Genetic diversity among tropical maize inbred lines as revealed by SSR markers

Genetic diversity and phenotypic superiority are important attributes of parental inbred lines for use in hybrid breeding programs. In this study, genetic diversity among 30 maize (Zea mays L.) inbred lines comprising of 28 introductions from the International Maize and Wheat Improvement Center (CIMMYT), one from Indonesia and a locally developed, were evaluated using 100 simple sequence repeat (SSR) markers, as early screening for potential parents of hybrid varieties. All markers were polymorphic, with a total of 550 unique alleles detected on the 100 loci from the 30 inbred lines. Allelic richness ranged from 2 to 13 per locus, with an average of 5.50 alleles (na). Number of effective alleles (ne) was 3.75 per locus, indicating their high effectiveness in revealing diversity among inbred lines. Average polymorphic information content (PIC) was 0.624, with values ranging from 0.178 to 0.874, indicating high informativeness of the markers. High gene diversity was observed on Chromosomes 8 and 4, with high number of effective alleles, indicating their potential usefulness for QTL analysis. The UPGMA dendrogram constructed identified four heterotic groups within a similarity index of 0.350, indicating that these markers were able to group the inbred lines. The three-dimensional PCoA plot also supports the dendrogram grouping, indicating that these two methods complement each other. Inbred lines in different heterotic groups have originated from different backgrounds and population sources. Information on genetic diversity among the maize inbred lines are useful in developing strategies exploiting heterosis in breeding programs

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Microsatellite marker-based genetic diversity of tropical-adapted shrunken-2 maize inbred lines and its relationship with normal endosperm inbred lines of known heterotic classification

Plant Genetic Resources ◽

10.1017/s1479262120000489 ◽

2021 ◽

pp. 1-8

Author(s):

J. E. Iboyi ◽

A. Abe ◽

V. O. Adetimirin

Keyword(s):

Genetic Diversity ◽

Gene Diversity ◽

Polymorphic Information Content ◽

Inbred Lines ◽

Heterotic Group ◽

Germplasm Management ◽

Maize Breeding ◽

Heterotic Groups ◽

Maize Population ◽

Maize Inbred Lines

Abstract Knowledge of the genetic diversity and relationships among maize inbred lines can facilitate germplasm management and plant breeding programmes. The study investigated the level of genetic diversity among S6 lines developed from a tropical-adapted shrunken-2 (sh-2) maize population and their relationship with normal endosperm tropical inbred lines of known heterotic groups. Ninety-one sh-2 maize inbred lines (UI1-UI91) developed in the University of Ibadan super-sweet Maize Breeding Programme were genotyped at 30 simple sequence repeat (SSR) loci, alongside five normal endosperm maize inbred lines viz. TZi3, TZi4, TZi10, TZi12 and TZi15, four of which belong to two heterotic groups. Twenty-three SSR markers were polymorphic and detected a total of 61 alleles, with a range of 2–7 and an average of 2.65 alleles per locus. The polymorphic information content ranged from 0.12 in bnlg1937 to 0.77 in phi126, with an average of 0.36. The gene diversity (He) averaged 0.43. Cluster analysis resulted in five groups consisting of 16, 36, 17, 23 and 3 inbred lines, with one sh-2 line ungrouped. TZi 12 and TZi 15, both of which are of the same heterotic group, clustered with TZi 3 of another heterotic group. Considerable genetic diversity exists among the 96 inbred lines. Only two of the five normal endosperm lines shared clusters with the sh-2 lines. The clustering of the normal endosperm inbred lines is not related to their established heterotic patterns. Inbred lines in two clusters offer the possibility of guiding the exploitation of heterosis among the sh-2 lines.

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MOLECULAR CHARACTERIZATION AND DIVERSITY ANALYSIS OF SELECTED MAIZE INBRED LINES USING SINGLE NUCLEOTIDE POLYMORPHISM MARKERS

Canadian Journal of Plant Science ◽

10.1139/cjps-2020-0051 ◽

2020 ◽

Author(s):

Mwaikonyole Zawadi ◽

Julia Sibiya ◽

Kingstone Mashingaidze ◽

Assefa B Amelework ◽

Aleck Kondwakwenda ◽

...

Keyword(s):

Genetic Diversity ◽

Single Nucleotide Polymorphism ◽

Agricultural Research ◽

Gene Diversity ◽

Polymorphic Information Content ◽

Inbred Lines ◽

Nucleotide Polymorphism ◽

Heterotic Groups ◽

Single Nucleotide ◽

Maize Inbred Lines

The level of genetic diversity among the available breeding materials determines the potential success of a breeding program. In this study, 92 maize inbred lines were genotyped with 3047 single nucleotide polymorphism (SNP) markers using a Kompetitive Allele-Specific Polymerase chain reaction (KASPTM) genotyping protocol. The objectives were to determine the level and pattern of genetic diversity and define potential heterotic groups of maize inbred lines developed by the Agricultural Research Council maize program of South Africa. More than 91% of the SNPs used were polymorphic with mean polymorphic information content (PIC) of 0.36. Gene diversity ranged from 0.35 to 0.37, with a mean of 0.36. Cluster analysis revealed the presence of three distinct subpopulations. Analysis of molecular variance revealed low but highly significant (p<0.0001) variations among populations, high within and among individual variations. Variation among individuals contributed 83% of the total variation, whereas variation within individuals and among populations contributed 14% and 3%, respectively. Low mean population differentiation observed in this study suggested that the inbred lines might be developed from parental genotypes with similar genetic backgrounds. The mean percentage of genetic purity among the inbred lines was 4.8, with more than 79% of the inbred lines exhibiting less than 5% heterozygosity, indicating the inbred lines are fixed. Genotypes in different clusters may be earmarked as belonging to distinct heterotic groups, and their crosses may result in better heterosis. Thus, the findings of this study set the basis for earmarking heterotic groups and parental selection.

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Changes of genetic diversity of maize inbred lines over four decades of hybrid breeding in the Bc institute revealed by SSR markers

Genetika ◽

10.2298/gensr1501233b ◽

2015 ◽

Vol 47 (1) ◽

pp. 233-243

Author(s):

Ivica Buhinicek ◽

Mirko Jukic ◽

Hrvoje Sarcevic ◽

Jerko Gunjaca ◽

Zdravko Kozic ◽

...

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Inbred Lines ◽

Hybrid Breeding ◽

Maize Breeding ◽

Hybrid Production ◽

The Past ◽

Maize Inbred Lines ◽

Heterotic Pattern ◽

Private Alleles

In this paper, changes of genetic diversity of the most important maize inbred lines used for hybrid production within the Bc Institute in the 1970s, 1980s, 1990s and 2000s were examined using the SSR markers. The average number of alleles per SSR locus was 3.14, 3.43, 3.07 and 3.25 for lines from 1970s, 1980s, 1990s and 2000s, whereas the number of private alleles for the same four decades was 8, 4, 0 and 6, respectively. Mean genetic distance among inbreds within decades steadily decreased over time from 0.64 in 1970s to 0.57 in 2000s, but the observed differences were not statistically significant. The clustering of the studied inbred lines indicates the exploitation of a known BSSS x LSC heterotic pattern within the Bc Institute maize breeding program. The overall results show that recycled inbred lines within these pools do not decline in genetic variation over the past 40 years.

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Genetic diversity of maize inbred lines as inferred from SSR markers

Genetika ◽

10.2298/gensr1502489n ◽

2015 ◽

Vol 47 (2) ◽

pp. 489-498

Author(s):

Ana Nikolic ◽

Dragana Ignjatovic-Micic ◽

Dragan Kovacevic ◽

Zoran Camdzija ◽

Milomir Filipovic ◽

...

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Principal Component ◽

Inbred Lines ◽

Yield Potential ◽

Pedigree Data ◽

Maize Breeding ◽

Breeding Programs ◽

Maize Inbred Lines ◽

The World

Creating new maize hybrids with greater yield potential is a permanent goal of breeding programs all over the world. Long-time existing and new problems related to different biotic and abiotic stresses and the growing needs of the world market require constant work on finding new ways for advancing maize production. Molecular marker technology is one of the fastest developing fields and its implementation has already given results in solving different problems related to maize breeding improvement. The aim of the study presented herein was characterization and genetic similarity assessment of twenty-nine maize inbred lines from Maize Research Institute collection using Simple Sequence Repeats (SSR) markers. The analysis was done using 20 pairs of SSR primers with clearly visible and reproducible results. A total of 119 alleles were detected with a mean of 5.8 per locus. PIC (Polymorphism Information Content) values were in the range from 0.45 to 0.92 (average 0.74). Genetic similarities calculated using Jaccard?s coefficient ranged from 0.27 to 0.99. Cluster and Principal Component Analysis (PCA) analysis were done using matrices of similarity in the NTSYSpc software, version 2.1. Results of both classifications were moderately in agreement with the pedigree data of analysed genotypes. The information about genetic diversity of maize inbred lines revealed by SSR markers could be useful in planning strategies for future maize breeding programs.

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Genetic Diversity, Population Structure and Inter-Trait Relationships of Combined Heat and Drought Tolerant Early-Maturing Maize Inbred Lines from West and Central Africa

Agronomy ◽

10.3390/agronomy10091324 ◽

2020 ◽

Vol 10 (9) ◽

pp. 1324

Author(s):

Alimatu Sadia Osuman ◽

Baffour Badu-Apraku ◽

Beatrice E. Ifie ◽

Pangirayi Tongoona ◽

Ebenezer Obeng-Bio ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Polymorphic Information Content ◽

Central Africa ◽

Inbred Lines ◽

Heterotic Groups ◽

Maize Inbred Lines ◽

Wide Range ◽

Early Maturing ◽

West And Central Africa

Adequate knowledge and understanding of the genetic diversity and inter-trait relationships among elite maize inbred lines are crucial for determining breeding strategies and predicting hybrid performance. The objectives of this study were to investigate the genetic diversity of 162 early maturing white and yellow tropical maize inbred lines, and to determine the population structure, heterotic groups and inter-trait relationships among the lines. Using 9684 DArT single nucleotide polymorphism (SNP) markers, a gene diversity (GD) of 0.30 was recorded for the inbred lines with polymorphic information content (PIC) ranging from 0.08 to 0.38. The genetic relatedness among the inbred lines evaluated revealed six different groups based on the history of selection, colour of endosperm and pedigree. The genotype-by-trait (GT) biplot analysis identified inbred 1 (TZEI 935) as outstanding in terms of combined heat and drought (HD) tolerance with the base index analysis identifying 15 superior inbreds in the HD environment. A wide range of genetic variability was observed among the inbred lines, indicating that they are an invaluable resource for breeding for HD tolerance in maize breeding programmes, especially in West and Central Africa.

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SSR-based and carotenoid diversity assessment of tropical yellow endosperm maize inbred lines

Plant Genetic Resources ◽

10.1017/s1479262113000294 ◽

2013 ◽

Vol 12 (1) ◽

pp. 67-73 ◽

Cited By ~ 2

Author(s):

Oyenike Adeyemo ◽

Olusesan Omidiji

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Polymorphic Information Content ◽

Vitamin A Deficiency ◽

Inbred Lines ◽

Reproductive Age ◽

Sub Saharan Africa ◽

Provitamin A ◽

Maize Inbred Lines ◽

Diversity Assessment

Yellow endosperm maize can be used to reduce vitamin A deficiency among many pre-school children and women of reproductive age in sub-Saharan Africa. Assessment of the genetic diversity of tropical yellow endosperm maize inbred lines will have genetic gains in breeding design to develop lines with an enhanced level of provitamin A. We screened 122 tropical yellow endosperm maize inbred lines with 62 simple sequence repeat (SSR) markers and 51 SSR loci were polymorphic. We detected 190 alleles with an average of 3.72 alleles per locus, and polymorphic information content values among the inbred lines varied from 0.12 to 0.74 with an average of 0.43. Genetic distance (GD) values among all the pairs of the 122 inbred lines varied from 0.02 to 0.61 with an average of 0.41 for the SSR markers. The inbred lines exhibited a substantial level of genetic diversity. Genetic diversity was also evaluated using carotenoid data. The Euclidean GDs varied from 1.00 to 9.97 with an average of 3.81 for the carotenoid data. Cluster and principal coordinate analyses revealed clear separation of maize inbred lines into SSR-based groupings and carotenoid-based groupings. Cluster based on SSR markers were predominantly consistent with known pedigree data of the inbred lines. The correlation using Mantel's test between carotenoid-based GD estimates and SSR marker-based GD estimates gave a low r value ( − 0.06). The grouping of lines will facilitate the selection of parental lines for making crosses to develop new lines with enhanced provitamin A content.

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Phenotypic and molecular characterization of a set of tropical maize inbred lines from a public breeding program in Brazil

BMC Genomics ◽

10.1186/s12864-021-08127-7 ◽

2022 ◽

Vol 23 (1) ◽

Author(s):

Sirlene Viana de Faria ◽

Leandro Tonello Zuffo ◽

Wemerson Mendonça Rezende ◽

Diego Gonçalves Caixeta ◽

Hélcio Duarte Pereira ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Inbred Lines ◽

Breeding Program ◽

Tropical Maize ◽

Maize Breeding ◽

Breeding Programs ◽

The Public ◽

Maize Inbred Lines

Abstract Background The characterization of genetic diversity and population differentiation for maize inbred lines from breeding programs is of great value in assisting breeders in maintaining and potentially increasing the rate of genetic gain. In our study, we characterized a set of 187 tropical maize inbred lines from the public breeding program of the Universidade Federal de Viçosa (UFV) in Brazil based on 18 agronomic traits and 3,083 single nucleotide polymorphisms (SNP) markers to evaluate whether this set of inbred lines represents a panel of tropical maize inbred lines for association mapping analysis and investigate the population structure and patterns of relationships among the inbred lines from UFV for better exploitation in our maize breeding program. Results Our results showed that there was large phenotypic and genotypic variation in the set of tropical maize inbred lines from the UFV maize breeding program. We also found high genetic diversity (GD = 0.34) and low pairwise kinship coefficients among the maize inbred lines (only approximately 4.00 % of the pairwise relative kinship was above 0.50) in the set of inbred lines. The LD decay distance over all ten chromosomes in the entire set of maize lines with r2 = 0.1 was 276,237 kb. Concerning the population structure, our results from the model-based STRUCTURE and principal component analysis methods distinguished the inbred lines into three subpopulations, with high consistency maintained between both results. Additionally, the clustering analysis based on phenotypic and molecular data grouped the inbred lines into 14 and 22 genetic divergence clusters, respectively. Conclusions Our results indicate that the set of tropical maize inbred lines from UFV maize breeding programs can comprise a panel of tropical maize inbred lines suitable for a genome-wide association study to dissect the variation of complex quantitative traits in maize, mainly in tropical environments. In addition, our results will be very useful for assisting us in the assignment of heterotic groups and the selection of the best parental combinations for new breeding crosses, mapping populations, mapping synthetic populations, guiding crosses that target highly heterotic and yielding hybrids, and predicting untested hybrids in the public breeding program UFV.

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Comparative analysis of genetic diversity among the maize inbred lines (Zea mays L.) obtained by RAPD and SSR markers

Brazilian Archives of Biology and Technology ◽

10.1590/s1516-89132008000100022 ◽

2008 ◽

Vol 51 (1) ◽

pp. 183-192 ◽

Cited By ~ 11

Author(s):

Silvia Graciele Hülse de Souza ◽

Valéria Carpentieri-Pípolo ◽

Claudete de Fátima Ruas ◽

Valdemar de Paula Carvalho ◽

Paulo Maurício Ruas ◽

...

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Zea Mays L ◽

Inbred Lines ◽

Pedigree Data ◽

Dice Coefficient ◽

Quantitative Characters ◽

Maize Inbred Lines ◽

Ssr Primers ◽

Selection Of

The RAPD and SSR markers were used to compare the genetic diversity among the 16 maize inbred lines. Twenty-two primers were used in the RAPD reactions, resulting in the amplification of 265 fragments, while 16 pairs of SSR primers resulted in 75 fragments. The similarity based on Dice coefficient for the RAPD ranged from 53 to 84% and for the SSR from 11 to 82%. The dendrogram obtained by the RAPD showed five groups, while dendrogram obtained by the SSR showed three groups and one isolated line. The association constructed from the markers and the principal coordinate’s analysis separated lines into two groups according to endosperm color, either orange or yellow. The RAPD were effective to validate pedigree data, while the SSR were effective to recognize the differences between the quantitative characters. Because they assess the distinct regions of the genome, the selection of one or other marker would depend on the characteristics of the material used and the objectives of the project.

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Applications of molecular markers in Genetic Diversity Studies of maize

Nigerian Journal of Biotechnology ◽

10.4314/njb.v37i1.11 ◽

2020 ◽

Vol 37 (1) ◽

pp. 101-108

Author(s):

Degife Asefa Zebire

Keyword(s):

Genetic Diversity ◽

Molecular Markers ◽

Inbred Lines ◽

Hybrid Breeding ◽

Diversity Analysis ◽

Crop Species ◽

Heterotic Groups ◽

Genetic Diversity Analysis ◽

Diversity Studies ◽

Genetic Diversity Study

Molecular markers are efficient for exploiting variations in genotypes as they are not influenced by environmental factors and also speed up breeding programs. They are used to detect large numbers of distinct divergence between genotypes at the DNA level. Genetic diversity study helps to estimate the relationship between inbred lines to make the best hybrid combinations. Lines which are clustered in different heterotic groups are considered as the best hybrid combinations to carry out further breeding activities. Molecular markers are used to meet a number of objectives, including genetic diversity analysis and prediction of hybrid performances in divergent crop species. Agro-morphological and molecular markers have been utilized to study genetic diversity so far. In maize, the uses of molecular markers are important for the evaluation of genetic diversity of inbred lines and in clustering them into heterotic groups. These markers determine genetic similarity of the lines and are used to assess the genetic diversity of maize. Molecular markers have proven valuable for genetic diversity analysis of many crop species and genetically diverse lines are important to improve hybrid breeding. Keyword: Molecular marker; Genetic diversity; Genetic variation, Diversity Array technology; cluster analysis

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