About

Amit Dhingra is a Professor and Department Head in the Department of Horticultural Sciences at Texas A&M University. His educational background includes a B.S. in Botany from the University of Delhi, a Postgraduate Diploma in Marketing Management from IGNOU in India, an M.S. in Botany from Agra University, and a Ph.D. in Plant Molecular Biology from the University of Delhi. He is a member of Texas A&M AgriLife, which encompasses the Texas A&M AgriLife Extension Service, Texas A&M AgriLife Research, and other related entities. His role involves leading the department, which offers various undergraduate and graduate programs in horticulture, and contributing to research and extension activities within the field of horticultural sciences.

Research topics

• Biology
• Biotechnology
• Business
• Genetics
• Agronomy
• Ecology
• Marketing
• Agroforestry
• Horticulture
• Botany

Selected publications

• Cell wall remodeling and inositol metabolism coexpression modules associated with nut size in Carya illinoinensis cvs. ‘Mahan’ and ‘Tiny Tim’

  Scientific Reports · 2026-02-10

  articleOpen accessSenior authorCorresponding

  Pecan is a tree nut crop native to the United States and Mexico, with a global market of over 2 billion USD. Nut size has been the most important target trait for crop improvement during the very limited breeding cycles. However, relatively little is known about the molecular basis of pecan nut ontogeny and the mechanisms underlying pecan nut sizing. Besides nut size, pecan fruit faces myriad physiological disorders throughout the growing season, making knowledge of essential genes at each growth stage a necessary first step in developing new cultivars and management practices to overcome these issues. To develop a deeper understanding of pecan fruit development and identify candidate genes underlying the large fruit phenotype, a time-course transcriptomic study of pecan fruit in two genotypes, ‘Mahan’ and ‘Tiny Tim’, was conducted. Weighted Gene-Coexpression Network Analysis (WGCNA) was employed to group transcripts into functional clusters, and hub transcripts were identified through module correlation analysis to select those that are potential drivers of these functional clusters. Modules related to cell wall biosynthesis, cell wall organization, and inositol metabolism in ‘Mahan’, and proteolysis and abscisic acid response in ‘Tiny Tim’ were found to be potentially associated with nut size.

  PublisherOA PDFDOI

• Pangenome Analysis of Pyrus Reveals Potential Role of Transcription Factors in Recent Adaptation to Arid Environments

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-01-22

  articleOpen accessSenior authorCorresponding

  Abstract Pears (genus Pyrus ) are among the most extensively cultivated tree fruits with a wide-reaching economic impact. Despite this, the genetic basis of most pear traits of interest, including abiotic stress tolerance, tree architecture, precocity, parthenocarpy, disease resistance, and fruit ripening, remains poorly understood. Although extensive efforts have been made to identify quantitative trait loci (QTLs) that explain the genetic basis of pear traits, many are poorly transferable, limiting their utility for informing genetic improvement or management of pears across most genetic backgrounds. To provide a whole-genome context and enable the exploration of functional variation in Pyrus , we developed a pangenome graph using 31 accessions representing 23 Pyrus species from the National Clonal Germplasm Repository. Whole-genome sequencing was performed solely with Oxford Nanopore, generating highly contiguous assemblies for pangenome construction, demonstrating the viability of a single-platform approach to pangenomic analysis in Viridiplantae. Exploration of the pangenome graph reveals genes present in some lineages, with potential functional implications. A group of arid-adapted Pyrus species exhibits signs of selective sweeps in regions associated with transcription factors, likely impacting abiotic stress tolerance. With the development of this pangenomic resource, resequencing analysis in Pyrus is now possible without the limitations imposed by single-reference genome assemblies.

  PublisherOA PDFDOI

• Extensive Novel Genomic Variations in Mutant European Pear Individuals Revealed by Mapping to a Pangenome Reference

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-03-04

  articleOpen accessSenior authorCorresponding

  Abstract European pear ( Pyrus communis ) is the most widely cultivated Pyrus species outside of Asia; however, production has been declining in Europe, Oceania, and North America. Most European pear cultivars are over 100 years old and face pressure from disease, a changing climate, and challenging postharvest characteristics, while demand for increased production efficiency rises. To generate germplasm with desirable characteristics to address these concerns, a mutation breeding approach was chosen, with crosses made between four economically significant cultivars (‘Bartlett’, ‘d’Anjou’, ‘Abbe Fetel’, and ‘Comice’) using gamma-irradiated pollen. This resulted in 49 viable offspring, of which 37 have survived at least 10 years. Nanopore whole-genome sequencing was used to test the success of this approach and screen for variants of interest. Sequence reads were mapped to both a lightweight, purpose-built pangenome derived from assemblies of parental haplotypes and a linear reference genome, enabling the high-quality discovery of variants of all sizes, ranging from single-base substitutions to megabase-scale deletions, with the overwhelming majority being small variants. The overall rate of mutation was 153 novel small variants and 0.228 novel structural variants per Gray of absorbed gamma radiation. Alternate ploidy levels were detected in four lines, which included three triploids and one tetraploid. While the resulting individuals appear incapable of floral development, they may be of utility as rootstock cultivars and a valuable genetic resource for understanding the underlying basis of structural traits.

  PublisherDOI

• Comparative transcriptome analysis of emerging young and mature leaves of <i>Bienertia sinuspersici,</i> a single-cell C4 plant

  PeerJ · 2025-04-29 · 1 citations

  articleOpen accessSenior author

  Background Efficient carbon capture by plants is crucial to meet the increasing demands for food, fiber, feed, and fuel worldwide. One potential strategy to improve the photosynthetic performance of plants is the conversion of C 3 -type crops to C 4 -type crops, enabling them to perform photosynthesis at higher temperatures and with less water. C 4 -type crops, such as corn, possess a distinct Kranz anatomy, where photosynthesis occurs in two distinct cell types. Remarkably, Bienertia sinuspersici is one of the four known land plant species that perform C 4 photosynthesis within a single cell. This unique single-cell C 4 (SCC 4 ) anatomy is characterized by dimorphic chloroplasts and corresponding intracellular biochemistry. Because young, emergent Bienertia leaves first exhibit C 3 anatomy and then differentiate into the C 4 anatomy as the leaves mature, Bienertia represents an excellent system to explore the basis for a C 3 to C 4 transition. Methods To gain insight into the genes and pathways associated with the C 3 to C 4 transition between emerging young and mature Bienertia sinuspersici leaves, a comparative transcriptome analysis was conducted in which global gene expression and gene ontologies were compared between the two stages. Results In the emergent leaf, differentially expressed genes and enrichment of ontologies associated with the cell cycle and cytoskeletal dynamics were observed, while the mature leaf displayed enrichment of processes associated with photosynthesis and cellular energetics. Additionally, numerous transcription factors (TFs) associated with metabolic homeostasis, hormone and stress signaling, and developmental regulation were expressed throughout development, with unique TF expression profiles at each stage. These data expand our insights into the molecular basis of Binertia’s unique cellular compartmentalization, chloroplast dimorphism, and single-cell C4 biochemistry and provide information that will be useful in the ongoing efforts to transform C 3 -type crops into C 4 type.

  PublisherDOI

• Co-expression Network Analysis in Carya illinoinensis cvs. ‘Tiny Tim’ and ‘Mahan’ Identifies Cell Wall Remodeling and Inositol Metabolism Modules Associated with Nut Size

  Research Square · 2025-10-30

  preprintOpen accessSenior author
  PublisherOA PDFDOI

• Efficient Stable Genetic Transformation of Pea (Pisum sativum)

  Research Square · 2025-10-29

  preprintOpen accessSenior author
  PublisherOA PDFDOI

• Tree Fruit and Nut Crops at the Dawn of the Pangenomic Era

  Preprints.org · 2025-11-10

  preprintOpen accessSenior author

  Tree fruit and nut crops are a critical component of the global economy, producing billions of dollars of value and nourishing billions of humans every year. Improved cultivars and growing practices depend upon an understanding of the molecular basis of tree traits and physiology. Over the past 20 years, the proliferation of reference genomes for tree fruit and nut crop species has transformed the study of genetics in these crops, providing a platform for resequencing analyses of large populations, enabling comparative genomic analyses between distant plant species, and allowing the development of molecular markers for use in breeding. Limitations exist, however, with reference bias and poor transferability of markers preventing widespread applicability in many instances. As third-generation sequencing has become more accurate and accessible, a greater number of reference genomes have become available, enabling higher-quality assemblies and wider sampling of genomic diversity. To facilitate the effective use of multiple closely related genomes to create a reference and comparative genomics platform, tools for the creation of pangenome graphs have been developed, allowing for singular representations of diversity within a species or even a wider genus. Pangenomic analyses at the genus-scale have been conducted for Malus and Citrus, and more tree fruit and nut species are likely to follow. As the number of genome sequences and pangenome resources increases, the importance of generating great quantities of transcriptomic and phenomic data will increase as well. This data is essential in the drive to connect genes to traits, as is needed to develop improved tree fruit and nut crops, which can satisfy global demand.

  PublisherOA PDFDOI

• Mineralization potential of spent coffee grounds and other nutrient sources

  Soil Science Society of America Journal · 2025-01-01 · 1 citations

  articleOpen accessSenior author

  Abstract Industrial‐scale coffee ground waste has the potential to serve as a nutrient‐rich soil amendment, which would offer growers an opportunity to reduce applications of traditional fertilizers. Composted spent coffee grounds (CSCGs) and noncomposted spent coffee grounds (NCSCGs) were evaluated for their potential as organic N fertilizers. Nitrogen mineralization of NCSCGs and CSCGs was compared to commonly used synthetic and organic N fertilizers: urea and Milorganite. Net N mineralization and microbial activity were measured in a fine sandy loam field soil at 25°C and 60% water holding capacity weekly for 100 days. Despite a C:N of 13:1, the CSCGs appeared to have slow mineralization. Total inorganic N was lower in both CSCGs and NCSCGs than the control throughout the 100‐day incubation with no additional N to the system. Greater CO 2 ─C respiration was recorded with SCGs, suggesting microbial activity is required for the breakdown of SCGs relative to other treatments. CSCGs may serve as a long‐term fertilizer due to the time it takes to mineralize; however, over a shorter period, it may increase the nutrient‐ and water‐holding capacity of soil, which can improve plant growth.

  PublisherOA PDFDOI

• Long-read metagenomic dataset from domestic rabbit manure and domestic rabbit manure-derived vermicompost

  Data in Brief · 2025-12-25

  articleOpen accessSenior authorCorresponding

  This dataset describes samples collected from two Domestic Rabbit manure sources and three Domestic Rabbit manure-derived vermicompost bins. Three samples were taken from each and total DNA was isolated. Nanopore sequencing was used to collect data from all isolated DNA samples. After length and quality filtering, 181.5 gigabases (Gb) of sequencing data was collected across 15 samples. Streptomyces, Bradyrhizobium, Mesorhizobium , and Microbacterium were in the top 5 genera for all vermicompost samples, but two vermicompost samples had very high proportions of Escherichia and Mycobacterium . Vermicomposting can enable the development of beneficial microbial communities, but often lacking a thermophilic phase, may also allow for the growth of potentially pathogenic microbes. The vermicomposts described by this dataset contains both beneficial and potentially harmful microbial communities and may be used to support comparisons between composts and vermicomposts of different backgrounds for safety and utility.

  PublisherDOI

• Both conventionally and organically fertilized tomatoes maintain fruit quality through uncontrolled green peach aphid infestation, with a transcriptional shift towards catabolism

  PLoS ONE · 2025-12-16

  articleOpen accessSenior authorCorresponding

  Aphids are a major pest of greenhouse-grown temperate crops, responsible for billions in crop damage yearly. As organic agriculture rapidly grows in popularity, understanding how plants grown under organic systems respond to insect pest pressure may give insights into better management practices and information about the genes of interest for crop improvement. We measured the response of tomato (Solanum lycopersicum) leaf and fruit transcriptome, as well as a few selected metabolites in the mature fruit, to an infestation of the generalist green peach aphid (Myzus persicae). The aphids were introduced approximately halfway through the lifecycle of the plants that were grown under conventional and organic fertilizer regimes. While plants provided with conventional fertilizer experienced greater aphid infestation, neither group suffered a significant loss in total yield or fruit quality. This result is likely a consequence of ample nutrient and water availability. Co-expression network analysis using WGCNA revealed that in leaf tissue, both treatment groups showed a general shift from diverse anabolic processes to catabolism, while fruit tissue experienced relatively minor changes. At the stage of infestation investigated, abscisic acid appeared to be the main phytohormone response. One coexpression network module showed a correlation with both organic fertilizer treatment and aphid infestation; its hub gene (Solyc02g078940.3) may be of interest in exploring unique responses to phloem feeding insect infestation under an organic fertilizer regime.

  PublisherDOI

Frequent coauthors

• Pamela S. Soltis

  Florida Museum of Natural History

  63 shared

• Seanna Hewitt

  Texas A&M University

  35 shared

• Michael J. Moore

  31 shared

• Jeremy Ramdial

  University of Florida

  28 shared

• Roolse Alexandre

  University of Florida

  26 shared

• Sunny Crawley

  Virginia Tech

  25 shared

• Khidir W. Hilu

  Virginia Tech

  25 shared

• Samuel F. Brockington

  University of Cambridge

  22 shared

Education

• B.S., Botany

  University of Delhi

• Other, Marketing Management

  IGNOU, India

• M.S., Botany

  Agra University

• Ph.D., Plant Molecular Biology

  University of Delhi