Genetic diversity and population structure of some Nigerian accessions of Bambara groundnut (Vigna subterranea (L.) Verdc.,) using DArT SNP markers

Osundare, Opeyemi T.; Akinyele, B. O.; Odiyi, A. C.; Paliwal, Rajneesh; Oyatomi, Olaniyi; Abberton, Michael T.

doi:10.1007/s10722-022-01472-w

Cited by 5 publications

(5 citation statements)

References 30 publications

(26 reference statements)

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“…These suggest that the two crops have a syntenic relationship, which might be due to their close evolutionary relationship. Similar results have been reported for another African indigenous legume (Bambara groundnut) having syntenic relationships with other legumes (common bean, adzuki bean, and mung bean) [ 96 , 97 ]. The five significant markers found in Phaseolus vulgaris genome at a location close to genes whose encoding proteins had been reported in other crops to regulate the same traits as those with which they are associated in AYB can also be considered candidate makers.…”

Section: Discussionsupporting

confidence: 86%

Genome-Wide Association Study Revealed SNP Alleles Associated with Seed Size Traits in African Yam Bean (Sphenostylis stenocarpa (Hochst ex. A. Rich.) Harms)

Olomitutu

Paliwal

Abe

et al. 2022

Genes

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Seed size is an important yield and quality-determining trait in higher plants and is also crucial to their evolutionary fitness. In African yam bean (AYB), seed size varies widely among different accessions. However, the genetic basis of such variation has not been adequately documented. A genome-wide marker-trait association study was conducted to identify genomic regions associated with four seed size traits (seed length, seed width, seed thickness, and 100-seed weight) in a panel of 195 AYB accessions. A total of 5416 SNP markers were generated from the diversity array technology sequence (DArTseq) genotype-by-sequencing (GBS)- approach, in which 2491 SNPs were retained after SNP quality control and used for marker-trait association analysis. Significant phenotypic variation was observed for the traits. Broad-sense heritability ranged from 50.0% (seed width) to 66.4% (seed length). The relationships among the traits were positive and significant. Genome-wide association study (GWAS) using the general linear model (GLM) and the mixed linear model (MLM) approaches identified 12 SNP markers significantly associated with seed size traits across the six test environments. The 12 makers explained 6.5–10.8% of the phenotypic variation. Two markers (29420334|F|0-52:C>G-52:C>G and 29420736|F|0-57:G>T-57:G>T) with pleiotropic effects associated with seed width and seed thickness were found. A candidate gene search identified five significant markers (100026424|F|0-37:C>T-37:C>T, 100041049|F|0-42:G>C-42:G>C, 100034480|F|0-31:C>A-31:C>A, 29420365|F|0-55:C>G-55:C>G, and 29420736|F|0-57:G>T-57:G>T) located close to 43 putative genes whose encoding protein products are known to regulate seed size traits. This study revealed significant makers not previously reported for seed size in AYB and could provide useful information for genomic-assisted breeding in AYB.

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Section: Discussionsupporting

confidence: 86%

Genome-Wide Association Study Revealed SNP Alleles Associated with Seed Size Traits in African Yam Bean (Sphenostylis stenocarpa (Hochst ex. A. Rich.) Harms)

Olomitutu

Paliwal

Abe

et al. 2022

Genes

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“…This suggests that different analysis methods can yield distinct results. This phenomenon has been observed in other species as well (Wienk et al, 2022;Osundare et al, 2023), possibly attributed to either lower levels of population differentiation or the presence of complex genetic structures. In addition, the Mantel analysis results indicated a moderate correlation between the molecular matrix and the geographic matrix, with a Mantel test value of only 0.09 in this study.…”

Section: Genetic Relationship Analysis Of Three Populationmentioning

confidence: 51%

Population structure and genetic diversity in Eucalyptus pellita based on SNP markers

Wang,

Lan,

Wang

et al. 2023

Front. Plant Sci.

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Eucalyptus pellita has the characteristics of rapid growth and high resistance. However, there is little research on molecular breeding of E. pellita, which is essential to shortening breeding life and selecting quality varieties. Therefore, a crucial step before selective breeding can be carried out to increase the wood quality of E. pellita is identifying genetic diversity and population structure using single nucleotide polymorphism (SNP) markers. In this study, the genetic diversity of 1st generation 196 E. pellita families from 23 geographically defined was assessed using 1,677,732 SNP markers identified by whole genome resequencing. SNP annotation showed that the ratio of non-synonymous to synonymous coding mutations was 0.83. Principal component analysis (PCA), phylogenetic tree, and population structure analysis permitted the families to be categorized into three groups, one of which (G2) contains most of the Indonesian (IDN) and Papua New Guinea (PNG) families. Genetic relationship analysis showed that IDN was closely related to PNG. Genetic diversity analysis showed that He, PIC, I, and H mean values were 0.2502, 0.2027, 0.3815, and 0.2680, respectively. PCA analysis classified various provenances in QLD into two categories (G1 and G3). The genetic diversity of G3 was higher than that of G2. The results of genetic differentiation (Fst) showed that PNG region was divided into two groups (PNG1 and PNG2), the Fst (0.172) between QLD and PNG2 region was higher than QLD and PNG1, and the Fst (0.024) between IDN and PNG1 is smaller than IDN and PNG2. A Mantel test revealed a positive correlation between the genetic and geographic distance of E. pellita. This study has a certain reference value for genetic identification, germplasm preservation, and breeding of E. pellita. Also, it provides a basis for subsequent association analysis to explore excellent alleles and introduction.

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“…Cluster 3 landrace characterized by desirable traits like higher number of pods, higher pod dry weight, higher seed weight, higher yield and lowest shelling percentage should be evaluated at different environments for years in other to select landraces adapted for yield improvement. Osundare et al (2022) noted that accessions which clustered in the same group have genetic relationship in the population. In addition, genotypes within this group that are from different genetic origins with high intra‐cluster distance showing potentials on yield component traits could be crossed to produce hybrids.…”

Section: Discussionmentioning

confidence: 99%

Exploring phenotypic variation of diverse bambara groundnut (Vigna subterranea L) origin and development of mini‐core collection for future breeding

Uba

Oselebe

Tesfaye

et al. 2023

Food and Energy Security

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Understanding the phenotypic variation and designing a mini-core collection is an efficient method to accelerate the genetic gain of bambara groundnut. A collection of 300 bambara groundnut landraces from 25 different countries of origin sourced from gene banks were used to analyze phenotypic variability among the landraces and develop a mini-core collection for future breeding. The landraces were evaluated in alpha lattice design with two replications for 2 years (2019 and 2020). The results showed highly significant differences (p < 0.001) among the bambara groundnut landraces for all the studied traits implying the selection of landraces with better agronomic traits could be achieved from the crop genetic pool. In addition, landrace x year interactions were significant for studied traits, except for shelling percentage and number of seeds per pod. The genotypic coefficient of variation values were high for most yield component traits, with the highest (65.39%) value obtained on seed dry weight. Furthermore, high heritability in conjunction with high genetic advance obtained in seed dry weight, pod dry weight, petiole length and plant height implies that these traits are majorly controlled by additive genetic action and could be improved through selection. Highly significant and positive correlations of yield were found with seed dry weight, pod dry weight, number of pod per plant, number of leaves, petiole length and plant height. A mini-core collection of 60 landraces (20%) was developed that represents the entire collection using Core Hunter algorithm. In general, the study provides insight into bambara groundnut germplasm that would enhance cultivar development and sustains the utilization of the crop. In addition, the mini-core collection established in the present study could be exploited for future bambara groundnut improvement efforts.

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Genetic diversity and population structure of some Nigerian accessions of Bambara groundnut (Vigna subterranea (L.) Verdc.,) using DArT SNP markers

Cited by 5 publications

References 30 publications

Genome-Wide Association Study Revealed SNP Alleles Associated with Seed Size Traits in African Yam Bean (Sphenostylis stenocarpa (Hochst ex. A. Rich.) Harms)

Genome-Wide Association Study Revealed SNP Alleles Associated with Seed Size Traits in African Yam Bean (Sphenostylis stenocarpa (Hochst ex. A. Rich.) Harms)

Population structure and genetic diversity in Eucalyptus pellita based on SNP markers

Exploring phenotypic variation of diverse bambara groundnut (Vigna subterranea L) origin and development of mini‐core collection for future breeding

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