RNA-Seq Provides Novel Genomic Resources for Noug (Guizotia abyssinica) and Reveals Microsatellite Frequency and Distribution in Its Transcriptome

Abstract

Genomic resources and tools are essential for improving crops and conserving their genetic resources. Guizotia abyssinica (noug), an outcrossing edible oilseed crop, has highly limited genomic resources. Hence, RNA-Seq based transcriptome sequencing of 30 noug genotypes was performed to generate novel genomic resources and assess their usefulness. The genotypes include self-compatible and self-incompatible types, which differ in maturity time, photoperiod sensitivity, or oil content and quality. RNA-Seq was performed on Illumina HiSeq 2500 platform, and the transcript was reconstructed de novo, resulting in 409,309 unigenes. The unigenes were characterized for simple sequence repeats (SSRs), and served as a reference for single nucleotide polymorphism (SNP) calling. In total, 40,776 SSRs were identified in 35,639 of the 409,309 unigenes. Of these, mono, di, tri, tetra, penta and hexanucleotide repeats accounted for 55.4, 20.8, 21.1, 2.3, 0.2, and 0.2%, respectively. The average G+C content of the unigenes and their SSRs were 40 and 22.1%, respectively. The vast majority of mononucleotide repeat SSRs (97%) were of the A/T type. AG/CT and CCA/TGG were the most frequent di and trinucleotide repeat SSRs. A different number of single nucleotide polymorphism (SNP) loci were discovered in each genotype, of which 1,687 were common to all 30 genotypes and 5,531 to 28 of them. The mean observed heterozygosity of the 5,531 SNPs was 0.22; 19.4% of them had polymorphism information content above 0.30 while 17.2% deviated significantly from Hardy-Weinberg equilibrium (P < 0.05). In both cluster and principal coordinate analyses, the genotypes were grouped into four major clusters. In terms of population structure, the genotypes are best represented by three genetic populations, with significant admixture within each. Genetic similarity between self-compatible genotypes was higher, due to the narrow genetic basis, than that between self-incompatible genotypes. The genotypes that shared desirable characteristics, such as early maturity, and high oil content were found to be genetically diverse, and hence superior cultivars with multiple desirable traits can be developed through crossbreeding. The genomic resources developed in this study are vital for advancing research in noug, such as genetic linkage mapping and genome-wide association studies, which could lead to genomic-led breeding.

Finger millet RNA-seq reveals differential gene expression associated with tolerance to aluminum toxicity and provides novel genomic resources

“…The abundance of CCG/CGG motifs in finger millet is consistent with previous findings in monocots (rice, maize, and wheat) (Morgante et al, 2002). In contrast, CCG/CGG motifs are rare in dicots (Arabidopsis, soybean, and noug) (Morgante et al, 2002;Gebeyehu et al, 2022). Tetra, penta, and hexanucleotide SSRs represent only 1% of all SSRs in the present study, indicating that they are relatively rare in finger millet transcriptomes.…”

“…Tetra, penta, and hexanucleotide SSRs represent only 1% of all SSRs in the present study, indicating that they are relatively rare in finger millet transcriptomes. In a similar study conducted on noug, these SSRs accounted for 2.7% of the total SSRs identified (Gebeyehu et al, 2022). In the case of the number of repeats of each SSR type, their frequency generally decreased as the number of repeats increased, which is consistent with various previous studies.…”

“…The G+C content in finger millet unigenes (46.4%) is higher than the G+C content of the SSRs derived from these unigenes (34.1%). A similar pattern was reported in Populus (Li and Yin, 2007) and noug (Gebeyehu et al, 2022). The G+C content of the mononucleotide repeat SSRs of finger millet (8.8%) revealed in this study was higher than that of noug (3.9%; Gebeyehu et al, 2022).…”

“…Transcriptome sequencing has opened a new way for the development of DNA markers such as simple sequence repeat (SSR) or microsatellites, and single nucleotide polymorphism (SNP). Microsatellites are co-dominant DNA markers of short tandem repeats consisting of 2-6 bp nucleotides that are extensively present across whole genomes, including within genes (Tsehay et al, 2020;Gebeyehu et al, 2022). They are major components of a genome and they play significant roles in the evolution and adaptation of plant species.…”

Development of molecular resources for the genetic improvement of noug (Guizotia abyssinica (L.f) Cass): a mini review

“…Interestingly, two of the compatible lines (C19-1 and K13-1) were utilized for transcriptome sequencing (Tsehay et al 2020). Additionally, self-compatible genotypes were developed through crossbreeding and selfing and were used for RNA-seq based sequencing (Gebeyehu et al 2022). Once self-compatible genotypes are identified, it is simple to generate pure-lines maintaining traits for generations.…”