Dataset Information

Genetic Variation Among Tropical Maize Inbred Lines from NARS and CGIAR Breeding Programs.

ABSTRACT: The use of molecular markers allows for precise estimates of genetic diversity, which is an important parameter that enables breeders to select parental lines and designing breeding systems. We assessed the level of genetic diversity and population structure in a panel of 151 tropical maize inbred lines using 10,940 SNP (single nucleotide polymorphism) markers generated through the DArTseq genotyping platform. The average gene diversity was 0.39 with expected heterozygosity ranging from 0.00 to 0.84, and a mean of 0.02. Analysis of molecular variance showed that 97% of allelic diversity was attributed to individual inbred lines within the populations while only 3% was distributed among the populations. Both neighbor-joining clustering and STRUCTURE analysis classified the inbred lines into four major groups. The crosses that involve inbred lines from most divergent subgroups are expected to generate maximum heterosis and produce wide variation. The results will be beneficial for breeders to better understand and exploit the genetic diversity available in the set of maize inbred lines we studied.

Supplementary information

The online version contains supplementary material available at 10.1007/s11105-022-01358-2.

SUBMITTER: Ayesiga SB

PROVIDER: S-EPMC10160135 | biostudies-literature | 2023

REPOSITORIES: biostudies-literature

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Genetic Variation Among Tropical Maize Inbred Lines from NARS and CGIAR Breeding Programs.

Ayesiga Stella Bigirwa SB Rubaihayo Patrick P Oloka Bonny Michael BM Dramadri Isaac Onziga IO Edema Richard R Sserumaga Julius Pyton JP

Plant molecular biology reporter 20220926 2

The use of molecular markers allows for precise estimates of genetic diversity, which is an important parameter that enables breeders to select parental lines and designing breeding systems. We assessed the level of genetic diversity and population structure in a panel of 151 tropical maize inbred lines using 10,940 SNP (single nucleotide polymorphism) markers generated through the DArTseq genotyping platform. The average gene diversity was 0.39 with expected heterozygosity ranging from 0.00 to ...[more]

PMID: 37159650

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Project description:BackgroundThe 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.ResultsOur 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.ConclusionsOur 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.

Project description:Analyses of the genetic distance and composition of inbred lines are a prerequisite for parental selection and to exploit heterosis in plant breeding programs. The study aimed to assess genetic diversity and population structure of a maize germplasm panel comprising 182 founder lines and 866 derived inbred lines using Single Nucleotide Polymorphism (SNP) markers to identify genetically unique lines for hybrid breeding. The founder lines were genotyped with 1201 SNPs, and the derived lines with 1484 SNPs. Moderate genetic variation, with genetic diversity ranging from 0.004 to 0.44 with a mean of 0.25, was recorded for the founder lines, while corresponding values of 0.004 to 0.34 with a mean of 0.13 were recorded for the derived lines. Heterozygosity values ranging from 0.00 to 0.24 and a mean of 0.08 were recorded for both lines. Of the SNP markers used, 82% of the 1201 markers and 84% of the 1484 markers exhibited polymorphism information content ranging from 0.25 to 0.50. Analysis of molecular variance revealed significant genetic differences (P ≤ 0.001) among and within populations in the founder and derived lines. Most detected variations, i.e., 97% and 88.38%, were attributed to within populations in the founder and derived lines, respectively. Population structure analysis identified three distinct subpopulations among founder lines and two among derived lines. Cluster analysis supported the population structure The following genetically distant founder and derived inbred lines were selected: G15NL337 and G15NL312 (Cluster 1), 15ARG152 and RGS-PL44 (Cluster 2), RGS-PL44 and 15ARG149 (Cluster 2), and RGS-PL33 and RGS-PL44 (Cluster 2), respectively. The selected lines are genetically distinct and recommended for marker-assisted hybrid maize breeding to exploit the frequency of beneficial alleles. This study provides valuable insights for maize breeding programs, enabling the exploitation of beneficial alleles and contributing to improved crop yields and food security through hybrid breeding.

Project description:BackgroundTemperate maize inbred lines with expired Plant Variety Protection Act certificates (Ex-PVP) are potential sources of desirable alleles for tropical germplasm improvement. Up to now, the usefulness of the Ex-PVP inbred lines as a potential source of novel beneficial alleles for Striga hermonthica resistance breeding to enhance genetic gain in tropical maize has not been reported.ResultsThis study was thus conducted to characterize the combining ability of 24 Ex-PVP inbred lines in crosses with two tropical Striga resistant inbred testers under Striga-infested and non-infested conditions and across three locations for 2 years. Many testcrosses between Ex-PVP inbred lines and the first tester (T1) produced competitive or significantly higher grain yields compared to the hybrid between the two resistant testers under Striga infested and non-infested conditions and across multiple test locations. Also, most of the testcrosses with positive heterosis for grain yield and negative heterosis for Striga damage and emerged Striga count involved T1 as a tester. Our study identified six Ex-PVP inbred lines with positive GCA effects for grain yield under Striga infested and non-infested conditions and across multiple test locations. Amongst these, inbred lines HB8229-1 and WIL900-1 also displayed negative GCA effects for emerged Striga count and Striga damage rating. The inbred line HB8229-1 showed positive SCA effects for grain yield with T2, whereas WIL900-1 had positive SCA effects for grain yield with T1. Over 70% of the Ex-PVP inbred lines were consistently assigned to specific heterotic groups using yield-based classifying methods (mean grain yield and SCA effects).ConclusionsThese results could facilitate systematic introgression of the Ex-PVP inbred lines into the existing Striga resistant heterotic groups in IITA. The Ex-PVP inbred lines with positive GCA effects and producing high grain yields in hybrid combinations could be useful parents for enhancing Striga resistance and agronomic performance of tropical maize hybrids.

Dataset Information

Genetic Variation Among Tropical Maize Inbred Lines from NARS and CGIAR Breeding Programs.

Supplementary information

Publications

Genetic Variation Among Tropical Maize Inbred Lines from NARS and CGIAR Breeding Programs.

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