An Exome-seq Based Tool for Mapping and Selection of Candidate Genes in Maize Deletion Mutants

Despite the large number of genomic and transcriptomic resources in maize, there is still much to learn about the function of genes in developmental and biochemical processes. Some maize mutants that were generated by gamma-irradiation showed clear segregation for the kernel phenotypes in B73 ? Mo17 F2 ears. To better understand the functional genomics of kernel development,we developed a mapping and gene identi?cation pipeline, bulked segregant exome sequencing(BSEx-seq), to map mutants with kernel phenotypes including opaque endosperm and reduced kernel size. BSEx-seq generates and compares the sequence of the exon fraction from mutant and normal plant F2 DNA pools. The comparison can derive mapping peaks, identify deletions within the mapping peak, and suggest candidate genes within the deleted regions. We then used the public kernel-speci?c expression data to narrow down the list of candidate genes/mutations and identi?ed deletions ranging from several kb to more than 1 Mb. A full deletion allele of the Opaque-2 gene was identi?ed in mutant 531, which occurs within a $200-kb deletion. Opaque mutant 1486 has a 6248-bp deletion in the mapping interval containing two candidate genes encoding RNA-directed DNA methylation 4(RdDM4) and AMP-binding protein, respectively. This study demonstrates the ef?-ciency and cost-effectiveness of BSEx-seq for causal mutation mapping and candidate gene selection,providing a new option in mapping-by-sequencing for maize functional genomics studies.

An update on the maize zein-gene family in the post-genomics era

Maize(Zea mays)is a cereal crop of global food importance.However,the deficiency of essential amino acids,more importantly lysine,methionine and tryptophan,in the major seed storage zein proteins makes corn nutritionally of low value for human consumption.The idea of improving maize nutritional value prompted the search for maize natural mutants harboring low zein contents and higher amount of lysine.These studies resulted in the identification of more than dozens of maize opaque mutants in the previous few decades,o2 mutant being the most extensively studied one.However,the high lysine contents but soft kernel texture and chalky endosperm halted the widespread application and commercial success of maize opaque mutants,which ultimately paved the way for the development of Quality Protein Maize(QPM)by modifying the soft endosperm of o2 mutant into lysine-rich hard endosperm.The previous few decades have witnessed a marked progress in maize zein research.It includes elucidation of molecular mechanism underlying the role of different zein genes in seed endosperm development by cloning different components of zein family,exploring the general organization,function and evolution of zein family members within maize species and among other cereals,and elucidating the cis-and trans-regulatory elements modulating the regulation of different molecular players of maize seed endosperm development.The current advances in high quality reference genomes of maize lines B73 and Mo17 plus the completion of ongoing pan genome sequencing projects of more maize lines with NGS technologies are expected to revolutionize maize zein gene research in near future.This review highlights the recent advances in QPM development and its practical application in the post genomic era,genomic and physical composition and evolution of zein family,and expression,regulation and downstream role of zein genes in endosperm development.Moreover,recent genomic tools and methods developed for functional validation of maize zein genes are also discussed.