Molecular markers in tea plant (Camellia sinensis): Applications to evolution, genetic identification, and molecular breeding

Li, Jingwen; Li, Hui; Liu, Zhi-Wei; Wang, Yongxin; Chen, Yi; Yang, Ning; Hu, Zhi-Hang; Li, Tong; Zhuang, Jing

doi:10.1016/j.plaphy.2023.107704

Cited by 18 publications

(4 citation statements)

References 131 publications

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“…In Ivy gourd, presence of SSRs in the differentially expressed unigenes coding for transcription factors, biosynthesis of metabolites, ubiquitin mediated proteolysis, structural element and signalling pathways which are crucial in fleshy fruit development and ripening ( Jia et al., 2023 ; Wang et al., 2023 ), indicates their potential for developing functional molecular markers. Our initial assessment also indicates that few of the SSRs are polymorphic in nature, and associated with genes encoding Leucine-rich repeat extensin-like protein, Trihelix transcription factor and 3-hydroxybutyryl-CoA dehydrogenase, implying that analysis and subsequent sequencing efforts at larger scales will help identify numerous polymorphic SSRs in C.grandis that can be used for marker assisted selection for crop breeding as well as for diversity analysis in plants ( Kapoor et al., 2023 ; Li et al., 2023 ).…”

Section: Discussionmentioning

confidence: 93%

Transcriptomics reveal useful resources for examining fruit development and variation in fruit size in Coccinia grandis

Panda,

Pradhan,

Mukherjee

2024

Front. Plant Sci.

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IntroductionThe Cucurbitaceae family comprises many agronomically important members, that bear nutritious fruits and vegetables of great economic importance. Coccinia grandis, commonly known as Ivy gourd, belongs to this family and is widely consumed as a vegetable. Members of this family are known to display an impressive range of variation in fruit morphology. Although there have been studies on flower development in Ivy gourd, fruit development remains unexplored in this crop.MethodsIn this study, comparative transcriptomics of two Ivy gourd cultivars namely “Arka Neelachal Kunkhi” (larger fruit size) and “Arka Neelachal Sabuja” (smaller fruit size) differing in their average fruit size was performed. A de novo transcriptome assembly for Ivy gourd was developed by collecting fruits at different stages of development (5, 10, 15, and 20 days after anthesis i.e. DAA) from these two varieties. The transcriptome was analyzed to identify differentially expressed genes, transcription factors, and molecular markers.ResultsThe transcriptome of Ivy gourd consisted of 155205 unigenes having an average contig size of 1472bp. Unigenes were annotated on publicly available databases to categorize them into different biological functions. Out of these, 7635 unigenes were classified into 38 transcription factor (TF) families, of which Trihelix TFs were most abundant. A total of 11,165 unigenes were found to be differentially expressed in both the varieties and the in silico expression results were validated through real-time PCR. Also, 98768 simple sequence repeats (SSRs) were identified in the transcriptome of Ivy gourd.DiscussionThis study has identified a number of genes, including transcription factors, that could play a crucial role in the determination of fruit shape and size in Ivy gourd. The presence of polymorphic SSRs indicated a possibility for marker-assisted selection for crop breeding in Ivy gourd. The information obtained can help select candidate genes that may be implicated in regulating fruit development and size in other fruit crops.

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Section: Discussionmentioning

confidence: 93%

Transcriptomics reveal useful resources for examining fruit development and variation in fruit size in Coccinia grandis

Panda,

Pradhan,

Mukherjee

2024

Front. Plant Sci.

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“…Among simple PCR-based markers, ILPs demonstrated gene specificity, high variability, environmental neutrality, and co-dominance, resulting in a high transferability rate through related species [ 18 ]. The advancement of whole-genome sequencing along with the availability of robust in silico tools can accelerate the development of low-cost, highly efficient gene-associated functional molecular markers for genotyping [ 10 ]. Therefore, by harnessing the advantage of publicly available genome sequences of tea species [ 9 , 15 , 26 ], we identified introns in the whole genome to exploit their length polymorphism as molecular markers in plants.…”

Section: Discussionmentioning

confidence: 99%

“…The early classification and identification of tea plants were primarily based on morphological characteristics. However, due to a limited understanding of the genetic information in the tea genome, traditional breeding methods have been somewhat blind and inefficient [ 10 ]. This limitation poses challenges in meeting the evolving market demands for diverse tea cultivars [ 11 ].…”

Section: Introductionmentioning

confidence: 99%

Development of Genome-Wide Intron Length Polymorphism (ILP) Markers in Tea Plant (Camellia sinensis) and Related Applications for Genetics Research

Shen,

He,

et al. 2024

IJMS

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The market value of tea is largely dependent on the tea species and cultivar. Therefore, it is important to develop efficient molecular markers covering the entire tea genome that can be used for the identification of tea varieties, marker-assisted breeding, and mapping important quantitative trait loci for beneficial traits. In this study, genome-wide molecular markers based on intron length polymorphism (ILP) were developed for tea trees. A total of 479, 1393, and 1342 tea ILP markers were identified using the PCR method in silico from the ‘Shuchazao’ scaffold genome, the chromosome-level genome of ‘Longjing 43’, and the ancient tea DASZ chromosome-level genome, respectively. A total of 230 tea ILP markers were used to amplify six tea tree species. Among these, 213 pairs of primers successfully characterize products in all six species, with 112 primer pairs exhibiting polymorphism. The polymorphism rate of primer pairs increased with the improvement in reference genome assembly quality level. The cross-species transferability analysis of 35 primer pairs of tea ILP markers showed an average amplification rate of 85.17% through 11 species in 6 families, with high transferability in Camellia reticulata and tobacco. We also used 40 pairs of tea ILP primers to evaluate the genetic diversity and population structure of C. tetracocca with 176 plants from Puan County, Guizhou Province, China. These genome-wide markers will be a valuable resource for genetic diversity analysis, marker-assisted breeding, and variety identification in tea, providing important information for the tea industry.

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“…Tea plants ( Camellia sinensis ) are perennial evergreen woody plants, and naturally growing tea plants can be classified into three types: arbors, small arbors, and shrubs (Lu et al., 2021). The leaves of tea plants are processed to produce non‐alcoholic tea beverages that are popular worldwide because of their health benefits and unique flavors (Li, Li, et al., 2023). Lignin is an aromatic heteropolymer that plays a crucial role in plant growth and development.…”

Section: Introductionunclassified

CsPAT1, a GRAS transcription factor, promotes lignin accumulation by antagonistic interacting with CsWRKY13 in tea plants

Li,

Zhou,

et al. 2024

The Plant Journal

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SUMMARYLignin is an important component of plant cell walls and plays crucial roles in the essential agronomic traits of tea quality and tenderness. However, the molecular mechanisms underlying the regulation of lignin biosynthesis in tea plants remain unclear. CsWRKY13 acts as a negative regulator of lignin biosynthesis in tea plants. In this study, we identified a GRAS transcription factor, phytochrome A signal transduction 1 (CsPAT1), that interacts with CsWRKY13. Silencing CsPAT1 expression in tea plants and heterologous overexpression in Arabidopsis demonstrated that CsPAT1 positively regulates lignin accumulation. Further investigation revealed that CsWRKY13 directly binds to the promoters of CsPAL and CsC4H and suppresses transcription of CsPAL and CsC4H. CsPAT1 indirectly affects the promoter activities of CsPAL and CsC4H by interacting with CsWRKY13, thereby facilitating lignin biosynthesis in tea plants. Compared with the expression of CsWRKY13 alone, the co‐expression of CsPAT1 and CsWRKY13 in Oryza sativa significantly increased lignin biosynthesis. Conversely, compared with the expression of CsPAT1 alone, the co‐expression of CsPAT1 and CsWRKY13 in O. sativa significantly reduced lignin accumulation. These results demonstrated the antagonistic regulation of the lignin biosynthesis pathway by CsPAT1 and CsWRKY13. These findings improve our understanding of lignin biosynthesis mechanisms in tea plants and provide insights into the role of the GRAS transcription factor family in lignin accumulation.

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Molecular markers in tea plant (Camellia sinensis): Applications to evolution, genetic identification, and molecular breeding

Cited by 18 publications

References 131 publications

Transcriptomics reveal useful resources for examining fruit development and variation in fruit size in Coccinia grandis

Transcriptomics reveal useful resources for examining fruit development and variation in fruit size in Coccinia grandis

Development of Genome-Wide Intron Length Polymorphism (ILP) Markers in Tea Plant (Camellia sinensis) and Related Applications for Genetics Research

CsPAT1, a GRAS transcription factor, promotes lignin accumulation by antagonistic interacting with CsWRKY13 in tea plants

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