| Maize(Zea mays L.)is one of the most important crops in the world.Heterosis plays an important role in maize production.Maize was native to the tropics and adapted to the temperate environment by domestication and breeding.The heterosis has been investigated from various aspects for more than a century.However,there is no widely accepted theory due to the complex genetic mechanism of heterosis.In this paper,a novel population,multiple-hybrid population(MHP),was developed for genome-wide association study(GWAS)to address the shortcomings of traditional natural populations used for GWAS.Three subpopulations of an MHP were developed:(1)a temperate diallel consisting of 325 crosses;(2)a temperate and tropical NCⅡ consisting of 263 hybrids;(3)a tropical diallel consisting of 136 crosses.MHPs have several advantages,including(1)they can be used to analyze the phenotype,combining ability and heterosis for self-pollination and hybrid crops,(2)large-scale hybrid populations can be shared through sharing parental lines,(3)the genotypes for n(n-1)/2 hybrids can be deduced by genotyping n parents for savings in genotyping,(4)different hybrid populations can be developed with great flexibility according to the requirements of trials and breeding designs,(5)an MHP can be tested across diverse environments because of its greater adaptability compared to its parents and(6)the performance for all possible hybrids with genomic information can be predicted using a part of MHP hybrids and genomewide prediction can be done for hybrid performance,combining ability and heterosis.By combining the phenotype and deduced genotype from 51 genotyped parents,GWAS for phenotype,combining ability and heterosis was performed with candidate genes selected,making it possible to complete GWAS for hybrids.1.Heterosis for plant height,flowering and yield related traits for maize of different ecological typesThe temperate diallel hybrids showed a lower level of heterosis for plant and ear heights and flowering traits.However,NCⅡ hybrids showed a higher level of heterosis for yield related traits,indicating the potential of tropical germplasm for improvement of temperate maize lines.Correlation analysis of heterosis revealed negative correlation between flowering traits and grain weight per plant.Significantly positive correlation was found between the marker polymorphisms between parents and mid-parent heterosis for all of traits,except for the flowering traits where a negative correlation was found.Significantly positive correlation between the marker polymorphism between the parents and high-parent heterosis was only found for grain number.A consistent correlation was found between genetic distance and mid-parent heterosis and between genetic distance and high-parent heterosis.Highly significant correlation was found for all the traits,except that only significant correction was found for plant height in addition to ear height,days to silk,grain number and grain weight per plant.Highest correlation between genetic distance and heterosis(both mid-and high-parent)was found for plant height.2.Combining ability for plant height,flowering and yield related traits of maize with different ecological typesAdditive effect accounted for the main part of the agronomic traits,as revealed by the mean square ratios of general to special combining abilities.A significantly positive correlation of combining ability was revealed for plant height,flowering traits and yield traits.However special combining ability for ASI was negatively correlated with that of yield traits.Heterosis was significant correlated with special combining ability,and a significant correlation was observed between the sum of combining abilities and hybrid performance.Therefore,hybrid performance can be predicted by combining ability and mid-parent heterosis.3.GWAS analysis of hybrid phenotype,combining ability and heterosis with the multiple hybrid populationThree GWAS methods were used for phenotype,combining ability and heterosis with the multiple hybrid population.The candidate genes were inferred for significant SNPs,with 18,6,8 and 4 candidate genes were inferred for hybrid phenotype,combining ability,mid-and high-parent heterosis,respectively.Two candidate genes(GRMZM2G130389 and GRMZM5G836910)were identified for the special combining ability for flowering traits,ear length and diameter.The candidate gene GRMZM2G130389 encodes S-locus lectin protein kinase family protein,which is involved in protein amino acid phosphorylation and pollen recognition.The gene GRMZM5G836910 encodes a plastid-localized aspartate aminotransferase involved in photosynthesis for C4 plants.The candidate gene GRMZM2G038636,identified for special combining ability of grain number,was also detected as a candidate gene for grain number per se.The inferred candidate genes include both the cloned genes such as fea2 and the genes revealed by position cloning or homologous gene non-functional analysis.Therefore,it is necessary to do further functional analysis for these genes.Epistasis interactions played an important role in polygenic effect for combining ability and heterosis,and thus a more attention should be given to the analysis of various interaction effects.4.Genomic prediction for ungenerated hybridsThe GS models of BRR,Bayes A,Bayes B,GBLUP and RKHS were used to predict ungenerated hybrids for the MHP.High prediction accuracy was showed in plant height for Bayes B model and flowering,yield traits for Bayes A model when 500 hybrids randomly selected from the generated hybrids were used as a training population to predict the rest 224 hybrids.And then the 724 maize hybrids were used as a training population to predict the 551 ungenerated hybrids.The top 100 hybrids were then selected,which showed a great yield increase compared with the mean yield of all possible hybrids.GWAS and candidate gene screening were performed using the 1275 hybrids(with measured or predicted phenotype)with the easyGWAS platform.The candidate gene,GRMZM2G308064,identified for grain weight per plant using all 1275 possible hybrids was also found for the special combining ability of flowering traits and grain weight per plant when the 724 tested hybrids were used.The prediction indicates that a subset of the hybrids developed can be used to predict all possible hybrids that can be developed by a set of parents,by which breeding testing scale can be largely reduced and thus the breeding efficiency can be improved. |
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