Fine-mapping and gene candidate analysis for AhRt1, a major dominant locus responsible for testa color in cultivated peanut

Chen, Hao; Chen, Xiangyu; Xu, Ruirong; Liu, Wenjing; Liu, Nian; Huang, Li; Luo, Huaiyong; Huai, Dongxin; Lan, Xinlong; Zhang, Yumei; Hu, Runfang; Chen, Jianhong; Tang, Zhaoxiu; Lin, Ge; Jiang, Huifang

doi:10.1007/s00122-021-03924-w

Cited by 14 publications

(21 citation statements)

References 31 publications

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“…These characteristics were selected so that purple testa could be distinguished as a true hybrid based on testa color in F 2 populations, thus improving the accuracy and efficiency of hybrid selection. Similar cross combinations were used in the study of Chen et al (2021) . At the same time, stable high oleic acid homozygous individual plants could be selected from F 2 by way of KASP.…”

Section: Discussionmentioning

confidence: 99%

Multi-Omics and miRNA Interaction Joint Analysis Highlight New Insights Into Anthocyanin Biosynthesis in Peanuts (Arachis hypogaea L.)

et al. 2022

Front. Plant Sci.

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Peanut (Arachis hypogaea L.) is one of the most important economic and oil crops in the world. At present, peanut varieties with rich anthocyanin in testa are rare in the market, but the selection and breeding of varieties with the related traits has always attracted the attention of breeders. In this study, two peanut varieties with the pink and purple testa, G110 (G) and Z18-40 (Z) were used to conduct interaction joint analysis of multi-omics and miRNA-target gene. The anthocyanin content of Z18-40 was 7.49–8.62-folds higher than G110 on 30 DAF (days after flowering) and 45 DAF via Ultraviolet-visible Spectrophotometer (UV-5800, Shanghai, China). And then, a total of 14 candidate genes related with the anthocyanin biosynthesis were identified for correlation in different comparison groups (R2 ≥ 0.80), among of a novel gene Ah21440 related with hydroxycinnamoyl transferase (HCT) biosynthesis was identified. In addition, Cyanidin 3-O-glucoside (Kuromanin, pmb0550) was the only common differentially accumulated metabolite (DAM) identified using multi-omics joint analysis in G1_vs_G2, Z1_vs_Z2, G1_vs_Z1, and G2_vs_Z2, respectively. Correlation analysis of miRNA-target genes and DEGs in the transcriptome shows that, AhmiR2950, AhmiR398, AhmiR50, and AhmiR51 regulated to HCT and chalcone biosynthesis related candidate genes (Ah21440, AhCHS, AhCHI). Lastly, all of 14 candidate genes and 4 differentially expressed miRNAs were validated using quantitative real-time PCR (qRT-PCR), which trends were consistent with that of the former transcriptome data. The results provide important reference for in-depth research on the anthocyanin metabolism mechanism in peanut testa.

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Section: Discussionmentioning

confidence: 99%

Multi-Omics and miRNA Interaction Joint Analysis Highlight New Insights Into Anthocyanin Biosynthesis in Peanuts (Arachis hypogaea L.)

et al. 2022

Front. Plant Sci.

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“…High-throughput sequencing technology has enabled not only the assembly of high-quality reference genomes for most crops but also the rapid detection of sequence variations, such as SNPs and Indels. By combining bulk segregation analysis and sequencing approach, BSA-seq has been successfully applied in many crops ( Lee et al., 2020 ; Chen et al., 2021 ; Wu et al., 2022 ; Zhang et al., 2022 ). However, due to the linkage disequilibrium and the incomplete coverage of the sequencing reads, the QTL regions identified using BSA-seq are usually large and need to be narrowed down further ( Chen et al., 2021 ; Zhang et al., 2022 ).…”

Section: Discussionmentioning

confidence: 99%

“…By combining bulk segregation analysis and sequencing approach, BSA-seq has been successfully applied in many crops ( Lee et al., 2020 ; Chen et al., 2021 ; Wu et al., 2022 ; Zhang et al., 2022 ). However, due to the linkage disequilibrium and the incomplete coverage of the sequencing reads, the QTL regions identified using BSA-seq are usually large and need to be narrowed down further ( Chen et al., 2021 ; Zhang et al., 2022 ). Therefore, the traditional mapping approach cannot be completely replaced by BSA-seq and is still needed in the fine-mapping procedure.…”

Section: Discussionmentioning

confidence: 99%

“…The rapid development of molecular biology and sequencing technologies provided various tools for modern crop breeding. Map-based cloning of genes involving significant agronomical traits and marker-assisted selection (MAS) have been widely applied in crops ( Chen et al., 2021 ; Koppolu et al., 2022 ). Bulked segregant analysis with whole-genome resequencing (BAS-seq) is an effective approach for the identification of candidate genes and has been successfully utilized ( Lee et al., 2020 ; Wu et al., 2022 ; Zhang et al., 2022 ).…”

Section: Introductionmentioning

confidence: 99%

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Identification and fine-mapping of a major QTL (PH1.1) conferring plant height in broomcorn millet (Panicum miliaceum)

Liu

et al. 2022

Front. Plant Sci.

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The plant height of broomcorn millet (Panicum miliaceum) is a significant agronomic trait that is closely related to its plant architecture, lodging resistance, and final yield. However, the genes underlying the regulation of plant height in broomcorn millet are rarely reported. Here, an F2 population derived from a cross between a normal variety, “Longmi12,” and a dwarf mutant, “Zhang778,” was constructed. Genetic analysis for the F2 and F2:3 populations revealed that the plant height was controlled by more than one locus. A major quantitative trait locus (QTL), PH1.1, was preliminarily identified in chromosome 1 using bulked segregant analysis sequencing (BSA-seq). PH1.1 was fine-mapped to a 109-kb genomic region with 15 genes using a high-density map. Among them, longmi011482 and longmi011489, containing nonsynonymous variations in their coding regions, and longmi011496, covering multiple insertion/deletion sequences in the promoter regions, may be possible candidate genes for PH1.1. Three diagnostic markers closely linked to PH1.1 were developed to validate the PH1.1 region in broomcorn millet germplasm. These findings laid the foundation for further understanding of the molecular mechanism of plant height regulation in broomcorn millet and are also beneficial to the breeding program for developing new varieties with optimal height.

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“…A high-throughput sequencing of "M-8070" DNA library was carried out by Illumina NovaSeq platform with NovaSeq 6000 S4 Reagent Kit. In addition, we got the high-throughput sequencing data of "FH 8" from a previous study [21]. Then, the clean data of "M-8070" and "FH 8" were mapped to a reference genome of cultivated peanut (Tifrunner_V20190521, https://www.peanutbase.…”

Section: Identification and Annotation Of Ems-induced Mutationsmentioning

confidence: 99%

Construction of EMS-Induced Peanut Mutant Libraries and Identification of Pod-Related Traits Mutant Lines

Chen¹,

Xiong²,

Xu³

et al. 2023

Phyton

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Peanut (Arachis hypogaea L.) is an oil and economic crop of vital importance, and peanut pod is the key organ influencing the yield and processing quality. Hence, the Pod-related traits (PRTs) are considered as important agronomic traits in peanut breeding. To broaden the variability of PRTs in current peanut germplasms, three elite peanut cultivars were used to construct Ethyl methane sulfonate (EMS)-induced mutant libraries in this study. The optimal EMS treatment conditions for the three peanut varieties were determined. It was found that the median lethal dose (LD50) of EMS treatment varied greatly among different genotypes. Finally, the EMS-induced peanut mutant libraries were constructed and a total of 124 mutant lines for PRTs were identified and evaluated. Furthermore, "M-8070", one of the mutant lines for pod constriction, was re-sequenced via high-throughput sequencing technology. The genome-wide variations between "M-8070" and its wild parent "Fuhua 8" (FH 8) were detected. 2994 EMS-induced single nucleotide polymorphisms (SNPs) and 1188 insertion-deletions (InDels) between "M-8070" and its wild parent were identified. The predominant SNP mutation type was C/G to T/A transitions, while the predominant InDel mutation type was "1-bp". We analyzed the distribution of identified mutations and annotated their functions. Most of the mutations (91.68% of the SNPs and 77.69% of the InDels) were located in the intergenic region. 72 SNPs were identified in the exonic region, leading to 27 synonymous, 43 nonsynonymous and 2 stop-gain variation for gene structure. 13 Indels were identified in the exonic region, leading to 4 frame-shift, 8 non-frame-shift and 1 stop-gain variations of genes. These mutations may lead to the phenotypic variation of "M-8070". Our study provided valuable resources for peanut improvement and functional genomic research.

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Fine-mapping and gene candidate analysis for AhRt1, a major dominant locus responsible for testa color in cultivated peanut

Cited by 14 publications

References 31 publications

Multi-Omics and miRNA Interaction Joint Analysis Highlight New Insights Into Anthocyanin Biosynthesis in Peanuts (Arachis hypogaea L.)

Multi-Omics and miRNA Interaction Joint Analysis Highlight New Insights Into Anthocyanin Biosynthesis in Peanuts (Arachis hypogaea L.)

Identification and fine-mapping of a major QTL (PH1.1) conferring plant height in broomcorn millet (Panicum miliaceum)

Construction of EMS-Induced Peanut Mutant Libraries and Identification of Pod-Related Traits Mutant Lines

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