scholarly journals 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 ◽  
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.

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

2020 ◽  
pp. 2010-2019
Author(s):  
Maizura Abu Sin ◽  
Ghizan Saleh ◽  
Nur Ashikin Psyquay Abdullah ◽  
Pedram Kashiani
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Gene Diversity ◽  
Polymorphic Information Content ◽  
Similarity Index ◽  
Inbred Lines ◽  
Hybrid Breeding ◽  
Heterotic Groups ◽  
Breeding Programs ◽  
Maize Inbred Lines

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

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

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.

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

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.

scholarly journals Genetic diversity and population structure of early and extra-early maturing maize germplasm adapted to sub-Saharan Africa

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Baffour Badu-Apraku ◽  
Ana Luísa Garcia-Oliveira ◽  
César Daniel Petroli ◽  
Sarah Hearne ◽  
Samuel Adeyemi Adewale ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Inbred Lines ◽  
Snp Markers ◽  
Rapid Expansion ◽  
Sub Saharan Africa ◽  
Heterotic Groups ◽  
Breeding Programs ◽  
Early Maturing ◽  
Sub Saharan

Abstract Background Assessment and effective utilization of genetic diversity in breeding programs is crucial for sustainable genetic improvement and rapid adaptation to changing breeding objectives. During the past two decades, the commercialization of the early and extra-early maturing cultivars has contributed to rapid expansion of maize into different agro-ecologies of sub-Saharan Africa (SSA) where maize has become an important component of the agricultural economy and played a vital role in food and nutritional security. The present study aimed at understanding the population structure and genetic variability among 439 early and extra-early maize inbred lines developed from three narrow-based and twenty-seven broad-based populations by the International Iinstitute of Tropical Agriculture Maize Improvement Program (IITA-MIP). These inbreds were genotyped using 9642 DArTseq-based single nucleotide polymorphism (SNP) markers distributed uniformly throughout the maize genome. Results About 40.8% SNP markers were found highly informative and exhibited polymorphic information content (PIC) greater than 0.25. The minor allele frequency and PIC ranged from 0.015 to 0.500 and 0.029 to 0.375, respectively. The STRUCTURE, neighbour-joining phylogenetic tree and principal coordinate analysis (PCoA) grouped the inbred lines into four major classes generally consistent with the selection history, ancestry and kernel colour of the inbreds but indicated a complex pattern of the genetic structure. The pattern of grouping of the lines based on the STRUCTURE analysis was in concordance with the results of the PCoA and suggested greater number of sub-populations (K = 10). Generally, the classification of the inbred lines into heterotic groups based on SNP markers was reasonably reliable and in agreement with defined heterotic groups of previously identified testers based on combining ability studies. Conclusions Complete understanding of potential heterotic groups would be difficult to portray by depending solely on molecular markers. Therefore, planned crosses involving representative testers from opposing heterotic groups would be required to refine the existing heterotic groups. It is anticipated that the present set of inbreds could contribute new beneficial alleles for population improvement, development of hybrids and lines with potential to strengthen future breeding programs. Results of this study would help breeders in formulating breeding strategies for genetic enhancement and sustainable maize production in SSA.

scholarly journals Performance of provitamin A- quality protein maize inbred lines and derived hybrids in contrasting environments

2019 ◽  
Author(s):  
Ebenezer Obeng-Bio ◽  
Baffour Badu-Apraku ◽  
Beatrice Elohor Ifie ◽  
Agyemang Danquah ◽  
Essie Blay ◽  
...  
Keyword(s):  
Grain Yield ◽  
Central Africa ◽  
Inbred Lines ◽  
Provitamin A ◽  
Quality Protein Maize ◽  
Whole Grain ◽  
Maize Inbred Lines ◽  
Early Maturing ◽  
West And Central Africa ◽  
The Relationship

Abstract Background Early maturing provitamin A (PVA) quality protein maize (QPM) inbred lines with tolerance to drought and low-N are needed to develop superior hybrids in West and Central Africa (WCA). This study aimed to (i) identify inbred lines that combined drought and low-N tolerance with increased levels of PVA and tryptophan and (ii) assess the relationship among PVA carotenoids, tryptophan and grain yield. Sixty-four inbred lines plus six inbred checks were evaluated under induced drought, low-N and optimal conditions in 2016 and 2017 in Nigeria. The inbred lines were assayed for PVA and tryptophan contents. Results Thirty-three of the lines were found to be tolerant to drought and low-N. Ninety percent of the inbred lines had tryptophan contents > 0.075 % per sample in whole grain substantiating the presence of the QPM trait in the inbred lines. Inbred lines TZEIORQ 55 and TZEIORQ 29 combined high PVA contents (15.38 and 12.10μg g-1, respectively) with low-N tolerance while nine inbred lines combined moderate PVA levels (5.06 – 8.34μg g-1) with drought and low-N tolerance. Conclusions These maize inbred lines could be utilized to develop superior drought and low-N tolerant hybrids and synthetics with elevated levels of PVA and tryptophan for WCA. The correlations observed among grain yield, PVA and tryptophan of the lines were not significant suggesting that these traits could be improved independently.

scholarly journals Genetic diversity and population structure of early-maturing tropical maize inbred lines using SNP markers

PLoS ONE ◽  
2019 ◽  
Vol 14 (4) ◽  
pp. e0214810 ◽  
Author(s):  
Gloria Boakyewaa Adu ◽  
Baffour Badu-Apraku ◽  
Richard Akromah ◽  
Ana Luisa Garcia-Oliveira ◽  
Frederick Justice Awuku ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Inbred Lines ◽  
Snp Markers ◽  
Tropical Maize ◽  
Maize Inbred Lines ◽  
Early Maturing

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

BMC Genomics ◽  
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.

scholarly journals Transcriptome wide SSR discovery cross-taxa transferability and development of marker database for studying genetic diversity population structure of Lilium species

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Manosh Kumar Biswas ◽  
Mita Bagchi ◽  
Ujjal Kumar Nath ◽  
Dhiman Biswas ◽  
Sathishkumar Natarajan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Large Scale ◽  
Polymorphic Information Content ◽  
Pcr Amplification ◽  
Efficient Manner ◽  
Lilium Species ◽  
Population Structure Analysis ◽  
Wide Range ◽  
Functional Molecular Markers

Abstract Lily belongs to family liliaceae, which mainly propagates vegetatively. Therefore, sufficient number of polymorphic, informative, and functional molecular markers are essential for studying a wide range of genetic parameters in Lilium species. We attempted to develop, characterize and design SSR (simple sequence repeat) markers using online genetic resources for analyzing genetic diversity and population structure of Lilium species. We found di-nucleotide repeat motif were more frequent (4684) within 0.14 gb (giga bases) transcriptome than other repeats, of which was two times higher than tetra-repeat motifs. Frequency of di-(AG/CT), tri-(AGG/CTT), tetra-(AAAT), penta-(AGAGG), and hexa-(AGAGGG) repeats was 34.9%, 7.0%, 0.4%, 0.3%, and 0.2%, respectively. A total of 3607 non-redundant SSR primer pairs was designed based on the sequences of CDS, 5′-UTR and 3′-UTR region covering 34%, 14%, 23%, respectively. Among them, a sub set of primers (245 SSR) was validated using polymerase chain reaction (PCR) amplification, of which 167 primers gave expected PCR amplicon and 101 primers showed polymorphism. Each locus contained 2 to 12 alleles on average 0.82 PIC (polymorphic information content) value. A total of 87 lily accessions was subjected to genetic diversity analysis using polymorphic SSRs and found to separate into seven groups with 0.73 to 0.79 heterozygosity. Our data on large scale SSR based genetic diversity and population structure analysis may help to accelerate the breeding programs of lily through utilizing different genomes, understanding genetics and characterizing germplasm with efficient manner.

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