Abstract
SUMMARY Plant height (PH) is an important trait affecting the plant architecture, seed yield, and harvest index. However, the molecular mechanisms underlying PH heterosis remain unclear. In addition, useful PH‐related genes must be urgently identified to facilitate ideal plant architecture breeding in rice ( Oryza sativa L.). In the present study, to explore rice quantitative trait loci (QTLs) and heterosis‐related loci of PH in rice, we developed a high‐generation (>F 15 ) population of 272 recombinant inbred lines (RIL) from a cross of two elite varieties, Luohui 9 ( in dica/ xian ) × RPY geng ( japonica / geng) , and two testcross hybrid populations derived from the crosses of RILs and two cytoplasmic male sterile lines (YTA [ indica ] and Z7A [ japonica ]). Using deep resequencing data, a high‐density genetic map containing 4758 bin markers was constructed, with a total map distance of 2356.41 cM. Finally, 31 PH‐related QTLs for different PH component lengths or tiller numbers across five seasons were identified. Two major environment‐specific PH QTLs were stably detected in Hainan ( qPH‐3.1 ) or Hubei ( qPH‐5.1 ), which have undergone significant functional alterations in rice with changes in geographical environment. Based on comparative genomics, gene function annotation, homolog identification, and existing literature (pioneering studies), candidate genes for multiple QTLs were fine‐mapped, and the candidate genes qPH‐3.1 and qPH‐5.1 for PH were further validated using CRISPR–Cas9 gene editing. Specifically, qPH‐3.1 was characterized as a pleiotropic gene, and the qPH‐3.1 knockout line showed reduced PH, delayed heading, a decreased seed setting rate, and increased tiller numbers. Importantly, 10 PH heterosis‐related QTLs were identified in the testcross populations, and a better‐parent heterosis locus ( qBPH‐5.2 ) completely covered qPH‐5.1 . Furthermore, the cross results of fixed‐genotype RILs verified the dominant effects of qPH‐3.1 and qPH‐5.1 . Together, these findings further our understanding of the genetic mechanisms of PH and offer multiple highly reliable gene targets for breeding rice varieties with ideal architecture and high yield potential in the immediate future.
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Claims 14
Claim · model-written summary
A rice genetic map contained 4758 bin markers and spanned 2356.41 cM.
- Taxon
- rice
Oryza sativat0 - Outcome
- high‐density genetic mape0
- Value
- 4758 bin markerse0
- Qualifier
- 2356.41 cMe0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“a high‐density genetic map containing 4758 bin markers was constructed, with a total map distance of 2356.41 cM.”
t0“breeding in rice ( Oryza sativa L.)”
Claim · model-written summary
Thirty-one rice plant-height QTLs were identified across five seasons.
- Taxon
- riceOryza sativat0
- Outcome
- PH‐related QTLse0
- Value
- 31e0
- Qualifier
- across five seasonse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“31 PH‐related QTLs for different PH component lengths or tiller numbers across five seasons were identified.”
t0“breeding in rice ( Oryza sativa L.)”
Claim · model-written summary
qPH‐3.1 was stably detected in Hainan.
- Taxon
- riceOryza sativat0
- Gene
- qPH‐3.1e0
- Outcome
- stably detectede0
- Setting
- Hainane0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Two major environment‐specific PH QTLs were stably detected in Hainan ( qPH‐3.1 ) or Hubei ( qPH‐5.1 )”
t0“breeding in rice ( Oryza sativa L.)”
Claim · model-written summary
qPH‐5.1 was stably detected in Hubei.
- Taxon
- riceOryza sativat0
- Gene
- qPH‐5.1e0
- Outcome
- stably detectede0
- Setting
- Hubeie0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Two major environment‐specific PH QTLs were stably detected in Hainan ( qPH‐3.1 ) or Hubei ( qPH‐5.1 )”
t0“breeding in rice ( Oryza sativa L.)”
Claim · model-written summary
Candidate genes qPH‐3.1 and qPH‐5.1 were validated with CRISPR–Cas9 editing.
- Taxon
- riceOryza sativat0
- Gene
- qPH‐3.1 and qPH‐5.1e0
- Outcome
- validatede0
- Value
- qPH‐3.1 and qPH‐5.1e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“the candidate genes qPH‐3.1 and qPH‐5.1 for PH were further validated using CRISPR–Cas9 gene editing.”
t0“breeding in rice ( Oryza sativa L.)”
Claim · model-written summary
qPH‐3.1 was characterized as pleiotropic.
- Taxon
- riceOryza sativat0
- Gene
- qPH‐3.1e0
- Outcome
- pleiotropic genee0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“qPH‐3.1 was characterized as a pleiotropic gene”
t0“breeding in rice ( Oryza sativa L.)”
Claim · model-written summary
Knocking out qPH‐3.1 reduced rice plant height.
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“the qPH‐3.1 knockout line showed reduced PH, delayed heading, a decreased seed setting rate, and increased tiller numbers.”
t0“breeding in rice ( Oryza sativa L.)”
Claim · model-written summary
Knocking out qPH‐3.1 delayed heading.
- Taxon
- riceOryza sativat0
- Treatment
- qPH‐3.1 knockout linee0
- Gene
- qPH‐3.1e0
- Outcome
- headinge0
- Direction
- delayede0
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“the qPH‐3.1 knockout line showed reduced PH, delayed heading, a decreased seed setting rate, and increased tiller numbers.”
t0“breeding in rice ( Oryza sativa L.)”
Claim · model-written summary
Knocking out qPH‐3.1 decreased seed-setting rate.
- Taxon
- riceOryza sativat0
- Treatment
- qPH‐3.1 knockout linee0
- Gene
- qPH‐3.1e0
- Outcome
- seed setting ratee0
- Direction
- decreasede0
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“the qPH‐3.1 knockout line showed reduced PH, delayed heading, a decreased seed setting rate, and increased tiller numbers.”
t0“breeding in rice ( Oryza sativa L.)”
Claim · model-written summary
Knocking out qPH‐3.1 increased tiller numbers.
- Taxon
- riceOryza sativat0
- Treatment
- qPH‐3.1 knockout linee0
- Gene
- qPH‐3.1e0
- Outcome
- tiller numberse0
- Direction
- increasede0
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“the qPH‐3.1 knockout line showed reduced PH, delayed heading, a decreased seed setting rate, and increased tiller numbers.”
t0“breeding in rice ( Oryza sativa L.)”
Claim · model-written summary
Ten plant-height heterosis QTLs were identified in testcross populations.
- Taxon
- riceOryza sativat0
- Material
- testcross populationse0
- Outcome
- PH heterosis‐related QTLse0
- Value
- 10e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“10 PH heterosis‐related QTLs were identified in the testcross populations”
t0“breeding in rice ( Oryza sativa L.)”
Claim · model-written summary
The better-parent heterosis locus qBPH‐5.2 completely covered qPH‐5.1.
- Taxon
- riceOryza sativat0
- Gene
- qBPH‐5.2e0
- Outcome
- completely covered qPH‐5.1e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“a better‐parent heterosis locus ( qBPH‐5.2 ) completely covered qPH‐5.1”
t0“breeding in rice ( Oryza sativa L.)”
Claim · model-written summary
Fixed-genotype crosses verified a dominant effect of qPH‐3.1.
- Taxon
- riceOryza sativat0
- Material
- fixed‐genotype RILse0
- Gene
- qPH‐3.1e0
- Outcome
- dominant effectse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“the cross results of fixed‐genotype RILs verified the dominant effects of qPH‐3.1 and qPH‐5.1”
t0“breeding in rice ( Oryza sativa L.)”
Claim · model-written summary
Fixed-genotype crosses verified a dominant effect of qPH‐5.1.
- Taxon
- riceOryza sativat0
- Material
- fixed‐genotype RILse0
- Gene
- qPH‐5.1e0
- Outcome
- dominant effectse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“the cross results of fixed‐genotype RILs verified the dominant effects of qPH‐3.1 and qPH‐5.1”
t0“breeding in rice ( Oryza sativa L.)”
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