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

ABSTRACT: Information on genetic diversity and population structure are very important in any breeding programme for the improvement of traits of interest and the development of outstanding products for commercialization. In the present study, we assessed the genetic diversity of 94 early-maturing white and yellow tropical maize inbred lines using single nucleotide polymorphism (SNP) markers. The larger number of SNP markers used in this study allowed a clearer inference of the population structure of the 94 inbred lines. Cluster analysis resolved the inbred lines into different clusters based on their pedigree, selection history and endosperm colour. However, three heterotic groups were revealed by population structure analysis, but additional field evaluation could be more informative to confirm the heterotic groups identified. Nevertheless, wide genetic variability existed among the inbred lines making them unique with the potential to contribute new beneficial alleles to maize breeding programmes in the tropics, especially in the West and Central Africa (WCA) sub-region.

SUBMITTER: Boakyewaa Adu G

PROVIDER: S-EPMC6456193 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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

Boakyewaa Adu Gloria G Badu-Apraku Baffour B Akromah Richard R Garcia-Oliveira Ana Luisa AL Awuku Frederick Justice FJ Gedil Melaku M

PloS one 20190409 4

Information on genetic diversity and population structure are very important in any breeding programme for the improvement of traits of interest and the development of outstanding products for commercialization. In the present study, we assessed the genetic diversity of 94 early-maturing white and yellow tropical maize inbred lines using single nucleotide polymorphism (SNP) markers. The larger number of SNP markers used in this study allowed a clearer inference of the population structure of the ...[more]

PMID: 30964890

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Project description:BACKGROUND:Striga hermonthica (Benth.) parasitism militates against increased maize production and productivity in savannas of sub-Saharan Africa (SSA). Identification of Striga resistance genes is important in developing genotypes with durable resistance. So far, there is only one report on the existence of QTL for Striga resistance on chromosome 6 of maize. The objective of this study was to identify genomic regions significantly associated with grain yield and other agronomic traits under artificial Striga field infestation. A panel of 132 early-maturing maize inbreds were phenotyped for key agronomic traits under Striga-infested and Striga-free conditions. The inbred lines were also genotyped using 47,440 DArTseq markers from which 7224 markers were retained for population structure analysis and genome-wide association study (GWAS). RESULTS:The inbred lines were grouped into two major clusters based on structure analysis as well as the neighbor-joining hierarchical clustering. A total of 24 SNPs significantly associated with grain yield, Striga damage at 8 and 10?weeks after planting (WAP), ears per plant and ear aspect under Striga infestation were detected. Under Striga-free conditions, 11 SNPs significantly associated with grain yield, number of ears per plant and ear aspect were identified. Three markers physically located close to the putative genes GRMZM2G164743 (bin 10.05), GRMZM2G060216 (bin 3.06) and GRMZM2G103085 (bin 5.07) were detected, linked to grain yield, Striga damage at 8 and 10 WAP and number of ears per plant under Striga infestation, explaining 9 to 42% of the phenotypic variance. Furthermore, the S9_154,978,426 locus on chromosome 9 was found at 2.61?Mb close to the ZmCCD1 gene known to be associated with the reduction of strigolactone production in the maize roots. CONCLUSIONS:Presented in this study is the first report of the identification of significant loci on chromosomes 9 and 10 of maize that are closely linked to ZmCCD1 and amt5 genes, respectively and may be related to plant defense mechanisms against Striga parasitism. After validation, the identified loci could be targets for breeders for marker-assisted selection (MAS) to accelerate genetic enhancement of maize for Striga resistance in the tropics, particularly in SSA, where the parasitic weed is endemic.

Project description:BackgroundMolecular characterization is important for efficient utilization of germplasm and development of improved varieties. In the present study, we investigated the genetic purity, relatedness and population structure of 265 maize inbred lines from the Ethiopian Institute of Agricultural Research (EIAR), the International Maize and Wheat Improvement Centre (CIMMYT) and the International Institute of Tropical Agriculture (IITA) using 220,878 single nucleotide polymorphic (SNP) markers obtained using genotyping by sequencing (GBS).ResultsOnly 22% of the inbred lines were considered pure with <5% heterogeneity, while the remaining 78% of the inbred lines had a heterogeneity ranging from 5.1 to 31.5%. Pairwise genetic distances among the 265 inbred lines varied from 0.011 to 0.345, with 89% of the pairs falling between 0.301 and 0.345. Only <1% of the pairs had a genetic distance lower than 0.200, which included 14 pairs of sister lines that were nearly identical. Relative kinship analysis showed that the kinship coefficients for 59% of the pairs of lines was close to zero, which agrees with the genetic distance estimates. Principal coordinate analysis, discriminant analysis of principal components (DAPC) and the model-based population structure analysis consistently suggested the presence of three groups, which generally agreed with pedigree information (genetic background). Although not distinct enough, the SNP markers showed some level of separation between the two CIMMYT heterotic groups A and B established based on pedigree and combining ability information.ConclusionsThe high level of heterogeneity detected in most of the inbred lines suggested the requirement for purification or further inbreeding except those deliberately maintained at early inbreeding level. The genetic distance and relative kinship analysis clearly indicated the uniqueness of most of the inbred lines in the maize germplasm available for breeders in the mid-altitude maize breeding program of Ethiopia. Results from the present study facilitate the maize breeding work in Ethiopia and germplasm exchange among breeding programs in Africa. We suggest the incorporation of high density molecular marker information in future heterotic group assignments.

Dataset Information

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

Publications

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

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