The genetic mechanism of heterosis utilization in maize improvement

Yingjie Xiao,Jianbing Yan,Chuang Ma,Haijun Liu,Shuqin Jiang,Yijiang Meng,Qian Cheng,Wenhao Song,Jingyun Luo,Jiuran Zhao,Feng Qiao,Jun Yan,Wenyu Yang,Xiangfeng Wang,Wenqiang Li,Xiaqing Wang,Ruyang Zhang,Marilyn L Warburton

doi:10.1186/s13059-021-02370-7

Abstract

BackgroundIn maize hybrid breeding, complementary pools of parental lines with reshuffled genetic variants are established for superior hybrid performance. To comprehensively decipher the genetics of heterosis, we present a new design of multiple linked F1 populations with 42,840 F1 maize hybrids, generated by crossing a synthetic population of 1428 maternal lines with 30 elite testers from diverse genetic backgrounds and phenotyped for agronomic traits.ResultsWe show that, although yield heterosis is correlated with the widespread, minor-effect epistatic QTLs, it may be resulted from a few major-effect additive and dominant QTLs in early developmental stages. Floral transition is probably one critical stage for heterosis formation, in which epistatic QTLs are activated by paternal contributions of alleles that counteract the recessive, deleterious maternal alleles. These deleterious alleles, while rare, epistatically repress other favorable QTLs. We demonstrate this with one example, showing that Brachytic2 represses the Ubiquitin3 locus in the maternal lines; in hybrids, the paternal allele alleviates this repression, which in turn recovers the height of the plant and enhances the weight of the ear. Finally, we propose a molecular design breeding by manipulating key genes underlying the transition from vegetative-to-reproductive growth.ConclusionThe new population design is used to dissect the genetic basis of heterosis which accelerates maize molecular design breeding by diminishing deleterious epistatic interactions.

Highlights

In maize hybrid breeding, complementary pools of parental lines with reshuffled genetic variants are established for superior hybrid performance
The genome-wide association studies (GWAS) detection of true positives is declared by a significant threshold based on a series of type I errors (α) from 0.05 to 0.95 hybrid set when using measured mid-parent heterosis (MPH).plant height (PH) values and was absent when using predicted MPH.PH values, most likely reflecting the extremely low minor allele frequency (MAF = 0.023) of the peak single nucleotide polymorphisms (SNPs) among the 1428 hybrids. These results demonstrate that G2P prediction is an effective strategy that greatly reduces field labor and phenotyping expense without sacrificing GWAS power
In a long genomic region spanning from ~ 75 to ~ 88 Mbp on chromosome 8 upstream the ZEA CENTRORADIALIS 8 (ZCN8)/RAP2.7 QTLs (~ 123 Mbp), we identified a series of fragmented QTLs for MPH.days to tasseling (DTT) in 22 F1 populations, this region does not contain previously reported flowering time genes (Fig. 3b and Additional file 5)

Summary

Introduction

Complementary pools of parental lines with reshuffled genetic variants are established for superior hybrid performance. Crop improvement involves the selection of additional sets of genes, and useful variants at these sequences accumulated over time in improved germplasm [5, 6]. Various breeding goals and adaptation to diverse environments have caused a widely differing distribution of alleles across populations with more subtle effects on phenotypic morphology, as compared to variation in domestication-related alleles [7]. While this rich pool of potential genetic variants may further improve future crop yield, their minor effects on desirable traits complicate their identification and isolation in the analysis of small populations

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Discussion

Conclusion