scholarly journals Breeding Strategy for Resistance to Striga Asiatica Based on Genetic Diversity and Population Structure of Tropical Maize Lines

2021 ◽  
Author(s):  
Edmore Gasura ◽  
Brian Nyandoro ◽  
Stanford Mabasa ◽  
Peter S. Setimela ◽  
Martina Kyalo ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Grain Yield ◽  
Southern Africa ◽  
Inbred Lines ◽  
Breeding Strategy ◽  
Breeding Program ◽  
Heterotic Groups ◽  
Molecular Variance ◽  
Striga Asiatica

Abstract Maize (Zea mays L.) is a major staple crop in southern Africa and is produced on millions of hectares. However, its yield is greatly reduced by Striga spp, a parasitic weed which is causing US$ 7 billion losses annually. Use of host resistance could be an effective way of controlling Striga and resistance to Striga is quantitative, mainly controlled by additive gene action. Understanding the population structure and genetic diversity is therefore key in designing an effective breeding program targeting grain yield heterosis and resistance to Striga. The aim of this study was to determine the genetic diversity and population structure of the key germplasm from tropical Africa. This information could guide in the identification of heterotic groups and potential testers required to kick start a maize breeding program for Striga asiatica in southern Africa. A total of 222 maize inbred lines from IITA and CIMMYT were used in this study. The materials were genotyped using the genotyping-by-sequencing method. A total of 45 000 SNP markers were revealed, and these were subjected to analysis of molecular variance, structure analysis and clustering using the Gower’s distance and neighbor joining algorithm. Molecular variance was lager within individuals (91%) than among populations (9%). The inbred lines clustered into three major groups, with the IITA germplasm clustering separately from CIMMYT germplasm. A breeding strategy for Striga asiatica resistance was proposed with the aim of increasing genetic gains in both the resistance and grain yield.

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 Genetic variation and population structure in China summer maize germplasm

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Guoping Shu ◽  
Gangqiang Cao ◽  
Niannian Li ◽  
Aifang Wang ◽  
Fang Wei ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variation ◽  
Linkage Disequilibrium ◽  
Germplasm Collection ◽  
Genotyping By Sequencing ◽  
Inbred Lines ◽  
Summer Maize ◽  
Heterotic Groups ◽  
Breeding Germplasm

AbstractMaize (Zea mays L.) germplasm in China Summer maize ecological region (CSM) or central corn-belt of China is diverse but has not been systematically characterized at molecular level. In this study, genetic variation, genome diversity, linkage disequilibrium patterns, population structure, and characteristics of different heterotic groups were studied using 525,141 SNPs obtained by Genotyping-By-Sequencing (GBS) for 490 inbred lines collected from researchers at CSM region. The SNP density is lower near centromere, but higher near telomere region of maize chromosome, the degree of linkage disequilibrium (r2) vary at different chromosome regions. Majority of the inbred lines (66.05%) show pairwise relative kinship near zero, indicating a large genetic diversity in the CSM breeding germplasm. Using 4849 tagSNPs derived from 3618 haplotype blocks, the 490 inbred lines were delineated into 3 supergroups, 6 groups, and 10 subgroups using ADMIXTURE software. A procedure of assigning inbred lines into heterotic groups using genomic data and tag-SNPs was developed and validated. Genome differentiation among different subgroups measured by Fst, and the genetic diversity within each subgroup measured by GD are both large. The share of heterotic groups that have significant North American germplasm contribution: P, SS, IDT, and X, accounts about 54% of the CSM breeding germplasm collection and has increased significantly in the last two decades. Two predominant types of heterotic pattern in CSM region are: M-Reid group × TSPT group, and X subgroup × Local subgroups.

scholarly journals Genetic Diversity and Heterotic Orientation of South Africa Maize Inbred Lines Towards Tropical and Temperate Testers

2021 ◽  
Author(s):  
Siphiwokuhle Funani Shandu ◽  
John Derera ◽  
Kingston Mashingaidze ◽  
Edmore Gasura
Keyword(s):  
South Africa ◽  
Genetic Diversity ◽  
Grain Yield ◽  
Combining Ability ◽  
Molecular Genetic ◽  
Inbred Lines ◽  
Genetic Distances ◽  
Specific Combining Ability ◽  
Heterotic Groups ◽  
Maize Inbred Lines

Abstract An efficient hybrid breeding program defines and utilizes few heterotic groups. The objectives of this study were to determine genetic diversity and alignment of South Africa maize inbred lines collection towards tropical and temperate testers. Forty-two maize inbred lines were genotyped with 56110 single nucleotide polymorphism (SNP) DNA markers, using the Illumina MaizeSNP50 Bead chip. The 42 lines were crossed to two tropical and two temperate inbred line testers. The testcrosses were evaluated across seven environments, in South Africa, during 2014-2016. Genotypes and specific combining ability (SCA) effects of hybrids were significantly different (P<0.05) for grain yield. There was a weak correlation between molecular genetic distances and both grain yield mean and specific combining ability effects of hybrids, indicating that productivity of maize inbred lines could not be reliably determined based on molecular genetic distances. The SCA data was capable of classifying these maize inbred lines into three heterotic groups with respect to both tropical and temperate testers. Only a few lines could not be grouped on the basis of SCA data. The study also indicated high level of diversity among the maize inbred lines, which was shown by both the dendogram and molecular genetic distances. The SNP marker data classified the inbred lines into 11 clusters that could be simplified into three major groups of normal maize endosperm and two groups of quality protein maize (QPM) endosperm types. However, the SNP data indicated that maize lines were more aligned towards tropical than temperate inbred testers. This information would be useful for simplifying heterotic classification of the lines with profound implications for breeding progress.

scholarly journals Genomic diversity in pearl millet inbred lines derived from landraces and improved varieties

2020 ◽  
Author(s):  
Desalegn D. Serba ◽  
Ghislain Kanfany ◽  
Davina Rhodes ◽  
Paul St. Amand ◽  
Amy Bernardo ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Pearl Millet ◽  
Nutritional Quality ◽  
Inbred Lines ◽  
Genomic Diversity ◽  
Hybrid Breeding ◽  
Heterotic Groups ◽  
Improved Varieties ◽  
Different Levels

Abstract Background: Genetic improvement of pearl millet is lagging behind most of the major crops. Development of genomic resources is expected to expedite breeding for improved agronomic traits, stress tolerance, yield, and nutritional quality. Genotyping a breeding population with high throughput markers enables exploration of genetic diversity, population structure, and linkage disequilibrium (LD) which are important preludes for marker-trait association studies and application of genomic-assisted breeding. Results: Genotyping-by-sequencing (GBS) libraries of 309 inbred lines derived from landraces and improved varieties from Africa and India generated 54,770 high quality single nucleotide polymorphism (SNP) markers. On average one SNP per 29 Kb was mapped in the reference genome, with the telomeric regions more densely mapped than the pericentromeric regions of the chromosomes. Population structure analysis using 30,208 SNPs evenly distributed in the genome divided 309 accessions into five subpopulations with different levels of admixture. Pairwise genetic distance (GD) between accessions varied from 0.09 to 0.33 with the average distance of 0.28. Rapid LD decay implied low tendency of markers inherited together. Genetic differentiation estimates were the highest between subgroups 4 and 5, and the lowest between subgroups 1 and 2. Conclusions: Population genomic analysis of pearl millet inbred lines derived from diverse geographic and agroecological features identified five subgroups mostly following pedigree differences with different levels of admixture. It also revealed the prevalence of high genetic diversity in pearl millet, which is very useful in defining heterotic groups for hybrid breeding, trait mapping, and holds promise for improving pearl millet for yield and nutritional quality. The short LD decay observed suggests an absence of persistent haplotype blocks in pearl millet. The diverse genetic background of these lines and their low LD make this set of germplasm useful for traits mapping.

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 Genomic diversity in pearl millet inbred lines derived from landraces and improved varieties

2020 ◽  
Author(s):  
Desalegn D. Serba ◽  
Ghislain Kanfany ◽  
Davina Rhodes ◽  
Paul St. Amand ◽  
Amy Bernardo ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Pearl Millet ◽  
Nutritional Quality ◽  
Inbred Lines ◽  
Genomic Diversity ◽  
Hybrid Breeding ◽  
Heterotic Groups ◽  
Improved Varieties ◽  
Different Levels

Abstract Background: Genetic improvement of pearl millet is lagging behind most of the major crops. Development of genomic resources is expected to expedite breeding for improved agronomic traits, stress tolerance, yield, and nutritional quality. Genotyping a breeding population with high throughput markers enables exploration of genetic diversity, population structure, and linkage disequilibrium (LD) which are important preludes for marker-trait association studies and application of genomic-assisted breeding. Results: Sequencing the genotyping-by-sequencing (GBS) libraries of 309 inbred lines derived from landraces and improved varieties from Africa and India generated 54,770 high quality single nucleotide polymorphism (SNP) markers. On average one SNP per 29 Kb was mapped in the reference genome, with the telomeric regions more densely mapped than the pericentromeric regions of the chromosomes. Population structure analysis using 30,208 SNPs evenly distributed in the genome divided 309 accessions into five subpopulations with different levels of admixture. Pairwise genetic distance (GD) between accessions varied from 0.09 to 0.33 with the average distance of 0.28. Rapid LD decay implied low tendency of markers inherited together. Genetic differentiation estimates were the highest between subgroups 4 and 5, and the lowest between subgroups 1 and 2. Conclusions: Population genomic analysis of pearl millet inbred lines derived from diverse geographic and agroecological features identified five subgroups mostly following pedigree differences with different levels of admixture. It also revealed the prevalence of high genetic diversity in pearl millet, which is very useful in defining heterotic groups for hybrid breeding, trait mapping, and holds promise for improving pearl millet for yield and nutritional quality. The short LD decay observed suggests an absence of persistent haplotype blocks in pearl millet. The diverse genetic background of these lines and their low LD make this set of germplasm useful for traits mapping.

scholarly journals Genetic diversity and inter-trait relationship of tropical extra-early maturing quality protein maize inbred lines under low soil nitrogen stress

PLoS ONE ◽  
2021 ◽  
Vol 16 (6) ◽  
pp. e0252506
Author(s):  
Pearl Abu ◽  
Baffour Badu-Apraku ◽  
Beatrice E. Ifie ◽  
Pangirayi Tongoona ◽  
Leander D. Melomey ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Grain Yield ◽  
Soil Nitrogen ◽  
Inbred Lines ◽  
Indirect Selection ◽  
Genetic Distances ◽  
Quality Protein Maize ◽  
Tryptophan Content ◽  
Selection For

Information on the genetic diversity, population structure, and trait associations of germplasm resources is crucial for predicting hybrid performance. The objective of this study was to dissect the genetic diversity and population structure of extra-early yellow and orange quality protein maize (QPM) inbred lines and identify secondary traits for indirect selection for enhanced grain yield under low-soil nitrogen (LN). One hundred and ten inbred lines were assessed under LN (30 kg ha -1) and assayed for tryptophan content. The lines were genotyped using 2500 single nucleotide polymorphism (SNP) markers. Majority (85.4%) of the inbred lines exhibited wide pairwise genetic distances between 0.4801 and 0.600. Genetic distances were wider between yellow and orange endosperm lines and predicted high heterosis in crosses between parents of different endosperm colors. The unweighted pair group method with arithmetic mean (UPGMA) and the admixture model-based population structure method both grouped the lines into five clusters. The clustering was based on endosperm color, pedigree, and selection history but not on LN tolerance or tryptophan content. Genotype by trait biplot analysis revealed association of grain yield with plant height and ear height. TZEEQI 394 and TZEEIORQ 73A had high expressivity for these traits. Indirect selection for high grain yield among the inbred lines could be achieved using plant and ear heights as selection criteria. The wide genetic variability observed in this study suggested that the inbred lines could be important sources of beneficial alleles for LN breeding programs in SSA.

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 Genomic diversity in pearl millet inbred lines derived from landraces and improved varieties

2020 ◽  
Author(s):  
Ghislain Kanfany ◽  
Desalegn D. Serba ◽  
Davina Rhodes ◽  
Paul St. Amand ◽  
Amy Bernardo ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Pearl Millet ◽  
Nutritional Quality ◽  
Inbred Lines ◽  
Genomic Diversity ◽  
Hybrid Breeding ◽  
Heterotic Groups ◽  
Improved Varieties ◽  
Different Levels

Abstract Background: Genetic improvement of pearl millet is lagging behind most of the major crops. Development of genomic resources is expected to expedite breeding for improved agronomic traits, stress tolerance, yield, and nutritional quality. Genotyping a breeding population with high throughput markers enables exploration of genetic diversity, population structure, and linkage disequilibrium (LD) which are important preludes for marker-trait association studies and application of genomic-assisted breeding. Results: Genotyping-by-sequencing (GBS) libraries of 309 inbred lines derived from landraces and improved varieties from Africa and India generated 54,770 high quality single nucleotide polymorphism (SNP) markers. On average one SNP per 29 Kb was mapped in the reference genome, with the telomeric regions more densely mapped than the pericentromeric regions of the chromosomes. Population structure analysis using 30,208 SNPs evenly distributed in the genome divided 309 accessions into five subpopulations with different levels of admixture. Pairwise genetic distance (GD) between accessions varied from 0.09 to 0.33 with the average distance of 0.28. Rapid LD decay implied low tendency of markers inherited together. Genetic differentiation estimates were the highest between subgroups 4 and 5, and the lowest between subgroups 1 and 2. Conclusions: Population genomic analysis of pearl millet inbred lines derived from diverse geographic and agroecological features identified five subgroups mostly following pedigree differences with different levels of admixture. It also revealed the prevalence of high genetic diversity in pearl millet, which is very useful in defining heterotic groups for hybrid breeding, trait mapping, and holds promise for improving pearl millet for yield and nutritional quality. The short LD decay observed suggests an absence of persistent haplotype blocks in pearl millet. The diverse genetic background of these lines and their low LD make this set of germplasm useful for traits mapping.

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