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Article: Breeding of ZhongKeFaZaoGeng1 by molecular design.

Chen, Ming-Jiang / Liu, Guifu / Xiao, Ye-Qing / Yu, Hong / Li, Jiayang

Yi chuan = Hereditas

2023 Volume 45, Issue 9, Page(s) 829–834

Abstract: Double-cropping early-season rice is one important part of staple crop rice. In recent years, great progress has been made in breeding the double-cropping early- ... ...

Abstract	Double-cropping early-season rice is one important part of staple crop rice. In recent years, great progress has been made in breeding the double-cropping early-season
MeSH term(s)	Plant Breeding ; Agriculture ; Oryza/genetics ; Seasons
Language	English
Publishing date	2023-09-20
Publishing country	China
Document type	Journal Article
ISSN	0253-9772
ISSN	0253-9772
DOI	10.16288/j.yczz.23-129
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Article: Pyramiding of Low Chalkiness QTLs Is an Effective Way to Reduce Rice Chalkiness.

Yang, Weifeng / Chen, Songliang / Hao, Qingwen / Zhu, Haitao / Tan, Quanya / Lin, Shaojun / Chen, Guodong / Li, Zhan / Bu, Suhong / Liu, Zupei / Liu, Guifu / Wang, Shaokui / Zhang, Guiquan

Rice (New York, N.Y.)

2024 Volume 17, Issue 1, Page(s) 4

Abstract: Rice chalkiness is a key limiting factor of high-quality rice. The breeding of low chalkiness varieties has always been a challenging task due to the complexity of chalkiness and its susceptibility to environmental factors. In previous studies, we ... ...

Abstract	Rice chalkiness is a key limiting factor of high-quality rice. The breeding of low chalkiness varieties has always been a challenging task due to the complexity of chalkiness and its susceptibility to environmental factors. In previous studies, we identified six QTLs for the percentage of grain chalkiness (PGC), named qPGC5, qPGC6, qPGC8.1, qPGC8.2, qPGC9 and qPGC11, using single-segment substitution lines (SSSLs) with genetic background of Huajingxian 74 (HJX74). In this study, we utilized the six low chalkiness QTLs to develop 17 pyramiding lines with 2-4 QTLs. The results showed that the PGC decreased with the increase of QTLs in the pyramiding lines. The pyramiding lines with 4 QTLs significantly reduced the chalkiness of rice and reached the best quality level. Among the six QTLs, qPGC5 and qPGC6 showed greater additive effects and were classified as Group A, while the other four QTLs showed smaller additive effects and were classified as Group B. In pyramiding lines, although the presence of epistasis, additivity remained the main component of QTL effects. qPGC5 and qPGC6 showed stronger ability to reduce rice chalkiness, particularly in the environment of high temperature (HT) in the first cropping season (FCS). Our research demonstrates that by pyramiding low chalkiness QTLs, it is feasible to develop the high-quality rice varieties with low chalkiness at the best quality level even in the HT environment of FCS.
Language	English
Publishing date	2024-01-08
Publishing country	United States
Document type	Journal Article
ZDB-ID	2457103-9
ISSN	1939-8433 ; 1939-8425
ISSN (online)	1939-8433
ISSN	1939-8425
DOI	10.1186/s12284-023-00680-x
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Article ; Online: QTL epistasis plays a role of homeostasis on heading date in rice.

Huang, Lilong / Tang, Jichun / Zhu, Bihuang / Chen, Guodong / Chen, Leyi / Bu, Suhong / Zhu, Haitao / Liu, Zupei / Li, Zhan / Meng, Lijun / Liu, Guifu / Wang, Shaokui

Scientific reports

2024 Volume 14, Issue 1, Page(s) 373

Abstract: If there was no gene interaction, the gene aggregation effect would increase infinitely with the increase of gene number. Epistasis avoids the endless accumulation of gene effects, playing a role of homeostasis. To confirm the role, QTL epistases were ... ...

Abstract	If there was no gene interaction, the gene aggregation effect would increase infinitely with the increase of gene number. Epistasis avoids the endless accumulation of gene effects, playing a role of homeostasis. To confirm the role, QTL epistases were analyzed by four single-segment substitution lines with heading date QTLs in this paper. We found that QTLs of three positive effects and one negative effect generated 62.5% negative dual QTL epistatic effects and 57.7% positive triple QTL epistatic effects, forming the relationship "positive QTLs-negative one order interactions-positive two order interactions". In this way, the aggregation effect of QTLs was partially neutralized by the opposite epistatic effect sum. There also were two exceptions, QTL OsMADS50 and gene Hd3a-2 were always with consistent effect directions with their epistases, implying they could be employed in pyramiding breeding with different objectives. This study elucidated the mechanism of epistatic interactions among four QTLs and provided valuable genetic resources for improving heading date in rice.
MeSH term(s)	Chromosome Mapping ; Oryza/genetics ; Phenotype ; Epistasis, Genetic ; Chromosomes, Plant ; Plant Breeding ; Homeostasis/genetics
Language	English
Publishing date	2024-01-03
Publishing country	England
Document type	Journal Article
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-023-50786-x
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Article ; Online: LAZY3 interacts with LAZY2 to regulate tiller angle by modulating shoot gravity perception in rice

Cai, Yueyue / Huang, Linzhou / Song, Yuqi / Yuan, Yundong / Xu, Shuo / Wang, Xueping / Liang, Yan / Zhou, Jie / Liu, Guifu / Li, Jiayang / Wang, Wenguang / Wang, Yonghong

Plant Biotechnology Journal. 2023 June, v. 21, no. 6 p.1217-1228

2023

Abstract: Starch biosynthesis in gravity‐sensing tissues of rice shoot determines the magnitude of rice shoot gravitropism and thus tiller angle. However, the molecular mechanism underlying starch biosynthesis in rice gravity‐sensing tissues is still unclear. We ... ...

Abstract	Starch biosynthesis in gravity‐sensing tissues of rice shoot determines the magnitude of rice shoot gravitropism and thus tiller angle. However, the molecular mechanism underlying starch biosynthesis in rice gravity‐sensing tissues is still unclear. We characterized a novel tiller angle gene LAZY3 (LA3) in rice through map‐based cloning. Biochemical, molecular and genetic studies further demonstrated the essential roles of LA3 in gravity perception of rice shoot and tiller angle control. The shoot gravitropism and lateral auxin transport were defective in la3 mutant upon gravistimulation. We showed that LA3 encodes a chloroplast‐localized tryptophan‐rich protein associated with starch granules via Tryptophan‐rich region (TRR) domain. Moreover, LA3 could interact with the starch biosynthesis regulator LA2, determining starch granule formation in shoot gravity‐sensing tissues. LA3 and LA2 negatively regulate tiller angle in the same pathway acting upstream of LA1 to mediate asymmetric distribution of auxin. Our study defined LA3 as an indispensable factor of starch biosynthesis in rice gravity‐sensing tissues that greatly broadens current understanding in the molecular mechanisms underlying the starch granule formation in gravity‐sensing tissues, and provides new insights into the regulatory mechanism of shoot gravitropism and rice tiller angle.
Keywords	auxins ; biosynthesis ; biotechnology ; genes ; gravitropism ; gravity sensing ; mutants ; rice ; starch granules
Language	English
Dates of publication	2023-06
Size	p. 1217-1228.
Publishing place	John Wiley & Sons, Ltd
Document type	Article ; Online
Note	JOURNAL ARTICLE
ZDB-ID	2136367-5
ISSN	1467-7652 ; 1467-7644
ISSN (online)	1467-7652
ISSN	1467-7644
DOI	10.1111/pbi.14031
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Article: Functional mapping of tillering QTLs using the Wang–Lan–Ding model and a SSSL population

Luan, Xin / Xiong, Liang / Xu, Haiming / Zhu, Haitao / Bu, Suhong / Meng, Lijun / Liu, Guifu / Wang, Shaokui

Molecular genetics and genomics. 2021 Nov., v. 296, no. 6

2021

Abstract: Understanding dynamic changes in the genetic architecture of quantitative traits is crucial in developmental genetics. Functional mapping is an appropriate method that passes a mathematical equation to describe a biological developmental process with the ...

Abstract	Understanding dynamic changes in the genetic architecture of quantitative traits is crucial in developmental genetics. Functional mapping is an appropriate method that passes a mathematical equation to describe a biological developmental process with the genetic mapping framework. Appropriate genetic model and applicable mapping population are indispensable condition for functional mapping of important agronomic traits in plants. Based on the Wang–Lan–Ding model, we ever applied a DH population to carry out functional mapping QTLs underlying growth trajectory on tiller number. However, inconsistent genetic background among the DH lines might disturb the mapping results. With the advent of innovative research materials, single segment substitution lines, allows us to do more precise genetic analyses. Thus functional mapping was again conducted on tiller number using the Wang–Lan–Ding model and a single segment substitution line population with the genetic background of Huajingxian 74 so as to explore QTL dynamic mechanism to regulate developmental traits. We detected that all five single segment substitution lines harbored tillering QTLs with additives and/or dominances to influence the four functional parameters, the optimum tillering time (t₀), the maximum tiller number (K), the tillering increased rate (r) and the tillering decreased rate (c), which were estimated from the Wang–Lan–Ding model and with some biological meaning. They mainly brought the inflexion point (t₀) delay, the peak increase (K) and the degradation (c) acceleration, while the growth (r) slow down. Moreover, epistatic interactions among these QTLs were confirmed to be prevalent. A total of 39 significant epistatic effects were detected to associate with the four parameters, occupying 34.8% of 112 pairs of epistatic interactions investigated. Contrary to the QTL effects, these epistatic effects largely decreased t₀, K and c, while increased r. Our results indicated that the five QTL effects and their epistatic effects significantly changed the shape and trajectory of tiller number via influence of the four functional parameters. Rational use of these QTLs is expected to improve tillering number of rice by molecular design breeding.
Keywords	epistasis ; equations ; genetic background ; genetic models ; genomics ; rice ; substitution lines ; tillering
Language	English
Dates of publication	2021-11
Size	p. 1279-1286.
Publishing place	Springer Berlin Heidelberg
Document type	Article
ISSN	1617-4615
DOI	10.1007/s00438-021-01819-5
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Article ; Online: Identification, Interaction, Expression, and Function of QTLs on Leaf Numbers with Single-Segment Substitution Lines in Rice

Bu, Suhong / Zhan, Penglin / Huang, Lilong / Tang, Jichun / Chen, Leyi / Zhu, Haitao / Liu, Zupei / Meng, Lijun / Liu, Guifu / Wang, Shaokui

Agronomy. 2022 Nov. 25, v. 12, no. 12

2022

Abstract: Rice leaf is a solar panel of photosynthesis and determines the light energy utilization and yield of plants. Leaf numbers appear as S-type or parabola-type growth curves throughout their development. However, the ways in which the genes regulate the ... ...

Abstract	Rice leaf is a solar panel of photosynthesis and determines the light energy utilization and yield of plants. Leaf numbers appear as S-type or parabola-type growth curves throughout their development. However, the ways in which the genes regulate the process of leaf numbers still remain poorly understood. This paper first identified five QTLs associated with leaf numbers using single-segment substitution lines (SSSLs). Then, the epistatic effects between double QTLs were estimated via the decomposition of the QTL polymerization effects. Additionally, further the expression patterns and functions for these five QTLs and their epistasis were revealed by the methodologies of conditional QTL mapping and functional QTL mapping, respectively. The five SSSLs were detected as having significant additive and/or dominant effects at one or more stages, all of which increased the leaf numbers, except for the negative additive effect of the first SSSL. Seven pairs of QTLs interacted each other via three or four epistatic components, with the opposite effects in the case of single genes, i.e., most epistatic effects were negative. The five QTLs expressed their effects mainly in three stages, namely within 14 days, from 28 days to 42 days, and from 49 days to 63 days after transplantation. Positive effects and negative interactions of the QTLs were observed in the early and the late stages, but opposite interactions were observed in the middle stage. Mainly, three functional parameters, including the inflexion point, the peak value, and the degradation rate, were regulated via the QTL effects and their opposite interactions. This paper uncovered the genetic rule of five QTLs on the leaf numbers, including the interaction, expression, and function features. The information will be helpful to understand the genetic mechanism for developmental traits.
Keywords	additive effect ; agronomy ; energy ; epistasis ; leaves ; photosynthesis ; polymerization ; solar collectors
Language	English
Dates of publication	2022-1125
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article ; Online
ZDB-ID	2607043-1
ISSN	2073-4395
ISSN	2073-4395
DOI	10.3390/agronomy12122968
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Article: OsMPK4 promotes phosphorylation and degradation of IPA1 in response to salt stress to confer salt tolerance in rice

Jia, Meiru / Luo, Nan / Meng, Xiangbing / Song, Xiaoguang / Jing, Yanhui / Kou, Liquan / Liu, Guifu / Huang, Xiahe / Wang, Yingchun / Li, Jiayang / Wang, Bing / Yu, Hong

Journal of genetics and genomics. 2022 June 30,

2022

Abstract: Salt stress adversely affects plant growth, development, and crop yield. Rice (Oryza sativa L.) is one of the most salt-sensitive cereal crops, especially at the early seedling stage. Mitogen-activated protein kinase (MAPK/MPK) cascades have been shown ... ...

Abstract	Salt stress adversely affects plant growth, development, and crop yield. Rice (Oryza sativa L.) is one of the most salt-sensitive cereal crops, especially at the early seedling stage. Mitogen-activated protein kinase (MAPK/MPK) cascades have been shown to play critical roles in salt response in Arabidopsis. However, the roles of the MPK cascade signaling in rice salt response and substrates of OsMPK remain largely unknown. Here, we report that the salt-induced OsMPK4-Ideal Plant Architecture 1 (IPA1) signaling pathway regulates the salt tolerance in rice. Under salt stress, OsMPK4 could interact with IPA1 and phosphorylate IPA1 at Thr180, leading to degradation of IPA1. Genetic evidence shows that IPA1 is a negative regulator of salt tolerance in rice, whereas OsMPK4 promotes salt response in an IPA1-dependent manner. Taken together, our results uncover an OsMPK4-IPA1 signal cascade that modulates the salt stress response in rice and sheds new light on the breeding of salt-tolerant rice varieties.
Keywords	Arabidopsis ; Oryza sativa ; crop yield ; genomics ; mitogen-activated protein kinase ; phosphorylation ; plant architecture ; plant growth ; rice ; salt stress ; salt tolerance ; seedlings ; stress response
Language	English
Dates of publication	2022-0630
Publishing place	Elsevier Ltd
Document type	Article
Note	Pre-press version
ZDB-ID	2374568-X
ISSN	1873-5533 ; 1673-8527
ISSN (online)	1873-5533
ISSN	1673-8527
DOI	10.1016/j.jgg.2022.06.009
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Article: An engineered platform for reconstituting functional multisubunit SCF E3 ligase in vitro

Liu, Huihui / Liu, Simiao / Yu, Hong / Huang, Xiahe / Wang, Yingchun / Jiang, Liang / Meng, Xiangbing / Liu, Guifu / Chen, Mingjiang / Jing, Yanhui / Yu, Feifei / Wang, Bing / Li, Jiayang

Molecular plant. 2022 June 21,

2022

Abstract: Multisubunit SKP1/Cullin1/F-box (SCF) E3 ligases play essential roles in regulating the stability of crucial regulatory factors and controlling growth and development in eukaryotes. Detecting E3 ligase activity in vitro is important for exploring the ... ...

Abstract	Multisubunit SKP1/Cullin1/F-box (SCF) E3 ligases play essential roles in regulating the stability of crucial regulatory factors and controlling growth and development in eukaryotes. Detecting E3 ligase activity in vitro is important for exploring the molecular mechanism of protein ubiquitination. However, in vitro ubiquitination assay systems for multisubunit E3 ligases remain difficult to achieve, especially in plants, mainly due to difficulties in achieving active components of multisubunit E3 ligases with high purity and characterizing specific E2 and E3 pairs. In this study, we characterized components of the rice SCFᴰᵂᴬᴿF³ (SCFᴰ³) E3 ligase, screened the coordinated E2, and reconstituted active SCFᴰ³ E3 ligase in vitro. We further engineered SCFᴰ³ E3 ligase using a fused SKP1-Cullin1-RBX1 (eSCR) protein and found that both the wild-type SCFᴰ³ E3 ligase and the engineered SCFᴰ³ E3 ligase catalyzed ubiquitination of the substrate D53, which is the key transcriptional repressor in strigolactone signaling. Finally, we replaced D3 with other F-box proteins from rice and humans, and reconstituted active eSCF E3 ligases, including eSCFᴳᴵᴰ², eSCFFᴮXᴸ¹⁸ and eSCFCᴰC⁴ E3 ligases. Together, this work reconstitutes functional SCF E3 ligases in vitro and generates an engineered system with interchangeable F-box proteins, providing a powerful platform to study the mechanisms of multisubunit SCF E3 ligases in eukaryotes.
Keywords	catalytic activity ; eukaryotic cells ; growth and development ; repressor proteins ; rice ; strigolactones ; ubiquitin-protein ligase ; ubiquitination
Language	English
Dates of publication	2022-0621
Publishing place	Elsevier Inc.
Document type	Article
Note	Pre-press version
ZDB-ID	2393618-6
ISSN	1752-9867 ; 1674-2052
ISSN (online)	1752-9867
ISSN	1674-2052
DOI	10.1016/j.molp.2022.06.011
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Article ; Online: LAZY3 interacts with LAZY2 to regulate tiller angle by modulating shoot gravity perception in rice.

Cai, Yueyue / Huang, Linzhou / Song, Yuqi / Yuan, Yundong / Xu, Shuo / Wang, Xueping / Liang, Yan / Zhou, Jie / Liu, Guifu / Li, Jiayang / Wang, Wenguang / Wang, Yonghong

Plant biotechnology journal

2023 Volume 21, Issue 6, Page(s) 1217–1228

Abstract: Starch biosynthesis in gravity-sensing tissues of rice shoot determines the magnitude of rice shoot gravitropism and thus tiller angle. However, the molecular mechanism underlying starch biosynthesis in rice gravity-sensing tissues is still unclear. We ... ...

Abstract	Starch biosynthesis in gravity-sensing tissues of rice shoot determines the magnitude of rice shoot gravitropism and thus tiller angle. However, the molecular mechanism underlying starch biosynthesis in rice gravity-sensing tissues is still unclear. We characterized a novel tiller angle gene LAZY3 (LA3) in rice through map-based cloning. Biochemical, molecular and genetic studies further demonstrated the essential roles of LA3 in gravity perception of rice shoot and tiller angle control. The shoot gravitropism and lateral auxin transport were defective in la3 mutant upon gravistimulation. We showed that LA3 encodes a chloroplast-localized tryptophan-rich protein associated with starch granules via Tryptophan-rich region (TRR) domain. Moreover, LA3 could interact with the starch biosynthesis regulator LA2, determining starch granule formation in shoot gravity-sensing tissues. LA3 and LA2 negatively regulate tiller angle in the same pathway acting upstream of LA1 to mediate asymmetric distribution of auxin. Our study defined LA3 as an indispensable factor of starch biosynthesis in rice gravity-sensing tissues that greatly broadens current understanding in the molecular mechanisms underlying the starch granule formation in gravity-sensing tissues, and provides new insights into the regulatory mechanism of shoot gravitropism and rice tiller angle.
MeSH term(s)	Oryza/metabolism ; Plant Proteins/genetics ; Plant Proteins/metabolism ; Plant Shoots/genetics ; Gravity Sensing/genetics ; Tryptophan/metabolism ; Indoleacetic Acids/metabolism ; Gravitropism/genetics ; Starch/metabolism
Chemical Substances	Plant Proteins ; Tryptophan (8DUH1N11BX) ; Indoleacetic Acids ; Starch (9005-25-8)
Language	English
Publishing date	2023-02-28
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2136367-5
ISSN	1467-7652 ; 1467-7652
ISSN (online)	1467-7652
ISSN	1467-7652
DOI	10.1111/pbi.14031
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Article: Grain shape is a factor affecting the stigma exsertion rate in rice.

Tan, Quanya / Chen, Songliang / Gan, Zhenpeng / Lu, Qimiao / Yan, Zhenguang / Chen, Guodong / Lin, Shaojun / Yang, Weifeng / Zhao, Jiao / Ba, Yuanyuan / Zhu, Haitao / Bu, Suhong / Liu, Guifu / Liu, Zupei / Wang, Shaokui / Zhang, Guiquan

Frontiers in plant science

2023 Volume 14, Page(s) 1087285

Abstract: Stigma exsertion rate (SER) is an index of outcrossing ability in rice and is a key trait of male sterile lines (MSLs) in hybrid rice. In this study, it was found that the maintainer lines ... ...

Abstract	Stigma exsertion rate (SER) is an index of outcrossing ability in rice and is a key trait of male sterile lines (MSLs) in hybrid rice. In this study, it was found that the maintainer lines carrying
Language	English
Publishing date	2023-01-31
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2613694-6
ISSN	1664-462X
ISSN	1664-462X
DOI	10.3389/fpls.2023.1087285
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