Genome sequence and analysis of the eggplant (<i>Solanum melongena</i>L.)

Li, Dandan; Qian, Jun; Li, Wenjia; Jiang, Yaqin; Gan, Guiyun; Li, Weiliu; Chen, Riyuan; Ning, Yu; Li, Yán; Wu, Yen‐Ju; DeXian, Kang; Lian, Jinmin; Niu, Yongchao; Wang, Yikui

doi:10.1101/824540

Cited by 8 publications

(8 citation statements)

References 79 publications

(98 reference statements)

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“…From 2794 F 2 individuals, 60 plants with extreme phenotypes (30 with green peel and 30 with white peel color) were selected to construct two pools, one green-skinned pool and one white-skinned pool. Association analysis was performed for the two F 2 pools and the parental pools, with “guiqie1” [ 42 ] as the reference genome. The pooled DNAs were used for DNA library preparation, and the qualified library was sequenced on the Illumina HiSeq™ PE150 platform (San Diego, CA, USA).…”

Section: Methodsmentioning

confidence: 99%

Fine Mapping and Identification of SmAPRR2 Regulating Rind Color in Eggplant (Solanum melongena L.)

Fang

Wang

et al. 2023

IJMS

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Rind color is an economically important agronomic trait in eggplant that impacts consumer preferences. In this study, bulked segregant analysis and competitive allele-specific PCR were employed to identify the candidate gene for eggplant rind color through constructing a 2794 F2 population generated from a cross between “BL01” (green pericarp) and “B1” (white pericarp). Genetic analysis of rind color revealed that a single dominant gene controls green color of eggplant peel. Pigment content measurement and cytological observations demonstrated that chlorophyll content and chloroplast number in BL01 were higher than in B1. A candidate gene (EGP19168.1) was fine-mapped to a 20.36 Kb interval on chromosome 8, which was predicted to encode the two-component response regulator-like protein Arabidopsis pseudo-response regulator2 (APRR2). Subsequently, allelic sequence analysis revealed that a SNP deletion (ACT→AT) in white-skinned eggplant led to a premature termination codon. Genotypic validation of 113 breeding lines using the Indel marker closely linked to SmAPRR2 could predict the skin color (green/white) trait with an accuracy of 92.9%. This study will be valuable for molecular marker-assisted selection in eggplant breeding and provides theoretical foundation for analyzing the formation mechanism of eggplant peel color.

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Section: Methodsmentioning

confidence: 99%

Fine Mapping and Identification of SmAPRR2 Regulating Rind Color in Eggplant (Solanum melongena L.)

Fang

Wang

et al. 2023

IJMS

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“…After sequencing, raw reads were preprocessed to remove adaptors and low-quality reads (bp < 20). Duplicated reads were mapped onto the reference genome of eggplant [46] using BWA software (https://sourceforge.net/projects/bio-bwa/ (accessed on 8 May 2024)) with SAM tools [47]. Single-nucleotide polymorphisms (SNP) and insertion/deletions (indels) were called and filtered by removing heterozygous and missing SNPs as well as indels in the pools and parental lines using the GATK software (https://software.broadinstitute.org/gatk/2 (ac-cessed on 8 May 2024)) [48].…”

Section: Dna Extraction and Bulked Segregant Analysismentioning

confidence: 99%

Fine Mapping of Candidate Gene Controlling Anthocyanin Biosynthesis for Purple Peel in Solanum melongena L.

Xiao,

Tan,

Zhang

et al. 2024

IJMS

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Fruit color is an intuitive quality of horticultural crops that can be used as an evaluation criterion for fruit ripening and is an important factor affecting consumers’ purchase choices. In this study, a genetic population from the cross of green peel ‘Qidong’ and purple peel ‘8 guo’ revealed that the purple to green color of eggplant peel is dominant and controlled by a pair of alleles. Bulked segregant analysis (BSA), SNP haplotyping, and fine genetic mapping delimited candidate genes to a 350 kb region of eggplant chromosome 10 flanked by markers KA2381 and CA8828. One ANS gene (EGP22363) was predicted to be a candidate gene based on gene annotation and sequence alignment of the 350-kb region. Sequence analysis revealed that a single base mutation of ‘T’ to ‘C’ on the exon green peel, which caused hydrophobicity to become hydrophilic serine, led to a change in the three-level spatial structure. Additionally, EGP22363 was more highly expressed in purple peels than in green peels. Collectively, EGP22363 is a strong candidate gene for anthocyanin biosynthesis in purple eggplant peels. These results provide important information for molecular marker-assisted selection in eggplants, and a basis for analyzing the regulatory pathways responsible for anthocyanin biosynthesis in eggplants.

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“…From 2794 F 2 individuals, 60 plants with extreme phenotypes (30 with green peel and 30 with white peel color) were selected to construct two pools, one green-skinned pool and one white-skinned pool. The two F 2 pools of different colors and the parental pools were used for association analyses, and 'guiqie1' (Li 2019) was used as the reference genome. The pooled DNAs were used for DNA library preparation, and the quali ed library was sequenced on the Illumina HiSeq™ PE150 platform (San Diego, CA, United States).…”

Section: Bsaseq Mapping Approachmentioning

confidence: 99%

Fine mapping and identification of SmAPRR2 regulating rind color in eggplant (Solanum melongena L.)

Fang

Wang

Peng

et al. 2022

Preprint

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Rind color is an economically important agronomic trait in eggplant that impacts consumer preferences. However, the gene(s) regulating eggplant rind color have not been characterized. In this study, bulked segregant analysis (BSA) and kompetitive allele-specific PCR (KASP) were employed to identify a candidate gene for eggplant rind color through constructing an F2 population generated from a cross between 'BL01' (green pericarp) and 'B1' (white pericarp). Genetic analysis of rind color revealed that a single dominant gene controls green color of eggplant peel. Pigment content measurement and cytological observations demonstrated that chlorophyll and carotenoid content and the number of chloroplasts and thylakoids in BL01 were higher than in B1. Using a BSA-seq method and a recombinant mapping strategy in F2 plants, a candidate gene (EGP19168.1) was fine-mapped to a 20.36 Kb interval on chromosome 8. The gene is predicted to encode the two-component response regulator-like protein Arabidopsis pseudo-response regulator2 (APRR2). Subsequently, allelic sequence analysis revealed that a single-base deletion in white-skinned eggplant led to a premature termination codon. A credible molecular marker closely linked to the candidate gene was developed to genotype 45 diverse eggplant germplasms, which could predict the trait of rind color (green and white) with a 91.1% accuracy rate. This study will be valuable for molecular marker-assisted selection in eggplant breeding and provides theoretical foundation for analyzing the formation mechanism of eggplant peel color.

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Genome sequence and analysis of the eggplant (Solanum melongenaL.)

Cited by 8 publications

References 79 publications

Fine Mapping and Identification of SmAPRR2 Regulating Rind Color in Eggplant (Solanum melongena L.)

Fine Mapping and Identification of SmAPRR2 Regulating Rind Color in Eggplant (Solanum melongena L.)

Fine Mapping of Candidate Gene Controlling Anthocyanin Biosynthesis for Purple Peel in Solanum melongena L.

Fine mapping and identification of SmAPRR2 regulating rind color in eggplant (Solanum melongena L.)

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