Molecular regulation of seed development and strategies for engineering seed size in crop plants

Savadi, Siddanna

doi:10.1007/s10725-017-0355-3

Cited by 41 publications

(37 citation statements)

References 192 publications

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“…AGL62 (XS03G11771) encodes a MADS domain transcription factor, controlling cellularization during endosperm development [81]. Another MADS gene, PHERES1 (XS14G07914), has also been proven to be involved in seed development [82]. In addition, DIVARICATA (XS07G17645), a MYB family transcription factor controlling the dorsoventral asymmetry of flowers in Antirrhinum , was specifically expressed in hermaphrodite flower, implying that the regulatory mechanisms underlying corolla formation in the 2 flower types of yellowhorn might be different [83].…”

Section: Resultsmentioning

confidence: 99%

The genome assembly and annotation of yellowhorn (Xanthoceras sorbifolium Bunge)

Qiang

Li³

et al. 2019

GigaScience

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Background Yellowhorn ( Xanthoceras sorbifolium Bunge), a deciduous shrub or small tree native to north China, is of great economic value. Seeds of yellowhorn are rich in oil containing unsaturated long-chain fatty acids that have been used for producing edible oil and nervonic acid capsules. However, the lack of a high-quality genome sequence hampers the understanding of its evolution and gene functions. Findings In this study, a whole genome of yellowhorn was sequenced and assembled by integration of Illumina sequencing, Pacific Biosciences single-molecule real-time sequencing, 10X Genomics linked reads, Bionano optical maps, and Hi-C. The yellowhorn genome assembly was 439.97 Mb, which comprised 15 pseudo-chromosomes covering 95.42% (419.84 Mb) of the assembled genome. The repetitive fractions accounted for 56.39% of the yellowhorn genome. The genome contained 21,059 protein-coding genes. Of them, 18,503 (87.86%) genes were found to be functionally annotated with ≥1 "annotation" term by searching against other databases. Transcriptomic analysis showed that 341, 135, 125, 113, and 100 genes were specifically expressed in hermaphrodite flower, staminate flower, young fruit, leaf, and shoot, respectively. Phylogenetic analysis suggested that yellowhorn and Dimocarpus longan diverged from their most recent common ancestor ∼46 million years ago. Conclusions The availability and subsequent annotation of the yellowhorn genome, as well as the identification of tissue-specific functional genes, provides a valuable reference for plant comparative genomics, evolutionary studies, and molecular design breeding.

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Section: Resultsmentioning

confidence: 99%

The genome assembly and annotation of yellowhorn (Xanthoceras sorbifolium Bunge)

Qiang

Li³

et al. 2019

GigaScience

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“…For crops with seeds as the final target of production (for example, rice, wheat and soybean), seed size is also the determinant of productivity and yield (Fan et al, 2006;Chettoor et al, 2016;Hu et al, 2018). As such, increase of seed size has been one of the primary goals in breeding in cereal crops (Zhang et al, 2016;Savadi, 2018).…”

Section: Introductionmentioning

confidence: 99%

Quantitative Trait Loci for Seed Size Variation in Cucurbits – A Review

et al. 2020

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Cucurbits (Cucurbitaceae family) include many economically important fruit vegetable crops such as watermelon, pumpkin/squash, cucumber, and melon. Seed size (SS) is an important trait in cucurbits breeding, which is controlled by quantitative trait loci (QTL). Recent advances have deciphered several signaling pathways underlying seed size variation in model plants such as Arabidopsis and rice, but little is known on the genetic basis of SS variation in cucurbits. Here we conducted literature review on seed size QTL identified in watermelon, pumpkin/squash, cucumber and melon, and inferred 14, 9 and 13 consensus SS QTL based on their physical positions in respective draft genomes. Among them, four from watermelon (ClSS2.2, ClSS6.1, ClSS6.2, and ClSS8.2), two from cucumber (CsSS4.1 and CsSS5.1), and one from melon (CmSS11.1) were majoreffect, stable QTL for seed size and weight. Whole genome sequence alignment revealed that these major-effect QTL were located in syntenic regions across different genomes suggesting possible structural and functional conservation of some important genes for seed size control in cucurbit crops. Annotation of genes in the four watermelon consensus SS QTL regions identified genes that are known to play important roles in seed size control including members of the zinc finger protein and the E3 ubiquitinprotein ligase families. The present work highlights the utility of comparative analysis in understanding the genetic basis of seed size variation, which may help future mapping and cloning of seed size QTL in cucurbits.

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“…Seed or grain development is one of the most crucial processes in plant development. It not only determines the successful racial continuation of seed plants, but also affects the final seed yield and seed quality [1,2]. Generally, seed development can be broadly divided into two phases: Embryogenesis and maturation [3,4].…”

Section: Introductionmentioning

confidence: 99%

“…Seed development is predominantly regulated by genetic factors and is also greatly influenced by physiological pathways and environmental cues. At the physiological level, phytohormones—including auxins, cytokinins (CKs), gibberellins (GAs), brassinolides (BRs), abscisic acid (ABA), and ethylene (ET)—contribute to seed development [2]. At the molecular level, in the past two decades, many genes involved in seed development have been identified and their molecular pathways deciphered in the model plants Arabidopsis and rice through analysis of mutants, transcriptomes, and quantitative trait locus (QTLs) [2,5,6,7,8,9].…”

Section: Introductionmentioning

confidence: 99%

“…At the physiological level, phytohormones—including auxins, cytokinins (CKs), gibberellins (GAs), brassinolides (BRs), abscisic acid (ABA), and ethylene (ET)—contribute to seed development [2]. At the molecular level, in the past two decades, many genes involved in seed development have been identified and their molecular pathways deciphered in the model plants Arabidopsis and rice through analysis of mutants, transcriptomes, and quantitative trait locus (QTLs) [2,5,6,7,8,9]. Furthermore, in the last few years, investigations of the molecular mechanisms of seed development have also been undertaken in some crop plants such as maize [10,11], wheat [12,13], soybean [14,15,16], barley [4], Tartary buckwheat [17,18], chickpea [19], and Brassica napus [20,21] by transcriptome analysis.…”

Section: Introductionmentioning

confidence: 99%

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Transcriptome Analysis Reveals Key Seed-Development Genes in Common Buckwheat (Fagopyrum esculentum)

Deng

et al. 2019

IJMS

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Seed development is an essential and complex process, which is involved in seed size change and various nutrients accumulation, and determines crop yield and quality. Common buckwheat (Fagopyrum esculentum Moench) is a widely cultivated minor crop with excellent economic and nutritional value in temperate zones. However, little is known about the molecular mechanisms of seed development in common buckwheat (Fagopyrum esculentum). In this study, we performed RNA-Seq to investigate the transcriptional dynamics and identify the key genes involved in common buckwheat seed development at three different developmental stages. A total of 4619 differentially expressed genes (DEGs) were identified. Based on the results of Gene Ontology (GO) and KEGG analysis of DEGs, many key genes involved in the seed development, including the Ca2+ signal transduction pathway, the hormone signal transduction pathways, transcription factors (TFs), and starch biosynthesis-related genes, were identified. More importantly, 18 DEGs were identified as the key candidate genes for seed size through homologous query using the known seed size-related genes from different seed plants. Furthermore, 15 DEGs from these identified as the key genes of seed development were selected to confirm the validity of the data by using quantitative real-time PCR (qRT-PCR), and the results show high consistency with the RNA-Seq results. Taken together, our results revealed the underlying molecular mechanisms of common buckwheat seed development and could provide valuable information for further studies, especially for common buckwheat seed improvement.

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Molecular regulation of seed development and strategies for engineering seed size in crop plants

Cited by 41 publications

References 192 publications

The genome assembly and annotation of yellowhorn (Xanthoceras sorbifolium Bunge)

The genome assembly and annotation of yellowhorn (Xanthoceras sorbifolium Bunge)

Quantitative Trait Loci for Seed Size Variation in Cucurbits – A Review

Transcriptome Analysis Reveals Key Seed-Development Genes in Common Buckwheat (Fagopyrum esculentum)

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