Evolution of Gene Expression after Gene Amplification

Garcia, Nelson; Zhang, Wei; Wu, Yongrui; Messing, Joachim

doi:10.1093/gbe/evv075

Cited by 6 publications

(6 citation statements)

References 36 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“… b The percentages of different prolamin species in total prolamins were from a previous study ( Ogawa et al 1987 ). c The percentage of different types of teff prolamins in total prolamins was calculated by protein band densitometry from Image J, following a previous protocol ( Garcia et al 2015 ). d Percentages of different zeins in total maize prolamins were from previous reports ( Thompson and Larkins 1994 ; Wu et al 2009 ).…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Teff, an Orphan Cereal in theChloridoideae, Provides Insights into the Evolution of Storage Proteins in Grasses

Zhang

Bennetzen

et al. 2016

Genome Biol Evol

View full text Add to dashboard Cite

Seed storage proteins (SSP) in cereals provide essential nutrition for humans and animals. Genes encoding these proteins have undergone rapid evolution in different grass species. To better understand the degree of divergence, we analyzed this gene family in the subfamily Chloridoideae, where the genome of teff (Eragrostis tef) has been sequenced. We find gene duplications, deletions, and rapid mutations in protein-coding sequences. The main SSPs in teff, like other grasses, are prolamins, here called eragrostins. Teff has γ- and δ-prolamins, but has no β-prolamins. One δ-type prolamin (δ1) in teff has higher methionine (33%) levels than in maize (23–25%). The other δ-type prolamin (δ2) has reduced methionine residues (<10%) and is phylogenetically closer to α prolamins. Prolamin δ2 in teff represents an intermediate between δ and α types that appears to have been lost in maize and other Panicoideae, and was replaced by the expansion of α-prolamins. Teff also has considerably larger numbers of α-prolamin genes, which we further divide into five sub-groups, where α2 and α5 represent the most abundant α-prolamins both in number and in expression. In addition, indolines that determine kernel softness are present in teff and the panicoid cereal called foxtail millet (Setaria italica) but not in sorghum or maize, indicating that these genes were only recently lost in some members of the Panicoideae. Moreover, this study provides not only information on the evolution of SSPs in the grass family but also the importance of α-globulins in protein aggregation and germplasm divergence.

show abstract

Section: Discussionmentioning

confidence: 99%

“… c The percentage of different types of teff prolamins in total prolamins was calculated by protein band densitometry from Image J, following a previous protocol ( Garcia et al 2015 ). …”

Section: Discussionmentioning

confidence: 99%

Teff, an Orphan Cereal in theChloridoideae, Provides Insights into the Evolution of Storage Proteins in Grasses

Zhang

Bennetzen

et al. 2016

Genome Biol Evol

View full text Add to dashboard Cite

show abstract

“…S4B). Indeed, its regulator, the transcription factor Prolamin box binding factor 1 (Pbf1), whose function is conserved across cereals (15), is also reduced in the dek seeds (Fig. S4C).…”

Section: Significancementioning

confidence: 99%

Maize defective kernel mutant generated by insertion of a Ds element in a gene encoding a highly conserved TTI2 cochaperone

Garcia

Dooner

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

We have used the newly engineered transposable element to tag a gene that gives rise to a defective kernel () phenotype. requires the autonomous element for transposition. Upon excision, it leaves a short DNA footprint that can create in-frame and frameshift insertions in coding sequences. Therefore, we could create alleles of the tagged gene that confirmed causation of the phenotype by the insertion. The mutation, designated , is embryonic lethal, has a defective basal endosperm transfer (BETL) layer, and results in a smaller seed with highly underdeveloped endosperm. The maize gene encodes a TTI2 (Tel2-interacting protein 2) molecular cochaperone. In yeast and mammals, TTI2 associates with two other cochaperones, TEL2 (Telomere maintenance 2) and TTI1 (Tel2-interacting protein 1), to form the triple T complex that regulates DNA damage response. Therefore, we cloned the maize and homologs and showed that TEL2 can interact with both TTI1 and TTI2 in yeast two-hybrid assays. The three proteins regulate the cellular levels of phosphatidylinositol 3-kinase-related kinases (PIKKs) and localize to the cytoplasm and the nucleus, consistent with known subcellular locations of PIKKs. displays reduced pollen transmission, indicating TTI2's importance in male reproductive cell development.

show abstract

“…The OMA lines were used in the cytogenetic mapping system for maize genome ( Riera-Lizarazu, Rines & Phillips, 1996 ; Maquieira, 1997 ; Kynast et al, 2001 ; Kynast et al, 2002 ; Okagaki et al, 2001 ; Koumbaris & Bass, 2003 ), gene expression ( Jin et al, 2004 ), meiotic chromosome arrangements ( Bass et al, 2000 ), investigation of conservation of gene expression of prolamin storage protein ( Garcia et al, 2015 ) as well as investigation of genes transcriptional regulation in new genomic environments ( Dong et al, 2018 ). It was shown that the majority of maize genes displayed maize-specific transcription in the oat genomic environment.…”

Section: Introductionmentioning

confidence: 99%

Complex characterization of oat (Avena sativaL.) lines obtained by wide crossing with maize (Zea maysL.)

Skrzypek

Warzecha

Noga

et al. 2018

PeerJ

View full text Add to dashboard Cite

BackgroundThe oat × maize addition (OMA) lines are used for mapping of the maize genome, the studies of centromere-specific histone (CENH3), gene expression, meiotic chromosome behavior and also for introducing maize C4 photosynthetic system to oat. The aim of our study was the identification and molecular-cytogenetic characterization of oat × maize hybrids.MethodsOat DH lines and oat × maize hybrids were obtained using the wide crossing of Avena sativa L. with Zea mays L. The plants identified as having a Grande-1 retrotransposon fragment, which produced seeds, were used for genomic in situ hybridization (GISH).ResultsA total of 138 oat lines obtained by crossing of 2,314 oat plants from 80 genotypes with maize cv. Waza were tested for the presence of maize chromosomes. The presence of maize chromatin was indicated in 66 lines by amplification of the PCR product (500 bp) generated using primers specific for the maize retrotransposon Grande-1. Genomic in situ hybridization (GISH) detected whole maize chromosomes in eight lines (40%). All of the analyzed plants possessed full complement of oat chromosomes. The number of maize chromosomes differed between the OMA lines. Four OMA lines possessed two maize chromosomes similar in size, three OMA—one maize chromosome, and one OMA—four maize chromosomes. In most of the lines, the detected chromosomes were labeled uniformly. The presence of six 45S rDNA loci was detected in oat chromosomes, but none of the added maize chromosomes in any of the lines carried 45S rDNA locus. Twenty of the analyzed lines did not possess whole maize chromosomes, but the introgression of maize chromatin in the oat chromosomes. Five of 66 hybrids were shorter in height, grassy type without panicles. Twenty-seven OMA lines were fertile and produced seeds ranging in number from 1–102 (in total 613). Sixty-three fertile DH lines, out of 72 which did not have an addition of maize chromosomes or chromatin, produced seeds in the range of 1–343 (in total 3,758). Obtained DH and OMA lines were fertile and produced seeds.DiscussionIn wide hybridization of oat with maize, the complete or incomplete chromosomes elimination of maize occur. Hybrids of oat and maize had a complete set of oat chromosomes without maize chromosomes, and a complete set of oat chromosomes with one to four retained maize chromosomes.

show abstract

Evolution of Gene Expression after Gene Amplification

Cited by 6 publications

References 36 publications

Teff, an Orphan Cereal in theChloridoideae, Provides Insights into the Evolution of Storage Proteins in Grasses

Teff, an Orphan Cereal in theChloridoideae, Provides Insights into the Evolution of Storage Proteins in Grasses

Maize defective kernel mutant generated by insertion of a Ds element in a gene encoding a highly conserved TTI2 cochaperone

Complex characterization of oat (Avena sativaL.) lines obtained by wide crossing with maize (Zea maysL.)

Contact Info

Product

Resources

About