Abstract
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.
Highlights
Maize (Zea mays ssp. mays L.) is one of the top three crops globally in total production and is cultivated as a multi-purpose crop for food, feed, biofuel, and raw material for synthesis of various industrial products[1]
Most of the 298 inbred lines adapted to the African highland ecology showed high level of genetic heterogeneity than expected for lines extracted from S4 or later generations, which suggests the need for revising the line development strategy, including line finishing and use of genetically pure parental lines for line development; generating reference genotype data as one of the requirements for releasing lines; implementing quality assurance (QA) and quality control (QC) genotyping methods to regularly check genetic purity of key inbred lines during line maintenance; and more frequent use of doubled haploid (DH) technology in developing breeding lines
The germplasm used in the current study showed clear population www.nature.com/scientificreports structure, primarily by pedigree information and breeding history, and less so by heterotic groups and germplasm type
Summary
Maize (Zea mays ssp. mays L.) is one of the top three crops globally in total production and is cultivated as a multi-purpose crop for food, feed, biofuel, and raw material for synthesis of various industrial products[1]. (CIMMYT) started highland maize breeding program in Mexico in the 1970s with the intention of developing high yielding and cold tolerant improved germplasm from pools and populations carrying tropical and subtropical genetic backgrounds[5]. Various studies were conducted to determine the genetic diversity, relationship, population structure and heterotic grouping of maize inbred lines developed by CIMMYT7–13 and International Institute of Tropical Agriculture (IITA)[9,14,15,16] using different genotyping platforms and marker density. Previous genetic diversity studies conducted on highland maize inbred lines adapted to the African ecology were based on a small number of samples and low marker density[17,18,19,20,21]. Abakemal et al (2015) studied genetic purity and patterns of relationships among 36 maize inbred lines adapted to African highland agro-ecology using 25 SSR markers
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