Identification and fine mapping of a major QTL, qHD19, that plays pleiotropic roles in regulating the heading date in rice

Yang, Dewei; Cheng, Chaoping; Zheng, Xianghua; Ye, Xinfu; Ye, Ning; Huang, Fenghuang

doi:10.1007/s11032-020-1109-x

Cited by 7 publications

(3 citation statements)

References 38 publications

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“…The main feature of the NIL population is that each NIL contains only one or more donor chromosome fragments, which has a unique advantage for QTL identification, and by masking background genetic noise, QTLs can be visualized as a single Mendelian factor. Using the population of NILs, several QTLs have been identified or cloned [ 22 , 23 , 24 , 25 , 26 , 27 , 28 ]. In this study, we constructed 176 NILs using Jiafuzhan as the genetic background.…”

Section: Discussionmentioning

confidence: 99%

Fine Mapping and Cloning of a qRA2 Affect the Ratooning Ability in Rice (Oryza sativa L.)

Huang

Yang

2023

IJMS

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Ratooning ability is a key factor that influences the ratoon rice yield in areas where light and temperature are not sufficient for second-season rice. Near-isogenic lines (NILs) are the most powerful tools for the detection and precise mapping of quantitative trait loci (QTLs). In this study, using 176 NILs, we identified a novel QTL for ratooning ability in NIL128. First, we mapped the QTL between the markers Indel12-29 and Indel12-31, which encompass a region of 233 kb. The rice genome annotation indicated the existence of three candidate genes in this region that may be related to ratooning ability. Through gene prediction and cDNA sequencing, we speculated that the target gene of ratooning ability is LOC_Os02g51930 which encodes cytokinin glucosyl transferases (CGTs), hereafter named qRA2. Further analysis showed that qra2 was a 1-bp substitution in the first exon in NIL128, which resulted in the premature termination of qRA2. The results of the knockdown experiment showed that the Jiafuzhan knockdown mutants exhibited the ratooning ability phenotype of NIL128. Interestingly, the qRA2 gene was found to improve ratooning ability without affecting major agronomic traits. These results will help us better understand the genetic basis of rice ratooning ability and provide a valuable gene resource for breeding strong ratoon rice varieties.

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Section: Discussionmentioning

confidence: 99%

Fine Mapping and Cloning of a qRA2 Affect the Ratooning Ability in Rice (Oryza sativa L.)

Huang

Yang

2023

IJMS

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“…Each NIL carries one or more donor chromosome segments, which provide distinct advantages for QTLs identification, and a QTL can be visualized as a single Mendelian factor by blocking background genetic noise. Different types of QTLs have been identified and/or cloned using NIL populations, such as the drought resistance, qDTY 2.2 (Henry et al, 2015); the thermotolerance, TT1 (Li et al, 2015); the cold tolerance, QTLs (Zhou et al, 2012), the grain type, GS3 (Fan et al, 2006) and GW2 (Song et al, 2007); the heading stage, Ghd7 (Xue et al, 2008) and qHD19 (Yang et al, 2020); the spike type, DEP1 (Huang et al, 2009); the grain production, Cn1a (Ashikari et al, 2005) and 99 QTLs for different agronomic traits (Furuta et al, 2014). Although a number of plant height related genes/QTLs have been identified, and these genes/QTLs tend to have a function in hormone biosynthesis pathways including gibberellic acid, brassinosteroid, and strigolactone (Shearman et al, 2019), there are also hundreds of QTLs where the underlying cause remains unknown (Lei et al, 2018).…”

Section: Discussionmentioning

confidence: 99%

Fine Mapping and Cloning of a Major QTL qph12, Which Simultaneously Affects the Plant Height, Panicle Length, Spikelet Number and Yield in Rice (Oryza sativa L.)

Zhan

Huang

et al. 2022

Front. Plant Sci.

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Plant height is one of the most important agronomical traits in rice (Oryza sativa L.). Introducing the semidwarf rice in the 1960s significantly enhanced the rice yield potential in Asia. Implementing near-isogenic lines (NILs) is the most powerful tool for the identification and fine mapping of quantitative trait loci (QTLs). In this study, 176 NILs were produced from the crossing and back-crossing of two rice cultivars. Specifically, the indica rice cultivar Jiafuzhan served as a recipient, and the restorer japonica cultivar Hui1586 served as a donor. Using the 176 NILs, we identified a novel major QTL for reduced plant height in the NIL36 line. The qph12 QTL was mapped to a 31 kb genomic region between the indel markers Indel12-29 and Indel12-31. The rice genome annotation indicated the presence of three candidate genes in this genomic region. Through gene prediction and cDNA sequencing, we confirmed that LOC_Os12g40890 (qPH12) is the target gene in the NIL36 line. Further analysis showed that the qph12 QTL is caused by a 1 bp deletion in the first exon that resulted in premature termination of the qPH12. Knockout experiments showed that the qph12 QTL is responsible for the reduced plant height phenotype of the NIL36 line. Although the qph12 gene from the NIL36 line showed a shorter panicle length, fewer spikelets per panicle and a lower plant grain yield, the plant also exhibited a lower plant height. Taken together, our results revealed that the qph12 have good specific application prospects in future rice breeding.

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“…Several genes that cause mutant phenotypes were successfully cloned by map-based cloning from ion beaminduced rice mutants, such as Morita et al (2019) reported that long grain1 (lin1) mutant contributes to increasing grain weight. Several studies identified early heading date genes (Fujino et al 2013, Yang et al 2020, while Ichitani et al (2014) reported genes related to late heading date in rice. Fujita et al (2013) argued that the naturally varying SPIKE gene, located in the QTL cluster region of chromosome 4, had a significant impact on yield.…”

Section: Evaluation Of M2 Generationmentioning

confidence: 99%

Evaluation of Toraja (Indonesia) local aromatic rice mutant developed using heavy-ion beam irradiation

et al. 2021

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Abstract. Okasa AM, Sjahril R, Riadi M, Mahendradatta M, Sato T, Toriyama K, Ishii K, Hayashi Y, Abe T. 2021. Evaluation of Toraja (Indonesia) local aromatic rice mutant developed using heavy-ion beam irradiation. Biodiversitas 22: 3474-3481. The aromatic local Toraja rice "Pare Bau" has a good grain quality and aroma. However, it has some disadvantages, including a late heading and low yield for a modern farming system. This study aims to evaluate and select early heading as well as high yield mutant lines induced by heavy-ion beam irradiation. Furthermore, dry seeds of Pare Bau were irradiated with Argon-ion (300 keV/?m) and Carbon-ion (30 keV/?m) at RI-beam factory, RIKEN Nishina Center, Japan. The germination percentages of the M1 seeds were 49% for Pare Bau irradiated with Argon-ion (PB-A), 53% for Pare Bau irradiated with Carbon-ion (PB-C), and 70% for the Control. The 13 PB-A and 13 PB-C M1 plants were selected, and the seeds were sampled in the paddy field of Hasanuddin University (20 m asl.), Makassar. During the following planting season, the M2 generation plant was examined in Enrekang District (650 m asl.), South Sulawesi, Indonesia. Based on the early heading and a larger number of panicles, the 18 PB-A and one PB-C M3 line were selected from a total of 404 M2 survival plants. The selected lines and control were grouped into seven clusters based on the quantitative phenotypic traits, indicating the existence of genetic variability. The plant yield was significantly correlated with plant height, the number of tillers, the number of panicles, as well as grain weight per panicle, which showed that these traits are good criteria for selection.

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Identification and fine mapping of a major QTL, qHD19, that plays pleiotropic roles in regulating the heading date in rice

Cited by 7 publications

References 38 publications

Fine Mapping and Cloning of a qRA2 Affect the Ratooning Ability in Rice (Oryza sativa L.)

Fine Mapping and Cloning of a qRA2 Affect the Ratooning Ability in Rice (Oryza sativa L.)

Fine Mapping and Cloning of a Major QTL qph12, Which Simultaneously Affects the Plant Height, Panicle Length, Spikelet Number and Yield in Rice (Oryza sativa L.)

Evaluation of Toraja (Indonesia) local aromatic rice mutant developed using heavy-ion beam irradiation

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