BSA‑seq and genetic mapping reveals AhRt2 as a candidate gene responsible for red testa of peanut

Zhang, Kun; Yüan, Ming; Xia, Han; He, Lei; Ma, Jing; Wang, Mingxiao; Zhao, Hang; Hou, Lei; Zhao, Shuzhen; Li, Pengcheng; Tian, Ruizheng; Pan, Junxiao; Li, Guanghui; Thudi, Mahendar; Ma, Changle; Wang, Xingjun; Zhao, Chuanzhi

doi:10.1007/s00122-022-04051-w

Cited by 29 publications

(24 citation statements)

References 53 publications

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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%

“…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 ). However, genetic and genomic studies of broomcorn millet were more hysteretic than those of other crops.…”

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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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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 candidate gene controlling peanut purple testa was considered to be one of two MYB transcription factors (Zhao et al, 2019;Huang et al, 2020). Two independently inherited genes might be controlling peanut red testa, One encoded bHLH transcription factor and the other encoded anthocyanin reductase (Chen et al, 2021;Zhang et al, 2022). By analyzing the pink and red testa of peanut by transcriptome and metabolome, some CHS, F3 H, DFR, MYB, bHLH, and WD40 genes may be the key formation and regulatory genes controlling the formation of pink and red testa in peanut (Xue et al, 2021).…”

Section: Enrichment Analysis Of Metabolic Pathways and Flow Direction...mentioning

confidence: 99%

“…The candidate gene AhTc1 that controls the color of peanut purple testa has been mapped on chromosome 10 and encodes for R2R3-MYB transcription factor (Zhao et al, 2019). Two independently inherited genes controlling peanut red testa, AhRt1 and AhRt2, were identified on chromosomes 3 and 12, respectively (Chen et al, 2021;Zhang et al, 2022). Some other candidate genes and critical pathway were also predicted by combining transcriptome and metabolome methods between testa of two different colors, which enriched the study of gene function and the relationship between genes and metabolites in peanut testa (Wan et al, 2020;Xue et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

Targeted metabolome analysis reveals accumulation of metabolites in testa of four peanut germplasms

Zhang

Gangurde

et al. 2022

Front. Plant Sci.

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Cultivated peanut (Arachis hypogaea L.) is an important source of edible oil and protein. Peanut testa (seed coat) provides protection for seeds and serves as a carrier for diversity metabolites necessary for human health. There is significant diversity available for testa color in peanut germplasms. However, the kinds and type of metabolites in peanut testa has not been comprehensively investigated. In this study, we performed metabolite profiling using UPLC-MS/MS for four peanut germplasm lines with different testa colors, including pink, purple, red, and white. A total of 85 metabolites were identified in four peanuts. Comparative metabolomics analysis identified 78 differentially accumulated metabolites (DAMs). Some metabolites showed significant correlation with other metabolites. For instance, proanthocyanidins were positively correlated with cyanidin 3-O-rutinoside and malvin, and negatively correlated with pelargonidin-3-glucoside. We observed that the total proanthocyanidins are most abundant in pink peanut variety WH10. The red testa accumulated more isoflavones, flavonols and anthocyanidins compared with that in pink testa. These results provided valuable information about differential accumulation of metabolites in testa with different color, which are helpful for further investigation of the molecular mechanism underlying biosynthesis and accumulation of these metabolites in peanut.

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“…To identify candidate regions, a SNP-index association analysis and a Euclidean distance (ED) association analysis were conducted (Abe et al 2012;Zhang et al, 2022). The LOESS method was used for tting the ED and delta SNP-index values.…”

Section: Whole Genome Sequencing and Bsa-seq Analysismentioning

confidence: 99%

Genetic mapping, transcriptomic sequencing and metabolic profiling indicated a glutathione S-transferase is responsible for the red-spot-petals in Gossypium arboreum

et al. 2022

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Colored petal spots are correlated with insect pollination e ciency in Gossypium species. However, molecular mechanisms concerning the formation of red spots on Gossypium arboreum owers remain elusive. In the current study, the Shixiya1-R (SxyR, with red spots) × Shixiya1-W (SxyW, without red spots) segregating population was utilized to determine that the red-spot-petal phenotype was levered by a single dominant locus. This phenotype was expectedly related to the anthocyanin metabolites, wherein the cyanidin and delphinidin derivatives constituted the major partition. Subsequently, this dominant locus was narrowed to a 3.27 Mb range on chromosome 7 by genomic resequencing from the two parents and the two segregated progeny bulks that have spotted petals or not. Furthermore, differential expressed genes generated from the two bulks at either of three sequential ower developmental stages that spanning the spot formation were intersected with the annotated ones that allocated to the 3.27 Mb interval, which returned eight genes. A glutathione S-transferase-coding gene (Gar07G08900) out of the eight was the only one that exhibited simultaneously differential expression among all three developmental stages, and it was therefore considered to be the probable candidate. Finally, functional validation upon this candidate was achieved by the appearance of scattered petal spots with inhibited expression of Gar07G08900. In conclusion, the current report identi ed a key gene for the red spotted petal in G. arboretum under the scope of multi-omics approaches, such efforts and embedded molecular resources would bene t future applications underlying the ower color trait in cotton. Key MessageA GST for red-spot-petals in Gossypium arboretum was identi ed as the candidate under the scope of multi-omics approaches.

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BSA‑seq and genetic mapping reveals AhRt2 as a candidate gene responsible for red testa of peanut

Cited by 29 publications

References 53 publications

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

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

Targeted metabolome analysis reveals accumulation of metabolites in testa of four peanut germplasms

Genetic mapping, transcriptomic sequencing and metabolic profiling indicated a glutathione S-transferase is responsible for the red-spot-petals in Gossypium arboreum

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