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Fulltext Pulse Crop Genetics for a Sustainable Future: Where We Are Now and Where We Should Be Heading

Sahruzaini NA, Rejab NA, Harikrishna JA, Khairul Ikram NK, Ismail I, Kugan HM, et al.

Front Plant Sci, 2020;11:531.
PMID: 32431724 DOI: 10.3389/fpls.2020.00531

The last decade has witnessed dramatic changes in global food consumption patterns mainly because of population growth and economic development. Food substitutions for healthier eating, such as swapping regular servings of meat for protein-rich crops, is an emerging diet trend that may shape the future of food systems and the environment worldwide. To meet the erratic consumer demand in a rapidly changing world where resources become increasingly scarce due largely to anthropogenic activity, the need to develop crops that benefit both human health and the environment has become urgent. Legumes are often considered to be affordable plant-based sources of dietary proteins. Growing legumes provides significant benefits to cropping systems and the environment because of their natural ability to perform symbiotic nitrogen fixation, which enhances both soil fertility and water-use efficiency. In recent years, the focus in legume research has seen a transition from merely improving economically important species such as soybeans to increasingly turning attention to some promising underutilized species whose genetic resources hold the potential to address global challenges such as food security and climate change. Pulse crops have gained in popularity as an affordable source of food or feed; in fact, the United Nations designated 2016 as the International Year of Pulses, proclaiming their critical role in enhancing global food security. Given that many studies have been conducted on numerous underutilized pulse crops across the world, we provide a systematic review of the related literature to identify gaps and opportunities in pulse crop genetics research. We then discuss plausible strategies for developing and using pulse crops to strengthen food and nutrition security in the face of climate and anthropogenic changes.
Transcriptomic and Proteomic Analyses of Nepenthes ampullaria and Nepenthes rafflesiana Reveal Parental Molecular Expression in the Pitchers of Their Hybrid, Nepenthes × hookeriana

Zulkapli MM, Ab Ghani NS, Ting TY, Aizat WM, Goh HH

Front Plant Sci, 2020;11:625507.
PMID: 33552113 DOI: 10.3389/fpls.2020.625507

Nepenthes is a genus comprising carnivorous tropical pitcher plants that have evolved trapping organs at the tip of their leaves for nutrient acquisition from insect trapping. Recent studies have applied proteomics approaches to identify proteins in the pitcher fluids for better understanding the carnivory mechanism, but protein identification is hindered by limited species-specific transcriptomes for Nepenthes. In this study, the proteomics informed by transcriptomics (PIT) approach was utilized to identify and compare proteins in the pitcher fluids of Nepenthes ampullaria, Nepenthes rafflesiana, and their hybrid Nepenthes × hookeriana through PacBio isoform sequencing (Iso-Seq) and liquid chromatography-mass spectrometry (LC-MS) proteomic profiling. We generated full-length transcriptomes from all three species of 80,791 consensus isoforms with an average length of 1,692 bp as a reference for protein identification. The comparative analysis found that transcripts and proteins identified in the hybrid N. × hookeriana were more resembling N. rafflesiana, both of which are insectivorous compared with omnivorous N. ampullaria that can derive nutrients from leaf litters. Previously reported hydrolytic proteins were detected, including proteases, glucanases, chitinases, phosphatases, nucleases, peroxidases, lipid transfer protein, thaumatin-like protein, pathogenesis-related protein, and disease resistance proteins. Many new proteins with diverse predicted functions were also identified, such as amylase, invertase, catalase, kinases, ligases, synthases, esterases, transferases, transporters, and transcription factors. Despite the discovery of a few unique enzymes in N. ampullaria, we found no strong evidence of adaptive evolution to produce endogenous enzymes for the breakdown of leaf litter. A more complete picture of digestive fluid protein composition in this study provides important insights on the molecular physiology of pitchers and carnivory mechanism of Nepenthes species with distinct dietary habits.
Fulltext RNA-seq Analysis of Nepenthes ampullaria

Wan Zakaria WN, Loke KK, Zulkapli MM, Mohd Salleh F', Goh HH, Mohd Noor N

Front Plant Sci, 2015;6:1229.
PMID: 26793209 DOI: 10.3389/fpls.2015.01229
Fulltext Modeling induced resistance to plant disease using a dynamical systems approach

Abdul Latif NS, Wake GC, Reglinski T, Elmer PA, Taylor JT

Front Plant Sci, 2013;4:19.
PMID: 23424585 DOI: 10.3389/fpls.2013.00019
Fulltext Pluronic F-68 Improves Callus Proliferation of Recalcitrant Rice Cultivar via Enhanced Carbon and Nitrogen Metabolism and Nutrients Uptake

Kok AD, Mohd Yusoff NF, Sekeli R, Wee CY, Lamasudin DU, Ong-Abdullah J, et al.

Front Plant Sci, 2021;12:667434.
PMID: 34149763 DOI: 10.3389/fpls.2021.667434

Pluronic F-68 (PF-68) is a non-ionic surfactant used in plant tissue culture as a growth additive. Despite its usage as a plant growth enhancer, the mechanism underlying the growth-promoting effects of PF-68 remains largely unknown. Hence, this study was undertaken to elucidate the growth-promoting mechanism of PF-68 using recalcitrant MR 219 callus as a model. Supplementation of 0.04% PF-68 (optimum concentration) was shown to enhance callus proliferation. The treated callus recorded enhanced sugar content, protein content, and glutamate synthase activity as exemplified in the comparative proteome analysis, showing protein abundance involved in carbohydrate metabolism (alpha amylase), protein biosynthesis (ribosomal proteins), and nitrogen metabolism (glutamate synthase), which are crucial to plant growth and development. Moreover, an increase in nutrients uptake was also noted with potassium topping the list, suggesting a vital role of K in governing plant growth. In contrast, 0.10% PF-68 (high concentration) induced stress response in the callus, revealing an increment in phenylalanine ammonia lyase activity, malondialdehyde content, and peroxidase activity, which were consistent with high abundance of phenylalanine ammonia lyase, peroxidase, and peroxiredoxin proteins detected and concomitant with a reduced level of esterase activity. The data highlighted that incorporation of PF-68 at optimum concentration improved callus proliferation of recalcitrant MR 219 through enhanced carbohydrate metabolism, nitrogen metabolism, and nutrient uptake. However, growth-promoting effects of PF-68 are concentration dependent.
Fulltext Contrasting Phylogeographic Patterns in Lumnitzera Mangroves Across the Indo-West Pacific

Guo W, Banerjee AK, Wu H, Ng WL, Feng H, Qiao S, et al.

Front Plant Sci, 2021;12:637009.
PMID: 34249031 DOI: 10.3389/fpls.2021.637009

Mangroves are ecologically important forest communities in tropical and subtropical coasts, the effective management of which requires understanding of their phylogeographic patterns. However, these patterns often vary among different species, even among ecologically similar taxa or congeneric species. Here, we investigated the levels and patterns of genetic variation within Lumnitzera consisting of two species (L. racemosa and L. littorea) with nearly sympatric ranges across the Indo-West Pacific (IWP) region by sequencing three chloroplast DNA regions (for both species) and genotyping 11 nuclear microsatellite loci (for L. littorea). Consistent with findings in studies on other mangrove species, we found that both L. racemosa and L. littorea showed relatively high genetic variation among populations but low genetic variation within populations. Haplotype network and genetic clustering analyses indicated two well-differentiated clades in both L. racemosa and L. littorea. The relationship between geographic and genetic distances and divergence time estimates of the haplotypes indicated that limited dispersal ability of the propagules, emergence of land barriers during ancient sea-level changes, and contemporary oceanic circulation pattern in the IWP influenced the current population structure of the two species. However, the position of genetic break was found to vary between the two species: in L. racemosa, strong divergence was observed between populations from the Indian Ocean and the Pacific Ocean possibly due to land barrier effect of the Malay Peninsula; in L. littorea, the phylogeographic pattern was created by a more eastward genetic break along the biogeographic barrier identified as the Huxley's line. Overall, our findings strongly supported previous hypothesis of mangrove species divergence and revealed that the two Lumnitzera species have different phylogeographic patterns despite their close genetic relationship and similar current geographic distribution. The findings also provided references for the management of Lumnitzera mangroves, especially for the threatened L. littorea.
Fulltext Response of Plant Rhizosphere Microenvironment to Water Management in Soil- and Substrate-Based Controlled Environment Agriculture (CEA) Systems: A Review

Tan B, Li Y, Liu T, Tan X, He Y, You X, et al.

Front Plant Sci, 2021;12:691651.
PMID: 34456936 DOI: 10.3389/fpls.2021.691651

As natural agroecology deteriorates, controlled environment agriculture (CEA) systems become the backup support for coping with future resource consumption and potential food crises. Compared with natural agroecology, most of the environmental parameters of the CEA system rely on manual management. Such a system is dependent and fragile and prone to degradation, which includes harmful bacteria proliferation and productivity decline. Proper water management is significant for constructing a stabilized rhizosphere microenvironment. It has been proved that water is an efficient tool for changing the availability of nutrients, plant physiological processes, and microbial communities within. However, for CEA issues, relevant research is lacking at present. The article reviews the interactive mechanism between water management and rhizosphere microenvironments from the perspectives of physicochemical properties, physiological processes, and microbiology in CEA systems. We presented a synthesis of relevant research on water-root-microbes interplay, which aimed to provide detailed references to the conceptualization, research, diagnosis, and troubleshooting for CEA systems, and attempted to give suggestions for the construction of a high-tech artificial agricultural ecology.
Fulltext Deep structured populations of geographically isolated nipa (Nypa fruticans Wurmb.) in the Indo-West Pacific revealed using microsatellite markers

Mantiquilla JA, Shiao MS, Lu HY, Sridith K, Sidique SNM, Liyanage WK, et al.

Front Plant Sci, 2022;13:1038998.
PMID: 36388479 DOI: 10.3389/fpls.2022.1038998

Nipa (Nypa fruticans Wurmb.) is an important mangrove palm species, but it is understudied due to lack of information on genetic patterns within its distribution range. In this study, we identified 18 informative microsatellite markers to assess genetic variations among local populations in the Indo-West Pacific (IWP). Results showed population stratification based on high genetic differentiation (FST = 0.22131) with the Mantel test indicating significance to isolation-by-distance. We found a pronounced differentiation between the west populations in Sri Lanka and east populations in Southeast Asia. The east populations around the South China Sea were more genetically similar than those along the Malacca Strait and Java Sea. These genetic clines were shaped by ocean circulations and seasonal monsoon reversals as plausible factors. The Malacca Strait was confirmed as both a genetic and a geographic barrier rather than a corridor according to the Monmonier plot. Simulations of directional migration indicated a statistically strong contemporary genetic connectivity from west to east where Sri Lankan immigrants were detected as far as central Philippines via long-distance dispersal. This is the first report on the recent migration patterns of nipa using microsatellites. Assignment of first-generation (F0) immigrants suggested Mainland Southeast Asia as a melting pot due to the admixture associated with excess of homozygosity. The western populations were recent expansions that emerged in rapid succession based on a phylogram as supported by footprints of genetic drift based on bottleneck tests.
Fulltext An Efficient Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)/CRISPR-Associated Protein 9 Mutagenesis System for Oil Palm (Elaeis guineensis)

Yeap WC, Norkhairunnisa Che Mohd Khan, Norfadzilah Jamalludin, Muad MR, Appleton DR, Harikrishna Kulaveerasingam

Front Plant Sci, 2021;12:773656.
PMID: 34880893 DOI: 10.3389/fpls.2021.773656

The clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) system has emerged as a powerful tool for the precise editing of plant genomes for crop improvement. Rapid in vitro methods for the determination of guide RNA (gRNA) cleavage efficiency and an efficient DNA delivery system is essential for gene editing. However, we lack an efficient gene-editing system for palm species. In this study, we described the development of a transient oil palm protoplast assay to rapidly evaluate the cleavage efficiency of CRISPR/Cas9 mutagenesis and the generation of stable transformed oil palms using biolistic particle bombardment in immature embryos. Using the phytoene desaturase (EgPDS) gene, we found cleavage frequency of up to 25.49% in electro-transfected protoplast, which enables the production of transgenic oil palm shoots exhibiting chimeric albino phenotypes as a result of DNA insertions, deletions (InDels), and nucleotide substitutions, with a mutation efficiency of 62.5-83.33%. We further validated the mutagenesis efficiency and specificity of the CRISPR/Cas9 system in oil palm by targeting the brassinosteroid-insensitive 1 (EgBRI1) gene, which resulted in nucleotide substitutions in EgBRI1 with premature necrosis phenotype in oil palm transgenic shoots and stunted phenotype resulting from DNA InDels. Taken together, our results showed that effective and efficient editing of genes using the CRISPR/Cas9 system can be achieved in oil palm by optimizing the selection of efficient gRNA and DNA delivery methods. This newly designed strategy will enable new routes for the genetic improvement in oil palm and related species.
Fulltext Mitigation of Environmental Stress-Impacts in Plants: Role of Sole and Combinatory Exogenous Application of Glutathione

Koh YS, Wong SK, Ismail NH, Zengin G, Duangjai A, Saokaew S, et al.

Front Plant Sci, 2021;12:791205.
PMID: 35003181 DOI: 10.3389/fpls.2021.791205

Glutathione (GSH; γ-glutamyl-cysteinyl-glycine), a low-molecular-weight thiol, is the most pivotal metabolite involved in the antioxidative defense system of plants. The modulation of GSH on the plant in response to environmental stresses could be illustrated through key pathways such as reactive oxygen species (ROS) scavenging and signaling, methylglyoxal (MG) detoxification and signaling, upregulation of gene expression for antioxidant enzymes, and metal chelation and xenobiotic detoxification. However, under extreme stresses, the biosynthesis of GSH may get inhibited, causing an excess accumulation of ROS that induces oxidative damage on plants. Hence, this gives rise to the idea of exploring the use of exogenous GSH in mitigating various abiotic stresses. Extensive studies conducted borne positive results in plant growth with the integration of exogenous GSH. The same is being observed in terms of crop yield index and correlated intrinsic properties. Though, the improvement in plant growth and yield contributed by exogenous GSH is limited and subjected to the glutathione pool [GSH/GSSG; the ratio of reduced glutathione (GSH) to oxidized glutathione (GSSG)] homeostasis. Therefore, recent studies focused on the sequenced application of GSH was performed in order to complement the existing limitation. Along with various innovative approaches in combinatory use with different bioactive compounds (proline, citric acid, ascorbic acid, melatonin), biostimulants (putrescine, Moringa leaf extract, selenium, humic acid), and microorganisms (cyanobacteria) have resulted in significant improvements when compared to the individual application of GSH. In this review, we reinforced our understanding of biosynthesis, metabolism and consolidated different roles of exogenous GSH in response to environmental stresses. Strategy was also taken by focusing on the recent progress of research in this niche area by covering on its individualized and combinatory applications of GSH prominently in response to the abiotic stresses. In short, the review provides a holistic overview of GSH and may shed light on future studies and its uses.
Fulltext Vacuolar Processing Enzymes Modulating Susceptibility Response to Fusarium oxysporum f. sp. cubense Tropical Race 4 Infections in Banana

Wan Abdullah WMAN, Saidi NB, Yusof MT, Wee CY, Loh HS, Ong-Abdullah J, et al.

Front Plant Sci, 2021;12:769855.
PMID: 35095950 DOI: 10.3389/fpls.2021.769855

Fusarium oxysporum f. sp. cubense tropical race 4 (FocTR4) is a destructive necrotrophic fungal pathogen afflicting global banana production. Infection process involves the activation of programmed cell death (PCD). In this study, seven Musa acuminata vacuolar processing enzyme (MaVPE1-MaVPE7) genes associated with PCD were successfully identified. Phylogenetic analysis and tissue-specific expression categorized these MaVPEs into the seed and vegetative types. FocTR4 infection induced the majority of MaVPE expressions in the susceptible cultivar "Berangan" as compared to the resistant cultivar "Jari Buaya." Consistently, upon FocTR4 infection, high caspase-1 activity was detected in the susceptible cultivar, while low level of caspase-1 activity was recorded in the resistant cultivar. Furthermore, inhibition of MaVPE activities via caspase-1 inhibitor in the susceptible cultivar reduced tonoplast rupture, decreased lesion formation, and enhanced stress tolerance against FocTR4 infection. Additionally, the Arabidopsis VPE-null mutant exhibited higher tolerance to FocTR4 infection, indicated by reduced sporulation rate, low levels of H2O2 content, and high levels of cell viability. Comparative proteomic profiling analysis revealed increase in the abundance of cysteine proteinase in the inoculated susceptible cultivar, as opposed to cysteine proteinase inhibitors in the resistant cultivar. In conclusion, the increase in vacuolar processing enzyme (VPE)-mediated PCD played a crucial role in modulating susceptibility response during compatible interaction, which facilitated FocTR4 colonization in the host.
Fulltext Optimization and identification of siderophores produced by Pseudomonas monteilii strain MN759447 and its antagonism toward fungi associated with mortality in Dalbergia sissoo plantation forests

Srivastava P, Sahgal M, Sharma K, Enshasy HAE, Gafur A, Alfarraj S, et al.

Front Plant Sci, 2022;13:984522.
PMID: 36438130 DOI: 10.3389/fpls.2022.984522

Siderophore-positive bacteria present in the rhizosphere and in bulk soil assist plants by either inhibiting phytopathogen proliferation or increasing plant growth. The bacterial diversity of the Shisham forest ecosystem in the Tarai region of the Western Himalayas was studied and used for siderophore production, taking into account the large-scale dieback and wilt-induced mortality in Dalbergia sissoo (common name: shisham) plantation forests and the importance of soil microbes in tree health. In addition, Pseudomonas, Burkholderia, and Streptomyces were prominent siderophore-positive bacteria in Shisham forests. Pseudomonas species are known for their remarkable siderophore-producing ability. Bacterial siderophores inhibit pathogen growth by rapidly lowering the number of ferric ions in the rhizosphere. The Pseudomonas monteilii strain MN759447 was isolated from a D. sissoo plantation forest at the Agroforestry Research Centre, Pantnagar, Uttarakhand (28°58'N 79°25'E/28.97°N 79.41°E). It produces a significant number of siderophore units (80.36% in total). A two-stage optimization of growth factors was attempted in the strain MN759447 for better siderophore recovery. In the first-stage single-factor experiment, among the five variables studied, only pH, NH4NO3 concentration, and Fe concentration affected siderophore synthesis. In the second stage, an optimization of pH, NH4NO3 concentration, and Fe concentration for improved growth and enhanced siderophore production was carried out using a Box-Behnken design with response surface methodology. By using LC-MS, two derivatives of pseudomonine, salicylic acid, and kynurenic acid were detected as siderophores in the purified XAD-2 methanol extract of the P. monteilii strain MN759447. In addition to siderophore production, the P. monteilii strain MN759447 also exhibited a broad range of antagonistic activity against Aspergillus calidoustus (65%), Fusarium oxysporum (41.66%), Talaromyces pinophilus (65%), and Talaromyces verruculosus (65.1%) that are linked to sissoo mortality. To our knowledge, this is the first report on siderophore-producing bacteria isolated, identified, and characterized from the D. sissoo Roxb. forest habitat. This strain can also be developed as a commercial product.
Fulltext Allelopathic potential in rice - a biochemical tool for plant defence against weeds

Rahaman F, Shukor Juraimi A, Rafii MY, Uddin K, Hassan L, Chowdhury AK, et al.

Front Plant Sci, 2022;13:1072723.
PMID: 36589133 DOI: 10.3389/fpls.2022.1072723

Rice is a key crop for meeting the global food demand and ensuring food security. However, the crop has been facing great problems to combat the weed problem. Synthetic herbicides pose a severe threat to the long-term viability of agricultural output, agroecosystems, and human health. Allelochemicals, secondary metabolites of allelopathic plants, are a powerful tool for biological and eco-friendly weed management. The dynamics of weed species in various situations are determined by crop allelopathy. Phenolics and momilactones are the most common allelochemicals responsible for herbicidal effects in rice. The dispersion of allelochemicals is influenced not only by crop variety but also by climatic conditions. The most volatile chemicals, such as terpenoids, are usually emitted by crop plants in drought-stricken areas whereas the plants in humid zones release phytotoxins that are hydrophilic in nature, including phenolics, flavonoids, and alkaloids. The allelochemicals can disrupt the biochemical and physiological processes in weeds causing them to die finally. This study insight into the concepts of allelopathy and allelochemicals, types of allelochemicals, techniques of investigating allelopathic potential in rice, modes of action of allelochemicals, pathways of allelochemical production in plants, biosynthesis of allelochemicals in rice, factors influencing the production of allelochemicals in plants, genetical manipulation through breeding to develop allelopathic traits in rice, the significance of rice allelopathy in sustainable agriculture, etc. Understanding these biological phenomena may thus aid in the development of new and novel weed-control tactics while allowing farmers to manage weeds in an environmentally friendly manner.
Fulltext The potential of lactic acid bacteria in mediating the control of plant diseases and plant growth stimulation in crop production - A mini review

Jaffar NS, Jawan R, Chong KP

Front Plant Sci, 2022;13:1047945.
PMID: 36714743 DOI: 10.3389/fpls.2022.1047945

The microbial diseases cause significant damage in agriculture, resulting in major yield and quality losses. To control microbiological damage and promote plant growth, a number of chemical control agents such as pesticides, herbicides, and insecticides are available. However, the rising prevalence of chemical control agents has led to unintended consequences for agricultural quality, environmental devastation, and human health. Chemical agents are not naturally broken down by microbes and can be found in the soil and environment long after natural decomposition has occurred. As an alternative to chemical agents, biocontrol agents are employed to manage phytopathogens. Interest in lactic acid bacteria (LAB) research as another class of potentially useful bacteria against phytopathogens has increased in recent years. Due to the high level of biosafety, they possess and the processes they employ to stimulate plant growth, LAB is increasingly being recognized as a viable option. This paper will review the available information on the antagonistic and plant-promoting capabilities of LAB and its mechanisms of action as well as its limitation as BCA. This review aimed at underlining the benefits and inputs from LAB as potential alternatives to chemical usage in sustaining crop productivity.
Fulltext A comparison of 25 complete chloroplast genomes between sister mangrove species Kandelia obovata and Kandelia candel geographically separated by the South China Sea

Xu X, Shen Y, Zhang Y, Li Q, Wang W, Chen L, et al.

Front Plant Sci, 2022;13:1075353.
PMID: 36684775 DOI: 10.3389/fpls.2022.1075353

In 2003, Kandelia obovata was identified as a new mangrove species differentiated from Kandelia candel. However, little is known about their chloroplast (cp) genome differences and their possible ecological significance. In this study, 25 whole cp genomes, with seven samples of K. candel from Malaysia, Thailand, and Bangladesh and 18 samples of K. obovata from China, were sequenced for comparison. The cp genomes of both species encoded 128 genes, namely 83 protein-coding genes, 37 tRNA genes, and eight rRNA genes, but the cp genome size of K. obovata was ~2 kb larger than that of K. candle due to the presence of more and longer repeat sequences. Of these, tandem repeats and simple sequence repeats exhibited great differences. Principal component analysis based on indels, and phylogenetic tree analyses constructed with homologous protein genes from the single-copy genes, as well as 38 homologous pair genes among 13 mangrove species, gave strong support to the separation of the two species within the Kandelia genus. Homologous genes ndhD and atpA showed intraspecific consistency and interspecific differences. Molecular dynamics simulations of their corresponding proteins, NAD(P)H dehydrogenase chain 4 (NDH-D) and ATP synthase subunit alpha (ATP-A), predicted them to be significantly different in the functions of photosynthetic electron transport and ATP generation in the two species. These results suggest that the energy requirement was a pivotal factor in their adaptation to differential environments geographically separated by the South China Sea. Our results also provide clues for future research on their physiological and molecular adaptation mechanisms to light and temperature.
Fulltext Introgression of the QTL qSB11-1TT conferring sheath blight resistance in rice (Oryza sativa) into an elite variety, UKMRC 2, and evaluation of its backcross-derived plants

Hossain MK, Islam MR, Sundaram RM, Bhuiyan MAR, Wickneswari R

Front Plant Sci, 2022;13:981345.
PMID: 36699836 DOI: 10.3389/fpls.2022.981345

INTRODUCTION: Sheath blight (SB) is the most damaging fungal disease in rice caused by a soil-borne pathogenic fungus, Rhizoctonia solani Kuhn (R. solani). The disease resistance in rice is a complex quantitative trait controlled by a few major genes. UKMRC2 is a newly developed elite rice variety that possesses high yield potential but is susceptible to sheath blight disease indicating a huge risk of varietal promotion, mass cultivation, and large-scale adoption. The aim of our present study was the development of varietal resistance against R. solani in UKMRC2 to enhance its stability and durability in a wide range of environments and to validate the effects of an SB-resistance QTL on the new genetic background.
METHODS: In our study, we developed 290 BC1F1 backcross progenies from a cross between UKMRC2 and Tetep to introgress the QTL qSBR11-1TT into the UKMRC2 genetic background. Validation of the introgressed QTL region was performed via QTL analysis based on QTL-linked SSR marker genotyping and phenotyping against R. solani artificial field inoculation techniques.
RESULTS AND DISCUSSION: The QTL qSBR11-1TT was then authenticated with the results of LOD score (3.25) derived from composite interval mapping, percent phenotypic variance explained (14.6%), and additive effect (1.1) of the QTLs. The QTL region was accurately defined by a pair of flanking markers K39512 and RM7443 with a peak marker RM27360. We found that the presence of combination of alleles, RM224, RM27360 and K39512 demonstrate an improved resistance against the disease rather than any of the single allele. Thus, the presence of the QTL qSBR11-1TT has been validated and confirmed in the URMRC2 genetic background which reveals an opportunity to use the QTL linked with these resistance alleles opens an avenue to resume sheath blight resistance breeding in the future with marker-assisted selection program to boost up resistance in rice varieties.
Editorial: Genome editing and biotechnological advances for crop improvement and future agriculture

Hamdan MF, Hensel G, Alok A, Tan BC

Front Plant Sci, 2023;14:1132821.
PMID: 36798708 DOI: 10.3389/fpls.2023.1132821
Fulltext Resequencing of durian genomes reveals large genetic variations among different cultivars

Nawae W, Naktang C, Charoensri S, U-Thoomporn S, Narong N, Chusri O, et al.

Front Plant Sci, 2023;14:1137077.
PMID: 36875624 DOI: 10.3389/fpls.2023.1137077

Durian (Durio zibethinus), which yields the fruit known as the "King of Fruits," is an important economic crop in Southeast Asia. Several durian cultivars have been developed in this region. In this study, we resequenced the genomes of three popular durian cultivars in Thailand, including Kradumthong (KD), Monthong (MT), and Puangmanee (PM) to investigate genetic diversities of cultivated durians. KD, MT, and PM genome assemblies were 832.7, 762.6, and 821.6 Mb, and their annotations covered 95.7, 92.4, and 92.7% of the embryophyta core proteins, respectively. We constructed the draft durian pangenome and analyzed comparative genomes with related species in Malvales. Long terminal repeat (LTR) sequences and protein families in durian genomes had slower evolution rates than that in cotton genomes. However, protein families with transcriptional regulation function and protein phosphorylation function involved in abiotic and biotic stress responses appeared to evolve faster in durians. The analyses of phylogenetic relationships, copy number variations (CNVs), and presence/absence variations (PAVs) suggested that the genome evolution of Thai durians was different from that of the Malaysian durian, Musang King (MK). Among the three newly sequenced genomes, the PAV and CNV profiles of disease resistance genes and the expressions of methylesterase inhibitor domain containing genes involved in flowering and fruit maturation in MT were different from those in KD and PM. These genome assemblies and their analyses provide valuable resources to gain a better understanding of the genetic diversity of cultivated durians, which may be useful for the future development of new durian cultivars.
Fulltext Rainfed assessment of foxtail millet (Setaria italica L. beauv) germplasms through genotyping and principal component analysis

Singh D, Lawrence K, Marker S, Bhattacharjee I, Lawrence R, Choudhary R, et al.

Front Plant Sci, 2023;14:1017652.
PMID: 36968405 DOI: 10.3389/fpls.2023.1017652

INTRODUCTION: Foxtail millet (Setaria italica L. beauv) is an important crop in underdeveloped countries; however, yield levels are low. The use of varied germplasm in a breeding approach is critical for increasing productivity. Foxtail millet can be cultivated effectively in a wide range of environmental circumstances but it is best suited to hot and dry climates.
METHODS: In the current study, multivariant traits were used to define 50 genotypes in the first year and 10 genotypes in the second year. The phenotypic correlations among all traits in the entire germplasm were assessed, and the data acquired for all quantitative characters were subjected to analysis of variance for augmented block design. Furthermore, WINDOWS STAT statistical software was used to carry out a principal component analysis (PCA). The presence of substantial variations in most symptoms was shown by analysis of variance.
RESULTS: Genotypic coefficient of variation (GCV) projections for grain yields were the highest, followed by panicle lengths and biological yields. Plant height and leaf length had the highest PCV estimates, followed by leaf width. Low GCV and phenotypic coefficient of variation (PCV) were measured as leaf length and 50% flowering in days. According to the PCV study, direct selection based on characters, panicle weight, test weight, and straw weight had a high and positive effect on grain yield per plant in both the rainy and summer seasons, indicating the true relationship between these characters and grain yield per plant, which aids indirect selection for these traits and thus improves grain yield per plant. Variability in foxtail millet germplasm enables plant breeders to effectively select appropriate donor lines for foxtail millet genetic improvement.
DISCUSSION: Based on the average performance of genotypes considered superior in terms of grain yield components under Prayagraj agroclimatic conditions, the best five genotypes were: Kangni-7 (GS62), Kangni-1 (G5-14), Kangni-6 (GS-55), Kangni-5 (GS-389), and Kangni-4 (GS-368).
Fulltext Image-based phenotyping of seed architectural traits and prediction of seed weight using machine learning models in soybean

Duc NT, Ramlal A, Rajendran A, Raju D, Lal SK, Kumar S, et al.

Front Plant Sci, 2023;14:1206357.
PMID: 37771485 DOI: 10.3389/fpls.2023.1206357

Among seed attributes, weight is one of the main factors determining the soybean harvest index. Recently, the focus of soybean breeding has shifted to improving seed size and weight for crop optimization in terms of seed and oil yield. With recent technological advancements, there is an increasing application of imaging sensors that provide simple, real-time, non-destructive, and inexpensive image data for rapid image-based prediction of seed traits in plant breeding programs. The present work is related to digital image analysis of seed traits for the prediction of hundred-seed weight (HSW) in soybean. The image-based seed architectural traits (i-traits) measured were area size (AS), perimeter length (PL), length (L), width (W), length-to-width ratio (LWR), intersection of length and width (IS), seed circularity (CS), and distance between IS and CG (DS). The phenotypic investigation revealed significant genetic variability among 164 soybean genotypes for both i-traits and manually measured seed weight. Seven popular machine learning (ML) algorithms, namely Simple Linear Regression (SLR), Multiple Linear Regression (MLR), Random Forest (RF), Support Vector Regression (SVR), LASSO Regression (LR), Ridge Regression (RR), and Elastic Net Regression (EN), were used to create models that can predict the weight of soybean seeds based on the image-based novel features derived from the Red-Green-Blue (RGB)/visual image. Among the models, random forest and multiple linear regression models that use multiple explanatory variables related to seed size traits (AS, L, W, and DS) were identified as the best models for predicting seed weight with the highest prediction accuracy (coefficient of determination, R2=0.98 and 0.94, respectively) and the lowest prediction error, i.e., root mean square error (RMSE) and mean absolute error (MAE). Finally, principal components analysis (PCA) and a hierarchical clustering approach were used to identify IC538070 as a superior genotype with a larger seed size and weight. The identified donors/traits can potentially be used in soybean improvement programs.

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