Pleiotropic Effects of Rice Florigen Gene RFT1 on the Amino Acid Content of Unmilled Rice

Xie, Lihong; Yingguo, Zhu; Tang, Shaoqing; Wei, Xiangjin; Sheng, Zhonghua; Jiao, Guiai; Zhuang, Jie‐Yun

doi:10.3389/fgene.2020.00013

Cited by 8 publications

(4 citation statements)

References 32 publications

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“…The heading date is known to be associated with a range of agronomic traits affecting yield, such as plant height, panicle number, grain number, and weight, and those affecting eating and cooking quality, such as AC and PC [3,[27][28][29][30]. Therefore, to facilitate the use of different Hd1 alleles in rice molecular breeding, it is important to evaluate the pleiotropic effects of Hd1 and the effects of different Hd1 alleles on major agronomic traits.…”

Section: Discussionmentioning

confidence: 99%

Hd1 Allele Types and Their Associations with Major Agronomic Traits in Korean Rice Cultivars

Lee

Park

et al. 2021

Plants

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Optimizing flowering time in crop plants is critical for maximizing yield and quality under target environments. While there is a wide range of heading date variation in Korean rice cultivars, the underlying gene mechanisms are unclear. Here, we sequenced the protein coding regions of Hd1, the major rice heading date gene, from 293 Korean rice cultivars and investigated the associations between Hd1 allele types and major agronomic traits under four different environments. There were four functional Hd1 and five nonfunctional hd1 alleles distributed among the 293 Korean rice cultivars. The effects of the Hd1 allele types were highly significant for days to heading in all four environments, explaining 51.4–65.8% of the phenotypic variation. On average, cultivars carrying nonfunctional hd1 headed 13.7 days earlier than those carrying functional Hd1. While the Hd1 allele types exhibited highly significant effects on culm length and protein content under all four environments, the differences between cultivars carrying Hd1 and hd1 were minimal. The effects of the Hd1 allele types on amylose content were significant in only one of the four environments. Our results provide useful information for fine-tuning rice heading dates by utilizing different Hd1 alleles in rice breeding programs.

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Section: Discussionmentioning

confidence: 99%

Hd1 Allele Types and Their Associations with Major Agronomic Traits in Korean Rice Cultivars

Lee

Park

et al. 2021

Plants

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“… Zhang et al (2020) found that the regions of several QTLs for grain weight influence HD between the two parental varieties. Xie et al (2020) also reported the pleiotropic effects of the rice florigen gene RFT1 on the amino acid content of unmilled rice. Ouyang et al (2020) indicated that OsHG3 can affect rice palea development, grain yield, and quality at the same time.…”

Section: Discussionmentioning

confidence: 98%

Detection of QTLs for panicle-related traits using an indica × japonica recombinant inbred line population in rice

Guan

Cheng

Yin

et al. 2021

PeerJ

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Background The panicle is the most important organ in rice, and all the panicle-related traits are correlated with rice grain yield. Understanding the underlying genetic mechanisms controlling panicle development is very important for improving rice production. Methods Nine panicle-related traits including heading date, panicle length, number of primary branches, number of secondary branches, number of grains per panicle, number of panicles per plant, number of filled grains per plant, seed-setting rate, and grain yield per plant were investigated. To map the quantitative trait loci (QTLs) for the nine panicle-related traits, a PCR-based genetic map with 208 markers (including 121 simple sequence repeats and 87 InDels) and a high-density linkage map with 18,194 single nucleotide polymorphism (SNP) markers were both used. Results Using a recombinant inbred line population derived from an indica variety Huanghuazhan and a japonica line Jizi 1560, a total of 110 and 112 QTLs were detected for panicle-related traits by PCR-based genetic map and by high-density linkage map, respectively. Most of the QTLs were clustered on chromosomes 1, 2, 3, 6, and 7 while no QTLs were detected on chromosome 10. Almost all the QTLs with LOD values of more than 5.0 were repeatedly detected, indicating the accuracy of the two methods and the stability of the QTL effects. No genes for panicle-related traits have been previously reported in most of these regions. QTLs found in JD1006–JD1007 and RM1148–RM5556 with high LOD and additive values deserved further research. The results of this study are beneficial for marker-assisted breeding and provide research foundation for further fine-mapping and cloning of these QTLs for panicle-related traits.

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“…Trait selection heavily influences pleiotropy results. Small subsets of measured traits originating from the same phytomer or highly correlated traits such as amino acid content [ 60 ] or grain quality [ 61 ] may already share similar regulatory pathways leading to enrichment in pleiotropic loci [ 23 ]. This may lead to unrealistic expectations of the pervasiveness of pleiotropy genome-wide.…”

Section: Discussionmentioning

confidence: 99%

Elucidating the patterns of pleiotropy and its biological relevance in maize

et al. 2023

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Pleiotropy—when a single gene controls two or more seemingly unrelated traits—has been shown to impact genes with effects on flowering time, leaf architecture, and inflorescence morphology in maize. However, the genome-wide impact of biological pleiotropy across all maize phenotypes is largely unknown. Here, we investigate the extent to which biological pleiotropy impacts phenotypes within maize using GWAS summary statistics reanalyzed from previously published metabolite, field, and expression phenotypes across the Nested Association Mapping population and Goodman Association Panel. Through phenotypic saturation of 120,597 traits, we obtain over 480 million significant quantitative trait nucleotides. We estimate that only 1.56–32.3% of intervals show some degree of pleiotropy. We then assess the relationship between pleiotropy and various biological features such as gene expression, chromatin accessibility, sequence conservation, and enrichment for gene ontology terms. We find very little relationship between pleiotropy and these variables when compared to permuted pleiotropy. We hypothesize that biological pleiotropy of common alleles is not widespread in maize and is highly impacted by nuisance terms such as population structure and linkage disequilibrium. Natural selection on large standing natural variation in maize populations may target wide and large effect variants, leaving the prevalence of detectable pleiotropy relatively low.

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Pleiotropic Effects of Rice Florigen Gene RFT1 on the Amino Acid Content of Unmilled Rice

Cited by 8 publications

References 32 publications

Hd1 Allele Types and Their Associations with Major Agronomic Traits in Korean Rice Cultivars

Hd1 Allele Types and Their Associations with Major Agronomic Traits in Korean Rice Cultivars

Detection of QTLs for panicle-related traits using an indica × japonica recombinant inbred line population in rice

Elucidating the patterns of pleiotropy and its biological relevance in maize

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