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Molecular diversity and selective sweeps in maize inbred lines adapted to African highlands

By: Dagne Wegary Gissa.
Contributor(s): Chere, A.T | Prasanna, B.M | Berhanu Tadesse Ertiro | Alachiotis, N | Negera, D | Awas, G | Abakemal, D | Ogugo, V | Gowda, M | Fentaye Kassa Semagn.
Material type: materialTypeLabelArticlePublisher: London (United Kingdom) : Nature Publishing Group, 2019ISSN: 2045-2322 (Online).Subject(s): Genetic variation | Plant breeding | Highlands | Maize | AfricaOnline resources: Open Access through Dspace In: Nature Scientific Reports v. 9, art. 13490Summary: Little is known on maize germplasm adapted to the African highland agro-ecologies. In this study, we analyzed high-density genotyping by sequencing (GBS) data of 298 African highland adapted maize inbred lines to (i) assess the extent of genetic purity, genetic relatedness, and population structure, and (ii) identify genomic regions that have undergone selection (selective sweeps) in response to adaptation to highland environments. Nearly 91% of the pairs of inbred lines differed by 30–36% of the scored alleles, but only 32% of the pairs of the inbred lines had relative kinship coefficient <0.050, which suggests the presence of substantial redundancy in allelic composition that may be due to repeated use of fewer genetic backgrounds (source germplasm) during line development. Results from different genetic relatedness and population structure analyses revealed three different groups, which generally agrees with pedigree information and breeding history, but less so by heterotic groups and endosperm modification. We identified 944 single nucleotide polymorphic (SNP) markers that fell within 22 selective sweeps that harbored 265 protein-coding candidate genes of which some of the candidate genes had known functions. Details of the candidate genes with known functions and differences in nucleotide diversity among groups predicted based on multivariate methods have been discussed.
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Article CIMMYT Knowledge Center: John Woolston Library

Lic. Jose Juan Caballero Flores

 

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Little is known on maize germplasm adapted to the African highland agro-ecologies. In this study, we analyzed high-density genotyping by sequencing (GBS) data of 298 African highland adapted maize inbred lines to (i) assess the extent of genetic purity, genetic relatedness, and population structure, and (ii) identify genomic regions that have undergone selection (selective sweeps) in response to adaptation to highland environments. Nearly 91% of the pairs of inbred lines differed by 30–36% of the scored alleles, but only 32% of the pairs of the inbred lines had relative kinship coefficient <0.050, which suggests the presence of substantial redundancy in allelic composition that may be due to repeated use of fewer genetic backgrounds (source germplasm) during line development. Results from different genetic relatedness and population structure analyses revealed three different groups, which generally agrees with pedigree information and breeding history, but less so by heterotic groups and endosperm modification. We identified 944 single nucleotide polymorphic (SNP) markers that fell within 22 selective sweeps that harbored 265 protein-coding candidate genes of which some of the candidate genes had known functions. Details of the candidate genes with known functions and differences in nucleotide diversity among groups predicted based on multivariate methods have been discussed.

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Negera, D. : Not in IRS Staff list but CIMMYT Affiliation

Awas, G. : Not in IRS Staff list but CIMMYT Affiliation

Ogugo, V. : Not in IRS Staff list but CIMMYT Affiliation

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