Abstract
BackgroundThe harvest index for many crops can be improved through introduction of dwarf stature to increase lodging resistance, combined with early maturity. The inbred line Shen5003 has been widely used in maize breeding in China as a key donor line for the dwarf trait. Also, one major quantitative trait locus (QTL) controlling plant height has been identified in bin 5.05–5.06, across several maize bi-parental populations. With the progress of publicly available maize genome sequence, the objective of this work was to identify the candidate genes that affect plant height among Chinese maize inbred lines with genome wide association studies (GWAS).Methods and FindingsA total of 284 maize inbred lines were genotyped using over 55,000 evenly spaced SNPs, from which a set of 41,101 SNPs were filtered with stringent quality control for further data analysis. With the population structure controlled in a mixed linear model (MLM) implemented with the software TASSEL, we carried out a genome-wide association study (GWAS) for plant height. A total of 204 SNPs (P≤0.0001) and 105 genomic loci harboring coding regions were identified. Four loci containing genes associated with gibberellin (GA), auxin, and epigenetic pathways may be involved in natural variation that led to a dwarf phenotype in elite maize inbred lines. Among them, a favorable allele for dwarfing on chromosome 5 (SNP PZE-105115518) was also identified in six Shen5003 derivatives.ConclusionsThe fact that a large number of previously identified dwarf genes are missing from our study highlights the discovery of the consistently significant association of the gene harboring the SNP PZE-105115518 with plant height (P = 8.91e-10) and its confirmation in the Shen5003 introgression lines. Results from this study suggest that, in the maize breeding schema in China, specific alleles were selected, that have played important roles in maize production.
Highlights
Attaining high and stable yield has been one of the major goals in the production of crops, including maize
The fact that a large number of previously identified dwarf genes are missing from our study highlights the discovery of the consistently significant association of the gene harboring the SNP PZE-105115518 with plant height (P = 8.91e-10) and its confirmation in the Shen5003 introgression lines
Results from this study suggest that, in the maize breeding schema in China, specific alleles were selected, that have played important roles in maize production
Summary
Attaining high and stable yield has been one of the major goals in the production of crops, including maize. Semi-dwarfism, an important agronomic trait that contributes to crop yield, improves harvest index and nitrogen response, and increases lodging resistance [1]. Semi-dwarfism can be controlled by the reducing-height (RHT) gene, which encodes a DELLA protein involved in the GA signaling pathway [2]. A multidrug resistant-like (MDR-like) ABC transporter involved in polar auxin transport leads to reduced plant height in the maize br mutant [14]. An epigenetic effect is illustrated by Epi-d1, a spontaneous rice mutant that displays a metastable dwarf phenotype caused by silencing of the DWARF1 (D1) gene, which encodes a GTP-binding protein involved in giberellin signalling [15]. One major quantitative trait locus (QTL) controlling plant height has been identified in bin 5.05–5.06, across several maize bi-parental populations. With the progress of publicly available maize genome sequence, the objective of this work was to identify the candidate genes that affect plant height among Chinese maize inbred lines with genome wide association studies (GWAS)
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