Loss-of-Function Alleles of Heading date 1 (Hd1) Are Associated With Adaptation of Temperate Japonica Rice Plants to the Tropical Region

Kim, Sung-Ryul; Torollo, Gideon; Yoon, Min-Ho; Kwak, Jieun; Lee, Choon-Ki; Prahalada, G. D.; Choi, Il-Ryong; Yeo, Un-Sang; Jeong, O‐Young; Jena, Kshirod K.; Lee, Jeom‐Sig

doi:10.3389/fpls.2018.01827

Cited by 41 publications

(37 citation statements)

References 51 publications

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“…Thus, the authors suggested that Hd1 was a possible target of selection to generate different flowering-time responses in different regions. Kim et al [ 60 ] selected about 60 diverse rice accessions to analyze the Hd trait of various types, including 4 aus accessions, 20 indica accessions, 4 tropical japonica accessions, 17 temperate japonica accessions, and 12 tropical adapted temperate japonica accessions. The authors analyzed 7 major flowering genes, including Hd1 [ 9 ], OsPPR37 [ 61 ], DTH8 [ 62 ], Ghd7 [ 12 ], Ehd1 [ 10 ], RFT1 [ 63 ] and Hd3a [ 11 ] as well as heading behavior under 3 different field conditions in temperate and tropical regions.…”

Section: Discussionmentioning

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 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%

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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“…They included cultivars grown in Spain (Guara, J. Sendra, Puntal, Gleva, and Bomba), Italy (Loto, Gigante Vercelli, Maratelli, Galileo, and Selenio) and France (Gines) (Courtois et al 2012;Reig-Valiente et al 2016). A Taiwanese cultivar Tainung 67 (TN67) closely related to Japanese and Korean temperate japonica varieties (Kim et al 2018) was also included in this panel. Rice plants were grown in the greenhouse under controlled conditions (14 h/10 h day/night cycle, 28°C/25°C, and 60% humidity).…”

Section: Plant Materialsmentioning

confidence: 99%

Effect of Root Colonization by Arbuscular Mycorrhizal Fungi on Growth, Productivity and Blast Resistance in Rice

Campo

Martín-Cardoso

Olivé

et al. 2020

Rice

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Background: Arbuscular mycorrhizal (AM) fungi form symbiotic associations with roots in most land plants. AM symbiosis provides benefits to host plants by improving nutrition and fitness. AM symbiosis has also been associated with increased resistance to pathogen infection in several plant species. In rice, the effects of AM symbiosis is less studied, probably because rice is mostly cultivated in wetland areas, and plants in such ecosystems have traditionally been considered as non-mycorrhizal. In this study, we investigated the effect of AM inoculation on performance of elite rice cultivars (Oryza sativa, japonica subspecies) under greenhouse and field conditions, focusing on growth, resistance to the rice blast fungus Magnaporthe oryzae and productivity. Results: The response to inoculation with either Funneliformis mosseae or Rhizophagus irregularis was evaluated in a panel of 12 rice cultivars. Root colonization was confirmed in all rice varieties. Under controlled greenhouse conditions, R. irregularis showed higher levels of root colonization than F. mosseae. Compared to non-inoculated plants, the AM-inoculated plants had higher Pi content in leaves. Varietal differences were observed in the growth response of rice cultivars to inoculation with an AM fungus, which were also dependent on the identity of the fungus. Thus, positive, negligible, and negative responses to AM inoculation were observed among rice varieties. Inoculation with F. mosseae or R. irregularis also conferred protection to the rice blast fungus, but the level of mycorrhiza-induced blast resistance varied among host genotypes. Rice seedlings (Loto and Gines varieties) were pre-inoculated with R. irregularis, transplanted into flooded fields, and grown until maturity. A significant increase in grain yield was observed in mycorrhizal plants compared with non-mycorrhizal plants, which was related to an increase in the number of panicles. Conclusion: Results here presented support that rice plants benefit from the AM symbiosis while illustrating the potential of using AM fungi to improve productivity and blast resistance in cultivated rice. Differences observed in the mycorrhizal responsiveness among the different rice cultivars in terms of growth promotion and blast resistance indicate that evaluation of benefits received by the AM symbiosis needs to be carefully evaluated on a case-by-case basis for efficient exploitation of AM fungi in rice cultivation.

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“…The tenth exon of Hd16 was amplified by polymerase chain reaction (PCR) using the primers and conditions described in Supplementary Table S1 . The two exons of Hd1 and the two exons of Ghd7 were amplified by PCR as described in [ 22 ]. Sequencing of the PCR products was performed by Macrogen (Daejeon, Korea).…”

Section: Methodsmentioning

confidence: 99%

Characterization of QTLs and Candidate Genes for Days to Heading in Rice Recombinant Inbred Lines

Jeong

et al. 2020

Genes

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Understanding the gene mechanisms controlling days to heading (DH) is important in rice breeding for adaption in the target environment. Using a recombinant inbred line population derived from the cross between two japonica rice cultivars, Koshihikari and Baegilmi, we identified three consistent quantitative trait loci (QTLs) for DH for two years, qDH3, qDH6, and qDH7 on chromosomes 3, 6, and 7, respectively. While Baegilmi contributed the allele for early heading at qDH6 and qDH7 with the additive effect of five days each, Koshihikari contributed the allele for early heading at qDH3 with the additive effect of three days. Notably, pyramiding two or more alleles for early heading at these QTLs accelerated heading effectively. Sequencing of Hd16, Hd1, and Ghd7, the previously known heading date genes underlying qDH3, qDH6, and qDH7, respectively, revealed that Baegilmi and Koshihikari carry different alleles at the three genes. Molecular markers were developed to screen the allelic compositions of the three genes among 295 Korean commercial rice cultivars. The results showed that few cultivars carry alleles for early heading at the three genes, highlighting that DH can be further accelerated and fine-tuned in breeding programs by combining the desirable alleles of Hd16, Hd1, and Ghd7.

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Loss-of-Function Alleles of Heading date 1 (Hd1) Are Associated With Adaptation of Temperate Japonica Rice Plants to the Tropical Region

Cited by 41 publications

References 51 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

Effect of Root Colonization by Arbuscular Mycorrhizal Fungi on Growth, Productivity and Blast Resistance in Rice

Characterization of QTLs and Candidate Genes for Days to Heading in Rice Recombinant Inbred Lines

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