skip to main content
US FlagAn official website of the United States government
dot gov icon
Official websites use .gov
A .gov website belongs to an official government organization in the United States.
https lock icon
Secure .gov websites use HTTPS
A lock ( lock ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.

Explore Research Products in the PAR
It may take a few hours for recently added research products to appear in PAR search results.


Title: Exploring Genetic Diversity within aus Rice Germplasm: Insights into the Variations in Agro-morphological Traits
Abstract Theaus(Oryza sativaL.) varietal group comprises of aus, boro, ashina and rayada seasonal and/or field ecotypes, and exhibits unique stress tolerance traits, making it valuable for rice breeding. Despite its importance, the agro-morphological diversity and genetic control of yield traits inausrice remain poorly understood. To address this knowledge gap, we investigated the genetic structure of 181ausaccessions using 399,115 SNP markers and evaluated them for 11 morpho-agronomic traits. Through genome-wide association studies (GWAS), we aimed to identify key loci controlling yield and plant architectural traits. Our population genetic analysis unveiled six subpopulations with strong geographical patterns. Subpopulation-specific differences were observed in most phenotypic traits. Principal component analysis (PCA) of agronomic traits showed that principal component 1 (PC1) was primarily associated with panicle traits, plant height, and heading date, while PC2 and PC3 were linked to primary grain yield traits. GWAS using PC1 identifiedOsSAC1on Chromosome 7 as a significant gene influencing multiple agronomic traits. PC2-based GWAS highlighted the importance ofOsGLT1and OsPUP4/ Big Grain 3 in determining grain yield. Haplotype analysis of these genes in the 3,000 Rice Genome Panel revealed distinct genetic variations inausrice. In summary, this study offers valuable insights into the genetic structure and phenotypic diversity ofausrice accessions. We have identified significant loci associated with essential agronomic traits, withGLT1, PUP4, andSAC1genes emerging as key players in yield determination.  more » « less
Award ID(s):
2204374
PAR ID:
10615772
Author(s) / Creator(s):
; ; ; ; ; ; ; ; ; ; ; ; ; ;
Publisher / Repository:
Wiley
Date Published:
Journal Name:
Rice
Volume:
17
Issue:
1
ISSN:
1939-8425
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. ; ; ; ; ; ; ; ; ; ; et al (, Plant Physiology)
    Abstract Tomato (Solanum lycopersicum) is a highly valuable fruit crop, and yield is one of the most important agronomic traits. However, the genetic architecture underlying tomato yield-related traits has not been fully addressed. Based on ∼4.4 million single nucleotide polymorphisms obtained from 605 diverse accessions, we performed a comprehensive genome-wide association study for 27 agronomic traits in tomato. A total of 239 significant associations corresponding to 129 loci, harboring many previously reported and additional genes related to vegetative and reproductive development, were identified, and these loci explained an average of ∼8.8% of the phenotypic variance. A total of 51 loci associated with 25 traits have been under selection during tomato domestication and improvement. Furthermore, a candidate gene, Sl-ACTIVATED MALATE TRANSPORTER15, that encodes an aluminum-activated malate transporter was functionally characterized and shown to act as a pivotal regulator of leaf stomata formation, thereby affecting photosynthesis and drought resistance. This study provides valuable information for tomato genetic research and breeding. 
    more » « less
  2. ; ; ; ; ; (, Advances in Weed Science)
    The seed shattering trait has been repeatedly reshaped during rice evolution. Reduced in cultivated rice and increased in weedy rice, shattering is of great agronomic importance because of its association with yield losses. Since its first descriptions, the phenotypic patterns and the genetic regulation of cultivated and weedy rice seed shattering have been extensively studied, with a variety of methods and techniques. The aim of this review is to discuss and recommend the most suitable experimental methods for phenotypic and molecular evaluation of seed shattering in cultivated and weedy rice. Rice seed shattering must be quantified, preferably, by breaking tensile strength (BTS) assays, because other methods are more prone to human errors. The evaluation time is particularly important, and the developmental stages of the panicles measured need to be recorded. QTL analyses and GWAS studies are suitable for discovery of genes influencing shattering, but the resulting genes may only be relevant in the parental lines or the populations used. The variety of cultivated rice and evolutionary origin of weedy rice accessions has a great influence on results of rice seed shattering phenotypic and genotypic analyses and needs to always be taken into account. 
    more » « less
  3. ; ; ; ; ; ; ; ; ; ; et al (, New Phytologist)
    Summary A higher minimum (night‐time) temperature is considered a greater limiting factor for reduced rice yield than a similar increase in maximum (daytime) temperature. While the physiological impact of high night temperature (HNT) has been studied, the genetic and molecular basis of HNT stress response remains unexplored.We examined the phenotypic variation for mature grain size (length and width) in a diverse set of rice accessions under HNT stress. Genome‐wide association analysis identified several HNT‐specific loci regulating grain size as well as loci that are common for optimal and HNT stress conditions.A novel locus contributing to grain width under HNT conditions colocalized withFie1, a component of the FIS‐PRC2 complex. Our results suggest that the allelic difference controlling grain width under HNT is a result of differential transcript‐level response ofFie1in grains developing under HNT stress.We present evidence to support the role ofFie1in grain size regulation by testing overexpression (OE) and knockout mutants under heat stress. The OE mutants were either unaltered or had a positive impact on mature grain size under HNT, while the knockouts exhibited significant grain size reduction under these conditions. 
    more » « less
  4. ; ; ; ; ; ; ; (, Molecular Ecology)
    Abstract Weedy rice (Oryzaspp.) is a weedy relative of the cultivated rice that competes with the crop and causes significant production loss. The BHA (blackhull awned) US weedy rice group has evolved fromauscultivated rice and differs from its ancestors in several important weediness traits, including flowering time, plant height and seed shattering. Prior attempts to determine the genetic basis of weediness traits in plants using linkage mapping approaches have not often considered weed origins. However, the timing of divergence between crossed parents can affect the detection of quantitative trait loci (QTL) relevant to the evolution of weediness. Here, we used a QTL‐seq approach that combines bulked segregant analysis and high‐throughput whole genome resequencing to map the three important weediness traits in an F2population derived from a cross between BHA weedy rice with an ancestralauscultivar. We compared these QTLs with those previously detected in a cross of BHA with a more distantly related crop,indica. We identified multiple QTLs that overlapped with regions under selection during the evolution of weedy BHA rice and some candidate genes possibly underlying the evolution weediness traits in BHA. We showed that QTLs detected with ancestor–descendant crosses are more likely to be involved in the evolution of weediness traits than those detected from crosses of more diverged taxa. 
    more » « less
  5. ; ; ; ; ; ; ; ; ; ; et al (, Frontiers in Plant Science)
    Heat stress occurring during rice (Oryza sativa) grain development reduces grain quality, which often manifests as increased grain chalkiness. Although the impact of heat stress on grain yield is well-studied, the genetic basis of rice grain quality under heat stress is less explored as quantifying grain quality is less tractable than grain yield. To address this, we used an image-based colorimetric assay (Red, R; and Green, G) for genome-wide association analysis to identify genetic loci underlying the phenotypic variation in rice grains exposed to heat stress. We found the R to G pixel ratio (RG) derived from mature grain images to be effective in distinguishing chalky grains from translucent grains derived from control (28/24°C) and heat stressed (36/32°C) plants. Our analysis yielded a novel gene, riceChalky Grain 5(OsCG5) that regulates natural variation for grain chalkiness under heat stress.OsCG5encodes a grain-specific, expressed protein of unknown function. Accessions with lower transcript abundance ofOsCG5exhibit higher chalkiness, which correlates with higher RG values under stress. These findings are supported by increased chalkiness ofOsCG5knock-out (KO) mutants relative to wildtype (WT) under heat stress. Grains from plants overexpressingOsCG5are less chalky than KOs but comparable to WT under heat stress. Compared to WT and OE, KO mutants exhibit greater heat sensitivity for grain size and weight relative to controls. Collectively, these results show that the natural variation atOsCG5may contribute towards rice grain quality under heat stress. 
    more » « less
  • Citation Formats
  • MLA
  • APA
  • Chicago
  • BibTeX
  • Save / Share this Record
  • Send to Email