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.)

He, Ning; Zhan, Guanping; Huang, Fenghuang; Abou‐Elwafa, Salah Fatouh; Yang, Dewei

doi:10.3389/fpls.2022.878558

Cited by 7 publications

(8 citation statements)

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“…The genetic background of NIL128 homozygous material was analysed using 296 primers that showed polymorphism between Hui1586 and Jiafuzhan cultivars [ 20 ]. The results showed that five markers exhibited homozygous alleles of Hui 1586, including Ind1-3 on chromosome 1, RM7286 on chromosome 2, Ind3-18 on chromosome 3, RM566 on chromosome 9, and RM19 on chromosome 12.…”

Section: Resultsmentioning

confidence: 99%

“…The indica rice cultivar Jiafuzhan and the japonica rice cultivar Hui1586 were preserved at the Rice Research Institute, Fujian Academy of Agricultural Sciences, China. In the early stage, 176 NILs were constructed with the indica cultivar Jiafuzhan as the acceptor and the japonica cultivar Hui1586 as the donor [ 20 ].…”

Section: Methodsmentioning

confidence: 99%

“…DNA was extracted from rice leaves by the CTAB method and modified appropriately [ 36 ]. For PCR amplification, every 20-μL reaction mixture contained 30 ng DNA (2-μL), 0.4 μM of each primer (1-μL), 2× Es Tag MasterMix (Dye) (10-μL), and 6-μL sterile deionized water [ 20 ]. The amplified PCR products were stained by 3% agarose gel electrophoresis with ethidium bromide staining as the marker [ 37 ].…”

Section: Methodsmentioning

confidence: 99%

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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: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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

Huang

Yang

2023

IJMS

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“…Furthermore, validation of these identified and stable or previously reported QTLs in different genetic backgrounds is challenging, and very limited efforts have been made toward it. Several stable yield QTLs and genes have been identified and cloned in other crop species, such as rice ( Xing and Zhang, 2010 ; He et al., 2022 ). However, progress toward functional characterization of seed yield-related QTLs or genes is lagging in soybean.…”

Section: Challenges and Perspectivesmentioning

confidence: 99%

Molecular, genetic, and genomic basis of seed size and yield characteristics in soybean

Tayade,

Imran,

Ghimire

et al. 2023

Front. Plant Sci.

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Soybean (Glycine max L. Merr.) is a crucial oilseed cash crop grown worldwide and consumed as oil, protein, and food by humans and feed by animals. Comparatively, soybean seed yield is lower than cereal crops, such as maize, rice, and wheat, and the demand for soybean production does not keep up with the increasing consumption level. Therefore, increasing soybean yield per unit area is the most crucial breeding objective and is challenging for the scientific community. Moreover, yield and associated traits are extensively researched in cereal crops, but little is known about soybeans’ genetics, genomics, and molecular regulation of yield traits. Soybean seed yield is a complex quantitative trait governed by multiple genes. Understanding the genetic and molecular processes governing closely related attributes to seed yield is crucial to increasing soybean yield. Advances in sequencing technologies have made it possible to conduct functional genomic research to understand yield traits’ genetic and molecular underpinnings. Here, we provide an overview of recent progress in the genetic regulation of seed size in soybean, molecular, genetics, and genomic bases of yield, and related key seed yield traits. In addition, phytohormones, such as auxin, gibberellins, cytokinins, and abscisic acid, regulate seed size and yield. Hence, we also highlight the implications of these factors, challenges in soybean yield, and seed trait improvement. The information reviewed in this study will help expand the knowledge base and may provide the way forward for developing high-yielding soybean cultivars for future food demands.

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“…With the continuous advancement of research techniques and the utilization of new research materials, several new PH-related genes are being localized and cloned. For example, a PH major quantitative trait locus (QTL), qph12, was identified in rice, and knockout experiments verified that LOC_Os12g40490 is the key candidate gene, which is an auxin-responsive Aux/IAA gene family member (He et al, 2022). SD8 (LOC_Os08g45030), a PH-related IAA-associated gene, was also identified, which encodes an ATP-binding cassette-B (ABCB) transporter, and the mutant lines were able to reduce PH and adjust the flag leaf angle, thereby optimizing rice structure without affecting yield (Qu et al, 2022).…”

Section: Introductionmentioning

confidence: 99%

Transcriptome analysis reveals potential genes associated with plant height in rice

CHEN¹,

Feng²,

ZHANG³

et al. 2023

Biocell

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Plant height (PH) is a complex trait regulated by the environment and multiple genes. PH directly affects crop yield, harvest index, and lodging resistance. From plant dwarf mutants, many genes related to PH have been identified and described. Nonetheless, the molecular mechanism of height regulation in high-culm rice mutants has not been well studied. By using transcriptome and weighted gene co-expression network analysis (WGCNA), we identified the differentially expressed genes (DEGs) between high-culm rice mutants (MUT) and wild-type (WT) and explored the key pathways and potential candidate genes involved in PH regulation. Transcriptome analysis identified a total of 2,184 DEGs, of which 1,317 were identified at the jointing stage and 1,512 were identified at the heading stage. Kyoto Encyclopedia of Genes and Genomes enrichment showed that the enrichment pathways were mainly involved in plant hormone signal transduction, ABC transportation, and steroid hormone biosynthesis. Among these metabolic pathways, LOC_Os05g43910 and LOC_Os01g35030 were auxin (IAA)-related genes, up-regulated in MUT and LOC_Os02g08500 (LEPTO1), LOC_Os11g04720, and LOC_Os12g04500 were cytokinin (CK)-related genes, downregulated in MUT. The WGCNA identified four modules (light cyan, dark grey, grey, and pale turquoise) closely related to PH, and seven key genes were screened from these modules, of which two were up-regulated cell wallrelated genes (LOC_Os01g26174 (OsWAK5), LOC_Os06g05050) in MUT, and one gibberellic acid (GA) gene (LOC_Os06g37364, OsKO2) was also up-regulated. These genes might be closely related to PH regulation. These findings help us better understand the transcriptional regulation of rice plant growth and development and provide a theoretical basis for mapping and cloning the PH regulatory genes.

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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.)

Cited by 7 publications

References 46 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.)

Molecular, genetic, and genomic basis of seed size and yield characteristics in soybean

Transcriptome analysis reveals potential genes associated with plant height in rice

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