The C–S–A gene system regulates hull pigmentation and reveals evolution of anthocyanin biosynthesis pathway in rice

Sun, Xiaotao; Zhang, Zhanying; Chen, Chao; Wu, Wei; Ren, Nannan; Jiang, Conghui; Yu, Jianping; Zhao, Yan; Zheng, Xiaoming; Yang, Qingwen; Zhang, Hongliang; Li, Jinjie

doi:10.1093/jxb/ery001

Cited by 116 publications

(152 citation statements)

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“…The origin of cultivated rice is a continuing, controversial issue with variable lines of evidence for single and multiple origins. Multiple origins are currently supported by most academics (Choi et al ., ; Londo et al ., ; Sun et al ., ). Therefore, by combing previous studies and our results, we speculate that proto ‐japonica from wild rice in Southern China went through the An‐1 and GLA domestication steps prior to japonica/indica differentiation and produced domesticated proto ‐japonica varieties with the an‐1/gla genotype.…”

Section: Discussionmentioning

confidence: 97%

“…The reaction product was diluted three times as template. Quantitative RT‐PCR (qRT‐PCR) was carried out as previously reported (Sun et al ., ). OsActin1 was used for internal reference (Data S1).…”

Section: Methodsmentioning

confidence: 97%

“…The InDel1 and InDel3 alleles of GLA in 371 rice accessions (Data S2) were analysed from the sequencing results and then subjected to genotyping. Group analyses were carried out as previously reported (Sun et al ., ).…”

Section: Methodsmentioning

confidence: 97%

“…The 358 accessions (143 landraces and 215 improved accessions; Data S2 and S5) were analysed for the An‐1 , An‐2 and GLA functional loci controlling grain length or awn development and genotyped as non‐functional or functional alleles (Sun et al ., ).…”

Section: Methodsmentioning

confidence: 97%

“…ProGLA , Progla and Pro35S::LUC plasmid used as an internal control were co‐transferred into tobacco leaves. The ratios of GUS/LUC (luciferase) were used as relative promoter activities (Sun et al ., ; Zhang et al ., ). Three biological repeats, each with four technical replicates were analysed for each vector.…”

Section: Methodsmentioning

confidence: 99%

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Natural alleles of GLA for grain length and awn development were differently domesticated in rice subspecies japonica and indica

Zhang

Sun

et al. 2019

Plant Biotechnology Journal

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Summary Rice ( Oryza sativa L.) cultivars harbour morphological and physiological traits different from those of wild rice ( O. rufipogon Griff.), but the molecular mechanisms underlying domestication remain controversial. Here, we show that awn and long grain traits in the near‐isogenic NIL ‐ GLA are separately controlled by variations within the GLA ( Grain Length and Awn Development ) gene, a new allele of GAD 1 / RAE 2 , which encodes one member of the EFPL (epidermal patterning factor‐like protein) family. Haplotype analyses and transgenic studies revealed that InDel1 (variation for grain length, VGL ) in the promoter region of GLA ( GLA VGL ) increases grain length by promoting transcription of GLA . Absence of InDel3 (variation for awn formation, VA ) in the coding region ( CDS ) of GLA ( GLA va ) results in short awn or no awn phenotypes. Analyses of minimum spanning trees and introgression regions demonstrated that An‐1 , an important gene for awn formation, was preferentially domesticated and its mutation to an‐1 was followed by GLA and An‐2 . Gene flow then occurred between the evolved japonica and indica populations. Quality analysis showed that GLA causes poor grain quality. During genetic improvement, awnlessness was selected in ssp. indica , whereas short–grained and awnless phenotypes with good quality were selected in japonica . Our findings facilitate an understanding of rice domestication and provide a favourable allele for rice breeding.

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Section: Discussionmentioning

confidence: 97%

Section: Methodsmentioning

confidence: 97%

Section: Methodsmentioning

confidence: 97%

Section: Methodsmentioning

confidence: 97%

Section: Methodsmentioning

confidence: 99%

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Natural alleles of GLA for grain length and awn development were differently domesticated in rice subspecies japonica and indica

Zhang

Sun

et al. 2019

Plant Biotechnology Journal

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MYB Genes Involved in Domestication and Crop Improvement

Albert

Allan

2021

Annual Plant Reviews Online

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Domestication of the world's crop species has been achieved through improvements in yield, and product qualities, with or without the guidance of scientific knowledge. These selection pressures are applied by breeders (and before them, farmers) both intentionally and unintentionally to improve crop features, which have often been grouped into ‘production traits’ and ‘quality traits’. New approaches to breeding that incorporate genome sequencing, mapping, and identification of genes underlying traits have revealed new variants in the family of transcription factors (TFs) called MYBs as driving important features in both these categories of domestication traits. In this article, we review the progress in understanding the role of MYB TFs in crop performance, as well as reasons to predict further gains in yield and quality centred on the MYB TF family.

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Candidate genes for anthocyanin pigmentation in rice stem revealed by GWAS and whole‐genome resequencing

et al. 2022

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Anthocyanin pigment as a phenolic secondary metabolite is accumulated in areal organs of some rice cultivars. Despite several research attempts, the majority of genomic regions and candidate genes for purple‐colored stem (Ps) resulting from anthocyanin pigmentation of rice leaf sheath have not been identified. A genome‐wide association study (GWAS) and whole‐genome resequencing (WGR) analysis was applied for genetic dissection of anthocyanin pigmentation of rice stem. Using GWAS, the genomic regions (on chromosomes 2, 4, and 6) tagged to eight single‐nucleotide polymorphisms (SNPs) were identified to be significantly associated with purple stem, and in the vicinity of GWAS signals, 19 genes were highlighted as putative candidate genes. To narrow down the genomic regions more highly associated to the trait, a WGR study on recombinant inbred lines (RIL) with opposite phenotypes was conducted. After defining the DNA variation between reference genome, maternal parent and the two sister lines, a narrow genomic region on the short arm of chromosome 6 (4.7–6.2 Mbp interval) was identified to be highly associated with anthocyanin pigmentation of rice stem. In the interval, a few candidate genes with probable role in anthocyanin biosynthesis and accumulation were identified, which included five structural genes involved in the known pathways [one chalcone isomerase (CHI), two glycosyl transferases, and two UDP‐flavonoid‐3‐O‐glucosyl (UFGT) transferases] and two transcription factors [one basic helix–loop–helix (bHLH)‐ and one myeloblastosis (MYB)‐coding genes]. The identified candidate genes can be used in breeding programs of rice or other Gramineae species for anthocyanin accumulation in areal organs.

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The C–S–A gene system regulates hull pigmentation and reveals evolution of anthocyanin biosynthesis pathway in rice

Abstract: The C–S–A gene system determines rice hull pigmentation. A conserved color-producing model reveals the independent origin and evolution of the anthocyanin biosynthesis pathway in rice.

Cited by 116 publications

References 46 publications

Natural alleles of GLA for grain length and awn development were differently domesticated in rice subspecies japonica and indica

Natural alleles of GLA for grain length and awn development were differently domesticated in rice subspecies japonica and indica

MYB Genes Involved in Domestication and Crop Improvement

Candidate genes for anthocyanin pigmentation in rice stem revealed by GWAS and whole‐genome resequencing

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