Rice height QTLs in KDML105 chromosome segment substitution lines

Shearman, Jeremy R.; Vejchasarn, Phanchita; Naktang, Chaiwat; Phansenee, Yotwarit; Jomchai, Nukoon; Lanceras-Siangliw, J.; Tangphatsornruang, Sithichoke; Toojinda, Theerayut

doi:10.1016/j.ygeno.2019.09.003

Cited by 7 publications

(5 citation statements)

References 24 publications

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“…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). In the present study, we developed 176 NILs with a genetic background from the indica rice cultivar Jiafuzhan.…”

Section: Discussionmentioning

confidence: 99%

“…The sequencing results showed that the main cause of this mutation could be due to the mutation in the Hui1586 parent. Similarly, Shearman et al (2019) reported that the reduced plant height phenotype resulted from the introgression segments from IR62266 into KDML 105 is due to that the IR62266 has a deletion in the Gibberellin 20-oxidase 2 gene that corresponds to the semidwarf 1 locus, which led to the identification of a plant height QTL. Previous studies have showed that Aux/IAA genes play important roles in plant growth and development by regulating the expression of early auxin-responsive genes (Jain et al, 2006).…”

Section: Discussionmentioning

confidence: 99%

“…Moreover, using RILs, Han et al (2017) identified three QTLs designated qPh3.1, qPh1 and qPh7.1 for plant height. Furthermore, using the CSSL population, Shearman et al (2019) identified plant height QTLs on chromosomes 1 and 4. Most of the identified genes related to plant height, such as semidwarf1 (sd1; Sasaki et al, 2002), GA-insensitive dwarf1 (gid1; Ueguchi-Tanaka et al, 2005), GA-insensitive dwarf2 (gid2; Hirano et al, 2010), BR-deficient dwarf1 (brd1; Mori et al, 2002), BR-insensitive mutant (d61; Hong et al, 2003), and BR-deficient mutant (osdwarf4-1; Sakamoto et al, 2006), are related to the metabolism or signaling of the phytohormones gibberellin (GA) and brassinosteroid (BR; Deng et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

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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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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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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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“…Combining these components makes it possible to determine the type of plant needed partially. Shearman et al identified height QTLs on chromosome 1 using Chromosome Segment Substitution Line, and the significant QTL peaks were observed at 38.4 Mb [ 10 ]. This result is consistent with the current study, and many genes related to plant height were identified in this region.…”

Section: Discussionmentioning

confidence: 99%

“…To solve this problem, we need more robust rice varieties. Shorter plants spend fewer resources on stem growth, which can help increase stem diameter, thereby improving lodging resistance and yield [ 10 ]. The plant height of rice is determined by internode length, which has an important effect on the height of the center of gravity and the lodging resistance of the stem.…”

Section: Introductionmentioning

confidence: 99%

Identification of Candidate Gene for Internode Length in Rice to Enhance Resistance to Lodging Using QTL Analysis

Zhao

Son

Farooq

et al. 2021

Plants

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Internode length and stem diameter are the primary traits affecting the lodging resistance of rice. Traits related to the length of the panicle (LP), uppermost internode (LUI), second internode (LSI), third internode (LTI), fourth internode (LFI), lowest internode (LLI) as well as stem diameter at the uppermost internode (SDUI), second internode (SDSI), third internode (SDTI), fourth internode (SDFI), and lowest internode (SDLI) in 120 Cheongcheong/Nagdong doubled haploid population were investigated using a quantitative trait locus (QTL) analysis. Thirty-four QTL regions affected LP and the length of each internode. Twenty-six QTL regions were associated with the stem diameter of each internode. RM12285-RM212 on chromosome 1 contained 10 QTLs related to the internode length, which have overlapped for over 2 years. Twenty-three candidate genes were screened using mark interval. Among the candidate genes, Os01g0803900, named OsCYPq1, which is in the Cytochrome P450 family, might be involved in gibberellins (GA) synthesis. GA is an essential plant growth regulator that affects plant height. OsCYPq1 catalyzes oxidation steps in the middle part of the GA pathway. OsCYPq1 is expected to provide valuable information to improve the marker assessment for target traits and QTL gene cloning in rice.

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Identification of candidate genes and favourable haplotypes for yield traits in rice based on a genome-wide association study

Cheng,

Chang,

Sun

et al. 2023

Euphytica

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Rice height QTLs in KDML105 chromosome segment substitution lines

Cited by 7 publications

References 24 publications

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.)

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.)

Identification of Candidate Gene for Internode Length in Rice to Enhance Resistance to Lodging Using QTL Analysis

Identification of candidate genes and favourable haplotypes for yield traits in rice based on a genome-wide association study

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