Molecular Breeding Approaches Research Articles

Harnessing Genomic Resources and Molecular Breeding Techniques for Advancing Crop Resilience and Productivity

Crop improvement and adaptation are critical to ensure global food security in the face of climate change, population growth, and resource limitations. Exploiting genomic resources and molecular breeding techniques offers immense potential to accelerate the development of resilient, high-yielding crop varieties. This review provides an overview of the current state and future prospects of leveraging genomics and molecular breeding for crop improvement, with a focus on major food crops. We discuss key genomic resources such as reference genomes, transcriptomes, and pan-genomes, as well as powerful molecular breeding approaches like marker-assisted selection, genomic selection, and genome editing. Integrating these tools into crop breeding pipelines can greatly enhance the precision and efficiency of developing improved varieties with desirable traits such as abiotic stress tolerance, disease resistance, and enhanced nutritional quality. We also highlight successful examples of applying these techniques in crops like rice, wheat, maize, and legumes. Furthermore, we explore the role of big data, machine learning, and systems biology in extracting actionable insights from the vast genomic data being generated. Finally, we discuss the challenges and opportunities in translating genomic discoveries into improved crop varieties, emphasizing the need for multidisciplinary collaborations, capacity building, and public-private partnerships. Harnessing the power of genomics and molecular breeding will be pivotal in developing climate-resilient crops to feed the growing global population sustainably.

The transcription factors GmVOZ1A and GmWRI1a synergistically regulate oil biosynthesis in soybean.

Soybean [Glycine max (L.) Merr.] is a major oil-producing crop worldwide. Although several related proteins regulating soybean oil accumulation have been reported, little is known about the regulatory mechanisms. In this study, we characterized vascular plant one-zinc-finger 1A (GmVOZ1A) that interacts with WRINKLED 1a (GmWRI1a) using yeast two-hybrid library screening. The GmVOZ1A-GmWRI1a interaction was further verified by protein-protein interaction assays in vivo and in vitro. GmVOZ1A enhanced the seed fatty acid and oil contents by regulating genes involved in lipid biosynthesis. Conversely, a loss-of-function mutation in GmVOZ1A resulted in a reduction in triacylglycerol (TAG) content in soybean. Protein-DNA interaction assays revealed that GmVOZ1A and GmWRI1a cooperate to up-regulate the expression level of acyl-coenzymeA-binding protein 6a (GmACBP6a) and promote the accumulation of TAG. In addition, GmACBP6a overexpression promoted seed fatty acid and oil contents, as well as increased seed size and 100-seed weight. Taken together, these findings indicate that the transcription factor GmVOZ1A regulates soybean oil synthesis and cooperates with GmWRI1a to up-regulate GmACBP6a expression and oil biosynthesis in soybean. The results lay a foundation for a comprehensive understanding of the regulatory mechanisms underlying soybean oil biosynthesis and will contribute to improving soybean oil production through molecular breeding approaches.

Redesigning soybean with improved oil and meal traits.

Soybean seed oil and meal composition traits can be combined without interference to provide additional value to the crop. Soybean [Glycine max (L.) Merr.] is an important crop worldwide; its overall value comes from seed oil and high protein meal. The development of soybean varieties with allele combinations for improved oil and meal quality is expected to provide a compositional value bundle for soybean. The high oleic and low linolenic acid seed oil trait (HOLL; > 70% oleic and < 3% linolenic acid) is targeted to optimize the health and functional properties of soybean oil. For soybean meal, metabolizable energy is improved by altering the carbohydrate profile with increased sucrose and decreased anti-nutritional factors, raffinose family of oligosaccharides (RFOs). Previous research identified four variant alleles of fatty acid desaturase (FAD) genes and two raffinose synthase (RS) genes necessary for the HOLL trait in soybean oil and Low or Ultra-Low (UL) RFO traits in soybean meal, respectively. We employed a molecular marker-assisted breeding approach to combine six alleles conferring the desired soybean oil and meal value traits. Eight environment field trials were conducted with twenty-four soybean lines to evaluate phenotypic interactions among the variant alleles of FAD and RS genes. The results indicated that the four FAD gene alleles conditioned the HOLL fatty acid profile of the seed oil regardless of the allele status of the RS genes. Independent of the allele combination of the FAD genes, soybean with two variant alleles of the RS genes had the desired RFO trait in the seeds. The results confirm the feasibility of soybean variety development with this unique combination of oil and meal traits.

Using RNA sequencing to unravel molecular changes underlying the defense response in chickpea induced by Phytophthora medicaginis.

Phytophthora root rot (PRR), caused by Phytophthora medicaginis, is a major soil-borne disease of chickpea in Australia. Breeding for PRR resistance is an effective approach to avoid significant yield loss. Genetic resistance has been identified in cultivated chickpea (Cicer arietinum) and in the wild relative C. echinospermum, with previous studies identifying independent genetic loci associated with each of these sources. However, the molecular mechanisms associated with PRR resistance are not known. RNA sequencing analysis employed in this study identified changes in gene expression in roots of three chickpea genotypes grown hydroponically, early post-infection with P. medicaginis zoospores. Analyses of differentially expressed genes (DEG) identified the activation of a higher number of non-specific R-genes in a PRR-susceptible variety than in the resistant genotypes, suggesting a whole plant resistance response occurring in chickpea against the pathogen. Contrasting molecular changes in signaling profiles, proteolysis and transcription factor pathways were observed in the cultivated and wild Cicer-derived resistant genotypes. DEG patterns supported a hypothesis that increased root elongation and reduced adventitious root formation limit the pathogen entry points in the genotype containing the wild Cicer source of PRR resistance. Candidate resistance genes, including an aquaporin and a maltose transporter in the wild Cicer source and GDSL esterases/lipases in the cultivated source of resistance, were oppositely regulated. Increased knowledge of these genes and pathways will improve our understanding of molecular mechanisms controlling PRR resistance in chickpea, and support the development of elite chickpea varieties through molecular breeding approaches.

Retraction: The intervention of classical and molecular breeding approaches to enhance flooding stress tolerance in soybean - An review.

[This retracts the article DOI: 10.3389/fpls.2022.1085368.].

Unveiling alliinase gene candidates in shallots using resistance gene motif-based degenerate primers

Shallots are integral to Indonesian daily life, with annual production reaching two million tons. However, the superior varieties are often susceptible to disease, highlighting the need for new resistant varieties. Understanding the genetic basis of disease resistance is crucial for breeding efforts aimed at developing new varieties. Alliinase, an enzyme crucial for garlic defense, is a potential candidate for enhancing shallot resistance. This study aims to identify alliinase gene candidates in shallots using degenerate primers. Genomic DNA from the Bima Brebes genotype was isolated, and degenerate primers successfully amplified 600–800 bp fragments. Three sequences were selected for further analysis, with one sequence showing high similarity to known resistance genes. Multiple sequence alignment revealed characteristic resistance gene motifs, supporting their candidacy as resistance genes. Phylogenetic analysis grouped these sequences with known resistance genes, further supporting their potential. These findings provide valuable insights for breeding programs aiming to enhance resistance in shallots through a molecular breeding approach. The identified alliinase gene candidates can be used to develop disease-resistant shallot varieties. Incorporating these genes into breeding programs can enhance resistance, improving yield and stability in shallot production.

Grain and shoot iron (Fe) content and root phytosiderophore release are the major determinants of Fe-deficiency tolerance index (FeDTI) and the reliable screening markers to breed Fe-efficient rice (Oryza sativa L.)

There is a need to exploit the genetic variability in rice to improve the Fe deficiency tolerance, particularly under aerobic conditions, and to improve the Fe uptake and accumulation in the grain to facilitate biofortification. The present research was conducted to ascertain the regulators and determinants of Fe-deficiency tolerance in rice. Fifty-seven diverse genotypes were investigated under Fe-deficient (1 µM, FDS, -Fe) and Fe-sufficient (100 µM, FSS, +Fe) nutrient solution cultures for growth and physiological attributes, Fe uptake and accumulation and root release of phytosiderophores (PS), etc., and Fe-deficiency tolerance index (FeDTI). A strong positive correlation was observed between root traits and the PS release. Further, a higher release of PS was evidenced as a major determinant of shoot Fe and grain Fe in rice particularly under Fe deficiency. Based on FeDTI, a total of ten rice genotypes were identified, and their Fe deficiency response was further validated on Fe deficient (∼2.1 ppm Fe, FeDS) and Fe-sufficient soils (∼10 ppm Fe, FeSS) in pot culture. Maintenance of high active Fe content and consequently a higher leaf chlorophyll content throughout the plant growth were extremely important determinants of grain yield and grain Fe fortification in rice under Fe deficiency than under the Fe sufficient condition. Based on the FeDTI, this study further identifies the Fe-deficiency tolerant rice genotypes which can be exploited through conventional and molecular breeding approaches to improve the Fe uptake efficiency and grain Fe content of the high-yielding rice genotypes.

Development of early maturing salt-tolerant rice variety KKL(R) 3 using a combination of conventional and molecular breeding approaches.

Introduction: Soil salinity poses a severe threat to rice production, resulting in stunted growth, leaf damage, and substantial yield losses. This study focuses on developing an early maturing seedling stage salinity tolerant rice variety by integrating conventional breeding methods with marker assisted breeding (MAB) approaches. Methods: Seedling-stage salinity tolerance Quantitative Trait Locus (QTL) "Saltol" from the salt-tolerant parent FL478 was introduced into the high-yielding but salt-sensitive rice variety ADT 45. This was achieved through a combination of conventional breeding and MAB. The breeding process involved rigorous selection, screening, and physiological parameter assessments. Results: KKL(R) 3 (KR 15066) identified as the top performing Recombinant Inbred Line (RIL), consistently demonstrating maximum mean grain yields under both salinity (3435.6kg/ha) and normal (6421.8kg/ha) conditions. In comparison to the early maturing, salt-tolerant national check variety CSR 10, KKL(R) 3 exhibited a substantial yield increase over 50%. Discussion: The notable improvement observed in KKL(R) 3 positions it as a promising variety for release, offering a reliable solution to maximize yields, ensure food security, and promote agricultural sustainability in both saline and non-saline environments. The study highlights the effectiveness of MAB in developing salt-tolerant rice varieties and emphasizes the significance of the Saltol QTL in enhancing seedling stage salinity tolerance. The potential release of KKL(R) 3 has the capacity to revolutionize rice production in salt affected regions, providing farmers with a reliable solution to maximize yields and contribute to food security while ensuring agricultural sustainability.

Sulfate transport and metabolism: strategies to improve the seed protein quality.

Sulfur-containing amino acids (SAA), namely methionine, and cysteine are crucial essential amino acids (EAA) considering the dietary requirements of humans and animals. However, a few crop plants, especially legumes, are characterized with suboptimal levels of these EAA thereby limiting their nutritive value. Hence, improved comprehension of the mechanistic perspective of sulfur transport and assimilation into storage reserve, seed storage protein (SSP), is imperative. Efforts to augment the level of SAA in seed storage protein form an integral component of strategies to balance nutritive quality and quantity. In this review, we highlight the emerging trends in the sulfur biofortification approaches namely transgenics, genetic and molecular breeding, and proteomic rebalancing with sulfur nutrition. The transgenic 'push and pull strategy' could enhance sulfur capture and storage by expressing genes that function as efficient transporters, sulfate assimilatory enzymes, sulfur-rich foreign protein sinks, or by suppressing catabolic enzymes. Modern molecular breeding approaches that adopt high throughput screening strategies and machine learning algorithms are invaluable in identifying candidate genes and alleles associated with SAA content and developing improved crop varieties. Sulfur is an essential plant nutrient and its optimal uptake is crucial for seed sulfur metabolism, thereby affecting seed quality and yields through proteomic rebalance between sulfur-rich and sulfur-poor seed storage proteins.

Differential gene expression and potential regulatory network of fatty acid biosynthesis during fruit and leaf development in yellowhorn (Xanthoceras sorbifolium), an oil-producing tree with significant deployment values.

Xanthoceras sorbifolium (yellowhorn) is a woody oil plant with super stress resistance and excellent oil characteristics. The yellowhorn oil can be used as biofuel and edible oil with high nutritional and medicinal value. However, genetic studies on yellowhorn are just in the beginning, and fundamental biological questions regarding its very long-chain fatty acid (VLCFA) biosynthesis pathway remain largely unknown. In this study, we reconstructed the VLCFA biosynthesis pathway and annotated 137 genes encoding relevant enzymes. We identified four oleosin genes that package triacylglycerols (TAGs) and are specifically expressed in fruits, likely playing key roles in yellowhorn oil production. Especially, by examining time-ordered gene co-expression network (TO-GCN) constructed from fruit and leaf developments, we identified key enzymatic genes and potential regulatory transcription factors involved in VLCFA synthesis. In fruits, we further inferred a hierarchical regulatory network with MYB-related (XS03G0296800) and B3 (XS02G0057600) transcription factors as top-tier regulators, providing clues into factors controlling carbon flux into fatty acids. Our results offer new insights into key genes and transcriptional regulators governing fatty acid production in yellowhorn, laying the foundation for efforts to optimize oil content and fatty acid composition. Moreover, the gene expression patterns and putative regulatory relationships identified here will inform metabolic engineering and molecular breeding approaches tailored to meet biofuel and bioproduct demands.

Enhancing Crop Improvement through Synergistic Integration of Advanced Plant Breeding and Proximal Remote Sensing Techniques: A Review

Accelerating crop improvement with enhanced adaptability to changing climatic conditions and meeting the ever-increasing global food demand requires urgent action. To achieve this, we must employ advanced molecular breeding techniques, such as marker-assisted selection, marker-assisted backcrossing, genomic selection, genome editing, and targeted mutation. However, these approaches demand the screening of large populations to identify potential genes and genotypes. Unfortunately, a significant bottleneck lies in the absence of high-throughput plant phenotyping methods that can rapidly and cost-effectively facilitate data-driven genotype selection in plant breeding. Traditional phenotyping methods, reliant on trained experts, are slow, expensive, labour-intensive, subjective, and often require destructive sampling. Proximal remote sensing technologies, including RGB imaging, thermal imaging, hyperspectral imaging, multispectral imaging, and fluorescence imaging, offer a non-destructive and rapid collection of detailed phenotypic data, providing valuable insights into various plant traits at different growth stages. High-throughput phenotyping platforms, such as Conveyor-Type Indoor, Benchtop-Type Indoor, Unmanned Aerial Platform (UAP), and Manned Aerial Platform (MAP), utilize a combination of the aforementioned remote sensing technologies. This review article aims to explore the integration of proximal remote sensing and molecular breeding approaches, showcasing how this synergistic approach can expedite crop improvement efforts. By emphasizing the benefits, challenges, and future prospects of this integrative approach, we hope to pave the way for sustainable and productive agriculture, ensuring food security in the face of changing environmental conditions.

Wheat Septoria Disease Management and Molecular Breeding Approaches in Ethiopia: A Review

Septoria tritici blotch (STB) caused by the fungus Mycosphaerella graminicola, is one of the most important foliar diseases of wheat (T. aestivum spp., aestivum L.) worldwide. The disease is pervasive and economically significant throughout Ethiopia's wheat-growing regions. Naturally susceptible wheat cultivars of STB disease were found in the Central Highlands of Ethiopia, where incidence (98%) and severity (97%) of the disease, as well as yield loss (41%), were documented. This disease has been managed using a variety of techniques, including cultural control, chemical control, and genetic controls have been utilized to control this disease and subsequently reduce yield losses. The lack of information on the diversity of diseases worldwide and in Ethiopia now hampers the screening and selection of wheat genotypes for disease resistance. In this review, wheat septoria disease management and molecular breeding approaches in Ethiopia were assessed.

Delineation of novel genomic loci and putative candidate genes associated with seed iron and zinc content in lentil (Lens culinaris Medik.)

The use of molecular breeding approaches for development of lentil genotypes biofortified with essential micro-nutrients such as iron and zinc, could serve as a promising solution to address the problem of global malnutrition. Thus, genome-wide association study (GWAS) strategy was adopted in this study to identify the genomic regions associated with seed iron and zinc content in lentil. A panel of 95 diverse lentil genotypes, grown across three different geographical locations and evaluated for seed iron and zinc content, exhibited a wide range of variation. Genotyping-by-sequencing (GBS) analysis of the panel identified 33,745 significant single nucleotide polymorphisms (SNPs) that were distributed across all the 7 lentil chromosomes. Association mapping revealed 23 SNPs associated with seed iron content that were distributed across all the chromosomes except chromosome 3. Similarly, 14 SNPs associated with seed zinc content were also identified that were distributed across chromosomes 1, 2, 4, 5 and 6. Further, 80 genes were identified in the proximity of iron associated markers and 36 genes were identified in the proximity of zinc associated markers. Functional annotation of these genes revealed their putative involvement in iron and zinc metabolism. For seed iron content, two highly significant SNPs were found to be located within two putative candidate genes namely iron-sulfur cluster assembly (ISCA) and flavin binding monooxygenase (FMO) respectively. For zinc content, a highly significant SNP was detected in a gene encoding UPF0678 fatty acid-binding protein. Expression analysis of these genes and their putative interacting partners suggests their involvement in iron and zinc metabolism in lentil. Overall, in this study we have identified markers, putative candidate genes and predicted putative interacting protein partners significantly associated with iron and zinc metabolism that could be utilized in future breeding studies of lentil for nutrient biofortification.

A Review on Revolutionary Strategy for Crop Improvement: Genome Editing

Genome editing technology revolutionized crop improvement technology through sequence-specific, precise, site-directed, safe genetic manipulation and combat the major 21st century challenge such as achieving world food security meeting rising global food demand and improving food nutrition in the face of rapidly changing climate conditions. Crop improvement using conventional and molecular breeding approaches takes time, causing biosafety concerns and cannot equipoise with raising demand. Genome editing system like zinc finger nuclease (ZFN), transcription activator-like effector nucleases (TALEN), and clustered regularly interspaced short palindromic repeats (CRISPR) made a desirable targeted modification in crops for improving crop yield, nutraceutical quality and also enhance tolerance to environmental stress (biotic or abiotic) through add the desirable trait(s) and remove the undesirable. Genome manipulation tools progression creates new breakthroughs and speeds up crop improvement through site-directed mutagenesis efficiently for crop improvements to meet the ever-increasing global demand for food and produce more resilient crop with great flexibility to combat climate change.

Melatonin strongly enhances the Agrobacterium- mediated transformation of carnation in nitrogen-depleted media

With the rising demand for new cultivars of carnation, efficient transformation protocols are needed to enable the bioengineering of new traits. Here, we established a novel and efficient Agrobacterium-mediated transformation system using callus as the target explant for four commercial carnation cultivars. Leaf-derived calli of all cultivars were inoculated with Agrobacterium tumefaciens strain LBA4404 containing the plasmid pCAMBIA 2301 harboring genes for β-glucuronidase (uidA) and neomycin phosphotransferase (nptII). Polymerase chain reaction (PCR) and histochemical assays confirmed the presence of uidA and β-glucuronidase (GUS), respectively in transgenic shoots. The effect on transformation efficiency of medium composition and the presence of antioxidants during inoculation and co-cultivation was investigated. The transformation efficiency was increased in Murashige and Skoog (MS) medium lacking KNO3 and NH4NO3, and also in MS medium lacking macro and micro elements and Fe to 5% and 3.1% respectively, compared to 0.6% in full-strength medium. Transformation efficiency was increased dramatically to 24.4% across all carnation cultivars by the addition of 2 mg/l melatonin to nitrogen-depleted MS medium. Shoot regeneration was also doubled in this treatment. The establishment of this efficient and reliable transformation protocol can advance the development of novel carnation cultivars through molecular breeding approaches.

Review on the Strategies for Enhancing Plant Disease Resistance: Insights from Molecular Plant Pathology

Plant diseases pose significant threats to global food security, necessitating innovative strategies for enhancing plant disease resistance. This article explores cutting-edge insights from molecular plant pathology to develop effective strategies for mitigating the impact of pathogens on crops. Beginning with an introduction to the importance of plant disease resistance in agriculture, the article delves into the fundamentals of molecular plant pathology. It examines the intricacies of the plant immune system, elucidating the molecular mechanisms by which plants recognize and respond to pathogens, and extends to the strategies employed by pathogens to compromise plant defenses, providing a comprehensive understanding of the molecular underpinnings of pathogen virulence. Genetic strategies for disease resistance, including traditional breeding and genetic engineering, are explored, along with an analysis of molecular breeding approaches and their integration into conventional breeding programs. Furthermore, the article investigates the role of omics technologies in elucidating plant-pathogen interactions, emphasizing their contribution to unraveling disease resistance mechanisms. Biotechnological interventions, such as RNA interference, gene editing, and synthetic biology, are examined in the context of enhancing plant disease resistance, with a focus on successful applications and associated ethical considerations. It also explores the implications of disease resistance for sustainable agriculture, considering how enhanced resistance contributes to holistic pest and disease management. Finally, it outlines future directions and challenges, identifying emerging trends in the field and recommending areas for further research. By synthesizing knowledge from molecular plant pathology, this article aims to provide a comprehensive overview of the strategies available for enhancing plant disease resistance, offering valuable insights for researchers, practitioners, and policymakers engaged in the pursuit of resilient and sustainable agricultural practices.

Morpho-genetic variability of Rhizoctonia solani population causing sheath blight disease in rice (Oryza sativa L.)

Aim: The present study aims to investigate the morpho-pathological and molecular variability among the R. solani isolates from different geographical regions of India. Methodology: R. solani isolates were collected from sheath blight infected rice plants from diverse regions of Western Uttar Pradesh and Uttarakhand. Morphological variability among the isolates was studied in-vitro on PDA medium. The anastomosis grouping was determined by hyphal fusion reactions paired with tester strain and confirmed by AG-specific-PCR assay. Pathogenicity assay was conducted in-vivo on four rice varieties using artificial inoculation method under greenhouse conditions. Evolutionary relationship among the isolates was determined using rDNA-ITS-PCR with ITS1 &amp; ITS4 primers. Further, genetic variability among the isolates was assessed using ISSR primers. Results: A total of 21 isolates of R. solani were recovered and based on morphological and sclerotial features, significant variation was observed among the isolates. All the isolates belonged to AG1-IA group which was confirmed by AG-specific PCR assay. Based on pathogenicity, eight isolates were found highly virulent, eight were moderately virulent and six were less virulent. ISSR markers showed high level of polymorphism and grouped all isolates into three major clusters showing partial correlation with geographical origin of the isolates. Sequence variations in ITS region were observed in the form of insertions or deletions of the nucleotide when rDNA-ITS sequences were compared that led to the interspecies diversity and diversity was observed in clad-specific manner. The phylogenetic tree separated the isolates into ten distinct clades showing high level of genetic diversity. Interpretation: The results of the present study may be helpful for the phylogenetic classification of complex R. solani species and provide information on the genetic divergence and occurrence of pathogenic races. This information will be helpful for the development of effective disease management strategies based on the molecular breeding and other approaches. Key words: Anastomosis, Genetic diversity, ISSR, Pathogenicity, R. solani, Sheath blight

Outlier analyses and genome-wide association study identify glgC and ERD6-like 4 as candidate genes for foliar water-soluble carbohydrate accumulation in Trifolium repens.

Increasing water-soluble carbohydrate (WSC) content in white clover is important for improving nutritional quality and reducing environmental impacts from pastoral agriculture. Elucidation of genes responsible for foliar WSC variation would enhance genetic improvement by enabling molecular breeding approaches. The aim of the present study was to identify single nucleotide polymorphisms (SNPs) associated with variation in foliar WSC in white clover. A set of 935 white clover individuals, randomly sampled from five breeding pools selectively bred for divergent (low or high) WSC content, were assessed with 14,743 genotyping-by-sequencing SNPs, using three outlier detection methods: PCAdapt, BayeScan and KGD-FST. These analyses identified 33 SNPs as discriminating between high and low WSC populations and putatively under selection. One SNP was located in the intron of ERD6-like 4, a gene coding for a sugar transporter located on the vacuole membrane. A genome-wide association study using a subset of 605 white clover individuals and 5,757 SNPs, identified a further 12 SNPs, one of which was associated with a starch biosynthesis gene, glucose-1-phosphate adenylyltransferase, glgC. Our results provide insight into genomic regions underlying WSC accumulation in white clover, identify candidate genomic regions for further functional validation studies, and reveal valuable information for marker-assisted or genomic selection in white clover.

Genetic Diversity and Molecular Breeding of Melon (Cucumis melo L.): A review

Cucumis melo L. is an important horticultural crop that is widely cultivated for its edible fruit. The breeding of melon crop in order to improve its qualitative and quantitative yield is the objective of the current research. The recent melon breeding majorly focused on identification of novel genes, novel QTLs, and differentially expressed genes among the various populations. The publication of melon genome sequence in 2012, substantially accelerated the genetic dissection of candidate genes responsible for various desirable traits such as yield and yield contributing traits, fruit quality, disease resistance (Powdery mildew and Downey mildew resistance), salinity and temperature stress, and the genes involving in melon plant physiology. The molecular biology approaches such as whole-genome resequencing, bulked segregant analysis sequencing and the transcriptome analysis have been widely used to explore the genetic basis for the observed desirable phenotypic characteristics of the melon accessions in the germplasm to further aid in future molecular breeding of melon. Here, we summarized such research reports and categorized them under various sub sections. Overall, this current review presents the overview of very recent advances in melon crop improvement and developments in melon molecular breeding approaches as well as it provides the future directions for melon breeding. It would probably provide recent updates on melon crop improvement and help melon breeders to plan for their future breeding programmes.

Fruit Crop Improvement with Genome Editing, In Vitro and Transgenic Approaches

Fruit species contribute to nutritional and health security by providing micronutrients, antioxidants, and bioactive phytoconstituents, and hence fruit-based products are becoming functional foods presently and for the future. Although conventional breeding methods have yielded improved varieties having fruit quality, aroma, antioxidants, yield, and nutritional traits, the threat of climate change and need for improvement in several other traits such as biotic and abiotic stress tolerance and higher nutritional quality has demanded complementary novel strategies. Biotechnological research in fruit crops has offered immense scope for large-scale multiplication of elite clones, in vitro, mutagenesis, and genetic transformation. Advanced molecular methods, such as genome-wide association studies (GWAS), QTLomics, genomic selection for the development of novel germplasm having functional traits for agronomic and nutritional quality, and enrichment of bioactive constituents through metabolic pathway engineering and development of novel products, are now paving the way for trait-based improvement for developing genetically superior varieties in fruit plant species for enhanced nutritional quality and agronomic performance. In this article, we highlight the applications of in vitro and molecular breeding approaches for use in fruit breeding.