A functional chromogen gene C from wild rice is involved in a different anthocyanin biosynthesis pathway in indica and japonica

Qiao, Weihua; Wang, Yanyan; Xu, Rui; Yang, Ziyi; Sun, Yanyan; Su, Long; Zhang, Lizhen; Wang, Junrui; Huang, Jingfen; Zheng, Xiaoming; Liu, Shijia; Tian, Yunlu; Chen, Liangming; Liu, Xi; Lan, Jinhao; Yang, Qingwen

doi:10.1007/s00122-021-03787-1

Cited by 10 publications

(3 citation statements)

References 40 publications

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“…QTL mapping was performed based on phenotype and genotype association using the two CSSL populations described above. Some genes associated with domestication-related traits, such as sd1 for plant height 31 , 32 , sh4 for seed shattering 33 , and C1 for red or purple coloration 34 , 35 , were observed in the CSSL populations and fine-mapped to their exact positions (Supplementary Fig. 10 ).…”

Section: Resultsmentioning

confidence: 99%

Haplotype-resolved gapless genome and chromosome segment substitution lines facilitate gene identification in wild rice

Huang,

Zhang,

et al. 2024

Nat Commun

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The abundant genetic variation harbored by wild rice (Oryza rufipogon) has provided a reservoir of useful genes for rice breeding. However, the genome of wild rice has not yet been comprehensively assessed. Here, we report the haplotype-resolved gapless genome assembly and annotation of wild rice Y476. In addition, we develop two sets of chromosome segment substitution lines (CSSLs) using Y476 as the donor parent and cultivated rice as the recurrent parents. By analyzing the gapless reference genome and CSSL population, we identify 254 QTLs associated with agronomic traits, biotic and abiotic stresses. We clone a receptor-like kinase gene associated with rice blast resistance and confirm its wild rice allele improves rice blast resistance. Collectively, our study provides a haplotype-resolved gapless reference genome and demonstrates a highly efficient platform for gene identification from wild rice.

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Section: Resultsmentioning

confidence: 99%

Haplotype-resolved gapless genome and chromosome segment substitution lines facilitate gene identification in wild rice

Huang,

Zhang,

et al. 2024

Nat Commun

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“…The C - S - A gene system regulates rice hull color, involving C1 encoding the R2R3 MYB transcription factor, S1 encoding the bHLH protein and functioning tissue-specific, and A1 encoding a dihydroflavonol reductase has been proposed (Sun et al 2018 ; Qiao et al 2021 ). A protein–protein interaction occurs between the bHLH and R2R3 MYB domains, activating downstream genes in the structural anthocyanin biosynthesis pathway (Kim et al 2021 ; Kong et al 2012 ).…”

Section: Resultsmentioning

confidence: 99%

Flavonoid Metabolic Profiles and Gene Mapping of Rice (Oryza sativa L.) Purple Gradient Grain Hulls

Zhang

Yang

Huang

et al. 2022

Rice

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Rice (Oryza sativa L.) grain hull color is an easily observable trait and regarded as a crucial morphological marker in rice breeding. Here, a purple gradient grain hull mutant (pg) was found from natural mutations of a straw-white grain hull rice variety IARI 6184B (Orzya sativa L. subsp. indica). The color of the mutant grain hulls changed from straw-white to pink, then purple, and finally brownish-yellow. Ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) identified 217 flavonoids, including 18 anthocyanins, among which cyanidin O-syringic acid had the highest concentration in pink (66.2 × 106) and purple (68.0 × 106) grain hulls. The relative contents of hesperetin O-malonyl-hexoside, apigenin derivatives, genistein derivatives, and kaempferol 3-O derivatives were consistently downregulated during pg grain hull development. Conversely, 12 anthocyanins were upregulated in colored hulls, and cyanidin 3-O-malonylhexoside was abundant only in pink and purple grain hulls. Moreover, the candidate gene was mapped into a 1.38 Mb region on chromosome 4 through bulked segregant analysis based on deep sequencing (BSA-seq) and gene mapping approaches. These results increased our understanding of anthocyanin biosynthesis in rice grains, helping rice breeders to select new rice varieties with desirable grain traits.

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“…The QTLs mapping was performed based on the phenotype and genotype association using these two CSSL populations. Some domestication-related trait associated genes, such as sd1 for plant height 18,19 , sh4 for seeds shattering 20 , and C1 for red or purple traits 21,22 , were observed in these two CSSL populations and easily ne mapped on their exact positions (Supplementary Fig. 11).…”

Section: Development Of Chromosome Segments Substitution Lines In Dif...mentioning

confidence: 99%

Telomere-to-telomere gap-free genome assembly and chromosome segment substitution lines facilitated gene identification in wild rice

Huang

Zhang

et al. 2023

Preprint

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The abounding variations hidden in wild rice (Oryza rufipogon) provided potential reservoirs of useful genes for rice breeding. However, the genome of wild rice has not yet been comprehensively assessed. In this study, we constructed the telomere-to-telomere (T2T) genome assembly and annotation of wild rice Y476 with a total length of 421.1 Mb and 38,055 predicted protein-coding genes, which features evident improvements in the continuity and quality of sequence compared with the existing wild rice genomes. Of Y476 genome assembly, 128 Mb and 5,984 novel genes were not found in ‘Nipponbare’ reference, leading to 690 gene families expanded and 247 gene families contracted, including disease resistance and grain regulation gene family. Two sets of chromosome segments substitution lines (CSSLs) were constructed, using Y476 as the donor parent and cultivated rice as the recurrent parents, covering the whole genome of Y476, providing materials for introducing novel genes and identification of their function. Combining the T2T reference genome and CSSL population, 254 QTLs associated with agronomic traits, biotic and abiotic stresses were identified. A receptor-like kinase gene associated with rice blast resistance was identified, a 7.8-kb insertion was found in the intron of this gene which increased its expression level. Using CRISPR/Cas9 technology and transcriptomic data, we confirmed that this wild rice allele improves rice blast resistance via regulating OsMADS26 expression. Collectively, our findings provided not only a T2T gap-free reference genome but also a highly efficient platform for novel gene identification of O. rufipogon, and therefore, have important implications for wild rice utilization.

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A functional chromogen gene C from wild rice is involved in a different anthocyanin biosynthesis pathway in indica and japonica

Cited by 10 publications

References 40 publications

Haplotype-resolved gapless genome and chromosome segment substitution lines facilitate gene identification in wild rice

Haplotype-resolved gapless genome and chromosome segment substitution lines facilitate gene identification in wild rice

Flavonoid Metabolic Profiles and Gene Mapping of Rice (Oryza sativa L.) Purple Gradient Grain Hulls

Telomere-to-telomere gap-free genome assembly and chromosome segment substitution lines facilitated gene identification in wild rice

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