Mapping-by-Sequencing via MutMap Identifies a Mutation in ZmCLE7 Underlying Fasciation in a Newly Developed EMS Mutant Population in an Elite Tropical Maize Inbred

Abstract

Induced point mutations are important genetic resources for their ability to create hypo- and hypermorphic alleles that are useful for understanding gene functions and breeding. However, such mutant populations have only been developed for a few temperate maize varieties, mainly B73 and W22, yet no tropical maize inbred lines have been mutagenized and made available to the public to date. We developed a novel Ethyl Methanesulfonate (EMS) induced mutation resource in maize comprising 2050 independent M2 mutant families in the elite tropical maize inbred ML10. By phenotypic screening, we showed that this population is of comparable quality with other mutagenized populations in maize. To illustrate the usefulness of this population for gene discovery, we performed rapid mapping-by-sequencing to clone a fasciated-ear mutant and identify a causal promoter deletion in ZmCLE7 (CLE7). Our mapping procedure does not require crossing to an unrelated parent, thus is suitable for mapping subtle traits and ones affected by heterosis. This first EMS population in tropical maize is expected to be very useful for the maize research community. Also, the EMS mutagenesis and rapid mapping-by-sequencing pipeline described here illustrate the power of performing forward genetics in diverse maize germplasms of choice, which can lead to novel gene discovery due to divergent genetic backgrounds.

Genomic resources in plant breeding for sustainable agriculture

“…Using MutMap+ approach, novel mutant alleles for fine-tuning of cooked rice texture were identified in a rice starch branching enzyme IIb gene ( Nakata et al, 2018 ). Similarly, in maize, mapping-by-sequencing, an approach similar to MutMap, enabled identification of a mutation in ZmCLE7 underlying fasciation in a EMS mutant population ( Tran et al, 2020 ). MutMap was used also to map GDSL like lipase/acylhydrolase associated with drought tolerance in sorghum ( Jiao et al, 2018 ).…”

Next Generation Cereal Crop Yield Enhancement: From Knowledge of Inflorescence Development to Practical Engineering by Genome Editing

“…In this pathway, a homeodomain transcription factor, WUS, is expressed in the meristem organizing center and coordinates meristem activity by activating expression of the secreted peptide CLV3, which binds its receptor, CLV1 to repress WUS expression [ 24 , 25 , 26 , 27 , 28 , 29 ]. CLV orthologs in maize include the CLV1 ortholog THICK TASSEL DWARF1 ( TD1 ) [ 30 ], and CLV3 ortholog ZmCLAVATA3 / EMBRYO SURROUNDING REGION-RELATED7 ( ZmCLE7 ) [ 31 , 32 ], as well as a second CLE peptide, ZmFON2-LIKE CLE Protein1 ( ZmFCP1 ) [ 33 ], which acts in a distinct CLV pathway to repress WUS expression. Besides the CLV1 receptor, another LRR receptor-like protein FASCIATED EAR3 (FEA3) represses WUS from below a region of the meristem known as the organizing center, by perceiving ZmFCP1 [ 33 ].…”

“…The CLV2 ortholog in maize, FASCIATED EAR2 (FEA2), transmits signals from ZmCLE7 and ZmFCP1 through two different candidate downstream effectors, the maize heterotrimeric G proteins, COMPACT PLANT2 (CT2) and ZmGB1, and CORYNE (ZmCRN) [ 34 , 35 , 36 , 37 ]. Null mutants of these CLV genes cause meristem over-proliferation, leading to enlarged inflorescence stems and fasciated ears in maize [ 30 , 31 , 32 , 33 , 34 , 35 , 36 , 37 ].…”

“…Null alleles of maize clv genes cause meristem over-proliferation and fasciated ears that develop many more disorganized and shorter kernel rows with low grain yield [ 30 , 31 , 32 , 33 , 34 , 35 , 36 , 37 ]. However, weak coding sequence alleles of fea2 and fea3 generated by ethyl methanesulfonate mutagenesis cause a quantitative increase in kernel row number while maintaining meristem organization and ear length, highlighting the potential to quantitatively manipulate fea genes for yield enhancement [ 33 , 37 ].…”

E183K Mutation in Chalcone Synthase C2 Causes Protein Aggregation and Maize Colorless

“… Abe et al (2012) developed the MutMap strategy for chemical-induced mutation, in which the mutant line is crossed to the wild-type line with the same ecotype. These strategies have been implemented to accelerate the process of mutant mapping by direct genome sequencing in Arabidopsis ( Cuperus et al, 2010 ; Austin et al, 2011 ), rice ( Abe et al, 2012 ; Takagi et al, 2015 ), and maize ( Lu et al, 2018 ; Tran et al, 2020 ).…”