Fine Mapping and Candidate Gene Prediction of the Quantitative Trait Locus qPL8 for Panicle Length in Rice

Zhang, Lin; Zou, Yiting; Bian, Zhong; Xie, Dong; Yeilaghi, Hadi; Fan, Xiaolei; Zhao, Dongsheng; Liu, Qiaoquan

doi:10.32604/phyton.2021.014880

Cited by 3 publications

(2 citation statements)

References 40 publications

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“…For example, in RILs, the high recombination frequency is advantageous because of the occurrence of multiple meiotic events during repeated self-fertilization (Jansen, 2004). To directly perform fine-mapping, heterozygous plants are required such as NIL for population development and increasing an accuracy of phenotype determination (Zhang et al 2021). Additionally, the resolution for QTL mapping can be improved by using a large population size and greater marker density to more precisely detect recombination events (Chen et al 2014).…”

Section: Discussionmentioning

confidence: 99%

“…However, the validation and functional characterization of QTLs and genes are still required, as most of them are located in large genomic regions with limited low-density markers, and they do not provide accurate QTL information capable of controlling lodging-related traits (Wang et al 2011). Therefore, development of additional molecular markers is necessary to fine map or clone genes associated with important agronomical traits based on a high-resolution genetic map (Zhang et al 2021).…”

Section: Introductionmentioning

confidence: 99%

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Fine-Mapping of a Major Quantitative Trait Locusq2ID1for Rice Stem Diameter

Lee

et al. 2021

Plant Breed. Biotech.

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Rice culm is an important trait for determining rice lodging yield, and stem diameter has been suggested as a yield-related trait; however, studies for the genetic basis of its phenotypic variation are still required. In this study, we used 160 recombination inbred lines derived from a cross of two different rice varieties ['Milyang23' (Tongil rice) and 'Giho' (japonica)] for quantitative trait locus (QTL) mapping with nine stem traits. The analysis showed that QTLs for the diameters of the first, second, third and fourth internode traits were independently separated in the top of chromosome 1, whereas four lengths of internodes were estimated as being related to the semidwarf1 (sd1) gene. A major-effect QTL (q2ID1) was identified that the overlapped region of our previous mapping with a large genomic region. Therefore, we performed high-resolution genetic mapping for fine-mapping of q2ID1 to a ~140 kb region between Ind1_1 and Ind1_2 of genetic markers, with candidate genes predicted using a reference genome. We ultimately identified nine of the 15 candidate genes with specific gene functions and analyzed the sequence variations between two parents. These results offer valuable gene and/or genetic information on stem diameter to improve lodging resistance and yield.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Fine-Mapping of a Major Quantitative Trait Locusq2ID1for Rice Stem Diameter

Lee

et al. 2021

Plant Breed. Biotech.

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Characterization of qPL5, a Novel Quantitative Trait Locus (QTL) that controls Panicle Length in Rice (Oryza sativa L.)

Zhang¹,

Li²,

Du³

et al. 2022

Preprint

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Panicle length (PL) is an important trait that determines panicle architecture and strongly affects grain yield and quality in rice. However, this trait has not been well characterized genetically, and its contribution to yield improvement is not well understood. Characterization of novel genes related to PL is of great significance for breeding high-yielding rice varieties. In our previous research we identified qPL5, a quantitative trait locus for PL. In this study, we aimed to determine the exact position of qPL5 in the rice genome and identify the candidate gene. Through substitution mapping, we mapped qPL5 to a region of 21.86 kb flanked by the molecular marker loci STS5-99 and STS5-106 in which two candidate genes were predicted. By sequence analysis and relative expression analysis, LOC-Os05g41230, which putatively encodes a BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1 precursor, was considered to be the most likely candidate gene for qPL5. In addition, we successfully developed a pair of near-isogenic lines (NILs) for qPL5 in different genetic backgrounds to evaluate the genetic effects of qPL5. Agronomic trait analysis of the NILs indicated that qPL5 positively contributes to plant height, grain number per panicle, panicle length, grain yield per panicle, and flag leaf length, but it had no influence on heading date and grain-size-related traits. Therefore, qPL5 and the markers tightly linked to it should be available for molecular breeding of high-yielding varieties.

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Mining the candidate genes of rice panicle traits via a genome-wide association study

Liu,

Sun,

Zhang

et al. 2023

Front. Genet.

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Panicle traits are important for improving the panicle architecture and grain yield of rice. Therefore, we performed a genome-wide association study (GWAS) to analyze and determine the genetic determinants of five panicle traits. A total of 1.29 million single nucleotide polymorphism (SNP) loci were detected in 162 rice materials. We carried out a GWAS of panicle length (PL), total grain number per panicle (TGP), filled grain number per panicle (FGP), seed setting rate (SSR) and grain weight per panicle (GWP) in 2019, 2020 and 2021. Four quantitative trait loci (QTLs) for PL were detected on chromosomes 1, 6, and 9; one QTL for TGP, FGP, and GWP was detected on chromosome 4; two QTLs for FGP were detected on chromosomes 4 and 7; and one QTL for SSR was detected on chromosome 1. These QTLs were detected via a general linear model (GLM) and mixed linear model (MLM) in both years of the study period. In this study, the genomic best linear unbiased prediction (BLUP) method was used to verify the accuracy of the GWAS results. There are nine QTLs were both detected by the multi-environment GWAS method and the BLUP method. Moreover, further analysis revealed that three candidate genes, LOC_Os01g43700, LOC_Os09g25784, and LOC_Os04g47890, may be significantly related to panicle traits of rice. Haplotype analysis indicated that LOC_Os01g43700 and LOC_Os09g25784 are highly associated with PL and that LOC_Os04g47890 is highly associated with TGP, FGP, and GWP. Our results offer essential genetic information for the molecular improvement of panicle traits. The identified candidate genes and elite haplotypes could be used in marker-assisted selection to improve rice yield through pyramid breeding.

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Fine Mapping and Candidate Gene Prediction of the Quantitative Trait Locus qPL8 for Panicle Length in Rice

Cited by 3 publications

References 40 publications

Fine-Mapping of a Major Quantitative Trait Locusq2ID1for Rice Stem Diameter

Fine-Mapping of a Major Quantitative Trait Locusq2ID1for Rice Stem Diameter

Characterization of qPL5, a Novel Quantitative Trait Locus (QTL) that controls Panicle Length in Rice (Oryza sativa L.)

Mining the candidate genes of rice panicle traits via a genome-wide association study

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