Complementary Genes That Cause Black Ripening Hulls in F1Plants of Crosses betweenIndicaandJaponicaRice Cultivars

Fukuda, Akari; Shimizu, H.; Shiratsuchi, Hiroyuki; Yamaguchi, Hiromichi; Ohdaira, Youichi; Mochida, Hideyuki

doi:10.1626/pps.15.270

Cited by 13 publications

(16 citation statements)

References 15 publications

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“…( Figure S2A, S2B). These deletions are identical to those reported in other japonica cultivars (Fukuda et al, 2012). In addition, these deletions were reported to cause loss-of-function in the respective genes (Yu et al, 2008;Zhu et al, 2011).…”

Section: Identifying Candidate Genes Involved In Seed Hull Color Epissupporting

confidence: 83%

“…Thus, we conclude that Kaluheenati maintains the function of BH4 and Phr1, and Hitomebore cultivar probably lost their functions. Using a crossed line between an indica type cultivar "Habataki" and japonica type cultivar "Arroz da Terra", Fukuda et al (2012) reported that both BH4 and Phr1 are necessary for maintaining black hull phenotype. BH4 encodes a tyrosine transporter and Phr1 encodes a polyphenol oxidase of the tyrosinase family (Yu et al, 2008;Zhu et al, 2011).…”

Section: Identifying Candidate Genes Involved In Seed Hull Color Epismentioning

confidence: 99%

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RIL-StEp: epistasis analysis of recombinant inbred lines (RILs) reveals candidate interacting genes that control rice seed hull color

Sakai

Abe

Shimizu

et al. 2020

Preprint

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Studying epistatic gene interactions is important in understanding genetic architecture of complex traits in organisms. However, due to an enormous number of gene combinations to be analyzed, detection of epistatic gene-gene interactions has been computationally demanding. Here, we show a simple approach RIL-StEp, specialized to Recombinant Inbred Lines (RILs), to study epistasis using single nucleotide polymorphisms (SNPs) information of the genome. We applied the method to reveal epistasis affecting rice seed hull color phenotype, and successfully identified gene pairs that presumably control seed hull color. This method has a potential to enhancing our understanding of genetic architecture of various traits.

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Section: Identifying Candidate Genes Involved In Seed Hull Color Epissupporting

confidence: 83%

Section: Identifying Candidate Genes Involved In Seed Hull Color Epismentioning

confidence: 99%

RIL-StEp: epistasis analysis of recombinant inbred lines (RILs) reveals candidate interacting genes that control rice seed hull color

Sakai

Abe

Shimizu

et al. 2020

Preprint

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“…In plants, PPOs have been implicated in the browning response of damaged tissue, but their role in intact tissue is uncertain 27 . Some evidence has been presented to suggest that they participate in the synthesis of dark pigments in the rice husk 31 , but these particular pigments have not as yet been shown to be melanin.…”

Section: Discussionmentioning

confidence: 99%

Melanin formation in barley grain occurs within plastids of pericarp and husk cells

Shoeva

Mursalimov

Gracheva

et al. 2020

Sci Rep

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Melanins are a class of darkly pigmented biopolymers which are widely distributed among living organisms. the molecular and cellular mechanisms adopted by bacteria, fungi and animals to synthesize melanin, have been well described, but less is known regarding their production in plants. Here, a pair of barley near isogenic lines, bred to differ with respect to the pigmentation of the spike, was compared in order to understand the tissue and cellular location of melanin deposition. the melanic nature of the pigments purified from black spikes was confirmed by a series of solubility tests and Fourier transform infrared spectroscopy. An analysis of grains harvested at various stages of their development revealed that intracellular pigmented structures first appeared in the pericarp and the husk of black spike plants at early dough stage. The co-localization of these structures with red autofluorescence suggested that they form in chloroplast-derived plastids, here designated "melanoplasts". Differences in dynamics of plastid internal structure during grain ripening were detected between the lines by transmission electron microscopy. Both lines accumulated plastoglobuli inside plastids, which persisted in black grain pericarp tissue up to the hard dough stage, while neither plastoglobuli nor any plastids were observed in grain of the control line at this stage. the role of plastoglobuli in melanin synthesis is discussed.

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“…The black hull phenotype is controlled by at least two complementary genes that are linked in a cluster of domestication-related genes on rice chromosome 4 ( Fukuda et al, 2012 ). The gene Black Hull 4 (BH4) encodes a tyrosine transporter ( Zhu et al, 2011 ), and Phenol Reaction (Ph) encodes the polyphenol oxidase (PPO) enzyme which uses tyrosine as a substrate ( Yu et al, 2008 ; Table 4 and Figure 4 ).…”

Section: Resultsmentioning

confidence: 99%

A Coordinated Suite of Wild-Introgression Lines in Indica and Japonica Elite Backgrounds

Singh

Wang

Ali³

et al. 2020

Front. Plant Sci.

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Rice, Oryza sativa L., is a cultivated, inbreeding species that serves as the staple food for the largest number of people on earth. It has two strongly diverged varietal groups, Indica and Japonica, which result from a combination of natural and human selection. The genetic divergence of these groups reflects the underlying population structure of their wild ancestors, and suggests that a pre-breeding strategy designed to take advantage of existing genetic, geographic and ecological substructure may provide a rational approach to the utilization of crop wild ancestors in plant improvement. Here we describe the coordinated development of six introgression libraries (n = 63 to 81 lines per library) in both Indica (cv. IR64) and Japonica (cv. Cybonnet) backgrounds using three bio-geographically diverse wild donors representing the Oryza rufipogon Species Complex from China, Laos and Indonesia. The final libraries were genotyped using an Infinium 7K rice SNP array (C7AIR) and analyzed under greenhouse conditions for several simply inherited (Mendelian) traits. These six interspecific populations can be used as individual Chromosome Segment Substitution Line libraries and, when considered together, serve as a powerful genetic resource for systematic genetic dissection of agronomic, physiological and developmental traits in rice.

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Complementary Genes That Cause Black Ripening Hulls in F₁Plants of Crosses betweenIndicaandJaponicaRice Cultivars

Cited by 13 publications

References 15 publications

RIL-StEp: epistasis analysis of recombinant inbred lines (RILs) reveals candidate interacting genes that control rice seed hull color

RIL-StEp: epistasis analysis of recombinant inbred lines (RILs) reveals candidate interacting genes that control rice seed hull color

Melanin formation in barley grain occurs within plastids of pericarp and husk cells

A Coordinated Suite of Wild-Introgression Lines in Indica and Japonica Elite Backgrounds

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