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Analysis of the Segregation Distortion of FcRAN1 Genotypes Based on Whole-Genome Resequencing of Fig (Ficus carica L.) Breeding Parents.

ABSTRACT: The common fig (Ficus carica L.) has a gynodioecious breeding system, and its sex phenotype is an important trait for breeding because only female plant fruits are edible. During breeding to select for female plants, we analyzed the FcRAN1 genotype, which is strongly associated with the sex phenotype. In 12 F₁ populations derived from 13 cross combinations, the FcRAN1 genotype segregation ratio was 1:1, whereas the M119-226 × H238-107 hybridization resulted in an extremely male-biased segregation ratio (178:7 = male:female). This finding suggests that the segregation distortion was caused by some genetic factor(s). A whole-genome resequencing of breeding parents (paternal and maternal lines) identified 9,061 high-impact SNPs in the parents. A genome-wide linkage analysis exploring the gene(s) responsible for the distortion revealed 194 high-impact SNPs specific to Caprifig6085 (i.e., seed parent ancestor) and 215 high-impact SNPs specific to H238-107 (i.e., pollen parent) in 201 annotated genes. A comparison between the annotated genes and the genes required for normal embryo or gametophyte development and function identified several candidate genes possibly responsible for the segregation distortion. This is the first report describing segregation distortion in F. carica.

SUBMITTER: Ikegami H

PROVIDER: S-EPMC8384052 | biostudies-literature |

REPOSITORIES: biostudies-literature

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The Ficus erecta genome aids Ceratocystis canker resistance breeding in common fig (F. carica).

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| S-EPMC8127270 | biostudies-literature

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Project description:Ficus carica cultivar:fig Transcriptome or Gene expression

| PRJNA438437 | ENA

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| S-EPMC7873141 | biostudies-literature

Polygalacturonase gene family analysis identifies FcPG12 as a key player in fig (Ficus carica L.) fruit softening.

Project description:BackgroundThe fig (Ficus carica L.) tree has high economic value. However, its fruit have a short shelf life due to rapid softening. Polygalacturonases (PGs) are essential hydrolases, responsible for the pectin degradation that plays a key role in fruit softening. However, fig PG genes and their regulators have not yet been characterized.ResultsIn this study, 43 FcPGs were identified in the fig genome. They were non-uniformly distributed on 13 chromosomes, and tandem repeat PG gene clusters were found on chromosomes 4 and 5. Ka/Ks calculation and collinear analysis indicated negative selection as the main driver of FcPG family expansion. Fourteen FcPGs were found expressed in fig fruit with FPKM values > 10, of which seven were positively correlated, and three, negatively correlated with fruit softening. Eleven FcPGs were upregulated and two downregulated in response to ethephon treatment. FcPG12, a member of the tandem repeat cluster on chromosome 4, was selected for further analyses due to its sharp increment in transcript abundance during fruit softening and its response to ethephon treatment. Transient overexpression of FcPG12 led to decreased fig fruit firmness and increased PG enzyme activity in the tissue. Two ethylene response factor (ERF)-binding GCC-box sites were found on the FcPG12 promoter. Yeast one-hybrid and dual luciferase assays showed that FcERF5 binds directly to the FcPG12 promoter and upregulates its expression. Transient overexpression of FcERF5 upregulated FcPG12 expression, thereby increasing PG activity and fruit softening.ConclusionsOur study identified FcPG12 as a key PG gene in fig fruit softening, and its direct positive regulation by FcERF5. The results provide new information on the molecular regulation of fig fruit softening.

| S-EPMC10265768 | biostudies-literature

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| S-EPMC10285451 | biostudies-literature

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