Both Hd1 and Ehd1 are important for artificial selection of flowering time in cultivated rice

Wei, Fu‐Jin; Tsai, Yun-Long; Wu, Huimin; Huang, Lin‐Tzu; Chen, Yu‐Chi; Chen, Yifang; Wu, Cheng-Chieh; Tseng, Yi-Tzu; Hsing, Yue‐Ie C.

doi:10.1016/j.plantsci.2015.09.005

Cited by 45 publications

(49 citation statements)

References 37 publications

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“…In the current study, we classified it as type 19. In our previous study, we demonstrated that loss-of-function hd1 with this 1.9-kb insertion was introgressed from 2 Taiwan landraces, Muteka and Nakabo, to the early breeding generation of TC65 (Wei et al, 2016).…”

Section: Many Loss-of-function Haplotypes Are Present In Rice Accessionsmentioning

confidence: 85%

“…Type 12 was present only in Laos and it was positively selected. The mutation of type 19 occurred thousands of years ago in the aboriginal villages in Taiwan (Wei et al, 2016).…”

Section: The Origin Of the Loss-of-function Mutations In Hd1 Genementioning

confidence: 99%

“…Banglad esh 5 4 --4 78 35 --35 Bhutan 2 2 2 --2 2 1 1 Cambod ia --------1 1 Only types 7 and 13 are illustrated. Most are 3K data and we added some accessions from Taiwan aboriginal villages (Wei et al, 2016).…”

Section: Additional Filementioning

confidence: 99%

“…In total, 31 accessions type 19 hd1. Most are modern varieties, including TC65, Taichung 179 and Taichung 188.According to our previous study of the hd1 gene in Taiwan aboriginal rice accessions, 11 contained this haplotype(Wei et al, 2016). A total of 16 accessions contained type 20 hd1, all from India and all…”

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

Wei²,

Chiou

et al. 2020

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Background Plant domestication/adaptation is a good model for evo-devo studies. Mutations that caused morphological and physiological change, followed by human selection, finally led to improvement of phenotypes suitable for different kinds of environments. Originating from the Yangtze Valley, rice is a facultative short-day plant. Rice spread southward thousands of years ago, but one of the new traits beneficial to crop yield would be loss of sensitivity to photoperiod. That is, if rice could be cultivated 2 or 3 seasons each year, the production would at least double. Results We used the sequence information for Heading date 1 (Hd1) gene to reveal the relationship of sequence changes and flowering phenotypes of rice in different regions. Seven loss-of-function hd1 haplotypes were reported previously. By data mining the genome sequencing information in the public domain, we discovered another 3 types. Allele haplotypes are present in sub-tropical and tropical regions, which indicates human selection. Two of these alleles, types 7 and 13, must have occurred early in southern Asia and then were introgressed in many local landraces. According to the rice 3K database, more than one-third of the world’s rice accessions contain these 2 loss-of-function haplotypes. We also demonstrate that these haplotypes are present in weedy rice populations, again indicating 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. Conclusion In the current study, we analyzed how sequence changes in a rice flowering-control gene occurred, were selected and were retained during rice cultivation. Many loss-of-function hd1 alleles have existed in sub-tropical and tropical Asia rice-growing areas for a long time. Some of these haplotypes were present locally, but 2, types 7 and 13, were spread in many regions and are now included in most of the modern varieties in southern Asia.

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Section: Many Loss-of-function Haplotypes Are Present In Rice Accessionsmentioning

confidence: 85%

“…Type 12 was present only in Laos and it was positively selected. The mutation of type 19 occurred thousands of years ago in the aboriginal villages in Taiwan (Wei et al, 2016).…”

Section: The Origin Of the Loss-of-function Mutations In Hd1 Genementioning

confidence: 99%

Section: Additional Filementioning

confidence: 99%

mentioning

confidence: 99%

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

Wei²,

Chiou

et al. 2020

Preprint

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“…The trait frequency of heading, including early, late, or no heading, is very low in TRIM but higher in the other 2 resources. These differences might be related to the function of Heading date 1 ( Hd1 ) and Early heading date 1 ( Ehd1 ) in Nipponbare, which are lost in TNG67 [28]. In addition, TRIM features a higher frequency of dark-green, narrow, short leaf, short panicle, and small grain as compared with the other resources, which shows the relationship among varieties, cultivation locations, and cropping seasons.…”

Section: Data Validation and Quality Controlmentioning

confidence: 99%

Large-scale phenomics analysis of a T-DNA tagged mutant population

Wei

et al. 2017

GigaScience

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Rice, Oryza sativa L., is one of the most important crops in the world. With the rising world population, feeding people in a more sustainable and environmentally friendly way becomes increasingly important. Therefore, the rice research community needs to share resources to better understand the functions of rice genes that are the foundation for future agricultural biotechnology development, and one way to achieve this goal is via the extensive study of insertional mutants. We have constructed a large rice insertional mutant population in a japonica rice variety, Tainung 67. The collection contains about 93 000 mutant lines, among them 85% with phenomics data and 65% with flanking sequence data. We screened the phenotypes of 12 individual plants for each line grown under field conditions according to 68 subcategories and 3 quantitative traits. Both phenotypes and integration sites are searchable in the Taiwan Rice Insertional Mutants Database. Detailed analyses of phenomics data, T-DNA flanking sequences, and whole-genome sequencing data for rice insertional mutants can lead to the discovery of novel genes. In addition, studies of mutant phenotypes can reveal relationships among varieties, cultivation locations, and cropping seasons.

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Functional homoeologous alleles of CONSTANS contribute to seasonal crop type in rapeseed

Jin

Yin

et al. 2021

Theor Appl Genet

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Both Hd1 and Ehd1 are important for artificial selection of flowering time in cultivated rice

Cited by 45 publications

References 37 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

Large-scale phenomics analysis of a T-DNA tagged mutant population

Functional homoeologous alleles of CONSTANS contribute to seasonal crop type in rapeseed

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