Achievements and prospects of QTL mapping and beneficial genes and alleles mining for important quality and agronomic traits in tea plant (<i>Camellia sinensis</i>)

Zhihua Wang; Rong Huang; Doo-Gyung Moon; Sezai Ercisli; Liang Chen; Zhihua Wang; Rong Huang; Doo-Gyung Moon; Sezai Ercisli; Liang Chen

doi:10.48130/BPR-2023-0022

Figures (7) Tables (2)

Figure 1.
QTL mapping construction flow chart.
Figure 2.
Schematic presentation of catechin metabolism. PAL, phenylalanine ammonia-lyase; C4H, cinnamate 4-hydroxylase; 4CL, 4-coumarate-CoA ligase; CHS, chalcone synthase; CHI, chalcone isomerase; F3'H, flavonoid 3'-monooxygenase; F3H, flavanone 3-hydroxylase; F3'5'H, flavonoid 3', 5'-hydroxylase; FLS, flavonol synthase; DFR, dihydroflavonol-4-reductase; ANS, anthocyanidin synthase; ANR, anthocyanidin reductase; ECGT, 1-Ogalloyl-b-D-glucose O-galloyltransferase; UFGT, UDP-glucoseflavonoid-3-O-glucosyltransferase; LAR, leucoanthocyanidin reductase; DFR, dihydroflavonol reductase.
Figure 3.
Effect of different factors on theanine accumulation. (a) Theanine content in different tissues: young leaves > roots > old leaves > stems. (b) Theanine content in different tissues under shading (Data source is from Yang et al.^[60]). (c) Expression patterns of candidate genes in different tissues in theanine biosynthesis of cultivar 'Shuchazao': apical buds (AB), young leaves (YL), mature leaves (ML), old leaves (OL), young stems (ST), flowers (FL), young fruits (FR) and tender roots (RT) (Date source is from Wei et al.^[1]). (d) The content of theanine in different tissues of tea cultivar 'Shuchazao': The dry weight contents of theanine were detected by HPLC analysis in eight different tissues of tea cultivar 'Shuchazao' (Date source is from Wei et al.^[1]).
Figure 4.
Schematic representation of caffeine metabolism. 7-NMT, 7-Methylxanthosine synthase; N-MeNase, N-Methylnucleotidase; MXMT, Theobromine synthase; TCS, Tea caffeine synthase; SAM, S-Adenosyl methionine; SAH, S-Adenosyl-L-homocysteine.
Figure 5.
Route map of three low caffeine tea plant breeding technologies. CCT, 'Cocoa tea', a caffeine-free tea plant from Guangdong, China; HYC, 'Hongyacha', a naturally caffeine-free tea plant from Fujian, China; RY, 'Ruyuan', which contains low caffeine. (Data source is from Wang et al.^[81]).
Figure 6.
Timeline of research on tea plant genome databases and platforms.
Figure 7.
Growing number of articles on tea plant GWAS. The number of articles is implied by the amount of tea plants. All data were obtained from the web of science (www.webofscience.com) by searching the terms 'tea plants' and 'genome-wide association study'.

No.	Mapping population (♂ × ♀)	Population size	Marker type	Markers	Linkage groups	Total length (cM)	Average distance (cM)	Ref.
1	Yabukita	46	RAPD	23	6	−	−	[16]
1	Shizu-Inzaysu131	46	RAPD	36	6	−	−	[16]
2	Sayamakaori	54	RAPD	126	14	1550	11.7	[27]
2	Kana-CK17	54	RAPD	140	17	1640		[27]
3	SFS150	90	RAPD/AFLP	126	15	1349.7	11.7	[28]
3	TN14/3	90	RAPD/AFLP	−				[28]
4	Qimen 4	69	AFLP	208	17	2457.7	11.9	[29]
4	Chaoan Dawuye	69	AFLP	200	16	2545.3		[29]
5	Fuding Dabaicha	94	RAPD/ISSR	62	6	1180.9	15.7	[30]
6	TRI2043	141	SSR	139	15	1018	2.9	[31]
6	TRI2023	141	SSR	173	15	1192.9		[31]
7	Sayamakari	64	SSR/RAPD/CAPS/STS	571	17	3091	1.93	[32]
7	Kana-CK17	64	SSR/RAPD/CAPS/STS	632	15	3314		[32]
8	TRFCA SFS150	42	RAPD/AFLP/SSR	69	15	1012	14.1	[33]
8	AHP S15/10	42	RAPD/AFLP/SSR	31	19	399.5		[33]
9	Sayamakaori	54	SSR/RAPD/CAPS/STS	701	15	1305	1.93	[34]
9	Kana-CK17	54	SSR/RAPD/CAPS/STS	701	15	1298		[34]
10	Longjing43	170	SSR	237	15	1156.9	5.2	[35]
10	Baihaozao	170	SSR					[35]
11	Yingshuang	183	SSR	406	15	1143.5	3.0	[17]
11	Beiyue Danzhu	183	SSR					[17]
12	Yingshuang	148	SNP/SSR	6448	15	3965	1.0	[36]
12	Beiyue Danzhu	148	SNP/SSR					[36]
13	Longjing 43	170	SSR	483	15	1226.2	2.5	[22]
13	Baihaozao	170	SSR					[22]
14	Wuniuzao	174	SSR	175	16	1156.9	7.4	[37]
14	Longjing 43	174	SSR					[37]
15	Fushun	79	RAPD/AFLP/SSR	678	−	1441.6	4.7	[38]
15	Kemsull	79	RAPD/AFLP/SSR					[38]
16	TRFK 303/577	109	DArT-seq	187	15	1028.1	1.1	[25]
	GW Ejulu	109
	GW Ejulu	152		190	15	1026.6
	TRFK 303/577	152
17	Longjing 43	327	SNP	417	15	1678.52	0.4	[19]
17	Baihaoza	327	SNP					[19]
18	Ziyan	176	SNP	131	15	1062.7	9.48	[18]
19	Jinxuan	96	SNP	8956	15	1490.81	0.18	[24]
19	Yuncha1	96	SNP					[24]
20	Shuchazao	327	SNP	5325	15	2107.21	0.39	[39]
20	Longjing 43	327	SNP					[39]
21	Emei Wenchun	294	SNP	4244	15	1449.19	0.34	[23]
22	Longjing 43	198	SNP	2688	15	1846.32	0.69	[20]
22	Baijiguan	198	SNP					[20]
23	Huangdan	148	SNP	3770	15	1754.57	0.47	[21]
23	Jinxuan

Table 1.

Summarized papers of genetic map information in tea plants.

QTL mapping	GWAS mapping
Artificial populations with trait separation	Natural populations with rich variation
Bi-parental crosses	de-novo crossing and selfing
Less prone to false positives	High possibility of false positives
Fewer markers required	A larger number of individuals is required
Limited number of genotypes and low allele richness	Abundant alleles but low allele frequency
Lower resolution based on the number of recombination	High possibility of phenotypic variation
More robust in heterogeneity but single genetic basis	High map density but low heritability

Table 2.

The main characteristics of GWAS mapping and QTL mapping.