| Characterization of maize germplasm is an important work for founding allelomorphic gene, association analysis of complex traits, and breeding practice. Plant architecture trait is one of the main factors in maize yield formation. Plant architecture trait showes higher variantation and the ideal plant architecture will improve maize lodging resistance, photosynthesis, grain yield and so on. It is a primary work before QTL analysis and gene clone to found excellent allelomorphic gene included in maize germplasm with good plant architecture trait, which can not only for uncovering the genetic basis of plant architecture but also supplling molecular genetics proofs for plant architecture improving.Based on the larger and diverser collection of maize germplasm collected in our previous studies, a subset of367main inbred lines was constructed. Which was planted under different envirments among two years, five plant architecture related traits were investigated. On the molecular level, genetic diversity, population structure, pairvise kinship, and linkage disequilibrium (LD) were evaluated using high throughput’MaizeSNP50’including56110SNPs. Gentic comparing was done among43inbred lines derived from Huangzaosi. And158SNPs associated with plant architecture related traits were found. Main results are listed as follow:1. A total of41,819informative SNPs with minor allele number (MAF) of more than0.05were used to estimate the genetic diversity and relatedness, and16,827SNPs with MAF>0.1wore selected to estimate the LD decay. Totally1015SNPs which were evenly distributed in the genome were selected randomly to evaluate the population structure of these accessions. The results showed that two groups could be classified in the accessions, i.e. the introduced germplasm and the local germplasm. Further, five subgroups corresponding to different heterotic groups, that is, Reid, Lancaster, P, TSPT, and Tem-tropic I, were clustered. By using the re-sampling method, the genetic diversity of each subgroups was estimated, with the highest in the Tem-Tropic I and the lowest in the P. Most lines in this panel showed weak or modest relatedness with each other. Comparisons of gene diversity (GD) showed that there existed some conserved genetic regions for specific subgroup across10chromosomes of maize, i.e. seven in Lancaster, seven in Reid, six in TSPT, five in P, and two in Tem-Tropical I. Additionally, the results also revealed that there existed fifteen conservative regions transmitted from Huangzaosi, an important foundation parent, to its descendants, which are important for further studies since the outcomes may provide clues to understand why Huangzaosi could become a foundation parent in Chinese maize breeding. For the entire set, average LD distance was74.08kb and varied among different chromosomes as well as in different genomic regions of one chromosome. This analysis uncovered a rich natural genetic diversity of the elite maize inbred set, suggesting that the panel can be used in association study, esp. for temperate regions.2. Among this subset of367inbred lines, ANOVA analysis showed that there was significant deviation among5plant architecture related traits between any two inbred lines. The coefficient variation ranged from22.83%to11.87%. Plant height showed the highest coefficient variation of43.83%. The second two were Tassel primary branch number and Ear height with coefficient variation of34.59%and22.83%, respectively. The smallest coefficient variation was found in phenotype of Tassel length with11.87%, coefficient variation of "Ear height/Plant height" was14.69%. Otherwise, all the Shannon-Weaver indexes of5plant architecture related traits were beyond2. These results suggested that this subset used here were diverser in phehotypes.3.158SNPs were significant association with plant architecture related traits with P<0.0001.28SNPs were significant association with plant height, of which, six SNPs were found under two envirments at the same time, three SNPs were found under three envirments at the same time.50SNPs were significant association with ear height, of which, ten SNPs were found under two envirments at the same time, one SNPs were found under three envirments at the same time, three SNPs named PZE-105098995, SYN31958and PZE-105099028were found under four envirments at the same time, another important ear related SNP named PZE-104109619is on Chrom4, which was found under five envirments at the same time, the other ear height SNPs were found under one envirment only.34SNPs were significant association with "ear height/plant height", of which,4SNPs were found under two envirments at the same time, Eight SNPs were found under three envirments at the same time, two important SNPs named PZE-105090603and PZE-105090633, which were found under four envirments at the same time.14tassel length related SNPs and32tassel primary branch number related SNPs were found under one envirment only. These results revealed that genetic regions including these markers were close to genetic regions containing plant architecture related genes.BlastN search showed, among the158plant architecture related SNPs, some were in the regions with known plant architecture related genes. For example,3SNPs named PZE-101080319, PZE-101137671and SYN2469were close to the region with Rht gene which was related with plant height. PZE-102120220was close to the region with sdl gene which was related with plant architecture related traits. Except that, most significant association with plant architecture were found in the predication genes or intergenic regions, these variation may play important role in maize domestication and plant architecture formation. |
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