The breeding of tropical fruit trees for improving fruit traits is complicated, due to the long juvenile phase, generation cycle, parthenocarpy, polyploidy, polyembryony, heterozygosity and biotic and abiotic factors, as well as a lack of good genomic resources. Many molecular techniques have recently evolved to assist and hasten conventional breeding efforts. Molecular markers linked to fruit development and fruit quality traits such as fruit shape, size, texture, aroma, peel and pulp colour were identified in tropical fruit crops, facilitating Marker-assisted breeding (MAB). An increase in the availability of genome sequences of tropical fruits further aided in the discovery of SNP variants/Indels, QTLs and genes that can ascertain the genetic determinants of fruit characters. Through multi-omics approaches such as genomics, transcriptomics, metabolomics and proteomics, the identification and quantification of transcripts, including non-coding RNAs, involved in sugar metabolism, fruit development and ripening, shelf life, and the biotic and abiotic stress that impacts fruit quality were made possible. Utilizing genomic assisted breeding methods such as genome wide association (GWAS), genomic selection (GS) and genetic modifications using CRISPR/Cas9 and transgenics has paved the way to studying gene function and developing cultivars with desirable fruit traits by overcoming long breeding cycles. Such comprehensive multi-omics approaches related to fruit characters in tropical fruits and their applications in breeding strategies and crop improvement are reviewed, discussed and presented here.
With the globalization of seed trade and transgenic variety development, the application of molecular technologies for seed quality gained more significance in both the internal and international markets. Besides germination, genetic purity and seed health are the two most important seed quality parameters that determine the planting value of a seed lot. Compared to the conventional methods of testing, molecular marker technologies are more efficient for quality analysis as these are more accurate, robust, abundant, and faster. Among the various markers, simple sequence repeats (SSRs), due to their genome-wide presence, reproducibility, multi-allelic nature, and co-dominant inheritance, have emerged as the best markers, for establishing varietal distinctness, identity, and variety/hybrid seed purity testing. With the advent of the next-generation sequencing (NGS) technology, single nucleotide polymorphic (SNP) markers also became widely popular, and the closest to being an ideal marker besides SSRs, in seed genetic purity testing. With large-scale GM crop cultivation, testing for the adventitious presence and trait purity are two added components of seed quality testing. The methods of GM seed quality testing include DNA-based (conventional and real-time PCR), protein-based (lateral flow test and ELISA), and bioassay-based technologies. DNA-based methods including PCR/real-time PCR assays have been successfully employed to detect the adventitious presence of transgenic seeds in seed trade especially at international level, as well as in the national gene banks for germplasm conservation. ISTA plays a prominent role in international harmonization and providing universal guidelines on use of different methods to detect GM seeds. The BMT group of UPOV and the Working Group on DNA Methods of the Variety Committee of ISTA, work in tandem to standardize suitable molecular techniques for establishing variety identity and purity testing, respectively. In the area of seed health testing also, molecular detection assays such as, PCR (nested PCR, multiplex PCR, real-time PCR), loop-mediated isothermal amplification (LAMP), and DNA microarray with many advantages over the conventional assays have been proven highly useful. However, there is a need to validate the usefulness of molecular markers through stringent multi-laboratory tests for their reproducibility before recommending them in routine seed purity and health testing.
Tomato leaf curl Bangalore virus (ToLCBaV), often a woeful reason for complete failure of tomato crop in southern India. The plant response to virus infection is a complicated network involving several defence routes. Every defence route involves transcription factors (TFs) and other regulatory transcripts including lncRNA as important regulators of gene expression. These regulators act as both pro-viral and anti-viral factors involved in modulating disease symptoms. This study has reported and validated several TFs and lncRNAs from transcriptome study of tomato lines, IIHR2611 (R) and IIHR 2843 (S) in response to virus infection. Validation was done based on expression analysis of selected TFs and lncRNAs using qPCR at different intervals of ToLCBaV infection. TFs, DREB protein 1A and Protein RADIALIS-like 3 were induced upon ToLCBaV infection. Whereas, WRKY TF-53 was upregulated in S and down regulated in R plants upon virus infection. Four lncRNAs were found differentially expressed among R and S lines when analysed using qPCR. The differential temporal gene expression of TFs among S and R plants in response to ToLCBaV infection regulate the resistance or susceptibility. Further studies on the mechanism of resistance of TFs and lncRNAs will aid in unravelling novel antiviral defence pathways in tomato.
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