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Functional natural allelic variants of flavonoid 3′,5′-hydroxylase gene governing catechin traits in tea plant and its relatives

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Abstract

Main conclusion

Functional allelic variants of the flavonoid 3′,5′-hydroxylase (F3′5′H) gene provides new information of F3′5′H function of tea plant and its relatives. This insight may serve as the foundation upon which to advance molecular breeding in the tea plant.

Catechins are the active components of tea that determine its quality and health attributes. This study established the first integrated genomic strategy for deciphering the genetic basis of catechin traits of tea plant. With the RNA-sequencing analysis of bulked segregants representing the tails of a F1 population segregated for total catechin content, we identified a flavonoid 3′,5′-hydroxylase (F3′5′H) gene. F3′5′H had one copy in the genomic DNA of tea plant. Among 202 tea accessions, we identified 120 single nucleotide polymorphisms (SNPs) at F3′5′H locus. Seventeen significant marker-trait associations were identified by association mapping in multiple environments, which were involved in 10 SNP markers, and the traits including the ratio of di/tri-hydroxylated catechins and catechin contents. The associated individual and combination of SNPs explained 4.5–25.2 and 53.0–63.0% phenotypic variations, respectively. In the F1 population (validation population), the catechin trait variation percentages explained by F3′5′H diplotype were 6.9–74.3%. The genotype effects of ten functional SNPs in the F1 population were all consistent with the association population. Furthermore, the function of SNP−711/−655 within F3′5′H was validated by gene expression analysis. Altogether, our work indicated functional SNP allelic variants within F3′5′H governing the ratio of di/tri-hydroxylated catechins and catechin contents. The strong catechin-associated SNPs identified in this study can be used for future marker-assisted selection to improve tea quality.

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Abbreviations

BFR:

Bulk frequency ratio

BSR-Seq:

Bulked segregant RNA-seq

CI:

Catechin index

DIC:

Dihydroxylated catechins

DRR:

Downstream regulatory region

EC:

(–)-Epicatechin

ECG:

(–)-Epicatechin gallate

EGC:

(–)-Epigallocatechin

EGCG:

(–)-Epigallocatechin gallate

F3′H:

Flavonoid 3′-hydroxylase

F3′5′H:

Flavonoid 3′,5′-hydroxylase

FDR:

False discovery rate

FPKM:

Fragment per kilobase of exon model per million mapped reads

gDNA:

Genomic DNA

LD:

Linkage disequilibrium

MLM:

Mixed linear model

NGS:

Next generation sequencing

QTL:

Quantitative trait loci

r 2 :

The squared correlation of allele frequencies

RNA-seq:

RNA-sequencing

SNP:

Single nucleotide polymorphism

TC:

Total catechins

TRIC:

Trihydroxylated catechins

URR:

Upstream regulatory region

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Acknowledgements

This work was supported by the Earmarked Fund for China Agriculture Research System (CARS-023), the Chinese Academy of Agricultural Sciences through the Agricultural Science and Technology Innovation Program (CAASASTIP-2014-TRICAAS), National Natural Science Foundation of China (Nos. 31670685, 31500568, 31170624), National Science and Technology Support Program of China (2013BAD01B03-16), and the Natural Science Foundation of Zhejiang Province (No. LY13C160005).

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    1. Tea Research Institute of the Chinese Academy of Agricultural Sciences, National Center for Tea Improvement, Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, 9 South Meiling Road, Hangzhou, 310008, Zhejiang, China

      Ji-Qiang Jin, Jian-Qiang Ma, Ming-Zhe Yao, Chun-Lei Ma & Liang Chen

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    Correspondence to Liang Chen.

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    J.-Q. Jin and J.-Q. Ma contributed equally to this work.

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    Jin, JQ., Ma, JQ., Yao, MZ. et al. Functional natural allelic variants of flavonoid 3′,5′-hydroxylase gene governing catechin traits in tea plant and its relatives. Planta 245, 523–538 (2017). https://doi.org/10.1007/s00425-016-2620-5

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