Molecular diversity and selective sweeps in maize inbred lines adapted to African highlands.
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ABSTRACT:
SUBMITTER: Wegary D
PROVIDER: S-EPMC6748982 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Genetic diversity is fundamental for studying the complex architecture of the traits of agronomic importance, controlled by major and minor loci. Moreover, well-characterized germplasm collections are essential tools for dissecting and analyzing genetic and phenotypic diversity in crops. A panel of 360 entries, a subset of a larger collection maintained within the GenBank at CREA Bergamo, which includes the inbreds derived from traditional Italian maize open-pollinated (OP) varieties and advanced breeding ones (Elite Inbreds), was analyzed to identify SNP markers using the tGBS® genotyping-by-sequencing technology. A total of 797,368 SNPs were found during the initial analysis. Imputation and filtering processes were carried out based on the percentage of missing data, redundant markers, and rarest allele frequencies, resulting in a final dataset of 15,872 SNP markers for which a physical map position was identified. Using this dataset, the inbred panel was characterized for linkage disequilibrium (LD), genetic diversity, population structure, and genetic relationships. LD decay at a genome-wide level indicates that the collection is a suitable resource for association mapping. Population structure analyses, which were carried out with different clustering methods, showed stable grouping statistics for four groups, broadly corresponding to 'Insubria', 'Microsperma', and 'Scagliolino' genotypes, with a fourth group composed prevalently of elite accessions derived from Italian and US breeding programs. Based on these results, the CREA Italian maize collection, genetically characterized in this study, can be considered an important tool for the mapping and characterization of useful traits and associated loci/alleles, to be used in maize breeding programs.
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Project description:Knowledge of combining ability and genetic diversity are important prerequisites for the development of outstanding hybrids that are tolerant to high plant density. This work was carried out to assess general combining ability (GCA) and specific combining ability (SCA), identify promising hybrids, estimate genetic diversity among the inbred lines and correlate genetic distance to hybrid performance and SCA across different plant densities. A total of 28 F1 hybrids obtained by crossing eight adverse inbred lines (four local and four exotic) were evaluated under three plant densities 59,500 (D1), 71,400 (D2) and 83,300 (D3) plants ha-1 using spilt plot design with three replications at two locations during 2018 season. Increasing plant density from D1 to D3 significantly decreased leaf angle (LANG), chlorophyll content (CHLC), all ear characteristics and grain yield per plant (GYPP). Contrarily, days to silking (DTS), anthesis-silking interval (ASI), plant height (PLHT), ear height (EHT), and grain yield per hectare (GYPH) were significantly increased. Both additive and non-additive gene actions were involved in the inheritance of all the evaluated traits, but additive gene action was predominant for most traits. Inbred lines L1, L2, and L5 were the best general combiners for increasing grain yield and other desirable traits across research environments. Two hybrids L2 × L5 and L2 × L8 were found to be good specific combiners for ASI, LANG, GYPP and GYPH. Furthermore, these hybrids are ideal for further testing and promotion for commercialization under high plant density. Genetic distance (GD) among pairs of inbred lines ranged from 0.31 to 0.78, with an average of 0.61. Clustering based on molecular GD has effectively grouped the inbred lines according to their origin. No significant correlation was found between GD and both hybrid performance and SCA for grain yield and other traits and proved to be of no predictive value. Nevertheless, SCA could be used to predict the hybrid performance across all plant densities. Overall, this work presents useful information regarding the inheritance of maize grain yield and other important traits under high plant density.
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Project description:The maize RTCS gene, encoding a LOB domain transcription factor, plays important roles in the initiation of embryonic seminal and postembryonic shoot-borne root. In this study, the genomic sequences of this gene in 73 China elite inbred lines, including 63 lines from 5 temperate heteroric groups and 10 tropic germplasms, were obtained, and the nucleotide polymorphisms and haplotype diversity were detected. A total of 63 sequence variants, including 44 SNPs and 19 indels, were identified at this locus, and most of them were found to be located in the regions of UTR and intron. The coding region of this gene in all tested inbred lines carried 14 haplotypes, which encoding 7 deferring RTCS proteins. Analysis of the polymorphism sites revealed that at least 6 recombination events have occurred. Among all 6 groups tested, only the P heterotic group had a much lower nucleotide diversity than the whole set, and selection analysis also revealed that only this group was under strong negative selection. However, the set of Huangzaosi and its derived lines possessed a higher nucleotide diversity than the whole set, and no selection signal were identified.
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Project description:Key messageThe extent of molecular diversity parameters across three rice species was compared using large germplasm collection genotyped with genomewide SNPs and SNPs that fell within selective sweep regions. Previous studies conducted on limited number of accessions have reported very low genetic variation in African rice (Oryza glaberrima Steud.) as compared to its wild progenitor (O. barthii A. Chev.) and to Asian rice (O. sativa L.). Here, we characterized a large collection of African rice and compared its molecular diversity indices and population structure with the two other species using genomewide single nucleotide polymorphisms (SNPs) and SNPs that mapped within selective sweeps. A total of 3245 samples representing African rice (2358), Asian rice (772) and O. barthii (115) were genotyped with 26,073 physically mapped SNPs. Using all SNPs, the level of marker polymorphism, average genetic distance and nucleotide diversity in African rice accounted for 59.1%, 63.2% and 37.1% of that of O. barthii, respectively. SNP polymorphism and overall nucleotide diversity of the African rice accounted for 20.1-32.1 and 16.3-37.3% of that of the Asian rice, respectively. We identified 780 SNPs that fell within 37 candidate selective sweeps in African rice, which were distributed across all 12 rice chromosomes. Nucleotide diversity of the African rice estimated from the 780 SNPs was 8.3 × 10-4, which is not only 20-fold smaller than the value estimated from all genomewide SNPs (π = 1.6 × 10-2), but also accounted for just 4.1%, 0.9% and 2.1% of that of O. barthii, lowland Asian rice and upland Asian rice, respectively. The genotype data generated for a large collection of rice accessions conserved at the AfricaRice genebank will be highly useful for the global rice community and promote germplasm use.
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Project description: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.
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Project description:The propensity to capture and mobilize gene fragments by the highly abundant Helitron family of transposable elements likely impacts the evolution of genes in Zea mays. These elements provide a substrate for natural selection by giving birth to chimeric transcripts by intertwining exons of disparate genes. They also capture flanking exons by read-through transcription. Here, we describe the expression of selected Helitrons in different maize inbred lines. We recently reported that these Helitrons produce multiple isoforms of transcripts in inbred B73 via alternative splicing. Despite sharing high degrees of sequence similarity, the splicing profile of Helitrons differed among various maize inbred lines. The comparison of Helitron sequences identified unique polymorphisms in inbred B73, which potentially give rise to the alternatively spliced sites utilized by transcript isoforms. Some alterations in splicing, however, do not have obvious explanations. These observations not only add another level to the creation of transcript diversity by Helitrons among inbred lines but also provide novel insights into the cis-acting elements governing splice-site selection during pre-mRNA processing.
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Project description:We focused on a region encompassing a major maize domestication locus, Tb1, and a locus involved in the flowering time variation, Dwarf8 (D8), to investigate the consequences of two closely linked selective sweeps on nucleotide variation and gain some insights into maize geographical diffusion, through climate adaptation. First, we physically mapped D8 at approximately 300 kb 3' of Tb1. Second, we analyzed patterns of nucleotide variation at Tb1, D8, and seven short regions (400-700 bp) located in the Tb1-D8 region sequenced on a 40 maize inbred lines panel encompassing early-flowering temperate and late-flowering tropical lines. The pattern of polymorphism along the region is characterized by two valleys of depleted polymorphism while the region in between exhibits an appreciable amount of diversity. Our results reveal that a region approximately 100 kb upstream of the D8 gene exhibits hallmarks of divergent selection between temperate and tropical lines and is likely closer than the D8 gene to the target of selection for climate adaptation. Selection in the tropical lines appears more recent than in the temperate lines, suggesting an initial domestication of early-flowering maize. Simulation results indicate that the polymorphism pattern is consistent with two interfering selective sweeps at Tb1 and D8.
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