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

Sakai, Toshiyuki; Abe, Akira; Shimizu, Mitsuru; Terauchi, Ryohei

doi:10.1101/2020.06.09.141697

Cited by 2 publications

(2 citation statements)

References 55 publications

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“…Varga et al [ 15 ] found that the component of melanin in oat bracts was homopolymer of p -coumaric acid, one of the key intermediates in the anthocyanin biosynthesis pathway with phenylalanine as a precursor, which was catalyzed by cinnamate 4-hydroxylase (C4H) [ 16 , 17 ]. In wild rice, black is considered to be the original color in the bracts controlled by two complementary genes— Bh4 ( black hull 4 ) and Phr1 ( phenol reaction 1 )—encoding a tyrosine transporter and a polyphenol oxidase, respectively, which are involved in melanin biosynthesis [ 18 , 19 , 20 , 21 ]. Notably, recent studies have shown that the formation of melanin in barley ( Hordeum vulgare L.) bracts occurred in chloroplasts [ 22 ].…”

Section: Introductionmentioning

confidence: 99%

PSII Activity Was Inhibited at Flowering Stage with Developing Black Bracts of Oat

Liu

Zhang

Sun

et al. 2021

IJMS

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The color of bracts generally turns yellow or black from green during cereal grain development. However, the impact of these phenotypic changes on photosynthetic physiology during black bract formation remains unclear. Two oat cultivars (Avena sativa L.), ‘Triple Crown’ and ‘Qinghai 444’, with yellow and black bracts, respectively, were found to both have green bracts at the heading stage, but started to turn black at the flowering stage and become blackened at the milk stage for ‘Qinghai 444’. Their photosynthetic characteristics were analyzed and compared, and the key genes, proteins and regulatory pathways affecting photosynthetic physiology were determined in ‘Triple Crown’ and ‘Qinghai 444’ bracts. The results show that the actual PSII photochemical efficiency and PSII electron transfer rate of ‘Qinghai 444’ bracts had no significant changes at the heading and milk stages but decreased significantly (p < 0.05) at the flowering stage compared with ‘Triple Crown’. The chlorophyll content decreased, the LHCII involved in the assembly of supercomplexes in the thylakoid membrane was inhibited, and the expression of Lhcb1 and Lhcb5 was downregulated at the flowering stage. During this critical stage, the expression of Bh4 and C4H was upregulated, and the biosynthetic pathway of p-coumaric acid using tyrosine and phenylalanine as precursors was also enhanced. Moreover, the key upregulated genes (CHS, CHI and F3H) of anthocyanin biosynthesis might complement the impaired PSII activity until recovered at the milk stage. These findings provide a new insight into how photosynthesis alters during the process of oat bract color transition to black.

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Section: Introductionmentioning

confidence: 99%

PSII Activity Was Inhibited at Flowering Stage with Developing Black Bracts of Oat

Liu

Zhang

Sun

et al. 2021

IJMS

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“…Genotyping of RILs by whole-genome resequencing To obtain the genotypes of the RILs, we performed whole-genome resequencing of the parents and 125 RILs using the Illumina DNA sequencing platform. Genotyping of RILs was carried out according to the method described by Sakai et al (2021).…”

Section: Pikps-1 Rnaimentioning

confidence: 99%

Isolation of Pikps, an allele of Pik, from the aus rice cultivar Shoni

et al. 2022

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Blast disease caused by the filamentous fungus Pyricularia oryzae (syn. Magnaporthe oryzae) is one of the most destructive diseases of rice (Oryza sativa L.) around the globe. An aus cultivar, Shoni, showed resistance against at least four Japanese P. oryzae isolates. To understand Shoni's resistance against the P. oryzae isolate Naga69-150, genetic analysis was carried out using recombinant inbred lines developed by a cross between Shoni and the japonica cultivar Hitomebore, which is susceptible to Naga69-150. The result indicated that the resistance was controlled by a single locus, which was named Pi-Shoni. A QTL analysis identified Pi-Shoni as being located in the telomeric region of chromosome 11. A candidate gene approach in the region indicated that Pi-Shoni corresponds to the previously cloned Pik locus, and we named this allele Pikps. Loss of gene function mediated by RNA interference demonstrated that a head-to-head-orientated pair of NBS-LRR receptor genes (Pikps-1 and Pikps-2) are required for the Pikps-mediated resistance. Amino acid sequence comparison showed that Pikps-1 is 99% identical to Pikp-1, while Pikps-2 is identical to Pikp-2. Pikps-1 had one amino acid substitution (Pro351Ser) in the NBS domain as compared to Pikp-1. The recognition specificity of Pikps against known AVR-Pik alleles is identical to that of Pikp.

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

Cited by 2 publications

References 55 publications

PSII Activity Was Inhibited at Flowering Stage with Developing Black Bracts of Oat

PSII Activity Was Inhibited at Flowering Stage with Developing Black Bracts of Oat

Isolation of <i>Pikps</i>, an allele of <i>Pik</i>, from the <i>aus</i> rice cultivar Shoni

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