Short Communication - (2021) Volume 12, Issue 1
Received: 17-Nov-2020
Published:
29-Jan-2021
, DOI: 10.37421/2155-9929.2021.12.449
Citation: Aditya Pratap Singh. “Achievements in Genome Sequencing of Major Oilseeds.” J Mol Biomark Diagn 12 (2021): 449.
Copyright: © 2021 Singh AP. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
With the ever increasing human population around the world, food security and climate change are the major thurst areas of research for both public and private sectors alike. Having said that, the most resilient way to combat both issues is to develop high yielding yet stress tolerant crop varieties. Since traditional methods are time consuming, molecular breeding is the chosen one. Molecular breeding essentializes thorough knowledge of plants’ genome information. This can be achieved with various ways like gene mapping and cloning which are in turn dependent on genome sequence data.
The recent development of genome-sequencing technology has enabled the effective identification of SNPs and other genetic variations in a large genetic population [1] and novel method for SNP detection, mapping, and quantifying transcriptomes in one run, with the potential to overshadow limitations of traditional marker systems. RNA-seq technology has been applied to plant species, opening the entire transcriptional landscape of gene activity in a high-throughput and quantitative manner in diploid species [2]. For example, large-scale resequencing projects in the human genome have effectively identified millions of SNPs, and used these to identify many genes associated with various genetic diseases [3].
Whole-genome sequencing approaches can be employed using various methods for specific purposes. The RAD-seq method for example has been attempted for a number of species and can be efficient for producing large numbers of SNPs, but has not been used routinely yet in many polyploid species, nor may be as cost-efficient for marker-assisted breeding of large populations. High read depth can be achieved using Illumina short read technology, which has the potential to represent a significant part of the transcriptome and even identify transcription factors, which have important roles in stress response. High read depth also provides an opportunity to identify variants with high confidence, which could be potentially used as markers for selection of varieties.
Keeping in view these, an attempt has been made here to concisely review the significant achievements in genome sequencing of major oilseeds (number sequence of crops are not indicative of their importance).
Significance of genome sequencing in oilseed crops
Oilseeds are gaining importance for production of edible oils with health benefits, biofuels and in pharmaceutical industries. Sequencing of genomes helps us to study the genes and intergenic regions, various transposons in the crop and their evolution from wild types to cultivated ones and their contribution towards genetic diversity of the crop [4]. It also contributes towards identification of the genes involved in production of various components that are present in oil and their respective effects. Through sequencing we can also get information on various marker trait associations and also for development of co-dominant markers [5]. Complete sequence is required while developing a species-specific vector for transfer of desirable genes. One such development is done in sesame for gene transformation using chloroplast genome vector [6].
Achievements
Various methods of sequencing were adopted by scientists for sequencing of either whole genome or a part of genome or DNA containing organelles in different crops (Table 1).
| Crop | Strategy Used | Achievements |
|---|---|---|
| Sesame | GS-FLX pyrosequencing method and Genome Sequencer FLX system | Complete chloroplast DNA sequencing results in 155 contigs that gives 257,427 bp |
| Illumina HiSeq 2000 | Sequenced a contig N50 of 52.2 kb and scaffold N50 of 2.1 Mb | |
| Safflower | Illumina high-throughput sequencing | Characterization of miRNA transcriptomes |
| Illumina Solexa sequencing | Studied de novo transcriptomes and identified transcripts that are involved in flavonoids biosynthesis and oleosin production | |
| Illumina sequencing | Identified genes and pathways for secondary metabolites | |
| Illumina HiSeq 2000 | Developed SSR markers and assessed their cross-species transferability | |
| Illumina sequencing | Presented complete chloroplast genome | |
| Groundnut | Illumina sequencing | Analysed the sequences of four cultivars and identified potential SNPs |
| Genotyping-by-sequencing (NGS) | Analysed 38 accessions for whole genome re-sequencing and 3 for transcriptome sequencing for identification of SNPs | |
| Genotyping-by-sequencing | Generate SNP data and develop genetic map | |
| Rapeseed-Mustard | Illumina sequencing | Complete chloroplast genome was sequenced and SSRs were identified |
| 454 pyro-sequencing | Complete mitochondrial genome was sequenced of CMS hybrid | |
| Illumina sequencing | Conducted re-sequencing of whole genome and studied the genetic variation of the diversity in ecotypes | |
| Castor | Flow cytometry | Draft sequence of the castor bean genome by producing ~2.1 million high-quality sequences reads from plasmid and fosmid libraries. |
| Illumina sequencing by synthesis technology | Tissue-Specific Whole Transcriptome Sequencing in Castor for understanding Triacylglycerol Lipid Biosynthetic Pathways | |
| Sunflower | llumina or 454 | Final assembly of the sequences belonging to the six databases produced a whole genome set of 283,800 contigs. |
| Genome Analyzer II next generation sequencing platform (Illumina Inc. San Diego, CA). | A total of 271,445,770 sequence reads were generated. From these reads, 1,208,784 tags were generated. While 29.2% (353,304) of the sequence tags were uniquely aligned to the sunflower genome, 14.2% (172,196) of the tags were aligned to multiple positions. |
Sesame: Illumina Sequencing was adapted to sequence a contig N50 of 52.2 kb and a scaffold N50 of 2.1 Mb [2]. GS-FLX pyrosequencing was used to sequence the entire chloroplast DNA which shows that it contains 155 contigs comprising of 257,427 base pairs.
Safflower: High-throughput Illumina sequencing was adopted for characterization of miRNA transcriptomes as they play an important role in plant development and adaptation to various stresses [7]. Illumina Solexa sequencing technology was utilized for identification of transcripts involved in the biosynthesis of flavonoids such as carthamone, safflor yellow A, hydroxysafflor yellow A etc. and also studied genes responsible for oleosin production [8]. The component oleosin is found to prevent degradation of oil body present in seed during seed desiccation [9]. Using Illumina sequencing method, genes and pathways for secondary metabolites were identified in safflower tubular flower tissue transcriptome. Illumina sequencing was used to study the genome sequence for developing microsatellite markers and study their cross-species transferability [5]. This resulted in designing of 5716 novel microsatellite primers, of which 325 were validated and out of 325, 93 were found to be polymorphic in nature. A complete choloplast genome was presented using Illumina sequencing which shows that is contains 127 genes of which, 89 are protein encoding genes, 30 tRNA and 8 rRNA genes [10].
Groundnut: Illumina sequencing has been deployed to sequence the transcriptome of four market class cultivars namely OLin, New Mexico Valencia C, Tamrun OL07 and Jupiter and identified potential SNPs [11]. Genotypingby- sequencing method of NGS was used for whole genome re-sequencing of 38 accessions and transcriptome sequencing of 3 accessions and developed a high-density SNP array that consists of 58,233 unique and informative SNPs. Again, genotyping-by-sequencing method was used to sequence RIL population and generated a genetic map consisting of 585 SNPs [12].
Sunflower: In Helinthus annus species different approaches of de novo assembling sequence reads were obtained by NGS procedures (Illumina and 454) to gain a comprehensive characterization of the repetitive component by Natali et al. [13].
Celik et al. used Genome Analyzer II next generation sequencing platform (Illumina Inc. San Diego, CA) and observed a total of 271,445,770 sequence reads were generated. From these reads 1,208,784 tags were generated. While 29.2 % (353,304) of the sequence tags were uniquely aligned to the sunflower genome, 14.2 % (172,196) of the tags were aligned to multiple positions [14].
Castor: The castor bean genome, which is distributed across ten chromosomes, is estimated by flow cytometry to be ~320 Mb, a draft sequence of the castor bean genome by producing ~2.1 million high-quality sequence reads from plasmid and fosmid libraries [15]. High-throughput Illumina sequencing was adopted for tissue-specific whole transcriptome sequencing in Castor for understanding triacylglycerol lipid biosynthetic pathways [16].
Rapeseed-Mustard: Illumina sequencing method was used for the complete chloroplast D NA (cpDNA) sequencing of Brassica napus and found that it consists of 152,860 base pairs of nucleotides that contained a pair of 26,035 bp inverted repeat sequences. The gene coding region occupied the major portion of the cpDNA i.e., 56.4% and the average AT content was found to be 63.7% in Brassica napus. Also, a total of 86 SSRs were also identified [17]. Complete sequencing of heterogenous composition mitochondrial genome of Ogura-cms cybrid (oguC) rapeseed was carried out with the help of 454 pyro-sequencing methods. It was found to be composed of 258,473 bp which contain 33 protein coding genes, 23 tRNA genes and 3 rRNA genes. The genome of all the 5 species of genus Brassica i.e., B. napus, B. rapa, B. oleracea, B. carinata and B. juncea was compared and found six identical regions and concluded that they have a stable chloroplast genome source [18]. By using illumine sequencing, polymorphism in the rapeseed genome in its ecotypes was studied by re-sequencing of the worldwide accessions and provides insights into the evolution of rapeseed and flowering time diversity in the three ecotypes of rapeseed [19-21].
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