Genome‐wide identification and analysis of heterotic loci in three maize hybrids

Abstract

SummaryHeterosis, or hybrid vigour, is a predominant phenomenon in plant genetics, serving as the basis of crop hybrid breeding, but the causative loci and genes underlying heterosis remain unclear in many crops. Here, we present a large‐scale genetic analysis using 5360 offsprings from three elite maize hybrids, which identifies 628 loci underlying 19 yield‐related traits with relatively high mapping resolutions. Heterotic pattern investigations of the 628 loci show that numerous loci, mostly with complete–incomplete dominance (the major one) or overdominance effects (the secondary one) for heterozygous genotypes and nearly equal proportion of advantageous alleles from both parental lines, are the major causes of strong heterosis in these hybrids. Follow‐up studies for 17 heterotic loci in an independent experiment using 2225 F2 individuals suggest most heterotic effects are roughly stable between environments with a small variation. Candidate gene analysis for one major heterotic locus (ub3) in maize implies that there may exist some common genes contributing to crop heterosis. These results provide a community resource for genetics studies in maize and new implications for heterosis in plants.

Genome-wide identification of agronomically important genes in outcrossing crops using OutcrossSeq

“…In maize (Zea mays), a double-cross population (four inbred parents were sequenced with 46.83, 46.83, 43.83, and 43.43 coverage, Supplemental Figure 7) containing 800 individuals was sequenced with $0.33 coverage for each individual, genotyped using OutcrossSeq, and phenotyped for 11 agronomic traits (Supplemental Table 3). Overall, 64 QTLs were identified, of which 33 QTLs overlapped with those from previous reports (Liu et al, 2020a). Moreover, well-characterized genes in maize were detected within 12 QTLs (Supplemental Table 8).…”

Heterosis and Hybrid Crop Breeding: A Multidisciplinary Review

“…At the proteome level, hybrids generally show protein levels which deviate from the mid-parent, particularly in functional classes related to central metabolism and stress responses ( Marcon et al, 2010 ). Efforts to map heterosis for various traits generally do not reveal loci for which the association holds universally across genotypes, even for single traits within a species ( Huang et al, 2016 ; Liu et al, 2020 ). If a particular universal mechanism of heterosis were ultimately revealed, the genes involved would still have biologically additive, dominant, or epistatic gene action.…”

Transcriptome-wide analysis of epitranscriptome and translational efficiency associated with heterosis in maize

“…These modifications, in turn, yield advantages in growth, stress resistance, and adaptability of F 1 hybrids over their parents due to interactions between alleles of the parental genomes that alter regulatory networks of related genes ( Alonso-Peral et al , 2017 ; Shen et al , 2017 ). Genetic variation is widely studied to understand the molecular basis of heterosis ( Huang et al , 2015 ; Morris et al , 2016 ; Jiang et al , 2017 ; Liu et al , 2020 ). It is assumed that a combination of different genetic principles might run together to explain hybrid vigor ( Swanson-Wagner et al , 2006 ; Lippman and Zamir, 2007 ).…”

“…It is assumed that a combination of different genetic principles might run together to explain hybrid vigor ( Swanson-Wagner et al , 2006 ; Lippman and Zamir, 2007 ). To better decipher the processes underlying the manifestation of heterosis for various phenotypic traits, multifaceted molecular data have been collected at different regulatory levels including the genome ( Huang et al , 2015 ; Lin et al , 2020 ; Liu et al , 2020 ), epigenome ( Groszmann et al , 2011 ; Shen et al , 2012 ; He et al , 2013 ; Kawanabe et al , 2016 ; Shen et al , 2017 ; Zhu et al , 2017 ; Lauss et al , 2018 ; Sinha et al , 2020 ), transcriptome ( Paschold et al , 2012 ; Baldauf et al , 2016 ; Zhu et al , 2016 ; Alonso-Peral et al , 2017 ; Shen et al , 2017 ; Shao et al , 2019 ; Sinha et al , 2020 ), proteome ( Hoecker et al , 2008 ), and metabolome ( Romisch-Margl et al , 2010 ). However, to date we still lack, for any species, fundamental knowledge of how post-transcriptional activities are involved in heterosis.…”