Genetic Diversity and Population Structure of Normal Maize Germplasm Collected in South Sudan Revealed by SSR Markers

Mathiang, Emmanuel Andrea; Jin, Kyu; Park, Hyeon; Kim, Yeon Joon; Lee, Ju Kyong

doi:10.3390/plants11202787

Cited by 11 publications

(15 citation statements)

References 46 publications

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“…This result is peculiar to outcrosses, which show a higher degree of variability within populations than among populations [ 53 , 70 ]. The result is consistent with the findings of Nelimor et al [ 71 ], Mathiang et al [ 72 ], Ayesiga et al [ 53 ], and Zawadi et al [ 73 ] who reported 83–97% variability within maize populations. The presence of significantly higher variation within the three subpopulations of the tested inbred lines enables the effective selection of core sets of inbred lines that capture the maximum allelic richness of the respective subpopulations, resulting in the identification of genotypes with desirable traits [ 74 ].…”

Section: Discussionsupporting

confidence: 93%

DArTseq-based SNP markers reveal high genetic diversity among early generation fall armyworm tolerant maize inbred lines

Adu,

Awuku,

Garcia-Oliveira

et al. 2024

PLoS ONE

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Diversity analysis using molecular markers serves as a powerful tool in unravelling the intricacies of inclusivity within various populations and is an initial step in the assessment of populations and the development of inbred lines for host plant resistance in maize. This study was conducted to assess the genetic diversity and population structure of 242 newly developed S3 inbred lines using 3,305 single nucleotide polymorphism (SNP) markers and to also assess the level of homozygosity achieved in each of the inbred lines. A total of 1,184 SNP markers were found highly informative, with a mean polymorphic information content (PIC) of 0.23. Gene diversity was high among the inbred lines, ranging from 0.04 to 0.50, with an average of 0.27. The residual heterozygosity of the 242 S3 inbred lines averaged 8.8%, indicating moderately low heterozygosity levels among the inbred lines. Eighty-four percent of the 58,322 pairwise kinship coefficients among the inbred lines were near zero (0.00–0.05), with only 0.3% of them above 0.50. These results revealed that many of the inbred lines were distantly related, but none were redundant, suggesting each inbred line had a unique genetic makeup with great potential to provide novel alleles for maize improvement. The admixture-based structure analysis, principal coordinate analysis, and neighbour-joining clustering were concordant in dividing the 242 inbred lines into three subgroups based on the pedigree and selection history of the inbred lines. These findings could guide the effective use of the newly developed inbred lines and their evaluation in quantitative genetics and molecular studies to identify candidate lines for breeding locally adapted fall armyworm tolerant varieties in Ghana and other countries in West and Central Africa.

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Section: Discussionsupporting

confidence: 93%

DArTseq-based SNP markers reveal high genetic diversity among early generation fall armyworm tolerant maize inbred lines

Adu,

Awuku,

Garcia-Oliveira

et al. 2024

PLoS ONE

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“…These studies investigated the phenotypic traits of maize accessions from Italy, the north-eastern Himalayas, and Algeria respectively and found that the accessions were not clustered together based on their geographical region. Mixing of germplasm accessions among local farms could be the reason behind the weak relationship among the accessions from the same region, which is the same finding that was reported in our previous report for accession clustering based on microsatellite marker data (Mathiang et al 2022).…”

Section: Discussionsupporting

confidence: 87%

“…Utilization of this method will help in forming an accurate estimation of the level of phenotypic variation in maize accessions collected from South Sudan. In a previous study, we used simple sequence repeat (SSR) or microsatellite markers for genetic diversity studies of maize landrace accessions collected from South Sudan, and provided the first report about the genetic variation of maize landrace accessions of South Sudan (Mathiang et al 2022). Recently, many tools have become available for studying the genetic relationships between landrace germplasm using various molecular markers; however, morphological characterization is the first step in germplasm evaluation and classification (Smith et al 1990).…”

Section: Introductionmentioning

confidence: 99%

Morphological Variation in Normal Maize Landrace Accessions Collected from South Sudan

Mathiang

Jin

Park

et al. 2023

Plant Breed. Biotech.

Self Cite

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Morphological variation was investigated among 31 maize landrace accessions collected from the fields of various farmers in South Sudan by examining 7 quantitative agronomic characteristics. A significant positive correlation was found between days to tasseling (DT) and days to silking (DS), between plant height (PH) and ear height (EH) and stem width (SW), and between EH and SW and leaf length (LL). First and second principal components accounted for 69% of the total variance (40.9% and 28.6%, respectively). PH, EH, SW, LL, and leaf width (LW) were clearly characterized in a positive direction on the first axis. DT and DS were clearly characterized in a positive direction on the second axis. A scatter plot based on phenotypic data revealed the existence of 3 groups based on the most discriminating characteristics: Group I included 5 maize landrace accessions, Group II comprised 14 maize landrace accessions, and Group III included 10 maize landrace accessions. In principal component analysis, generally the investigated genotypes were not clearly grouped into their geographical origins owing to a weak geographic relationship among the accessions. In conclusion, even though the morphological characterization studies were conducted in the South Korean climate, this study revealed significant phenotypic variation among the explored maize landrace accessions collected from South Sudan. Therefore, this information about phenotypic divergence may be very useful for future breeding research programs as well as for genetic improvement of South Sudan maize accessions.

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“…The length of the burn-in period was set at 10,000, and the number of Markov chain Monte Carlo (MCMC) repeats after burn-in was set at 100,000 to estimate individual admixture proportions ( Q ). Evanno’s method [ 49 ] and the online software Structure Harvester [ 50 ] were used to determine the optimal grouping K values [ 51 , 52 , 53 ]. Principal coordinate analysis (PCoA) was performed using GenAlex 6.41 software [ 54 , 55 ].…”

Section: Methodsmentioning

confidence: 99%

Genetic Relationships of 118 Castanea Specific Germplasms and Construction of Their Molecular ID Based on Morphological Characteristics and SSR Markers

Bai

Zhang

et al. 2023

Plants

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To understand the genetic relationships of Castanea species, 16 phenotypic traits were measured, simple sequence repeat (SSR) markers were analyzed, and molecular identity cards (IDs) were constructed for 118 Castanea materials using fluorescent capillary electrophoresis. The coefficient of variation values of the 16 morphological traits of the test materials ranged from 11.11% to 60.38%. A total of 58 alleles were detected using six pairs of SSR core primers, with an average number of 9.7 alleles per locus. The average number of valid alleles per locus was 3.9419 and the proportion of valid alleles was 40.78%. A total of 105 genotypes were detected, and the number of genotypic species that could be amplified per primer pair ranged from 8 to 26. The mean value of the observed heterozygosity was 0.4986. The variation in the He, H, and PIC values was similar; the size of I value was approximately 2.21 times larger, and its mean number of variations was 0.7390, 0.7359, 0.6985, and 1.6015, respectively. The classification of 118 Castanea species was performed using three analytical methods: structure analysis, neighbor-joining (NJ) cluster analysis, and principal coordinate analysis (PCoA), and the results of the three methods were in high agreement. Six pairs of SSR core primers with high polymorphism and strong discriminatory properties were used to identify 118 Castanea plants, and a unique molecular ID card was constructed for each material. These results provide insight into the genetic diversity and population structure of Castanea plants and a theoretical basis for improving the phenomenon of mixed varieties and substandard plants in the Castanea plant market.

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Genetic Diversity and Population Structure of Normal Maize Germplasm Collected in South Sudan Revealed by SSR Markers

Cited by 11 publications

References 46 publications

DArTseq-based SNP markers reveal high genetic diversity among early generation fall armyworm tolerant maize inbred lines

DArTseq-based SNP markers reveal high genetic diversity among early generation fall armyworm tolerant maize inbred lines

Morphological Variation in Normal Maize Landrace Accessions Collected from South Sudan

Genetic Relationships of 118 Castanea Specific Germplasms and Construction of Their Molecular ID Based on Morphological Characteristics and SSR Markers

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