Dataset Information

Genetic Diversity and Population Structure of Maize Inbred Lines with Varying Levels of Resistance to Striga Hermonthica Using Agronomic Trait-Based and SNP Markers.

ABSTRACT: Striga hermonthica is a serious biotic stress limiting maize production in sub-Saharan Africa. The limited information on the patterns of genetic diversity among maize inbred lines derived from source germplasm with mixed genetic backgrounds limits the development of inbred lines, hybrids, and synthetics with durable resistance to S. hermonthica. This study was conducted to assess the level of genetic diversity in a panel of 150 diverse maize inbred lines using agronomic and molecular data and also to infer the population structure among the inbred lines. Ten Striga-resistance-related traits were used for the phenotypic characterization, and 16,735 high-quality single-nucleotide polymorphisms (SNPs), identified by genotyping-by-sequencing (GBS), were used for molecular diversity. The phenotypic and molecular hierarchical cluster analyses grouped the inbred lines into five clusters, respectively. However, the grouping patterns between the phenotypic and molecular hierarchical cluster analyses were inconsistent due to non-overlapping information between the phenotypic and molecular data. The correlation between the phenotypic and molecular diversity matrices was very low (0.001), which is in agreement with the inconsistencies observed between the clusters formed by the phenotypic and molecular diversity analyses. The joint phenotypic and genotypic diversity matrices grouped the inbred lines into three groups based on their reaction patterns to S. hermonthica, and this was able to exploit a broad estimate of the actual diversity among the inbred lines. The joint analysis shows an invaluable insight for measuring genetic diversity in the evaluated materials. The result indicates that wide genetic variability exists among the inbred lines and that the joint diversity analysis can be utilized to reliably assign the inbred lines into heterotic groups and also to enhance the level of resistance to Striga in new maize varieties.

SUBMITTER: Stanley A

PROVIDER: S-EPMC7570130 | biostudies-literature | 2020 Sep

REPOSITORIES: biostudies-literature

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Genetic Diversity and Population Structure of Maize Inbred Lines with Varying Levels of Resistance to Striga Hermonthica Using Agronomic Trait-Based and SNP Markers.

Stanley Adekemi A Menkir Abebe A Paterne Agre A Ifie Beatrice B Tongoona Pangirayi P Unachukwu Nnanna N Meseka Silvestro S Mengesha Wende W Gedil Melaku M

Plants (Basel, Switzerland) 20200917 9

Striga hermonthica is a serious biotic stress limiting maize production in sub-Saharan Africa. The limited information on the patterns of genetic diversity among maize inbred lines derived from source germplasm with mixed genetic backgrounds limits the development of inbred lines, hybrids, and synthetics with durable resistance to S. hermonthica. This study was conducted to assess the level of genetic diversity in a panel of 150 diverse maize inbred lines using agronomic and molecu ...[more]

PMID: 32957613

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Project description:Striga hermonthica (Sh) and S. asiatica (Sa) are major parasitic weeds limiting cereal crop production and productivity in sub-Saharan Africa (SSA). Under severe infestation, Striga causes yield losses of up to 100%. Breeding for Striga-resistant maize varieties is the most effective and economical approach to controlling the parasite. Well-characterized and genetically differentiated maize germplasm is vital to developing inbred lines, hybrids, and synthetic varieties with Striga resistance and desirable product profiles. The objective of this study was to determine the genetic diversity of 130 tropical and sub-tropical maize inbred lines, hybrids, and open-pollinated varieties germplasm using phenotypic traits and single nucleotide polymorphism (SNP) markers to select Striga-resistant and complementary genotypes for breeding. The test genotypes were phenotyped with Sh and Sa infestations using a 13x10 alpha lattice design with two replications. Agro-morphological traits and Striga-resistance damage parameters were recorded under a controlled environment. Further, high-density Diversity Array Technology Sequencing-derived SNP markers were used to profile the test genotypes. Significant phenotypic differences (P<0.001) were detected among the assessed genotypes for the assessed traits. The SNP markers revealed mean gene diversity and polymorphic information content of 0.34 and 0.44, respectively, supporting the phenotypic variation of the test genotypes. Higher significant variation was recorded within populations (85%) than between populations using the analysis of molecular variance. The Structure analysis allocated the test genotypes into eight major clusters (K = 8) in concordance with the principal coordinate analysis (PCoA). The following genetically distant inbred lines were selected, displaying good agronomic performance and Sa and Sh resistance: CML540, TZISTR25, TZISTR1248, CLHP0303, TZISTR1174, TZSTRI113, TZDEEI50, TZSTRI115, CML539, TZISTR1015, CZL99017, CML451, CML566, CLHP0343 and CML440. Genetically diverse and complementary lines were selected among the tropical and sub-tropical maize populations that will facilitate the breeding of maize varieties with Striga resistance and market-preferred traits.

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.

Dataset Information

Genetic Diversity and Population Structure of Maize Inbred Lines with Varying Levels of Resistance to Striga Hermonthica Using Agronomic Trait-Based and SNP Markers.

Publications

Genetic Diversity and Population Structure of Maize Inbred Lines with Varying Levels of Resistance to <i>Striga Hermonthica</i> Using Agronomic Trait-Based and SNP Markers.

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