A Tetratricopeptide Repeat Protein Regulates Carotenoid Biosynthesis and Chromoplast Development in Monkeyflowers (<i>Mimulus</i>)

Stanley, Lauren E.; Ding, Baoqing; Sun, Wei; Mou, Feng-Juan; Hill, Connor; Chen, Shilin; Yuan, Yao‐Wu

doi:10.1105/tpc.19.00755

Cited by 48 publications

(40 citation statements)

References 100 publications

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“…The same transcription factors were not found to significantly upregulate psy1 expression in these tissues, suggesting that other regulators in maize kernels remain unidentified. An R2R3-MYB transcription factor and MADS-box transcription factor were found in monkeyflower and citrus, respectively, to regulate homologs of multiple of the genes identified in this study (STANLEY et al 2020, LU et al 2018.…”

Section: Epistasis Between Identified Genesmentioning

confidence: 57%

Eleven biosynthetic genes explain the majority of natural variation for carotenoid levels in maize grain

Diepenbrock

Ilut

Magallanes‐Lundback

et al. 2020

Preprint

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Vitamin A deficiency remains prevalent in parts of Asia, Latin America and sub-Saharan Africa where maize is a food staple. Extensive natural variation exists for carotenoids in maize grain; to understand its genetic basis, we conducted a joint linkage and genome-wide association study in the U.S. maize nested association mapping panel. Eleven of the 44 detected quantitative trait loci (QTL) were resolved to individual genes. Six of these were expression QTL (eQTL), showing strong correlations between RNA-seq expression abundances and QTL allelic effect estimates across six stages of grain development. These six eQTL also had the largest percent phenotypic variance explained, and in major part comprised the three to five loci capturing the bulk of genetic variation for each trait. Most of these eQTL had highly correlated QTL allelic effect estimates across multiple traits, suggesting that pleiotropy within this pathway is largely regulated at the expression level. Significant pairwise epistatic interactions were also detected. These findings provide the most comprehensive genome-level understanding of the genetic and molecular control of carotenoids in any plant system, and a roadmap to accelerate breeding for provitamin A and other priority carotenoid traits in maize grain that should be readily extensible to other cereals.

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Section: Epistasis Between Identified Genesmentioning

confidence: 57%

Eleven biosynthetic genes explain the majority of natural variation for carotenoid levels in maize grain

Diepenbrock

Ilut

Magallanes‐Lundback

et al. 2020

Preprint

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“…Little is known of specific fruit retrograde signals that coordinate the expression of chloroplast‐targeted genes, at plastid biogenesis, including the transition from chloroplasts to chromoplasts (Pesaresi et al ., ). Related to our findings, a tetratricopeptide repeat protein (TPR) was recently shown to affect carotenoid biosynthesis and chloroplast development in Monkeyflowers, and was proposed to act through the chromoplast‐to‐nucleus retrograde signaling (Stanley et al ., ). The TPR family contains motifs that are related to the PPR (Small and Peeters, ).…”

Section: Discussionmentioning

confidence: 97%

Deciphering genetic factors that determine melon fruit‐quality traits using RNA‐Seq‐based high‐resolution QTL and eQTL mapping

et al. 2018

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Combined quantitative trait loci (QTL) and expression-QTL (eQTL) mapping analysis was performed to identify genetic factors affecting melon (Cucumis melo) fruit quality, by linking genotypic, metabolic and transcriptomic data from a melon recombinant inbred line (RIL) population. RNA sequencing (RNA-Seq) of fruit from 96 RILs yielded a highly saturated collection of > 58 000 single-nucleotide polymorphisms, identifying 6636 recombination events that separated the genome into 3663 genomic bins. Bin-based QTL analysis of 79 RILs and 129 fruit-quality traits affecting taste, aroma and color resulted in the mapping of 241 QTL. Thiol acyltransferase (CmThAT1) gene was identified within the QTL interval of its product, S-methyl-thioacetate, a key component of melon fruit aroma. Metabolic activity of CmThAT1-encoded protein was validated in bacteria and in vitro. QTL analysis of flesh color intensity identified a candidate white-flesh gene (CmPPR1), one of two major loci determining fruit flesh color in melon. CmPPR1 encodes a member of the pentatricopeptide protein family, involved in processing of RNA in plastids, where carotenoid and chlorophyll pigments accumulate. Network analysis of > 12 000 eQTL mapped for > 8000 differentially expressed fruit genes supported the role of CmPPR1 in determining the expression level of plastid targeted genes. We highlight the potential of RNA-Seq-based QTL analysis of small to moderate size, advanced RIL populations for precise marker-assisted breeding and gene discovery. We provide the following resources: a RIL population genotyped with a unique set of SNP markers, confined genomic segments that harbor QTL governing 129 traits and a saturated set of melon eQTLs.

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“…Another tetratricopeptide repeat protein, RCP2, was recently found to regulate carotenoid accumulation in the floral tissues of monkeyflowers [ 27 ]. While TPR proteins participate in diverse eukaryotic cell processes through mediating versatile protein–protein interactions [ 28 ], the intriguing possibility of molecular parallels between plant and animal colouration calls for further study.…”

Section: Discussionmentioning

confidence: 99%

Expression levels of the tetratricopeptide repeat protein gene ttc39b covary with carotenoid-based skin colour in cichlid fish

et al. 2020

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Carotenoid pigments play a major role in animal body colouration, generating strong interest in the genes involved in the metabolic processes that lead from their dietary uptake to their storage in the integument. Here, we used RNA sequencing (RNA-Seq) to test for differentially expressed genes in a taxonomically replicated design using three pairs of related cichlid fish taxa from the genera Tropheus and Aulonocara . Within each pair, taxa differed in terms of red and yellow body colouration, and high‐performance liquid chromatography (HPLC) analyses of skin extracts revealed different carotenoid profiles and concentrations across the studied taxa. Five genes were differentially expressed in all three yellow–red skin contrasts ( dhrsx , nlrc3 , tcaf2 , urah and ttc39b ), but only the tetratricopeptide repeat protein-coding gene ttc39b , whose gene product is linked to mammalian lipid metabolism, was consistently expressed more highly in the red skin samples. The RNA-Seq results were confirmed by quantitative PCR. We propose ttc39b as a compelling candidate gene for variation in animal carotenoid colouration. Since differential expression of ttc39b was correlated with the presence/absence of yellow carotenoids in a previous study, we suggest that ttc39b is more likely associated with the concentration of total carotenoids than with the metabolic formation of red carotenoids.

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A Tetratricopeptide Repeat Protein Regulates Carotenoid Biosynthesis and Chromoplast Development in Monkeyflowers (Mimulus)

Abstract: One-sentence summary: Mutant analysis and transgenic experiments in the model plant 19 monkeyflower (Mimulus) identify a tetratricopeptide repeat protein required for chromoplast 20 development and carotenoid biosynthesis.

Cited by 48 publications

References 100 publications

Eleven biosynthetic genes explain the majority of natural variation for carotenoid levels in maize grain

Eleven biosynthetic genes explain the majority of natural variation for carotenoid levels in maize grain

Deciphering genetic factors that determine melon fruit‐quality traits using RNA‐Seq‐based high‐resolution QTL and eQTL mapping

Expression levels of the tetratricopeptide repeat protein gene ttc39b covary with carotenoid-based skin colour in cichlid fish

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