About

Subas Malla is an Associate Professor in the Department of Horticultural Sciences at Texas A&M University. He is based at the Texas A&M AgriLife Research and Extension Center in Uvalde. His professional role involves research and extension activities related to horticulture, contributing to the advancement of sustainable horticultural practices. Malla's work supports the department's mission to promote high-impact learning experiences and research in horticulture, although specific details about his research focus or key contributions are not provided in the available page text.

Research topics

• Biology
• Agronomy
• Genetics
• Microbiology
• Biotechnology
• Animal science
• Food science
• Mathematics
• Botany
• Metallurgy
• Agroforestry
• Horticulture
• Materials science

Selected publications

• Identification of race 2 anthracnose resistance Quantitative Trait Loci using biparental and association panel of diverse watermelon germplasm accessions

  Theoretical and Applied Genetics · 2026-02-20

  articleSenior authorCorresponding
  PublisherDOI

• The concept of soil depletion factor revisited and applied to determine the crop-specific fraction of total available water

  2025-12-12

  articleOpen access

  Limited availability of irrigation water, coupled with irregular rainfall, is driving the search for better water-saving strategies. One strategy is to select more efficient crop varieties that can maintain profitable yields without requiring large amounts of water. In this study, we developed a new approach to determine the soil depletion factor (p) by considering maximum root zone water extraction. The model of Rijtema and Aboukled was modified to account for different initial soil water contents. Three onion varieties with distinct bulb characteristics, ‘Hornet’ (yellow), ‘Mata Hari’ (red) and ‘Amadea’ (white), were evaluated in a field experiment with drip irrigation, in which the plants were subjected to five stress levels measured at 0.20 m: –25, –50, –75, –100 and –125 kPa. The results showed that the estimated p for the three varieties was higher than the reference values proposed by the FAO (p of 0.30 – 0.35 for a crop evapotranspiration of 5.0 mm d-1). Amadea exhibited the highest p values, with an average of 0.58. Mata Hari presented intermediate values and Hornet the lowest, although their average p values (0.48 and 0.39, respectively) were statistically similar. Additionally, Amadea extracted more water than the two other varieties across all analyzed periods, particularly during the final crop stage. It also appeared to be more drought tolerant. Further study focusing on estimating p across different phenological stages is necessary. We conclude that the proposed approach offers an alternative method for estimating the depletion factor and it can be extended to other crops.

  PublisherOA PDFDOI

• First Report of <i>Serratia sarumanii</i> Causing Plant Disease: A Case from Onion

  Plant Disease · 2025-12-10 · 1 citations

  articleOpen accessSenior author

  Serratia is a genus of Gram-negative bacteria classified under the phylum Pseudomonadota, order Enterobacterales, and family Yersiniaceae. As of August 2025, the genus comprises 24 validly published species with correct names, as listed in the List of Prokaryotic names with Standing in Nomenclature and recognized under the rules of the International Code of Nomenclature of Prokaryotes (Parte et al. 2020). Among them, S. marcescens is the most frequently reported plant-pathogenic species, known to infect a wide range of crops, including cucurbits, pepper, and corn (Besler and Little 2017). In onion (Allium cepa L.), S. plymuthica remains the only S. species previously reported to cause disease (Kowalska et al. 2011). While S sarumanii is a newly described species within the genus, it was originally isolated from human clinical samples, including wound and urine specimens (Klages et al. 2024). In 2021, an isolated diseased onion bulb was collected from Las Cruces, New Mexico, USA, to investigate the bacterial communities associated with symptomatic tissues. The outer bulb scales exhibited clear signs of rot. Bacteria were isolated from the margins of symptomatic bulb lesions and screened for pathogenicity using red onion scale and bulb assays, following the procedures and controls described previously (Khanal et al. 2023). All isolates were identified by 16S rRNA gene sequencing. One pathogenic strain, isolated from a bulb exhibiting outer scale rot, was identified as a S. species (GenBank accession no. OP325569). For the scale assay, a 10 µL suspension containing 108 CFU/ml of the bacterium was applied to the center of 3 cm-wide sections of red onion scales that had been punctured with a sterile needle. After incubation at 25 °C for 4 days, necrotic lesions (3–5 mm in diameter) with a creamy light-yellow appearance developed at the inoculation sites, whereas PBS-treated controls remained symptomless. BLAST analysis of the 928-bp 16S rRNA gene sequence revealed 99.78% and 99.68% similarity to the type strains of S. nematodiphila and S. marcescens, respectively. Due to its high relatedness to multiple S. species, whole-genome sequencing was performed for this strain (Genbank assembly GCA_028307185.1). Genome-based taxonomic analysis using TYGS (https://tygs.dsmz.de/) (Meier-Kolthoff and Göker 2019) and JSpeciesWS (https://jspecies.ribohost.com/jspeciesws/) (Richter et al. 2016) identified the strain as S. sarumanii. The strain showed a digital DNA–DNA hybridization (dDDH) value of 90.2% and average nucleotide identity based on BLAST (ANIb) of 98.4% with the type strain K-M0706T (Genbank assembly GCA_029962605.1), exceeding the species delineation threshold (Chun et al. 2018) of 70% (dDDH) and 95% (ANI). To further confirm pathogenicity, a 500 µL suspension containing 108 CFU/mL of the bacterium was inoculated into the upper shoulder of three yellow onion bulbs using a needle-syringe. The bulbs were then incubated at 25 °C for 12 days. After incubation, the onion bulbs were sectioned and exhibited clear signs of rot, including disintegration of scale tissue and brown discoloration. The bulb inoculation assay was repeated twice, consistently producing similar symptoms across all tested bulbs. Five daughter isolates recovered from lesions on inoculated onion scales and bulbs were morphologically uniform and reproduced identical symptoms when re-inoculated onto healthy onion bulbs. Furthermore, 16S rRNA gene sequencing of these daughter isolates (GenBank accessions PX021965–PX021969) revealed complete identity with the original (mother) strain, thereby fulfilling Koch’s postulates. This report constitutes the first documented case of S. sarumanii causing bulb decay and rot in onion, establishing it as a novel plant pathogen. This finding underscores the potential risk of S. sarumanii to onion production and postharvest storage in New Mexico and other onion-growing regions, warranting further monitoring and management considerations.

  PublisherOA PDFDOI

• Plasmids encode and can mobilize onion pathogenicity in <i>Pantoea agglomerans</i>

  The ISME Journal · 2025-01-01 · 10 citations

  articleOpen access

  Pantoea agglomerans is one of four Pantoea species reported in the USA to cause bacterial rot of onion bulbs. However, not all P. agglomerans strains are pathogenic to onion. We characterized onion-associated strains of P. agglomerans to elucidate the genetic and genomic signatures of onion-pathogenic P. agglomerans. We collected >300 P. agglomerans strains associated with symptomatic onion plants and bulbs from public culture collections, research laboratories, and a multi-year survey in 11 states in the USA. Combining the 87 genome assemblies with 100 high-quality, public P. agglomerans genome assemblies we identified two well-supported P. agglomerans phylogroups. Strains causing severe symptoms on onion were only identified in Phylogroup II and encoded the HiVir pantaphos biosynthetic cluster, supporting the role of HiVir as a pathogenicity factor. The P. agglomerans HiVir cluster was encoded in two distinct plasmid contexts: (i) as an accessory gene cluster on a conserved P. agglomerans plasmid (pAggl), or (ii) on a mosaic cluster of plasmids common among onion strains (pOnion). Analysis of closed genomes revealed that the pOnion plasmids harbored alt genes conferring tolerance to Allium thiosulfinate defensive chemistry and many harbored cop genes conferring resistance to copper. We demonstrated that the pOnion plasmid pCB1C can act as a natively mobilizable pathogenicity plasmid that transforms P. agglomerans Phylogroup I strains, including environmental strains, into virulent pathogens of onion. This work indicates a central role for plasmids and plasmid ecology in mediating P. agglomerans interactions with onion plants, with potential implications for onion bacterial disease management.

  PublisherOA PDFDOI

• Factors Affecting Growth and Survival of &lt;em&gt;Salmonella &lt;/em&gt;in Onion Extracts and Onion Bulbs

  Preprints.org · 2024-11-15 · 1 citations

  preprintOpen access

  This study investigated the survival and growth of Salmonella in onion extracts and bulbs. Extracts of an array of onion varieties and germplasms were used to evaluate their ability to retard or inhibit Salmonella growth and the antimicrobial activity of extracts prepared from onions that were subjected to different types of light during curing. Separately, the survival of internalized and non-internalized Salmonella enterica ser. Newport was tested in red, white, and yellow onions by inoculating onion bulbs on the external and internal onion layers and by internalizing Salmonella using a syringe and needle to inject the inoculum inside the bulb. The inoculated onions were stored at room temperature and collecting samples at intervals during storage. Results showed that the varied lighting used for postharvest stimulation resulted in extracts with different antimicrobial effects (P &amp;lt; 0.05). Extracts from red and white onions treated with blue light inhibited Salmonella growth. Extracts from onions treated with white light revealed slow and fast growth of Salmonella in red and yellow, respectively. Of the extracts from the various germplasms, only one corresponding to red onion, inhibited Salmonella growth, whereas the rest showed varying levels of growth retardation (P &amp;lt; 0.05). In survival studies, Salmonella inoculated on the outer layer was reduced by 1.2, &amp;gt; 2.7, and &amp;gt; 2.4 log cycles on red, white, and yellow onions, respectively within 3 days of storage. In the inner layers, Salmonella grew by 2.4, 2.6, and 2.8 log cycles of red, white, and yellow onions re-spectively, over 18-d storage. In separate trials, the outer layer again did not support the survival of Salmonella Newport. While the inner scales on red onion did not allow growth of Salmonella Newport, those of white and yellow onions allowed growth during the first 3 days of storage, followed by reduction to nondetectable levels. Although the antimicrobial effect of onions is attributed mainly to the polyphenols, factors such as tissue integrity or water content in internal tissues may hinder the deleterious effects of poly-phenols against Salmonella.

  PublisherDOI

• Plasmids encode and can mobilize onion pathogenicity in <i>Pantoea agglomerans</i>

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-08-01

  preprintOpen access

  Abstract Pantoea agglomerans is one of four Pantoea species for which strains have been reported in the United States to cause bacterial rot of onion bulbs. However, not all P. agglomerans strains are pathogenic to onion. We characterized onion-associated strains of P. agglomerans to elucidate the genetic and genomic signatures of onion-pathogenic P. agglomerans . We collected &gt;300 P. agglomerans strains associated with symptomatic onion plants and bulbs from public culture collections, research laboratories, and a multi-year survey in 11 states in the USA. Genome assemblies were generated for 87 P. agglomerans strains that showed a range in onion virulence phenotypes. Combining the 87 genome assemblies with 100 high-quality, public P. agglomerans genome assemblies identified two well-represented and well-supported P. agglomerans phylogroups. Strains causing severe symptoms on onion leaves and bulbs were only identified in Phylogroup II and encoded the HiVir biosynthetic cluster for the phytotoxin pantaphos, supporting the role of HiVir as a crucial pathogenicity factor. Using a MASH-based plasmid classification system, the P. agglomerans HiVir cluster was determined to be encoded in two distinct plasmid contexts: 1) as an accessory gene cluster on a conserved P. agglomerans plasmid (pAggl), or 2) on a mosaic cluster of plasmids common among onion strains (pOnion). Analysis of closed genomes of P. agglomerans revealed that the pOnion plasmids harbored alt genes responsible for encoding tolerance to the thiosulfinate defensive chemistry in Allium spp. Additionally, many of these pOnion plasmids harbored cop gene clusters, which confer resistance to copper. However, the pOnion plasmids encoded the HiVir cluster less frequently. We demonstrated that the pOnion plasmid pCB1C, encoding HiVir and alt clusters as well as an intact conjugative type IV secretion system (T4SS), can act as a natively mobilizable pathogenicity plasmid that transforms P. agglomerans Phylogroup I strains, including environmental strains, into virulent pathogens of onion. This work indicates a central role for plasmids and plasmid ecology in mediating P. agglomerans interactions with onion plants, with potential implications for onion bacterial disease management.

  PublisherOA PDFDOI

• Factors Affecting Growth and Survival of Salmonella in Onion Extracts and Onion Bulbs

  Foods · 2024-12-24 · 3 citations

  articleOpen access

  This study investigated the survival and growth of Salmonella in onion extracts and bulbs. The inhibition or retardation of Salmonella growth by extracts of red, white, and yellow onions was tested against the onion germplasm and exposure to different light spectra during curing. Separately, survival of Salmonella Newport was tested on red, white, and yellow onion bulbs on the external and internal onion layers with a syringe and needle. Onions exposed to blue, red, and white LED light during curing produced extracts with variable antimicrobial effects (p &lt; 0.05), with those exposed to blue light showing the strongest inhibitory effect on red and white onions only. In survival studies, Salmonella inoculated on the outer scale was reduced by 1.2, &gt;2.7, and &gt;2.4 logs on red, white, and yellow onions, respectively, within 3 days, whereas it grew by 2.4, 2.6, and 2.8 logs inside red, white, and yellow onion bulbs, respectively, over 18 days. In separate trials, the outer layer again did not support the survival of Salmonella Newport. The aw increased significantly from 0.51 to 0.58 in the outer scales and 0.96 to 0.98 for the fourth inner scales. Despite being rich in antimicrobial polyphenols, tissue integrity and water content may still promote Salmonella growth in onions.

  PublisherOA PDFDOI

• Recent Advances in Molecular Genetics of Onion

  Horticulturae · 2024-03-07 · 13 citations

  articleOpen accessSenior authorCorresponding

  Onion is an important vegetable crop because it adds nutritional value and diversity to food preparation. Understanding recent advancements in onion molecular genetics is essential to improve production, quality, and disease resistance. Cutting-edge genomic technologies like genetic mapping and RNA sequencing reveal important genes and pathways. The review examines the progress in utilizing various molecular markers to study genetic divergence. The exploration extends to understanding the genes and pathways responsible for bulb color and chemical composition and the genetic factors influencing bulbing, flowering, and vernalization. Additionally, the article explores quantitative trait loci associated with resistance to major damaging diseases and delves into the role of different loci in male sterility and hybrid development. The recent publication of the whole genome sequence of onions will lead to further identification of genes and understanding their roles and functions in metabolic pathways.

  PublisherOA PDFDOI

• Draft Genome Sequence and Annotation of Pseudomonas carnis Strain 20TX0167, Isolated from an Onion (Allium cepa)

  Microbiology Resource Announcements · 2023-01-16 · 2 citations

  articleOpen accessSenior authorCorresponding

  The draft genome sequence of Pseudomonas carnis strain 20TX0167, isolated from a cold stored onion bulb, is described here. A comparative genomic study against the type strain of this species, B4-1 T , revealed differences in some genetic aspects.

  PublisherDOI

• Recent Advances and Challenges in Management of Colletotrichum orbiculare, the Causal Agent of Watermelon Anthracnose

  Horticulturae · 2023-10-13 · 10 citations

  articleOpen accessSenior authorCorresponding

  The fungus Colletotrichum orbiculare causes watermelon anthracnose and is an important pathogen of watermelon in the United States, causing a significant impact on yield and quality of the produce. The application of fungicides as preventative and post-occurrence control measures is currently being deployed by growers. Further study of the genetic and molecular basis of anthracnose resistance will help in guiding future watermelon breeding strategies. Several conserved virulence factors (effectors) in C. orbiculare have been reported to interact with the host, at times impairing the host immune machinery. A single dominant gene conferring race 1 anthracnose resistance was reported independently on two watermelon germplasm. The recent advances in genomics, transcriptomics, proteomics, and metabolomics could facilitate a better understanding of the interaction between C. orbiculare effectors and host resistance genes in the already sequenced watermelon genome. In this review, we encompass and discuss (i) the history of watermelon anthracnose, taxonomy, morphology, and diversity in races of C. orbiculare; (ii) the epidemiology of the anthracnose disease and host resistance; (iii) the genetics behind the pathogenesis; and (iv) the current advances in breeding and molecular efforts to elucidate anthracnose resistance.

  PublisherOA PDFDOI

Frequent coauthors

• Bed Prakash Bhatta

  Texas A&M University

  23 shared

• Carl A. Griffey

  Virginia Tech

  15 shared

• Manzeal Khanal

  14 shared

• Edgar Correa

  Texas A&M University

  13 shared

• Wade E. Thomason

  Virginia Tech

  11 shared

• Harry D. Behl

  Virginia Tech

  11 shared

• Amir M. H. Ibrahim

  10 shared

• Kimberly Cochran

  Texas A&M University

  9 shared

Education

• Ph.D., Horticultural Sciences

  Texas A&M University

  2007

• M.S., Horticulture

  University of Idaho

  2001

• B.S., Horticulture

  University of Idaho

  1999