Identifying loci controlling total starch content of leaf in Nicotiana tabacum through genome-wide association study

Xu, Xin; Wang, Zhong; Xu, Shixiao; Xu, Min; He, Lei; Zhang, Jianfeng; Luo, Zhiwei; Xie, Xiaodong; Wu, Mingzhu; Yang, Jianyun

doi:10.1007/s10142-022-00851-x

Cited by 6 publications

(6 citation statements)

References 64 publications

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“…The range of diosgenin production was wider in Hainan than Luohe, which is due to significant genotype by environmental interactions (Table 1). A similar effect has also been reported for starch production in other crops like Tobacco [44].…”

Section: Phenotypic Assessment Of Association Panelsupporting

confidence: 83%

“…GWAS is a powerful approach to reveal the genomic regions associated with complex quantitative traits. However, the relatedness among genotypes caused by population structure may result in false positive identifications [44]. In this study, the SNP marker-based population structure revealed four sub-populations by PCA and K-matrix.…”

Section: Population Structure Assessment Of Association Panelmentioning

confidence: 81%

“…The Type-I errors (false positives) in GWAS were controlled by involvement of covariates based on population structure, kinship matrix, and the principal components. The same strategy has been adopted by various researchers for precise GWAS evaluation [28,44,45].…”

Section: Population Structure Assessment Of Association Panelmentioning

confidence: 99%

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Identification of genetic variants controlling diosgenin content in Dioscorea zingiberensis tuber by genome-wide association study

Sun,

Li,

Jia

et al. 2024

BMC Plant Biol

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Background Diosgenin is an important steroidal precursor renowned for its diverse medicinal uses. It is predominantly sourced from Dioscorea species, particularly Dioscorea zingiberensis. Dioscorea zingiberensis has an ability to accumulate 2–16% diosgenin in its rhizomes. In this study, a diverse population of 180 D. zingiberensis accessions was used to evaluate the genomic regions associated with diosgenin biosynthesis by the genome wide association study approach (GWAS). Results The whole population was characterized for diosgenin contents from tubers by gas chromatography mass spectrometry. The individuals were genotyped by the genotyping-by-sequencing approach and 10,000 high-quality SNP markers were extracted for the GWAS. The highest significant marker-trait-association was observed as an SNP transversion (G to T) on chromosome 10, with 64% phenotypic variance explained. The SNP was located in the promoter region of CYP94D144 which is a member of P450 gene family involved in the independent biosynthesis of diosgenin from cholesterol. The transcription factor (TF) binding site enrichment analysis of the promoter region of CYP94D144 revealed NAC TF as a potential regulator. The results were further validated through expression profiling by qRT-PCR, and the comparison of high and low diosgenin producing hybrids obtained from a bi-parental population. Conclusions This study not only enhanced the understanding of the genetic basis of diosgenin biosynthesis but also serves as a valuable reference for future genomic investigations on CYP94D144, with the aim of augmenting diosgenin production in yam tubers.

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Section: Phenotypic Assessment Of Association Panelsupporting

confidence: 83%

Section: Population Structure Assessment Of Association Panelmentioning

confidence: 81%

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Identification of genetic variants controlling diosgenin content in Dioscorea zingiberensis tuber by genome-wide association study

Sun,

Li,

Jia

et al. 2024

BMC Plant Biol

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“…One encoded E3 ubiquitin protein ligase, and the other encoded FBA. The results indicated that tobacco plants harboring both genes exhibited higher starch content, implying their potential role in augmenting starch levels in tobacco leaves [38]. This study suggested that FBA in Moso bamboo could undergo cytoplasmic ubiquitination and proposed that CSN5 could enhance FBA protein stability and activity through deubiquitination, ultimately promoting glycolysis rates.…”

Section: Discussionmentioning

confidence: 83%

Unveiling the Biological Function of Phyllostachys edulis FBA6 (PeFBA6) through the Identification of the Fructose-1,6-Bisphosphate Aldolase Gene

Li,

Zhu

et al. 2024

Plants

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Fructose-1,6-bisphosphate aldolase (FBA) is a pivotal enzyme in various metabolic pathways, including glycolysis, gluconeogenesis, and the Calvin cycle. It plays a critical role in CO2 fixation. Building on previous studies on the FBA gene family in Moso bamboo, our study revealed the biological function of PeFBA6. To identify CSN5 candidate genes, this study conducted a yeast two-hybrid library screening experiment. Subsequently, the interaction between CSN5 and PeFBA6 was verified using yeast two-hybrid and LCI experiments. This investigation uncovered evidence that FBA may undergo deubiquitination to maintain glycolytic stability. To further assess the function of PeFBA6, it was overexpressed in rice. Various parameters were determined, including the light response curve, CO2 response curve, and the levels of glucose, fructose, sucrose, and starch in the leaves of overexpressing rice. The results demonstrated that overexpressed rice exhibited a higher saturation light intensity, net photosynthetic rate, maximum carboxylation rate, respiration rate, and increased levels of glucose, fructose, and starch than wild-type rice. These findings indicated that PeFBA6 not only enhanced the photoprotection ability of rice but also improved the photosynthetic carbon metabolism. Overall, this study enhanced our understanding of the function of FBA and revealed the biological function of PeFBA6, thereby providing a foundation for the development of excellent carbon fixation bamboo varieties through breeding.

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“…LD decay distance was used to determine the region of potential candidate genes in GWAS. In Xu’s study, an SNP located on chromosome 19 associated with the starch content of leaf in Nicotiana tabacum was selected for linkage disequilibrium analysis to obtain the target candidate region [ 41 ]. Compared with self-pollinated species, the LD of cross-pollinated species, such as tea plants, declines faster because the recombination efficiency of the latter was lower [ 42 , 43 ].…”

Section: Discussionmentioning

confidence: 99%

Genome-wide association study of leaf-related traits in tea plant in Guizhou based on genotyping-by-sequencing

et al. 2023

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Background Studying the genetic characteristics of tea plant (Camellia spp.) leaf traits is essential for improving yield and quality through breeding and selection. Guizhou Plateau, an important part of the original center of tea plants, has rich genetic resources. However, few studies have explored the associations between tea plant leaf traits and single nucleotide polymorphism (SNP) markers in Guizhou. Results In this study, we used the genotyping-by-sequencing (GBS) method to identify 100,829 SNP markers from 338 accessions of tea germplasm in Guizhou Plateau, a region with rich genetic resources. We assessed population structure based on high-quality SNPs, constructed phylogenetic relationships, and performed genome-wide association studies (GWASs). Four inferred pure groups (G-I, G-II, G-III, and G-IV) and one inferred admixture group (G-V), were identified by a population structure analysis, and verified by principal component analyses and phylogenetic analyses. Through GWAS, we identified six candidate genes associated with four leaf traits, including mature leaf size, texture, color and shape. Specifically, two candidate genes, located on chromosomes 1 and 9, were significantly associated with mature leaf size, while two genes, located on chromosomes 8 and 11, were significantly associated with mature leaf texture. Additionally, two candidate genes, located on chromosomes 1 and 2 were identified as being associated with mature leaf color and mature leaf shape, respectively. We verified the expression level of two candidate genes was verified using reverse transcription quantitative polymerase chain reaction (RT-qPCR) and designed a derived cleaved amplified polymorphism (dCAPS) marker that co-segregated with mature leaf size, which could be used for marker-assisted selection (MAS) breeding in Camellia sinensis. Conclusions In the present study, by using GWAS approaches with the 338 tea accessions population in Guizhou, we revealed a list of SNPs markers and candidate genes that were significantly associated with four leaf traits. This work provides theoretical and practical basis for the genetic breeding of related traits in tea plant leaves.

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Identifying loci controlling total starch content of leaf in Nicotiana tabacum through genome-wide association study

Cited by 6 publications

References 64 publications

Identification of genetic variants controlling diosgenin content in Dioscorea zingiberensis tuber by genome-wide association study

Identification of genetic variants controlling diosgenin content in Dioscorea zingiberensis tuber by genome-wide association study

Unveiling the Biological Function of Phyllostachys edulis FBA6 (PeFBA6) through the Identification of the Fructose-1,6-Bisphosphate Aldolase Gene

Genome-wide association study of leaf-related traits in tea plant in Guizhou based on genotyping-by-sequencing

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