New Transcriptome-Based SNP Markers for Noug (Guizotia abyssinica) and Their Conversion to KASP Markers for Population Genetics Analyses

Tsehay, Sewalem; Ortíz, Rodomiro; Johansson, Eva; Bekele, Endashaw; Tesfaye, Kassahun; Hammenhag, Cecilia; Geleta, Mulatu

doi:10.3390/genes11111373

Cited by 18 publications

(28 citation statements)

References 87 publications

(121 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Whereas the ecotypes from central Europe recorded a slightly higher F IS , suggesting the Scandinavian red clover may be more similar to that of United Kingdom than to those of central Europe. In a recent bi-allelic SNP marker-based study by Tsehay et al (2020) in Guizotia abyssinica (a strictly outcrossing diploid species; Geleta and Bryngelsson, 2010), a mean F IS value of 0.13 was reported, which is higher than the values obtained in red clover. This could suggest that red clover is as strictly outcrossing as G. abyssinica if not stricter.…”

Section: F-statistics Heterozygosity and Within Population Diversitymentioning

confidence: 78%

Insights Into the Genetic Diversity of Nordic Red Clover (Trifolium pratense) Revealed by SeqSNP-Based Genic Markers

et al. 2021

Self Cite

View full text Add to dashboard Cite

Red clover (Trifolium pratense) is one of the most important fodder crops worldwide. The knowledge of genetic diversity among red clover populations, however, is under development. This study provides insights into its genetic diversity, using single nucleotide polymorphism (SNP) markers to define population structure in wild and cultivated red clover. Twenty-nine accessions representing the genetic resources available at NordGen (the Nordic gene bank) and Lantmännen (a Swedish agricultural company with a red clover breeding program) were used for this study. Genotyping was performed via SeqSNP, a targeted genotype by sequencing method that offers the capability to target specific SNP loci and enables de novo discovery of new SNPs. The SNPs were identified through a SNP mining approach based on coding sequences of red clover genes known for their involvement in development and stress responses. After filtering the genotypic data using various criteria, 623 bi-allelic SNPs, including 327 originally targeted and 296 de novo discovered SNPs were used for population genetics analyses. Seventy-one of the SNP loci were under selection considering both Hardy-Weinberg equilibrium and pairwise FST distributions. The average observed heterozygosity (HO), within population diversity (HS) and overall diversity (HT) were 0.22, 0.21 and 0.22, respectively. The tetraploids had higher average HO (0.35) than diploids (0.21). The analysis of molecular variance (AMOVA) showed low but significant variation among accessions (5.4%; P < 0.001), and among diploids and tetraploids (1.08%; P = 0.02). This study revealed a low mean inbreeding coefficient (FIS = −0.04) exhibiting the strict outcrossing nature of red clover. As per cluster, principal coordinate and discriminant analyses, most wild populations were grouped together and were clearly differentiated from the cultivated types. The cultivated types of red clover had a similar level of genetic diversity, suggesting that modern red clover breeding programs did not negatively affect genetic diversity or population structure. Hence, the breeding material used by Lantmännen represents the major genetic resources in Scandinavia. This knowledge of how different types of red clover accessions relate to each other and the level of outcrossing and heterozygosity will be useful for future red clover breeding.

show abstract

Section: F-statistics Heterozygosity and Within Population Diversitymentioning

confidence: 78%

Insights Into the Genetic Diversity of Nordic Red Clover (Trifolium pratense) Revealed by SeqSNP-Based Genic Markers

et al. 2021

Self Cite

View full text Add to dashboard Cite

show abstract

“…], sesame (Sesamum indicum L.) and linseed (Linum usitatissimum L.) (1). Various molecular marker based population genetics studies revealed high genetic diversity in these crops [e.g., (2)(3)(4)(5)(6)(7)(8)]. These crops are primarily used as sources of edible oil for local consumption.…”

Section: Introductionmentioning

confidence: 99%

Fatty Acid Profile, Total Phenolic Content, and Antioxidant Activity of Niger Seed (Guizotia abyssinica) and Linseed (Linum usitatissimum)

et al. 2021

Self Cite

View full text Add to dashboard Cite

Fatty acid composition and antioxidant content are major determinants of vegetable oil quality. Antioxidants are important food components, and there is an increasing interest of replacing synthetic antioxidants with those from natural sources for food industry. The objective of this study was to evaluate fatty acid composition, total phenolic, carotenoid and chlorophyll contents, and antioxidant capacity of different varieties of two oilseed crops. Five niger seed and eight linseed varieties were used. For the analysis of fatty acid composition of the seed oil, gas chromatography method was used. Standard methods were used for total phenolic, carotenoid and chlorophyll contents, and antioxidant properties. In niger seed oil, linoleic acid (C18:2) was the dominant fatty acid, accounting for 73.3% (variety Esete) to 76.8% (variety Ginchi) of the total fatty acids. In linseed oil, linolenic acid (C18:3) was the dominant fatty acid accounting for 55.7 (variety Chilalo) to 60.1 (variety Belaye-96). The total phenolic content ranged from 22.4 mg GAE/g (variety Esete) to 27.9 mg GAE/g (variety Ginchi) in niger seed and from 20.5 mg GAE/g (variety Belay-96) to 25.4 mg GAE/g (variety Ci-1525) in linseed. In niger seed, variety Fogera had the highest values for FRAP and radical scavenging activity. The carotenoid content also showed significant variation among the varieties ranging from 2.57 (Esete) to 8.08 (Kuyu) μmol/g for niger and 4.13 (Tole) to 8.66 (Belay-96) μmol/g for linseed. The FRAP assay showed that variety Fogera of niger seed and variety Chilalo of linseed came on top among their respective varieties with values of 57.2 and 30.6, respectively. Both niger seed and linseed were shown to be rich in bioactive compounds. However, significant variation was observed among the varieties of each crop and among the two crops in their total phenolic and carotenoid contents as well as ferric reducing potential and radical scavenging capacity. Principal component analysis revealed the presence of more than one group in both niger seed and linseed. Hence, genetic variation among the varieties should be utilized for improving their desirable characteristics through breeding. Both oil crops can be used as the source of antioxidants for replacing synthetic compounds.

show abstract

“…Such difference in clustering pattern of different Guizotia species and populations was also observed in molecular markers based studies (Random amplified polymorphic DNA vs Amplified Fragment Length Polymorphism) [15,35]. A recent study using transcriptome based SNP markers revealed a weak population structure in noug grown in Ethiopia due to population admixture, which is mainly a result of strong gene flow between populations via pollen and a gradual nation-wide germplasm exchange [36]. The poor clustering pattern of the accessions in terms of geographic proximity in the present study also suggest strong gene flow between populations throughout the country.…”

Section: Discussionmentioning

confidence: 63%

Characterization of Oilseed Crop Noug (Guizotia abyssinica) Using Agro-Morphological Traits

et al. 2021

Self Cite

View full text Add to dashboard Cite

Noug (Guizotia abyssinica) is an outcrossing oilseed crop that serves as a source of edible oil and other nutrients although its seed yield is generally low. The analysis of agro-morphological traits in relation to seed and oil yields is important for improving the productivity of this crop. The present study aimed at assessing the variation and heritability of quantitative (10) and qualitative (6) traits in noug based on 60 landrace accessions collected from wide geographic area in Ethiopia. The field trial was conducted at two sites in Ethiopia using a square lattice design. The analysis of variance revealed significant variation (p < 0.05) among these accessions. The highest broad-sense heritability (H2) was recorded for days to 10% flowering (DTF10; 85.4%), whereas number of capitula per plant (NCPP) and number of seeds per capitulum (NSPC) showed medium heritability (H2 = 38.5% and 31.6%, respectively). NCPP and NSPC showed a highly significant (p < 0.01) positive and negative genotypic correlation with days to flowering, respectively. These three traits showed very low genotypic coefficient of variation (<1%). In the case of qualitative traits, small capitulum, large flower, green leaf, green stem and course leaf margin showed significant association with higher number of seeds per plant (NSPP). Euclidean distance-based cluster analysis revealed that the clustering pattern of the accessions poorly correlates with the geographic distance between sample collecting sites. Similarly, no clear clustering pattern of accessions was revealed by principal component analysis (PCA) that explained 66.3% and 53.6% of the total variation of quantitative traits and qualitative traits, respectively. The oil content of these accessions was previously investigated and accessions with high oil content show large differences in terms of days to flowering, NSPP and thousand seed weight (TSW). Among the accessions included in this research, Hr_B21; Gj_C17, Sh_I4 and Gr_F15 Gj_G18 and Tg-R13 are top ranking, as they have at least one the following highly desirable traits: early maturity, high oil content, NSPP and TSW. Hence, crossbreeding of their selected genotypes would lead to the development of new cultivars that combine early maturity and both high seed and oil yields.

show abstract

New Transcriptome-Based SNP Markers for Noug (Guizotia abyssinica) and Their Conversion to KASP Markers for Population Genetics Analyses

Cited by 18 publications

References 87 publications

Insights Into the Genetic Diversity of Nordic Red Clover (Trifolium pratense) Revealed by SeqSNP-Based Genic Markers

Insights Into the Genetic Diversity of Nordic Red Clover (Trifolium pratense) Revealed by SeqSNP-Based Genic Markers

Fatty Acid Profile, Total Phenolic Content, and Antioxidant Activity of Niger Seed (Guizotia abyssinica) and Linseed (Linum usitatissimum)

Characterization of Oilseed Crop Noug (Guizotia abyssinica) Using Agro-Morphological Traits

Contact Info

Product

Resources

About