DNA sequencing methods contributing to new directions in cereal research

High-quality Momordica balsamina genome elucidates its potential use in improving stress resilience and therapeutic properties of bitter gourd

Introduction

Momordica balsamina is the closest wild species that can be crossed with an important fruit vegetable crop, Momordica charantia, has immense medicinal value, and placed under II subclass of primary gene pool of bitter gourd. M. balsamina is tolerant to major biotic and abiotic stresses. Genome characterization of Momordica balsamina as a wild relative of bitter gourd will contribute to the knowledge of the gene pool available for improvement in bitter gourd. There is potential to transfer gene/s related to biotic resistance and medicinal importance from M. balsamina to M. charantia to produce high-quality, better yielding and stress tolerant bitter gourd genotypes.

Methods

The present study provides the first and high-quality chromosome-level genome assembly of M. balsamina with size 384.90 Mb and N50 30.96 Mb using sequence data from 10x Genomics, Nanopore, and Hi-C platforms.

Results

A total of 6,32,098 transposons elements; 2,15,379 simple sequence repeats; 5,67,483 transcription factor binding sites; 3,376 noncoding RNA genes; and 41,652 protein-coding genes were identified, and 4,347 disease resistance, 67 heat stress-related, 05 carotenoid-related, 15 salt stress-related, 229 cucurbitacin-related, 19 terpenes-related, 37 antioxidant activity, and 06 sex determination-related genes were characterized.

Conclusion

Genome sequencing of M. balsamina will facilitate interspecific introgression of desirable traits. This information is cataloged in the form of webgenomic resource available at http://webtom.cabgrid.res.in/mbger/. Our finding of comparative genome analysis will be useful to get insights into the patterns and processes associated with genome evolution and to uncover functional regions of cucurbit genomes.

Re-sequencing Resources to Improve Starch and Grain Quality in Rice

Next-generation sequencing can identify differences in the rice genome that explain the genetic basis of grain quality variation. Differences in rice grain quality are mainly associated with differences in the major component of the grain, starch. Association of rice quality variation with rice genome variation can be conducted at the gene or whole-genome level. Re-sequencing of specific genes or whole genomes can be used depending on the extent to which candidate genes for the traits of interest are known. Amplicon sequencing of genes involved in starch metabolism can help in targeted discovery of the molecular genetic basis of differences in starch related quality attributes. Whole-genome re-sequencing can complement this, when the genetic basis of the trait is expected to be outside the coding region of starch metabolism genes. These approaches have been used successfully to understand the rice genome at specific loci and over the whole genome.

Genomics of crop wild relatives: expanding the gene pool for crop improvement

Plant breeders require access to new genetic diversity to satisfy the demands of a growing human population for more food that can be produced in a variable or changing climate and to deliver the high-quality food with nutritional and health benefits demanded by consumers. The close relatives of domesticated plants, crop wild relatives (CWRs), represent a practical gene pool for use by plant breeders. Genomics of CWR generates data that support the use of CWR to expand the genetic diversity of crop plants. Advances in DNA sequencing technology are enabling the efficient sequencing of CWR and their increased use in crop improvement. As the sequencing of genomes of major crop species is completed, attention has shifted to analysis of the wider gene pool of major crops including CWR. A combination of de novo sequencing and resequencing is required to efficiently explore useful genetic variation in CWR. Analysis of the nuclear genome, transcriptome and maternal (chloroplast and mitochondrial) genome of CWR is facilitating their use in crop improvement. Genome analysis results in discovery of useful alleles in CWR and identification of regions of the genome in which diversity has been lost in domestication bottlenecks. Targeting of high priority CWR for sequencing will maximize the contribution of genome sequencing of CWR. Coordination of global efforts to apply genomics has the potential to accelerate access to and conservation of the biodiversity essential to the sustainability of agriculture and food production.

A method for discovery of genome-wide SNP between any two genotypes from whole-genome re-sequencing data

Advances in sequencing technologies have aided the discovery of millions of genome-wide DNA polymorphisms such as single-nucleotide polymorphisms (SNPs) and insertion-deletions (InDels) which are an invaluable resource for marker-assisted breeding. Presently available bioinformatics tools assist the discovery of polymorphisms between target genotypes and the reference genome for a range of species. The discovery of polymorphisms between two genotypes within a breeding program is complicated by several factors such as bias in the number of reads from each genotype and residual heterozygosity within each genotype. In this chapter, we describe a novel approach where polymorphisms between a pair of genotypes are discovered from whole-genome re-sequencing data.

Application of large-scale sequencing to marker discovery in plants

Advances in DNA sequencing provide tools for efficient large-scale discovery of markers for use in plants. Discovery options include large-scale amplicon sequencing, transcriptome sequencing, gene-enriched genome sequencing and whole genome sequencing. Examples of each of these approaches and their potential to generate molecular markers for specific applications have been described. Sequencing the whole genome of parents identifies all the polymorphisms available for analysis in their progeny. Sequencing PCR amplicons of sets of candidate genes from DNA bulks can be used to define the available variation in these genes that might be exploited in a population or germplasm collection. Sequencing of the transcriptomes of genotypes varying for the trait of interest may identify genes with patterns of expression that could explain the phenotypic variation. Sequencing genomic DNA enriched for genes by hybridization with probes for all or some of the known genes simplifies sequencing and analysis of differences in gene sequences between large numbers of genotypes and genes especially when working with complex genomes. Examples of application of the above-mentioned techniques have been described.