An integrated peach genome structural variation map uncovers genes associated with fruit traits

Guo, Jian; Cao, Ke; Deng, Cecilia; Li, Yong; Zhu, Guoqiang; Fang, Weichao; Chen, Chang Wen; Wang, Xinwei; Wu, Jinlong; Guan, Liping; Wu, Shan; Guo, Wen‐Wu; Yao, Jia‐Long; Fei, Zhangjun; Wang, Lirong

doi:10.1186/s13059-020-02169-y

Cited by 95 publications

(106 citation statements)

References 74 publications

(128 reference statements)

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“…2b). Gene expression pattern was consistent with their genotypes, as fruit abortion trait was recessive [6,8]. As well, tissue speci c analysis showed that this gene was mostly expressed in seed and fruit ( Fig.…”

Section: Identi Cation and Expression Analysis Of Ppsnrk1γsupporting

confidence: 66%

“…In order to elucidate the genetic basis for at fruit abortion, candidate gene identi cation was carried out. We have already identi ed a 1.67-Mb chromosome inversion co-segregated with at fruit shape and validated it in 336 peach accessions [8] (Fig. 2a).…”

Section: Identi Cation and Expression Analysis Of Ppsnrk1γmentioning

confidence: 60%

“…It was reported that quite a few fruits could be abnormally mature with no seeds and cracking fruit phenotypes in these aborting at peach progenies [11]. In addition, overexpression the at shape gene, PpOFP1, did not result in fruit abortion in tomato [8] and Arabidopsis [12]. These results indicated that PpOFP1 was the at shape gene and the at fruit abortion trait should be controlled by the adjacent Af gene locus.…”

Section: Discussionmentioning

confidence: 86%

“…We have already analyzed the four genes around the two breakpoints of this inversion, and found that the expression levels of Prupe.6G290900 (PpOFP1, at fruit shape gene) and Prupe.6G323700 were both related to the allelic genotypes of at and round peach [8]. Given that the close position between at shape and at fruit abortion locus, and the recessive trait, Prupe.6G323700 was hypothesized as the candidate gene responsible for at fruit abortion, which was annotated as γ subunit of SNF1-related protein kinase.…”

Section: Identi Cation and Expression Analysis Of Ppsnrk1γmentioning

confidence: 99%

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A subunit gene of sucrose non-fermenting 1 related kinase, PpSnRK1γ, confers flat fruit abortion in peach by regulating sugar and starch metabolism

Guo

Cao

Yao

et al. 2020

Preprint

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Background: Fruit abortion is a major limiting factor for fruit production. In flat peach, fruit abortion is present in the whole tree of some accessions during early fruit development. However, the physiological factors and genetic mechanism underlying flat fruit abortion remain largely elusive. Results: In this study, we have revealed that the fertilization process was accomplished and the reduction of sucrose and starch contents might result in flat fruit abortion. By combining association and gene expression analysis, a key candidate gene, PpSnRK1γ, was identified. A 1.67-Mb inversion co-segregated with flat fruit shape altered the promoter activity of PpSnRK1γ, resulting in much lower expression in aborting flat peach. Ectopic transformation in tomato and transient overexpression in peach fruit have shown that PpSnRK1γ could increase sugar and starch contents. Comparative transcriptome analysis further confirmed that PpSnRK1γ participated in carbohydrate metabolism. Subcellular localization found that PpSnRK1γ was located in nucleus. Conclusions: This study clarified the reason for flat fruit abortion and identified a critical candidate gene, PpSnRK1γ, responsible for fruit abortion in peach. The results would provide great help in peach breeding and facilitate gene identification for fruit abortion in other plant species.

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Section: Identi Cation and Expression Analysis Of Ppsnrk1γsupporting

confidence: 66%

Section: Identi Cation and Expression Analysis Of Ppsnrk1γmentioning

confidence: 60%

Section: Discussionmentioning

confidence: 86%

Section: Identi Cation and Expression Analysis Of Ppsnrk1γmentioning

confidence: 99%

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A subunit gene of sucrose non-fermenting 1 related kinase, PpSnRK1γ, confers flat fruit abortion in peach by regulating sugar and starch metabolism

Guo

Cao

Yao

et al. 2020

Preprint

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“…Likewise, GWAS based on the graph soybean pan-genome identified a PAV associated with variation in seed luster [ 24 ]. In peach, candidate causative SVs for early fruit maturity, flesh color around the stone, fruit shape, and flat shape formation have also been observed [ 121 ]. However, our understanding of the importance of SVs to phenotypic trait variation is still in its infancy.…”

Section: Introductionmentioning

confidence: 99%

How the pan-genome is changing crop genomics and improvement

et al. 2021

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Crop genomics has seen dramatic advances in recent years due to improvements in sequencing technology, assembly methods, and computational resources. These advances have led to the development of new tools to facilitate crop improvement. The study of structural variation within species and the characterization of the pan-genome has revealed extensive genome content variation among individuals within a species that is paradigm shifting to crop genomics and improvement. Here, we review advances in crop genomics and how utilization of these tools is shifting in light of pan-genomes that are becoming available for many crop species.

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A Functional InDel in the WRKY10 Promoter Controls the Degree of Flesh Red Pigmentation in Apple

Wang,

Liu,

Mei

et al. 2024

Advanced Science

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MYB transcription factors have been linked to anthocyanin synthesis and various color phenotypes in plants. In apple, MYB10 confers a red‐flesh phenotype due to a minisatellite insertion in its R6 promoter, but R6:MYB10 genotypes exhibit various degrees of red pigmentation in the flesh, suggesting the involvement of other genetic factors. Here, it is shown that MdWRKY10, a transcription factor identified via DNA pull‐down trapping, binds to the promoter of MdMYB10 and activates its transcription. MdWRKY10 specifically interacts with the WDR protein MdTTG1 to join the apple MYB‐bHLH‐WDR (MBW) complex, which significantly enhances its transcriptional activation activity. A 163‐bp InDel detected in the promoter region of the alleles of MdWRKY10 in a hybrid population of identical heterozygous genotypes regarding R6 by structural variation analysis, contains a typical W‐box element that MdWRKY10 binds to for transactivation. This leads to increased transcript levels of MdWRKY10 and MdMYB10 and enhanced anthocyanin synthesis in the flesh, largely accounting for the various degrees of flesh red pigmentation in the R6 background. These findings reveal a novel regulatory role of the WRKY‐containing protein complex in the formation of red flesh apple phenotypes and provide broader insights into the molecular mechanism governing anthocyanin synthesis in plants.

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An integrated peach genome structural variation map uncovers genes associated with fruit traits

Cited by 95 publications

References 74 publications

A subunit gene of sucrose non-fermenting 1 related kinase, PpSnRK1γ, confers flat fruit abortion in peach by regulating sugar and starch metabolism

A subunit gene of sucrose non-fermenting 1 related kinase, PpSnRK1γ, confers flat fruit abortion in peach by regulating sugar and starch metabolism

How the pan-genome is changing crop genomics and improvement

A Functional InDel in the WRKY10 Promoter Controls the Degree of Flesh Red Pigmentation in Apple

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