Abstract
The development and use of genomic resources are essential for understanding the population genetics of crops for their efficient conservation and enhancement. Noug (Guizotia abyssinica) is an economically important oilseed crop in Ethiopia and India. The present study sought to develop new DNA markers for this crop. Transcriptome sequencing was conducted on two genotypes and 628 transcript sequences containing 959 single nucleotide polymorphisms (SNPs) were developed. A competitive allele-specific PCR (KASP) assay was developed for the SNPs and used for genotyping of 24 accessions. A total of 554 loci were successfully genotyped across the accessions, and 202 polymorphic loci were used for population genetics analyses. Polymorphism information content (PIC) of the loci varied from 0.01 to 0.37 with a mean of 0.24, and about 49% of the loci showed significant deviation from the Hardy-Weinberg equilibrium. The mean expected heterozygosity was 0.27 suggesting moderately high genetic variation within accessions. Low but significant differentiation existed among accessions (FST = 0.045, p < 0.0001). Landrace populations from isolated areas may have useful mutations and should be conserved and used in breeding this crop. The genomic resources developed in this study were shown to be useful for population genetics research and can also be used in, e.g., association genetics.
Highlights
Noug (Guizotia abyssinica (L. f.) Cass.) is among the cultivated species of the family Asteraceae.Similar to other Guizotia species, noug is diploid (2n = 30) with relatively small chromosomes [1,2,3].It has a larger genome size (1C = 3.8 pg) than its closely related congeners despite having the same chromosome number [4]
The 202 polymorphic loci used in this study included loci with minor allele frequency (MAF) ranging from below 1% to almost 50%, and the single nucleotide polymorphisms (SNPs) discovery approach is not expected to affect the results of population genetics analyses
More than 50% of these SNPs were successfully converted to Kompetitive Allele-Specific PCR (KASP) markers and used for the genotyping of noug populations collected from wide geographic areas in Ethiopia
Summary
Noug (Guizotia abyssinica (L. f.) Cass.) is among the cultivated species of the family Asteraceae. Similar to other Guizotia species, noug is diploid (2n = 30) with relatively small chromosomes [1,2,3]. It has a larger genome size (1C = 3.8 pg) than its closely related congeners despite having the same chromosome number [4]. The genome size of G. scabra ssp. The smaller chromosomes of G. scabra ssp. Schimperi when compared with that of noug [1,3] explains the larger genome size in the latter. An increase in the noug genome over its evolutionary and domestication period is likely due to genetic mechanisms such as gene duplication [5,6] and retrotransposition [7]
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