Genomic adaptation of flowering‐time genes during the expansion of rice cultivation area

Itoh, Hironori; Wada, Kaede C.; Sakai, Hiroaki; Shibasaki, Kazuo; Fukuoka, Shuichi; Wu, Jianzhong; Yonemaru, Jun‐ichi; Yano, Masahiro; Izawa, Takeshi

doi:10.1111/tpj.13906

Cited by 33 publications

(43 citation statements)

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“…Previous studies using sequencing information of the Hd1 gene region of 60 landraces [ 27 ] or 429 CSSL materials [ 29 ] illustrated that multiple introgressions and thus dynamic rearrangements occurred around the Hd1 gene. In the present study, we showed that the type 7 mutation occurred in indica rice in insular Southeastern Asia areas.…”

Section: Discussionmentioning

confidence: 99%

“…Their studies also revealed that multiple introgressions in the Hd1 gene region had occurred and were important for rice accessions to adapt to different habitats. Furthermore, a set of chromosome segregation substitution lines was used to elucidate the allele variations of common rice flowering-time QTL [ 29 ]. Hd1 was one of the 8 genes under investigation.…”

Section: Introductionmentioning

confidence: 99%

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Studies of rice Hd1 haplotypes worldwide reveal adaptation of flowering time to different environments

Wei

Chiou

et al. 2020

PLoS ONE

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Rice domestication/adaptation is a good model for studies of the development and spread of this important crop. Mutations that caused morphological and physiological change, followed by human selection/expansion, finally led to the improvement of phenotypes suitable for different kinds of environments. We used the sequence information for Heading date 1 ( Hd1 ) gene to reveal the association between sequence changes and flowering phenotypes of rice in different regions. Seven loss-of-function hd1 haplotypes had been reported. By data-mining the genome sequencing information in the public domain, we discovered 3 other types. These loss-of-function allele haplotypes are present in subtropical and tropical regions, which indicates human selection. Some of these haplotypes are present locally. However, types 7 and 13 are present in more than one-third of the world’s rice accessions, including landraces and modern varieties. In the present study, phylogenetic, allele network and selection pressure analyses revealed that these two haplotypes might have occurred early in Southeastern Asia and then were introgressed in many local landraces in nearby regions. We also demonstrate that these haplotypes are present in weedy rice populations, which again indicates that these alleles were present in rice cultivation for long time. In comparing the wild rice sequence information, these loss-of-function haplotypes occurred in agro but were not from wild rice.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Studies of rice Hd1 haplotypes worldwide reveal adaptation of flowering time to different environments

Wei

Chiou

et al. 2020

PLoS ONE

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“…Rice (Oryza sativa) is a typical SD plant whose flowering is promoted under SD conditions, but delayed under LD conditions (Yano et al, 2000). During rice domestication and genetic breeding, rice has dramatically expanded its cultivating areas through modulation of the flowering regulatory pathways (Goretti et al, 2017;Itoh et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

Post‐transcriptional regulation of Ghd7 protein stability by phytochrome and OsGI in photoperiodic control of flowering in rice

et al. 2019

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Summary Rice (Oryza sativa) is a facultative short‐day (SD) plant, flowering early under SD and late under long‐day (LD) conditions. Ghd7 is a major regulator of flowering time in rice, which strongly delays flowering under LD. Induction of Ghd7 expression by phytochromes has been shown to contribute to photoperiodic regulation of flowering in rice. Here, we show that Ghd7 also is regulated by phytochromes at a post‐transcriptional level. We found that constitutive expression of Ghd7 delays flowering in the wild‐type (WT) background, but not in the se5 mutant background (deficient in functional phytochromes) under LD and that Ghd7 protein fails to accumulate in the se5 mutant. We also found that co‐expressing OsGIGANTEA (OsGI) with Ghd7 causes reduced accumulation of Ghd7 protein and partially suppresses the delayed flowering phenotype in the WT background, suggesting that phytochromes and OsGI play antagonist roles in regulating Ghd7 protein stability and flowering time. We show that OsPHYA, OsPHYB and OsGI could directly interact with Ghd7. Interestingly, OsPHYA and OsPHYB could inhibit the interaction between OsGI and Ghd7, thus helping to stabilize Ghd7 protein. Our results revealed a new level of Ghd7 regulation by phytochromes and OsGI in photoperiodic control of flowering in rice.

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“…Since domestication, rice cultivation expanded towards different agro-ecological environments by the generation of new cultivars through selection of adapted plants to the new conditions through intense and continuous breeding activities [ 8 ]. One of the barriers that rice overcame to reach temperate regions was the difference in day length that became one of the main determinants of plant adaptation to new areas [ 10 , 11 ]. As a consequence, the genetic distance between cultivars from tropical regions and those cultivated in temperate regions enlarged enough to produce strong reproductive barriers that hinder the genetic flow between tropical and temperate cultivars [ 12 ] and contributing to the constriction of the genetic pool of cultivars and the emergence of different subpopulations.…”

Section: Introductionmentioning

confidence: 99%

Genome-wide association study of agronomic traits in rice cultivated in temperate regions

Reig-Valiente

Marques²,

Talón

et al. 2018

BMC Genomics

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BackgroundRice plants are sensitive to the agro-climate conditions, being photoperiod one of main factor contributing to their adaptation to the region where they are grown. Dissecting the genetic bases underlying diversity in rice populations adapted to specific environmental conditions is a fundamental resource for breeding. In this study we have analysed a collection of japonica varieties adapted to temperate regions to perform association studies with traits of high agronomical interest such as heading date, plant height, number of panicles, panicle length and number of grains per panicle.ResultsWe have performed a genome wide association study using a panel of 1713 SNPs that, based on previous linkage disequilibrium estimations, provides a full coverage of the whole genome. We have found a total of 43 SNPs associated with variations in the different traits. The identified SNPs were distributed across the genome except in chromosome 12, where no associated SNPs were found. The inspection of the vicinity of these markers also revealed a set of genes associated with physiological functions strongly linked to agronomic traits. Of special relevance are two genes involved in gibberellin homeostasis that are associated with plant height and panicle length. We also detected novel associated sites with heading date, panicle length and number of grain per panicle.ConclusionWe have identified loci associated with important agronomic traits among cultivars adapted to temperate conditions. Some of these markers co-localized with already known genes or QTLs, but the association also provided novel molecular markers that can be of help to elucidate the complicated genetic mechanism controlling important agronomic traits, as flowering regulation in the non-dependent photoperiod pathway. The detected associated markers may provide important tools for the genetic improvement of rice cultivars in temperate regions.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5086-y) contains supplementary material, which is available to authorized users.

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Genomic adaptation of flowering‐time genes during the expansion of rice cultivation area

Cited by 33 publications

References 58 publications

Studies of rice Hd1 haplotypes worldwide reveal adaptation of flowering time to different environments

Studies of rice Hd1 haplotypes worldwide reveal adaptation of flowering time to different environments

Post‐transcriptional regulation of Ghd7 protein stability by phytochrome and OsGI in photoperiodic control of flowering in rice

Genome-wide association study of agronomic traits in rice cultivated in temperate regions

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