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At least 415 records · Page 23
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Phenome‐to‐genome insights for evaluating root system architecture in field studies of maize

Abstract Understanding the genetic basis of root system architecture (RSA) in crops requires innovative approaches that enable both high‐throughput and precise phenotyping in field conditions. In this study, we evaluated multiple phenotyping and analytical frameworks for quantifying RSA in mature, field‐grown maize in three field experiments. We used forward and reverse genetic approaches to evaluate >1700 maize root crowns, including a diversity panel, a biparental mapping population, and maize mutant and wild‐type alleles at two known RSA genes,DEEPER ROOTING 1(DRO1) andRootless1(Rt1). We show the utility of increasing the dimensionality of traditional two‐dimensional (2D) techniques, referred to as the “2D multi‐view” method, to improve the capture of whole root system information for mapping genetic variation influencing RSA. Comparison of univariate and multivariate genome‐wide association study (GWAS) approaches revealed that multivariate traits were effective at dissecting complex RSA phenotypes and identifying pleiotropic quantitative trait loci (QTLs). Overall, three‐dimensional (3D) root models generated from X‐ray computed tomography and digital phenotyping captured a larger proportion of RSA trait variations compared to other methods of root phenotyping, as evidenced by both genome‐wide and single‐gene analyses. Among the individual root traits, root pulling force emerged as a highly heritable estimate of RSA that identified the largest number of shared QTLs with 3D phenotypes. Our study shows that integrating complementary phenotyping technologies helps to provide a more comprehensive understanding of the genetic architecture of RSA in field‐grown maize.

Genetics & Heredity↗
DOE OSTI2025

Development and characterization of a wild emmer wheat backcross introgression population for hard winter wheat improvement

Abstract Wild emmer wheat (Triticum turgidumsubsp.dicoccoides) is the tetraploid progenitor of hexaploid bread wheat (Triticum aestivumL.) and is known to be a valuable source of genetic variation for wheat improvement. However, direct evaluation of wild emmer diversity for agronomic potential has limited value unless performed in the backgrounds of adapted cultivars. Here, we present a genetic characterization of a population of 1601 backcross recombinant inbred lines, with an average genome composition of 75% bread wheat and 25% wild emmer. Low‐coverage whole‐genome sequencing allowed introgressions and aneuploidies to be identified at a relatively low cost per sample. We identified a relatively large proportion of small introgressions (median length 38 Mb), and we found introgressions to be distributed across all chromosomes. Approximately 44% of genotyped progeny carried at least one aneuploidy, with monosomies being by far the most common. This population, which we have denoted as the Great Plains Wild Emmer/Hard Winter Wheat introgression population (GPWEW‐IP), is, to our knowledge, the first introgression population developed through the direct hybridization of wild emmer wheat and US‐adapted hard winter wheat. We believe that this population represents a valuable resource for wheat breeders and will accelerate the discovery and integration of useful variation from wild emmer wheat.

Genetics & Heredity↗
DOE OSTI2025

Identification of a QTL region for tomato brown rugose fruit virus resistance in Solanum pimpinellifolium

Abstract Tomato (Solanum lycopersicumL.), one of the most widely grown vegetables in the world, has been seriously impacted in the past decade by the emerging tomato brown rugose fruit virus (ToBRFV). ToBRFV is a seed-borne tobamovirus, with ability to overcome the commonly usedTm-2 2 resistance gene in tomato. The objective of this study was to conduct quantitative trait locus (QTL) mapping and identify single-nucleotide polymorphism (SNP) markers associated with ToBRFV resistance in tomato. Two F 2 populations were used for QTL mapping: One derived from a cross betweenS. pimpinellifoliumUSVL333 (PI 390718) × USVL332 (PI 390717) and another from ‘Moneymaker’ × USVL332 (PI 390717), with population sizes of 195 and 79 plants, respectively. The resistance trait was derived from theS. pimpinellifoliumaccession USVL332 (PI 390717). A major QTL for ToBRFV resistance was identified on chromosome 11 (SL4.0ch11), with the peak located at approximately 46.84 Mbp. This QTL spans a 22-kb interval between 46,825,788 bp and 46,847,421 bp, as determined through both genome-wide association study (GWAS) and QTL linkage mapping. Three SNP markers, SL4.0ch11_46825788, SL4.0ch11_46847421, and SL4.0ch11_46850215, demonstrated the most significant association with high LOD values (LOD = 13 in the Blink model) in GWAS analysis. In this genomic region, two disease resistance gene analogs, Solyc11g062150 (TIR-NBS-LRR resistance protein, Toll-Interleukin receptor) and Solyc11g062180 (disease resistance protein, leucine-rich repeat), were identified, which may serve as candidates for ToBRFV resistance. The QTL identified in this study could be valuable for plant breeders in facilitating tomato breeding with ToBRFV resistance.

Agriculture↗
DOE OSTI2024

Specialized protist communities on mycorrhizal fungal hyphae

Abstract Arbuscular mycorrhizal (AM) fungi not only play a crucial role in acquiring nutrients for plants but also serve as a habitat for soil microbes. Recent studies observed that AM fungal hyphae are colonized by specific bacterial communities. However, so far it has not been explored whether fungal hyphae and mycorrhizal networks also harbor specific communities of protists, a key group of microbes in the soil microbiome. Here, we characterized protist communities in soil in a compartment with plant roots and on hyphae collected from hyphal compartments without plant roots. We detected specific protist communities on fungal hyphae. Fourteen protistan amplicon sequences variants (ASVs) were significantly associated with fungal hyphae, half of which belonged to the Cercozoa group. This research, for the first-time detected specific protist ASVs directly associated with abundant AM fungus hyphae, highlighting the complexity of the hyphal food web.

Mycology↗
DOE OSTI2020

Host-specific and tissue-dependent orchestration of microbiome community structure in traditional rice paddy ecosystems

Abstract Background and aim Rice and duckweed are two monocotyledonous plants that naturally coexist in paddy fields. While the presence of duckweed in paddy fields significantly improves rice productivity, the interplay between soil microbes and the two plant hosts in this agroecosystem remains unexplored. Methods We compared the bacterial community structure between duckweed, rice and soil from multiple rice paddies. We also isolated bacteria from these communities and characterized their modes of bacterial colonization and plant growth-promotion using model plants. Results Our data indicate that host-specific and tissue-dependent factors reproducibly orchestrate the bacterial community structure associated with their plant hosts. This is corroborated by results from culture-dependent approaches in which the dominant genus Pantoea isolated from rice aerial tissues can strongly attach and colonize gnotobiotic duckweed in spite of the low representation of this bacterial genus in the natural duckweed microbiome. Our study identified a core of 254 bacterial taxa that are consistently found in all rice and duckweed tissue samples from rice paddy fields. Furthermore, characterizing auxin-producing bacteria isolates from both plant species identified potential plant growth-promoting bacteria that may improve growth for both duckweed and rice in paddy fields. Conclusions Results from this work provide evidence for the importance of the host tissue and species context in determining plant colonization by microbes in the paddy field system. The resources generated in this study could facilitate the agronomic deployment of microbes for more sustainable rice production.

Agriculture↗