A transient heat stress occurring during early seed development in rice (
Increasing global surface temperatures is posing a major food security challenge. Part of the solution to address this problem is to improve crop heat resilience, especially during grain development, along with agronomic decisions such as shift in planting time and increasing crop diversification. Rice is a major food crop consumed by more than 3 billion people. For rice, thermal sensitivity of reproductive development and grain filling is well‐documented, while knowledge concerning the impact of heat stress (HS) on early seed development is limited. Here, we aim to study the phenotypic variation in a set of diverse rice accessions for elucidating the HS response during early seed development. To explore the variation in HS sensitivity, we investigated
- PAR ID:
- 10197283
- Publisher / Repository:
- Wiley Blackwell (John Wiley & Sons)
- Date Published:
- Journal Name:
- Plant Direct
- Volume:
- 4
- Issue:
- 1
- ISSN:
- 2475-4455
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
more » « less
Abstract Oryza sativa ) reduces seed size by altering endosperm development. However, the relationship between the timing of the stress and specific developmental stage on heat sensitivity is not well‐understood. To address this, we imposed a series of non‐overlapping heat stress treatments and found that young seeds are most sensitive during the first two days after flowering. Temporal transcriptome analysis of developing, heat stressed (35°C) seeds during this window shows thatInositol‐requiring enzyme 1 (IRE1) ‐mediated endoplasmic reticulum (ER) stress response and jasmonic acid (JA) pathways are the early (1–3 h) drivers of heat stress response. We propose that increased JA levels under heat stress may precede ER stress response as JA application promotes the spliced form ofOsbZIP50, an ER response marker gene linked to IRE1‐specific pathway. This study presents temporal and mechanistic insights into the role of JA and ER stress signalling during early heat stress response of rice seeds that impact both grain size and quality. Modulating the heat sensitivity of the early sensing pathways and downstream endosperm development genes can enhance rice resilience to transient heat stress events. -
more » « less
Abstract Weedy rice, a pervasive and troublesome weed found across the globe, has often evolved through fertilization of rice cultivars with little importance of crop‐weed gene flow. In Argentina, weedy rice has been reported as an important constraint since the early 1970s, and, in the last few years, strains with herbicide‐resistance are suspected to evolve. Despite their importance, the origin and genetic composition of Argentinian weedy rice as well its adaptation to agricultural environments has not been explored so far. To study this, we conducted genotyping‐by‐sequencing on samples of Argentinian weedy and cultivated rice and compared them with published data from weedy, cultivated and wild rice accessions distributed worldwide. In addition, we conducted a phenotypic characterization for weedy‐related traits, a herbicide resistance screening and genotyped accessions for known mutations in the acetolactate synthase (
ALS ) gene, which confers herbicide resistance. Our results revealed large phenotypic variability in Argentinian weedy rice. Most strains were resistant to ALS‐inhibiting herbicides with a high frequency of the ALS mutation (A122T) present in Argentinian rice cultivars. Argentinian cultivars belonged to the three major genetic groups of rice:japonica ,indica andaus while weeds were mostlyaus oraus‐indica admixed, resembling weedy rice strains from the Southern Cone region. Phylogenetic analysis supports a single origin foraus‐like South American weeds, likely as seed contaminants from the United States, and then admixture with localindica cultivars. Our findings demonstrate that crop to weed introgression can facilitate rapid adaptation to agriculture environments. -
more » « less
Abstract Previous work has shown that inorganic As localizes in rice bran whereas DMA localizes in the endosperm, but less is known about co-localization of As and S species and how they are affected by growing conditions. We used high-resolution synchrotron X-ray fluorescence imaging to image As and S species in rice grain from plants grown to maturity in soil (field and pot) and hydroponically (DMA or arsenite dosed) at field-relevant As concentrations. In hydroponics, arsenite was localized in the ovular vascular trace (OVT) and the bran while DMA permeated the endosperm and was absent from the OVT in all grains analyzed, and As species had no affect on S species. In pot studies, soil amended with Si-rich rice husk with higher DMA shifted grain As into the endosperm for both japonica and indica ecotypes. In field-grown rice from low-As soil, As localized in the OVT as arsenite glutathione, arsenite, and DMA. Results support a circumferential model of grain filling for arsenite and DMA and show Si-rich soil amendments alter grain As localization, potentially lessening risk to rice consumers.
-
more » « less
Abstract Background Genome wide association (GWA) studies demonstrate linkages between genetic variants and traits of interest. Here, we tested associations between single nucleotide polymorphisms (SNPs) in rice (
Oryza sativa ) and two root hair traits, root hair length (RHL) and root hair density (RHD). Root hairs are outgrowths of single cells on the root epidermis that aid in nutrient and water acquisition and have also served as a model system to study cell differentiation and tip growth. Using lines from the Rice Diversity Panel-1, we explored the diversity of root hair length and density across four subpopulations of rice (aus ,indica ,temperate japonica , andtropical japonica ). GWA analysis was completed using the high-density rice array (HDRA) and the rice reference panel (RICE-RP) SNP sets.Results We identified 18 genomic regions related to root hair traits, 14 of which related to RHD and four to RHL. No genomic regions were significantly associated with both traits. Two regions overlapped with previously identified quantitative trait loci (QTL) associated with root hair density in rice. We identified candidate genes in these regions and present those with previously published expression data relevant to root hair development. We re-phenotyped a subset of lines with extreme RHD phenotypes and found that the variation in RHD was due to differences in cell differentiation, not cell size, indicating genes in an associated genomic region may influence root hair cell fate. The candidate genes that we identified showed little overlap with previously characterized genes in rice and
Arabidopsis .Conclusions Root hair length and density are quantitative traits with complex and independent genetic control in rice. The genomic regions described here could be used as the basis for QTL development and further analysis of the genetic control of root hair length and density. We present a list of candidate genes involved in root hair formation and growth in rice, many of which have not been previously identified as having a relation to root hair growth. Since little is known about root hair growth in grasses, these provide a guide for further research and crop improvement.
-
more » « less
Summary Alternative polyadenylation (
APA ) is a widespread post‐transcriptional mechanism that regulates gene expression throughmRNA metabolism, playing a pivotal role in modulating phenotypic traits in rice (Oryza sativa L.). However, little is known about theAPA ‐mediated regulation underlying the distinct characteristics between two major rice subspecies,indica andjaponica . Using a poly(A)‐tag sequencing approach, polyadenylation (poly(A)) site profiles were investigated and compared pairwise from germination to the mature stage betweenindica andjaponica , and extensive differentiation inAPA profiles was detected genome‐wide. Genes with subspecies‐specific poly(A) sites were found to contribute to subspecies characteristics, particularly in disease resistance ofindica and cold‐stress tolerance ofjaponica . In most tissues, differential usage ofAPA sites exhibited an apparent impact on the gene expression profiles between subspecies, and genes with those APA sites were significantly enriched in quantitative trait loci (QTL ) related to yield traits, such as spikelet number and 1000‐seed weight. In leaves of the booting stage,APA site‐switching genes displayed global shortening of 3′ untranslated regions with increased expression inindica compared withjaponica , and they were overrepresented in the porphyrin and chlorophyll metabolism pathways. This phenomenon may lead to a higher chlorophyll content and photosynthesis inindica than injaponica , being associated with their differential growth rates and yield potentials. We further constructed an online resource for querying and visualizing the poly(A) atlas in these two rice subspecies. Our results suggest thatAPA may be largely involved in developmental differentiations between two rice subspecies, especially in leaf characteristics and the stress response, broadening our knowledge of the post‐transcriptional genetic basis underlying the divergence of rice traits.
