Genes related to circadian rhythm are involved in regulating tuberization time in potato

Niu, Yumeng; Li, Guangcun; Jian, Yinqiao; Duan, Shaoguang; Liu, Ju; Xu, Jianfei; Jin, Liping

doi:10.1016/j.hpj.2021.09.003

Cited by 13 publications

(15 citation statements)

References 54 publications

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“…The circadian clock involves several biological processes, from primary metabolism, hormone signaling, growth, and development to metabolic processes [ 50 , 51 ]. The circadian clock genes, including StGI , StPRR, and StEFM , were significantly differentially expressed in potatoes, indicating that an essential role for the plant circadian pathway exists in regulating tuberization [ 52 ]. The circadian clock regulates the transcript levels of several starch biosynthesis-related genes [ 53 , 54 ].…”

Section: Discussionmentioning

confidence: 99%

Phylogenetic and Expression Analysis of the Sucrose Synthase and Sucrose Phosphate Synthase Gene Family in Potatoes

Hu,

Duan,

et al. 2024

Metabolites

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Sucrose synthase (SUS) and sucrose phosphate synthase (SPS) are essential in plant sucrose metabolism. The potato is an important crop worldwide, but systematic analyses of the StSUS and StSPS gene families in potatoes are still lacking. Ten sucrose metabolism-related genes were identified in this study. The SUSs and SPSs could each be split into three subgroups through phylogenetic analysis. StSUSIc was the most highly expressed gene in different developmental tissues. Ka/Ks analysis showed that StSUSIb and StSUSIc were subjected to more-significant homozygous selection pressure. Our cis-acting element analysis of the StSUS and StSPS promoter sequences showed four elements: defense- and stress-responsive, hormone-responsive, light-responsive, and transcription factor elements. The expression of StSUS and StSPS genes was found to be regulated by circadian rhythm. In the treatments of 1% to 5% sucrose, glucose, and fructose, the expression of StSUS and StSPS family genes was enhanced by sucrose, but inhibited at high-glucose and fructose concentrations. This study identified six StSUS and four StSPS genes and analyzed their gene structure, conserved motifs, chromosome position, promoter elements, phylogenetic tree, and tissue-specific expression patterns. Our results will motivate more research into the biological process underlying the genes of sucrose metabolism in potatoes.

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Section: Discussionmentioning

confidence: 99%

Phylogenetic and Expression Analysis of the Sucrose Synthase and Sucrose Phosphate Synthase Gene Family in Potatoes

Hu,

Duan,

et al. 2024

Metabolites

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“…Tuberization, affected by daylength and early maturity and plant growth, as measured by its canopy and vine senescence, are complex quantitative traits and their multi-genic nature (e.g. circadian clone genes regulating tuberization [21,22], or phytochromes light receptors [23], among others) makes these characteristics difficult to evaluate in the early stages of the potato breeding cycle, particularly in long day sites with short cropping season. Furthermore, daylength fluctuations promote flowering time and tuber differentiation plus bulking in potato, both of which, as summarized by Rodríguez-Falcón et al [24], share common regulatory pathways.…”

Section: Discussionmentioning

confidence: 99%

Inbreeding effects on the performance and genomic prediction for polysomic tetraploid potato offspring grown at high Nordic latitudes

Ortíz

Reslow

Vetukuri

et al. 2023

Preprint

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Background. Inbreeding depression (ID) is caused by an increased homozygosity in the offspring after selfing. Although the self-compatible, highly heterozygous, tetrasomic polyploid potato (Solanum tuberosum L.) suffers from ID, some argue that the potential genetic gains from using inbred lines in a sexual propagation system of potato are too large to be ignored. The aim of this research was to assess the effects of inbreeding in potato offspring performance under a high latitude and the accuracy of genomic prediction of breeding values (GEBV) for further use in selection. Results. There were 16 parents (6 breeding clones and 10 cultivars) used in the crossing block. Four of them underwent selfing producing 113 ± 42 S1 seeds, while the seed set in the F1 hybrid offspring was 149 ± 29, suggesting inbreeding did not affect the crossing outcome but may have influenced the seed set. Four inbred (S1) and two hybrid (F1) offspring, and their parents (S0) were used in the experiment, with a field layout of an augmented design with the four S0 replicated in nine incomplete blocks comprising 100, 4-plant plots at Umeå (63°49′30″N 20°15′50″E), Sweden. The S0 was significantly (P < 0.01) better than both S1 and F1 offspring for tuber weight (total and according to five grading sizes), tuber shape and size uniformity, tuber eye depth and reducing sugars in the tuber flesh, while the F1 was significantly (P < 0.01) better than S1 for all tuber weight and uniformity traits. Some F1 hybrid offspring (15–19%) had better total tuber yield than the best performing parent. The GEBV accuracy ranged from -0.3928 to 0.4436. Overall, tuber shape uniformity had the highest GEBV accuracy, while tuber weight traits exhibited the lowest. The F1 full sib’s GEBV accuracy was higher, on average, than that of the S1. Conclusion. Accuracy estimates suggest a non-related training population (either S1 or F1) should not be used for early stages of genomic selection in potato breeding population. Genomic prediction may facilitate eliminating undesired inbred or hybrid offspring for further use in the genetic betterment of potato.

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“…Our analysis showed that genomes of Russian cultivars adapted to the long-day high northern latitudes and short-day adapted Andean landraces differ in their CNV occurrence for 4 of 48 known genes related to tuber formation and response to photoperiod changes ( Table 5 ). One of them is phytochrome A, which is involved in circadian clock control in potatoes [ 26 ] and potentially involved in resistance to adverse factors [ 64 ], three were identified as differentially expressed in two tetraploid cultivars with short and long tuberization times [ 25 ].…”

Section: Discussionmentioning

confidence: 99%

“…For this purpose, the initial list of tuberization and photoperiodicity-related genes was taken from a review [ 24 ] based on references given there [ 67 , 99 , 100 , 101 , 102 , 103 , 104 , 105 ] and supplemented with genes from refs. [ 25 , 26 ]. A total of 48 potato genes were included in the list ( Supplementary File S3 ).…”

Section: Methodsmentioning

confidence: 99%

Analysis of Genome Structure and Its Variations in Potato Cultivars Grown in Russia

Karetnikov

Vasiliev

Toshchakov

et al. 2023

IJMS

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Solanum tuberosum L. (common potato) is one of the most important crops produced almost all over the world. Genomic sequences of potato opens the way for studying the molecular variations related to diversification. We performed a reconstruction of genomic sequences for 15 tetraploid potato cultivars grown in Russia using short reads. Protein-coding genes were identified; conserved and variable parts of pan-genome and the repertoire of the NBS-LRR genes were characterized. For comparison, we used additional genomic sequences for twelve South American potato accessions, performed analysis of genetic diversity, and identified the copy number variations (CNVs) in two these groups of potato. Genomes of Russian potato cultivars were more homogeneous by CNV characteristics and have smaller maximum deletion size in comparison with South American ones. Genes with different CNV occurrences in two these groups of potato accessions were identified. We revealed genes of immune/abiotic stress response, transport and five genes related to tuberization and photoperiod control among them. Four genes related to tuberization and photoperiod were investigated in potatoes previously (phytochrome A among them). A novel gene, homologous to the poly(ADP-ribose) glycohydrolase (PARG) of Arabidopsis, was identified that may be involved in circadian rhythm control and contribute to the acclimatization processes of Russian potato cultivars.

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Genes related to circadian rhythm are involved in regulating tuberization time in potato

Cited by 13 publications

References 54 publications

Phylogenetic and Expression Analysis of the Sucrose Synthase and Sucrose Phosphate Synthase Gene Family in Potatoes

Phylogenetic and Expression Analysis of the Sucrose Synthase and Sucrose Phosphate Synthase Gene Family in Potatoes

Inbreeding effects on the performance and genomic prediction for polysomic tetraploid potato offspring grown at high Nordic latitudes

Analysis of Genome Structure and Its Variations in Potato Cultivars Grown in Russia

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