A Review of Omics Technologies and Bioinformatics to Accelerate Improvement of Papaya Traits

Zainal-Abidin, Rabiatul-Adawiah; Ruhaizat-Ooi, Insyirah-Hannah; Harun, Sarahani

doi:10.3390/agronomy11071356

Cited by 10 publications

(7 citation statements)

References 101 publications

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“…Target genes related to papaya's important agronomic traits, including tolerance/ resistance to abiotic and biotic stresses and fruit quality, were explored through omics and bioinformatics [26]. The papaya genome includes NBS genes which are diseaseresistant genes with nucleotide-binding site motifs in the Toll/interleukin-1 receptor (TIR) and non-TIR subclasses [27].…”

Section: Agronomic Characteristicsmentioning

confidence: 99%

Papaya: The Versatile Tropical Fruit

Burns¹,

Saengmanee²,

Doung-ngern³

2023

Tropical Plant Species and Technological Interventions for Improvement

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Papaya (Carica papaya L) is a versatile tropical fruit with its usage ranging from consumption, cosmetics, to pharmaceuticals. In 2020, it was the third most-produced tropical fruit crop in the world. Papaya is a trioecious herbaceous plant with distinct flower and fruit morphological appearances. The fruits from hermaphrodite papaya are favorable for both consumption and processing due to their superior quality. Papaya has a genome size of 372 Mb and chromosome of 2n =18. The male and hermaphrodite papaya have XY and XYh sex chromosomes, respectively, while the female has XX. Using omics and bioinformatics approaches, papaya cultivars with desired fruit quality can be selected and identified from germplasm for incorporation in breeding programs. Papaya production can be done either in open fields or under protected cultivation. Open field cultivation provides for large-scale production, but with the disadvantages of variability in fruit yield, quality, and limitations on growing and harvesting seasons. Under protected cultivation, papaya can be cultivated in all seasons, whilst delivering higher yields. Conversely, multidisciplinary approaches with selected papaya cultivars, good farm management, and suitable conditions provide high yields of quality fruit for both consumption and processing, whilst minimizing the adverse effects related to environmental conditions.

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Section: Agronomic Characteristicsmentioning

confidence: 99%

Papaya: The Versatile Tropical Fruit

Burns¹,

Saengmanee²,

Doung-ngern³

2023

Tropical Plant Species and Technological Interventions for Improvement

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“…High-throughput next-generation sequencing is a revolutionary tool in transcriptomics that can overcome the limitations of array-based approaches because it can capture all sequences [ 143 , 149 ] and its popularity grew surprisingly after 2008 when more advanced Illumina technologies recorded 10 9 transcript sequences with accurate quantitation [ 150 ]. Later, PacBio and Oxford Nanopore Technologies came to dominate plant genome studies due to their high-quality sequences, large sequence reads and lower error rates [ 151 ]. Remarkable stress-inducible transcripts were also identified in rice using RNA-seq.…”

Section: Omics Platforms Used For Rice Improvementmentioning

confidence: 99%

A Review of Integrative Omic Approaches for Understanding Rice Salt Response Mechanisms

Ullah

Abdullah‐Zawawi

Zainal-Abidin

et al. 2022

Plants

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Soil salinity is one of the most serious environmental challenges, posing a growing threat to agriculture across the world. Soil salinity has a significant impact on rice growth, development, and production. Hence, improving rice varieties’ resistance to salt stress is a viable solution for meeting global food demand. Adaptation to salt stress is a multifaceted process that involves interacting physiological traits, biochemical or metabolic pathways, and molecular mechanisms. The integration of multi-omics approaches contributes to a better understanding of molecular mechanisms as well as the improvement of salt-resistant and tolerant rice varieties. Firstly, we present a thorough review of current knowledge about salt stress effects on rice and mechanisms behind rice salt tolerance and salt stress signalling. This review focuses on the use of multi-omics approaches to improve next-generation rice breeding for salinity resistance and tolerance, including genomics, transcriptomics, proteomics, metabolomics and phenomics. Integrating multi-omics data effectively is critical to gaining a more comprehensive and in-depth understanding of the molecular pathways, enzyme activity and interacting networks of genes controlling salinity tolerance in rice. The key data mining strategies within the artificial intelligence to analyse big and complex data sets that will allow more accurate prediction of outcomes and modernise traditional breeding programmes and also expedite precision rice breeding such as genetic engineering and genome editing.

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“…Carica papaya, generally known as papaya, is a significant tropical fruit consumed worldwide [59]. The essential nutrients produced by papaya facilitate the initial papaya development to secure several aspects, including the growth of various parts of the plant, including its foliage, trunks, and roots, leading to higher papaya productivity [60,61]. This tropical plant can be used as an alternative medicine since the leaves, fruits, stems, seeds, and roots could be used for an alternative medical treatment of various disorders, including cancers, ulcers, and gastritis [62].…”

Section: The Identification Of Glucosinolate (Gsl) and Cyanogenic Gly...mentioning

confidence: 99%

Understanding the Complex Functional Interplay between Glucosinolates and Cyanogenic Glycosides in Carica papaya

et al. 2022

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Glucosinolates (GSLs) and cyanogenic glycosides (CGs) fulfil functions in plant defence and have been reported to be anticancer agents. Generally, GSL-containing plants do not produce CG, and vice versa, CG-containing plants do not synthesise GSLs. However, the production of both GSL and CG compounds was observed in Carica papaya. Additionally, several studies found both GSL glucotropaeolin and CG prunasin in papaya leaves. The advancement of genome technologies can be explored to elucidate the gene functions and other molecular discoveries in plants that might relate to GSLs and CGs. This review aims to discuss the complex interplay of the rare events whereby these two compounds (GSL and CG) co-occur in a bifurcation pathway in papaya. To our knowledge, this is the first review that highlights novel GSL and CG genes in papaya. Furthermore, species-specific pathways in papaya are also discussed and comprehensively described. The transcription factors involved in regulating GSL and CG biosynthesis pathways are also discussed, accompanied by relevant bioinformatic approaches that can help discover potential regulatory genes that control the production of prunasin and glucotropaeolin in papaya.

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A Review of Omics Technologies and Bioinformatics to Accelerate Improvement of Papaya Traits

Cited by 10 publications

References 101 publications

Papaya: The Versatile Tropical Fruit

Papaya: The Versatile Tropical Fruit

A Review of Integrative Omic Approaches for Understanding Rice Salt Response Mechanisms

Understanding the Complex Functional Interplay between Glucosinolates and Cyanogenic Glycosides in Carica papaya

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