Genome-wide association study reveals novel QTLs and candidate genes for panicle number in rice DOI Creative Commons
Jiangfan Guo,

Wenbin Wang,

Wěi Li

et al.

Frontiers in Genetics, Journal Year: 2024, Volume and Issue: 15

Published: Nov. 5, 2024

Introduction Panicle number (PN) is one of the three key yield components in rice, maintaining stable tiller and PN a crucial characteristic an ideal plant architecture. Understanding molecular mechanisms underlying essential for breeders aiming to improve rice yield. Methods To dissect genetic architecture panicle number, genome-wide association study (GWAS) was conducted 411 japonica varieties. GWAS analysis carried out with mixed linear model using 743,678 high-quality SNPs. Results Over two experimental years, we detected total seven quantitative trait loci (QTLs), located on chromosomes 1, 4, 6, 8, 11, 12; notably, qPN1.1 qPN8 were consistently both years. By combining haplotype expression analyses, OsCKX11 identified as candidate gene , while LOC_Os01g07870 LOC_Os01g07950 genes . Significant differences observed among haplotypes these genes. Additionally, qRT-PCR results showed that levels significantly lower accessions high numbers compared those low numbers. Discussion understand natural biological function genes, further research involving overexpression or silencing needed. Despite challenges, our will lay foundation development provide valuable resources developing high-panicle-number cultivars engineering breeding.

Language: Английский

Engineering source-sink relations by prime editing confers heat-stress resilience in tomato and rice DOI

H. F. Lou,

Shujia Li,

Zihang Shi

et al.

Cell, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 1, 2024

Language: Английский

Citations

12
The rice genome annotation project: an updated database for mining the rice genome DOI Creative Commons
John P. Hamilton, Chenxin Li, C. Robin Buell

et al.

Nucleic Acids Research, Journal Year: 2024, Volume and Issue: 53(D1), P. D1614 - D1622

Published: Nov. 18, 2024

Abstract Rice (Oryza sativa L.) is a major cereal crop that provides calories across the world. With small genome, rice has been used extensively as model for genetic and genomic studies in Poaceae. Since release of first genome sequence 2002, an improved reference assembly, multiple whole assemblies, extensive gene expression profiles, resequencing data from over 3000 accessions have generated. To facilitate access to plant biologists, we updated Genome Annotation Project database (RGAP; https://rice.uga.edu) with new datasets including 16 assemblies variants generated pan-genome projects Genomes Project. We abundance 80 RNA-sequencing function discovery, performed coexpression resulting 39 modules capture highly connected sets co-regulated genes. comparative analyses, 32 335 syntelogs were identified between Nipponbare other genomes 19 371 four Poaceae genomes. Infrastructure improvements RGAP include upgraded browser portals, enhanced website security increased performance website.

Language: Английский

Citations

4
Florigen‐like protein OsFTL1 promotes flowering without essential florigens Hd3a and RFT1 in rice DOI Open Access
Shaobo Wei,

Long Cheng,

Hongge Qian

et al.

Journal of Integrative Plant Biology, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 17, 2025

ABSTRACT Flowering time is a critical agronomic trait in rice, directly influencing grain yield and adaptability to specific planting regions seasons. Florigens, including FLOWERING LOCUS T (FT) proteins Hd3a (OsFTL2) RFT1 (OsFTL3), play central roles transmitting flowering signals through rice's photoperiod regulatory network. While have been extensively studied, the functions interactions of other FT‐like remain unclear, limiting advancements breeding strategies for early‐maturing rice varieties. Here, we demonstrate that florigen‐like protein OsFTL1 forms florigen activation complex (FAC) promotes under both short‐day long‐day conditions. localizes nucleus cytoplasm, with predominant expression shoot base, facilitating its mobilization apical meristem (SAM) initiate flowering. Overexpression ( ‐OE) leaves or bases significantly accelerates alters plant architecture. In nucleus, interacts GF14c OsFD1 form an FAC, activating OsMADS14 OsMADS15 drive Markedly, ‐OE plants deficient exhibited earlier compared wild‐type plants, indicating can independently promote Furthermore, haplotype analysis identified OsFTL1‐Hap3 , beneficial variant associated early comparable yields. These findings revealed substitute FAC formation, promoting across photoperiods, highlighting potential application early‐maturing, high‐yield varieties suitable diverse environments.

Language: Английский

Citations

0
Identification of QTLs and a candidate gene affecting rice grain volume via high-density genetic mapping DOI Creative Commons

Zhiguang Sun,

Hongzhou An,

Zeyu Qiu

et al.

Frontiers in Plant Science, Journal Year: 2025, Volume and Issue: 16

Published: March 31, 2025

Grain volume is a key agronomic trait of rice. It coordinately determined by grain length, width, thickness, and roundness, which influences the rice yield quality, yet molecular mechanism still not fully understood. In this study, mapping population Ludao (weedy rice) Guangbaixiangzhan (GBXZ) was developed in Lianyungang, Jiangsu province, China, employed to construct high-density genetic map use RICE 1 K mGPS chip 2021. The QTLs carried out with IciMapping software using inclusive composite interval (ICIM) method. A total eight for volume, explained 4.22-19.75% phenotypic variation, were detected LOD scores ranging from 3.33 13.25. Among these loci, five are known genes or loci related size, three qGV4-2, qGV7-1, qGV7-2, newly identified. major QTL, highest validated NIL pairs. By combining gene functional annotation, expression analysis sequence comparison within candidate (LOC_Os07g15540), encoding an ethylene receptor, OsETR4, Further haplotype-phenotype revealed be significantly associated thousand-grain weight. Thus we identified LOC_Os07g15540 as most likely gene. Taken together, our findings provide basis research on broaden understanding role factors regulating thus providing important resource improvement

Language: Английский

Citations

0
Integrated multi‐omics analyses provide new insights into genomic variation landscape and regulatory network candidate genes associated with walnut endocarp DOI
Hengzhao Liu, Huijuan Zhou, Hang Ye

et al.

The Plant Journal, Journal Year: 2025, Volume and Issue: 122(1)

Published: March 31, 2025

SUMMARY Persian walnut ( Juglans regia ) is an economically important nut oil tree; the fruit has a hard endocarp/shell to protect seeds, thus playing key role in its evolution, and shell thickness trait for breeding. However, genomic landscape gene regulatory networks associated with development remain be systematically elucidated. Here, we report high‐quality genome assembly of cultivar ‘Xiangling’ construct graphic structure pan‐genome eight species reveal genetic variations at level. We re‐sequence 285 accessions characterize variation landscape. Through genome‐wide association studies (GWAS), identified 19 loci more than 268 that underwent selection during domestication improvement. Multi‐omics analyses, including transcriptomics, metabolomics, DNA methylation, spatial transcriptomics across eleven developmental stages, revealed several candidate genes related secondary cell biosynthesis lignin accumulation. This integrated multi‐omics approach accumulation, such as UGP , MYB308, MYB83 NAC043 NAC073 CCoAOMT1 CCoAOMT7 CHS2 CESA7 LAC7 COBL4 IRX12 . Overexpression JrUGP JrMYB308 Arabidopsis thaliana confirmed their roles wall thickening. Consequently, our comprehensive findings offer novel insights into network regulation endocarp thickness, which enable further genome‐informed breeding strategies

Language: Английский

Citations

0
Deciphering rice feralization: insights from genomics of weedy rice DOI

Yunqi Cong,

Yijie Gui,

Kaicheng Yong

et al.

Published: Jan. 1, 2025

Language: Английский

Citations

0
The next Green Revolution: integrating crop architectype and physiotype DOI Creative Commons
Xia Li,

Xie Chen,

Lin Cheng

et al.

Trends in biotechnology, Journal Year: 2025, Volume and Issue: unknown

Published: April 1, 2025

Language: Английский

Citations

0
Genetic interaction network of quantitative trait genes for heading date in rice DOI Creative Commons
Mengjiao Chen, Yifeng Hong, Jiongjiong Fan

et al.

Journal of genetics and genomics/Journal of Genetics and Genomics, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 1, 2025

Language: Английский

Citations

0
Characterization of a stable QTL for quality-related traits and its effects on yields in wheat (Triticum aestivum L.) DOI

Hongke Ding,

Yankun Li,

Jinlian Ou

et al.

Theoretical and Applied Genetics, Journal Year: 2025, Volume and Issue: 138(3)

Published: Feb. 26, 2025

Language: Английский

Citations

0
OsMADS22 interacts with OsMADS50 to regulate floral transition in rice DOI
Dongyang Wang, Yisheng Chai, Suhui Chen

et al.

Biochemical and Biophysical Research Communications, Journal Year: 2025, Volume and Issue: 757, P. 151607 - 151607

Published: March 11, 2025

Language: Английский

Citations

0