ATP-dependent DNA helicase (TaDHL), a Novel Reduced-Height (Rht) Gene in Wheat

Guo, Baojin; Jin, Xin; Chen, Jingchuan; Xu, Hui; Zhang, Mingxia; Lü, Xing; Wu, Rugang; Zhao, Yan; Guo, Ying; An, Yanrong; Li, Sishen

doi:10.3390/genes13060979

Cited by 12 publications

(10 citation statements)

References 42 publications

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“…In addition, many genes could be cloned for other traits using RIL populations. For example, we have cloned a quality gene XIP (Xylanase Inhibitor Protein) (Sun et al, 2022) and a Rht gene TaDHL ( ATP-dependent DNA helicase ) (Guo et al, 2022) from QTLs of the TL-RILs. Seven other Rht genes were also confirmed via CRISPR/Cas9 technology from QTLs of the TL-RILs and “Shannong0431 × Lumai21” RILs (unpublished data).…”

Section: Discussionmentioning

confidence: 99%

Efficient cloning of genes for wheat yield component traits from QTLs via sequencing of the RIL population

Zhang,

Han,

Wang

et al. 2024

Preprint

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In wheat (Triticum aestivumL.), yield component traits (YCTs) are the most important yield traits. Only several genes for YCTs have been originally cloned. The efficient cloning of genes for YCTs directly from wheat remains a challenge. Here, we proposed a strategy for cloning genes from quantitative trait loci (QTLs) by sequencing of recombinant inbred lines (RILs) (QTL-Seq-RIL). Using the ‘TN18 × LM6’ RIL population as an example, we identified 138 candidate unigenes (CUGs) for YCTs from 77 stable QTLs. The average of CUGs per QTL was 1.8, which enabled us to confirm the CUGs directly. We have confirmed seven CUGs,TaIFABPL, TaDdRp, TaRLK, TaTD, TaTFC3, TaKMTandTaSPL17, via the CRISPR/Cas9 system. Of these, six genes were found firstly to regulate YCTs in crops except forTaSPL17. Five CUGs (includeTaSPL17) for which orthologous genes have been cloned previously with the same or similar agronomic functions. It is to say, 11 CUGs were preliminarily validated using a single RIL population. QTL-Seq-RIL provides an efficient method for rapid gene cloning using existing RIL populations.

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Section: Discussionmentioning

confidence: 99%

Efficient cloning of genes for wheat yield component traits from QTLs via sequencing of the RIL population

Zhang,

Han,

Wang

et al. 2024

Preprint

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“…Meanwhile, there are some methods about gene mining. For example, whole genome association analyses to locate gene loci related to plant height ( Guo et al., 2022 ), yield ( Li et al., 2021 ), and disease resistance ( Tsai et al., 2020 ). They only localize the relevant gene loci into a segment containing many candidate genes.…”

Section: Discussionmentioning

confidence: 99%

A new model construction based on the knowledge graph for mining elite polyphenotype genes in crops

Zhang,

Zhao,

Xian

et al. 2024

Front. Plant Sci.

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Identifying polyphenotype genes that simultaneously regulate important agronomic traits (e.g., plant height, yield, and disease resistance) is critical for developing novel high-quality crop varieties. Predicting the associations between genes and traits requires the organization and analysis of multi-dimensional scientific data. The existing methods for establishing the relationships between genomic data and phenotypic data can only elucidate the associations between genes and individual traits. However, there are relatively few methods for detecting elite polyphenotype genes. In this study, a knowledge graph for traits regulating-genes was constructed by collecting data from the PubMed database and eight other databases related to the staple food crops rice, maize, and wheat as well as the model plant Arabidopsis thaliana. On the basis of the knowledge graph, a model for predicting traits regulating-genes was constructed by combining the data attributes of the gene nodes and the topological relationship attributes of the gene nodes. Additionally, a scoring method for predicting the genes regulating specific traits was developed to screen for elite polyphenotype genes. A total of 125,591 nodes and 547,224 semantic relationships were included in the knowledge graph. The accuracy of the knowledge graph-based model for predicting traits regulating-genes was 0.89, the precision rate was 0.91, the recall rate was 0.96, and the F1 value was 0.94. Moreover, 4,447 polyphenotype genes for 31 trait combinations were identified, among which the rice polyphenotype gene IPA1 and the A. thaliana polyphenotype gene CUC2 were verified via a literature search. Furthermore, the wheat gene TraesCS5A02G275900 was revealed as a potential polyphenotype gene that will need to be further characterized. Meanwhile, the result of venn diagram analysis between the polyphenotype gene datasets (consists of genes that are predicted by our model) and the transcriptome gene datasets (consists of genes that were differential expression in response to disease, drought or salt) showed approximately 70% and 54% polyphenotype genes were identified in the transcriptome datasets of Arabidopsis and rice, respectively. The application of the model driven by knowledge graph for predicting traits regulating-genes represents a novel method for detecting elite polyphenotype genes.

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“…Using the QTL location of UG-Map for TL-RILs, we previously cloned two genes, the XIP ( Xylanase Inhibitor Protein ) gene, which regulates the SDS-sedimentation value and dough stability time [ 40 ], and the TaDHL ( ATP-dependent DNA helicase ) gene, which regulates the plant height [ 41 ]. These results further showed that the candidate genes in this study are favorable for corresponding gene cloning.…”

Section: Discussionmentioning

confidence: 99%

QTL Mapping and Candidate Gene Identifying for N, P, and K Use Efficiency at the Maturity Stages in Wheat

Han

Zhang

Gao

et al. 2023

Genes

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Nitrogen (N), phosphorus (P), and potassium (K) are the three most important mineral nutrients for crop growth and development. We previously constructed a genetic map of unigenes (UG-Map) based on their physical positions using a RIL population derived from the cross of “TN18 × LM6” (TL-RILs). In this study, a total of 18 traits related to mineral use efficiency (MUE) of N/P/K were investigated under three growing seasons using TL-RILs. A total of 54 stable QTLs were detected, distributed across 19 chromosomes except for 3A and 5B. There were 50 QTLs associated with only one trait, and the other four QTLs were associated with two traits. A total of 73 candidate genes for stable QTLs were identified. Of these, 50 candidate genes were annotated in Chinese Spring (CS) RefSeq v1.1. The average number of candidate genes per QTL was 1.35, with 45 QTLs containing only one candidate gene and nine QTLs containing two or more candidate genes. The candidate gene TraesCS6D02G132100 (TaPTR gene) for QGnc-6D-3306 belongs to the NPF (NRT1/PTR) gene family. We speculate that the TaPTR gene should regulate the GNC trait.

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ATP-dependent DNA helicase (TaDHL), a Novel Reduced-Height (Rht) Gene in Wheat

Cited by 12 publications

References 42 publications

Efficient cloning of genes for wheat yield component traits from QTLs via sequencing of the RIL population

Efficient cloning of genes for wheat yield component traits from QTLs via sequencing of the RIL population

A new model construction based on the knowledge graph for mining elite polyphenotype genes in crops

QTL Mapping and Candidate Gene Identifying for N, P, and K Use Efficiency at the Maturity Stages in Wheat

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