Genome-wide association study of traits in sacred lotus uncovers MITE-associated variants underlying stamen petaloid and petal number variations

Gao, Zhiyan; Liang, Yuting; Wang, Yuhan; Xiao, Yingjie; Chen, Jin‐Ming; Shi, Tao

doi:10.3389/fpls.2022.973347

Cited by 3 publications

(1 citation statement)

References 122 publications

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“…Therefore, it is used not only as a vegetable but also as a medicinal herb, tea, and dessert. Lotus is beneficial to the food economy, hence more and more research has been done on it recently 15 , 16 , including transcriptome, genome, polymorphic markers and gene identification 17 , 18 . However, there is no scientific analysis on the selection of normalised reference genes in different developmental stages and stress treatments in Lotus.…”

Section: Introductionmentioning

confidence: 99%

Evaluation and validation of suitable reference genes for quantitative real-time PCR analysis in lotus (Nelumbo nucifera Gaertn.)

Wang,

Zhu,

Zheng

et al. 2024

Sci Rep

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The qRT-PCR technique has been regarded as an important tool for assessing gene expression diversity. Selection of appropriate reference genes is essential for validating deviation and obtaining reliable and accurate results. Lotus (Nelumbo nucifera Gaertn) is a common aquatic plant with important aesthetic, commercial, and cultural values. Twelve candidate genes, which are typically used as reference genes for qRT-PCR in other plants, were selected for this study. These candidate reference genes were cloned with, specific primers designed based on published sequences. In particular, the expression level of each gene was examined in different tissues and growth stages of Lotus. Notably, the expression stability of these candidate genes was assessed using the software programs geNorm and NormFinder. As a result, the most efficient reference genes for rootstock expansion were TBP and UBQ. In addition, TBP and EF-1α were the most efficient reference genes in various floral tissues, while ACT and GAPDH were the most stable genes at all developmental stages of the seed. CYP and GAPDH were the best reference genes at different stages of leaf development, but TUA was the least stable. Meanwhile, the gene expression profile of NnEXPA was analyzed to confirm the validity of the findings. It was concluded that, TBP and GAPDH were identified as the best reference genes. The results of this study may help researchers to select appropriate reference genes and thus obtain credible results for further quantitative RT-qPCR gene expression analyses in Lotus.

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Section: Introductionmentioning

confidence: 99%

Evaluation and validation of suitable reference genes for quantitative real-time PCR analysis in lotus (Nelumbo nucifera Gaertn.)

Wang,

Zhu,

Zheng

et al. 2024

Sci Rep

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Smart breeding driven by advances in sequencing technology

et al. 2023

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Crop breeding has undergone numerous advancements throughout history with the next revolution being uncertain. This review provides an overview of breeding techniques from traditional selective breeding and crossbreeding to modern breeding based on molecular marker‐assisted and genomic selection. Systematic analysis of the mainstream genotyping approaches based on principle, application scenario and supporting software revealed that the changes in genotyping technology have led to an explosion in data. This data expansion will drive a breakthrough in sequencing technology and integrate artificial intelligence with automation. The review also discusses the technological changes associated with breeding during the big data era, including breeding models, genotyping technologies and future intelligent breeding, to provide references for crop breeders. The paper highlights the potential of smart breeding technologies driven by advances in sequencing technology, which will lead to the development of new breeding strategies and accelerate the breeding process.

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A single dominant GLOBOSA allele accounts for repeated origins of hose-in-hose flowers in Sinningia (Gesneriaceae)

Yang,

Liu,

Wang

et al. 2024

The Plant Cell

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Plants bearing double flowers have long been cultivated as ornamental plants. Hose-in-hose flowers, bearing 2-whorled corolla tubes in whorls 1 and 2, are uncommon but recur in Sinningia (Gesnerioideae, Gesneriaceae). In this study, we selected 15 hose-in-hose cultivars as materials to explore the underlying molecular and genetic mechanisms of this floral architecture. We found that they originated from different hybridization events within the Dircaea clade. Three B-class MADS-box genes were globally expressed in all floral whorls, but only GLOBOSA1 (GLO1) has accumulated a dominant mutation, i.e., the insertion of a hAT-like miniature inverted-repeat transposable element (MITE) into its promoter, that co-segregated with the hose-in-hose phenotype. In addition, all 15 hose-in-hose cultivars contained the same dominant GLO1 allele. Transient gene expression assays confirmed the role of this MITE insertion in up-regulating the promoter activity of GLO1 by providing several cis-regulatory elements. Genetic transformation in heterologous Chirita pumila (Didymocarpoideae, Gesneriaceae) verified that this dominant GLO1 allele is sufficient to confer the hose-in-hose phenotype. We further demonstrated that both the GLO1 allele and the hAT-like MITE descended from wild S. cardinalis with single flowers. This study highlights the significance of wide hybridization in frequent gains of the dominant GLO1 allele and thereafter repeated occurrence of hose-in-hose flowers in Sinningia.

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Genome-wide association study of traits in sacred lotus uncovers MITE-associated variants underlying stamen petaloid and petal number variations

Cited by 3 publications

References 122 publications

Evaluation and validation of suitable reference genes for quantitative real-time PCR analysis in lotus (Nelumbo nucifera Gaertn.)

Evaluation and validation of suitable reference genes for quantitative real-time PCR analysis in lotus (Nelumbo nucifera Gaertn.)

Smart breeding driven by advances in sequencing technology

A single dominant GLOBOSA allele accounts for repeated origins of hose-in-hose flowers in Sinningia (Gesneriaceae)

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