Nearly Identical Paralogs: Implications for Maize (<i>Zea mays</i> L.) Genome Evolution

Emrich, Scott J.; Li, Li; Wen, Tsui-Jung; Yandeau‐Nelson, Marna D.; Fu, Yan; Guo, Ling; Chou, Hui-Hsien; Aluru, Srinivas; Ashlock, Daniel; Schnable, Patrick S.

doi:10.1534/genetics.106.064006

Cited by 61 publications

(49 citation statements)

References 53 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Polymorphisms could be detected at the primer binding sites for 90% (9/10) of the SNP markers that yielded significantly larger peak areas for B73 than Mo17 alleles in the F 1 . In contrast, 0% of the 13 SNP markers that yielded (Emrich et al 2007b) e Ten of these SNPs are non-unique. f Nine of these SNPs are non-unique.…”

Section: Snp Validation and Map Constructionmentioning

confidence: 98%

High-Throughput Genetic Mapping of Mutants via Quantitative Single Nucleotide Polymorphism Typing

Liu

Chen²,

Makarevitch

et al. 2010

Genetics

Self Cite

View full text Add to dashboard Cite

Advances in next-generation sequencing technology have facilitated the discovery of single nucleotide polymorphisms (SNPs). Sequenom-based SNP-typing assays were developed for 1359 maize SNPs identified via comparative next-generation transcriptomic sequencing. Approximately 75% of these SNPs were successfully converted into genetic markers that can be scored reliably and used to generate a SNPbased genetic map by genotyping recombinant inbred lines from the intermated B73 3 Mo17 population. The quantitative nature of Sequenom-based SNP assays led to the development of a time-and costefficient strategy to genetically map mutants via quantitative bulked segregant analysis. This strategy was used to rapidly map the loci associated with several dozen recessive mutants. Because a mutant can be mapped using as few as eight multiplexed sets of SNP assays on a bulk of as few as 20 mutant F 2 individuals, this strategy is expected to be widely adopted for mapping in many species. W ITH the availability of a sequenced genome it is feasibletoundertakechromosomewalking projects to clone genes responsible for mutant phenotypes (Alleman et al. 2006;Briggs et al. 2007;Menzel et al. 2007;Song et al. 2007) and quantitative trait loci (QTL) (Glazier et al. 2002;Korstanje and Paigen 2002;Salvi et al. 2007). However, it can be logistically difficult and time-consuming to map mutants with current technologies. A high-throughput system to map phenotypic mutants would be very useful in converting the wealth of phenotypic mutants into an understanding of the molecular basis.Single nucleotide polymorphisms (SNPs) can be converted into genetic markers that are scored in mapping populations using various high-throughput SNP-typing technologies ( Maize (Zea mays L.) is an important model organism with substantial economic value. In this species, SNPs occur at a rate of one per 28-214 bp (Tenaillon et al. 2001;Barbazuk et al. 2007). Using our 454-based SNP discovery pipeline, we identified .7000 putative SNPs, .85% (94/ 110) of which could be validated via Sanger sequencing (Barbazuk et al. 2007). Here, we report the analysis of 1359 of these putative SNPs. Approximately 75% of the tested SNPs could be converted into genetic markers, and only 3% were deemed to be false positives. These SNP-based markers were used to construct a genetic map that can be used to address diverse biological questions. Finally, we apply the combination of quantitative SNP typing and bulked segregant analysis (BSA) (Michelmore et al. 1991) to efficiently map phenotypic mutants. MATERIALS AND METHODSGenetic materials: Using a high-throughput protocol (Dietrich et al. 2002) (Table S1, supporting information), the 25 non-B73 parents of the nested association mapping (NAM) population , and mutant and non-mutant pools of DNAs for BSA. For BSA, tissues from all mutant (or non-mutant) individuals from within the same F 2 family were pooled, and a single DNA isolation was performed or DNA was isolated from each individual and then equal amounts from each individ...

show abstract

Section: Snp Validation and Map Constructionmentioning

confidence: 98%

High-Throughput Genetic Mapping of Mutants via Quantitative Single Nucleotide Polymorphism Typing

Liu

Chen²,

Makarevitch

et al. 2010

Genetics

Self Cite

View full text Add to dashboard Cite

show abstract

“…Differential expression of related, duplicated genes has been linked to functional diversity within species (Gu et al, 2004), and subfunctionalization can provide a basis for genome evolution (Moore and Purugganan, 2005;Emrich et al, 2007b). The impetus for resolving expression among paralogs is further motivated by the extent of polyploidy, which is estimated to affect 50% to 80% of angiosperm species, including maize, wheat (Triticum aestivum), cotton (Gossypium hirsutum), and other important crops (Osborn et al, 2003;Blanc and Wolfe, 2004).…”

mentioning

confidence: 99%

Transcript Profiling by 3′-Untranslated Region Sequencing Resolves Expression of Gene Families

2007

View full text Add to dashboard Cite

Differences in gene expression underlie central questions in plant biology extending from gene function to evolutionary mechanisms and quantitative traits. However, resolving expression of closely related genes (e.g. alleles and gene family members) is challenging on a genome-wide scale due to extensive sequence similarity and frequently incomplete genome sequence data. We present a new expression-profiling strategy that utilizes long-read, high-throughput sequencing to capture the information-rich 3#-untranslated region (UTR) of messenger RNAs (mRNAs). Resulting sequences resolve gene-specific transcripts independent of a sequenced genome. Analysis of approximately 229,000 3#-anchored sequences from maize (Zea mays) ovaries identified 14,822 unique transcripts represented by at least two sequence reads. Total RNA from ovaries of drought-stressed wild-type and viviparous-1 mutant plants was used to construct a multiplex cDNA library. Each sample was labeled by incorporating one of 16 unique three-base key codes into the 3#-cDNA fragments, and combined samples were sequenced using a GS 20 454 instrument. Transcript abundance was quantified by frequency of sequences identifying each unique mRNA. At least 202 unique transcripts showed highly significant differences in abundance between wild-type and mutant samples. For a subset of mRNAs, quantitative differences were validated by real-time reverse transcription-polymerase chain reaction. The 3#-UTR profile resolved 12 unique cellulose synthase (CesA) transcripts in maize ovaries and identified previously uncharacterized members of a histone H1 gene family. In addition, this method resolved nearly identical paralogs, as illustrated by two auxin-repressed, dormancyassociated (Arda) transcripts, which showed reciprocal mRNA abundance in wild-type and mutant samples. Our results demonstrate the potential of 3#-UTR profiling for resolving gene-and allele-specific transcripts.

show abstract

“…Tetraploidization of maize after the divergence from Sorghum created a large collection of duplicated genes. It has been reported that at least one-third of maize genes are tandemly duplicated , 1% of maize genes have at least one NIP, and 80% of maize NIP families are differentially expressed in at least one tissue (Emrich et al, 2007). ZmIPK1 can provide a system to explore the biological significance of widespread gene duplications in maize.…”

Section: Discussionmentioning

confidence: 99%

Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase from Maize: Molecular and Biochemical Characterization

Sun¹,

Thompson²,

Lin³

et al. 2007

Plant Physiol.

View full text Add to dashboard Cite

Discovery R&D, Dow AgroSciences, Indianapolis, Indiana 46268 Inositol 1,3,4,5,6-pentakisphosphate 2-kinase, an enzyme encoded by the gene IPK1, catalyzes the terminal step in the phytic acid biosynthetic pathway. We report here the isolation and characterization of IPK1 cDNA and genomic clones from maize (Zea mays). DNA Southern-blot analysis revealed that ZmIPK1 in the maize genome constitutes a small gene family with two members. Two nearly identical ZmIPK1 paralogs, designated as ZmIPK1A and ZmIPK1B, were identified. The transcripts of ZmIPK1A were detected in various maize tissues, including leaves, silks, immature ears, seeds at 12 d after pollination, midstage endosperm, and maturing embryos. However, the transcripts of ZmIPK1B were exclusively detected in roots. A variety of alternative splicing products of ZmIPK1A were discovered in maize leaves and seeds. These products are derived from alternative acceptor sites, alternative donor sites, and retained introns in the transcripts. Consequently, up to 50% of the ZmIPK1A transcripts in maize seeds and leaves have an interrupted open reading frame. In contrast, only one type of splicing product of ZmIPK1B was detected in roots. When expressed in Escherichia coli and subsequently purified, the ZmIPK1 enzyme catalyzes the conversion of myo-inositol 1,3,4,5,6-pentakisphosphate to phytic acid. In addition, it is also capable of catalyzing the phosphorylation of myo-inositol 1,4,6-trisphosphate, myo-inositol 1,4,5,6-tetrakisphosphate, and myo-inositol 3,4,5,6-tetrakisphosphate. Nuclear magnetic resonance spectroscopy analysis indicates that the phosphorylation product of myoinositol 1,4,6-trisphosphate is inositol 1,2,4,6-tetrakisphosphate. Kinetic studies showed that the K m for ZmIPK1 using myo-inositol 1,3,4,5,6-pentakisphosphate as a substrate is 119 mM with a V max at 625 nmol/min/mg. These data describing the tissue-specific accumulation and alternative splicing of the transcripts from two nearly identical ZmIPK1 paralogs suggest that maize has a highly sophisticated regulatory mechanism controlling phytic acid biosynthesis.

show abstract

Nearly Identical Paralogs: Implications for Maize (Zea mays L.) Genome Evolution

Cited by 61 publications

References 53 publications

High-Throughput Genetic Mapping of Mutants via Quantitative Single Nucleotide Polymorphism Typing

High-Throughput Genetic Mapping of Mutants via Quantitative Single Nucleotide Polymorphism Typing

Transcript Profiling by 3′-Untranslated Region Sequencing Resolves Expression of Gene Families

Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase from Maize: Molecular and Biochemical Characterization

Contact Info

Product

Resources

About