance at quantitative trait locus, qSRI.A9.1 is controlled by a SHATTERPROOF1 (SHP1) paralog in B. napus (BnSHP1.A9). Expression analysis by quantitative RT-PCR showed that BnSHP1.A9 was specifically expressed in flower buds, flowers and developing siliques in the oilseed rape line (R1) carrying the qSRI.A9.1 allele with negative effect, but not expressed in any tissue of the line (R2) carrying the positive effect qSRI.A9.1 allele. Transgenic plants constitutively expressing BnSHP1.A9 alleles from pod resistant and pod shattering parental lines showed that both alleles are responsible for pod shattering via promoting lignification of enb layer, which indicated allelic difference of BnSHP1.A9 gene per se is not the causal factor of the QTL. The upstream sequence of BnSHP1.A9 in the promotor region harboring highly methylated long terminal repeat retrotransposon insertion (LTR, 4803bp) in R2 repressed the expression of BnSHP.A9, and thus contributed to the positive effect on pod shatter resistance. Genetic and association analysis revealed that the copia LTR retrotransposon based marker BnSHP1.A9-R2 can be used for breeding for pod shatter resistant varieties and reducing the loss of seed yield in oilseed rape.

genetics↗

bioRxiv2019

GWAS hints at pleiotropic roles for FLOWERING LOCUS T in flowering time and yield-related traits in canola

Transition to flowering at the right time is critical for local adaptation and to maximize seed yield in canola, which is an important oilseed crop. There is extensive variation among canola varieties in flowering time. However, our understanding of underlying genes and their role in canola productivity is still limited. We reveal natural variation in flowering time and response to photoperiod in a diverse GWAS panel (up to 368 accessions) of canola and identify associated SNPs across multiple experiments. Complementary QTL and eQTL mapping studies were also conducted in an Australian doubled haploid (DH) population for flowering time and other grain yield related traits. We show that several associations that were repeatedly detected across experiments map in the vicinity of FLOWERING LOCUS T (FT) paralogues and its known transcriptional regulators. QTL mapping study in a DH population detected consistent genomic regions close to FT paralogs. FT sequences vary between accessions and FT expression in field and controlled environment grown plants was correlated with flowering time. FT paralogs displayed association not only with flowering time, but also with plant emergence, shoot biomass and grain yield. Our findings suggest that FT paralogs not only modulate flowering time but also modulate yield-related productivity traits in canola. HighlightThe genetic association, eQTL and expression analyses suggest that FT paralogs have multifaceted roles in canola flowering time, plant development and productivity traits.

plant biology↗

bioRxiv2017

Speed breeding: a powerful tool to accelerate crop research and breeding

The growing human population and a changing environment have raised significant concern for global food security, with the current improvement rate of several important crops inadequate to meet future demand [1]. This slow improvement rate is attributed partly to the long generation times of crop plants. Here we present a method called speed breeding, which greatly shortens generation time and accelerates breeding and research programs. Speed breeding can be used to achieve up to 6 generations per year for spring wheat (Triticum aestivum), durum wheat (T. durum), barley (Hordeum vulgare), chickpea (Cicer arietinum), and pea (Pisum sativum) and 4 generations for canola (Brassica napus), instead of 2-3 under normal glasshouse conditions. We demonstrate that speed breeding in fully-enclosed controlled-environment growth chambers can accelerate plant development for research purposes, including phenotyping of adult plant traits, mutant studies, and transformation. The use of supplemental lighting in a glasshouse environment allows rapid generation cycling through single seed descent and potential for adaptation to larger-scale crop improvement programs. Cost-saving through LED supplemental lighting is also outlined. We envisage great potential for integrating speed breeding with other modern crop breeding technologies, including high-throughput genotyping, genome editing, and genomic selection, accelerating the rate of crop improvement.

plant biology↗