Quantitative Trait Locus Mapping of High Photosynthetic Efficiency and Biomass in Oryza longistaminata

doi:10.1016/j.rsci.2022.01.011

Abstract

Abstract:

Photosynthetic efficiency, a key trait that determines yield potential in rice, is quantitatively regulated by multiple genes. Utilization of valuable genetic resources hidden in wild rice is an effective way to improve rice photosynthesis and yield potential. In this study, 152 backcross inbred lines derived from wild rice Oryza longistaminata were explored for QTL mapping of photosynthetic rate (Pn) and biomass (BM) in natural fields. Five novel QTLs for Pn and seven QTLs for BM or daily biomass (DBM) derived from O. longistaminata were identified. One of these QTLs, qPn8.1, could significantly improve Pn and was located in a 68-kb region containing only 11 candidate genes. Meanwhile, qBM1.1 and qDBM1.1 for BM and DBM on chromosome 1 were overlapped with qPn1.1 for Pn from 9311, and could affect both Pn and BM in natural fields. These QTLs identified in O. longistaminata may provide a novel alternative to explore new genes and resources for yield potentiality, highlighting the important role of wild rice in rice breeding programs.

Key words: QTL, Oryza longistaminata, photosynthetic rate, biomass, wild rice

Si Fengfeng, Fan Fengfeng, Wei Xiao, He Shihao, Li Xianlong, Peng Xiaojue, Li Shaoqing. Quantitative Trait Locus Mapping of High Photosynthetic Efficiency and Biomass in Oryza longistaminata[J]. Rice Science, 2022, 29(6): 569-576.

Figures/Tables 7

Table 1. Pn and BM of backcross inbred lines in different sites.

Site	Trait	9311 (Mean ± SD, n = 5)	Backcross inbred line
Site	Trait	9311 (Mean ± SD, n = 5)	Mean ± SD (n = 5)	CV (%)	Range
Ezhou	Pn [µmol/(m²·s)]	19.90 ± 1.00	22.00 ± 5.70	25.90	10.30-36.20
	Gs [mol/(m²·s)]	0.75 ± 0.06	0.68 ± 0.19	27.91	0.30-1.21
	BM (g)	41.17 ± 1.11	55.89 ± 9.43	16.72	23.95-89.00
	DBM (g/d)	0.29 ± 0.01	0.39 ± 0.06	16.70	0.06-0.61
Lingshui	Pn [µmol/(m²·s)]	25.00 ± 0.69	26.20 ± 3.40	12.83	17.20-32.60
	Gs [mol/(m²·s)]	0.85 ± 0.13	0.80 ± 0.22	27.82	0.31-1.32
	BM (g)	33.31 ± 4.75	56.25 ± 8.21	15.01	34.05-73.98
	DBM (g/d)	0.24 ± 0.03	0.41 ± 0.06	15.14	0.06-0.54

Fig. 1. Frequency distributions of photosynthetic rate (A), stomatal conductance (B), biomass (C) and daily biomass (D) of backcross inbred lines (BILs) in different sites.

Table 2. Correlation coefficients among photosynthesis and biomass of backcross inbred lines in Ezhou (upper right) and Lingshui (lower left), China.

Trait	Pn	Gs	BM	DBM
Pn		0.437**	0.168*	0.174*
Gs	0.588**		-0.042	-0.022
BM	0.202*	-0.049		0.988**
DBM	0.256**	-0.011	0.958**

Fig. 2. QTL analysis of photosynthesis of backcross inbred line population in different sites. Upward direction indicates the allele showing positive effects, while downward direction indicates the allele showing negative effects. Pn, Photosynthetic rate; Gs, Stomatal conductance; BM, Biomass; DBM, Daily biomass.

Table 3. QTL information for photosynthic rate and biomass of backcross inbred lines in fields.

QTL	Site	Chr.	L/Bin	R/Bin	LOD	PVE (%)	Add
qPn1.1	Lingshui	1	1-143	1-144	3.5	11.9	-1.1381
qPn2.1	Lingshui	2	2-25	2-26	2.9	9.2	-1.1851
qPn5.1	Ezhou	5	5-86	5-87	3.1	7.9	-2.6304
qPn8.1	Ezhou	8	8-85	8-86	3.6	9.2	3.2571
qPn8.1	Lingshui	8	8-85	8-86	2.7	8.4	1.5921
qPn12.1	Ezhou	12	12-121	12-122	2.8	7.0	-1.7882
qGs2.1	Ezhou	2	2-256	2-257	3.9	11.7	-0.1334
qBM1.1	Ezhou	1	1-143	1-144	3.0	8.2	3.1844
qBM1.1	Lingshui	1	1-143	1-144	4.5	15.0	3.6097
qBM6.1	Ezhou	6	6-107	6-108	3.0	8.1	5.2379
qDBM1.1	Ezhou	1	1-143	1-144	4.5	8.1	0.0243
qDBM1.1	Lingshui	1	1-143	1-144	3.4	13.0	0.0240
qDBM3.1	Ezhou	3	3-179	3-180	2.7	4.5	-0.0326
qDBM4.1	Ezhou	4	4-99	4-100	4.4	7.7	-0.0332
qDBM6.1	Ezhou	6	6-106	6-107	5.3	9.3	0.0422
qDBM12.1	Ezhou	12	12-54	12-55	3.0	5.0	-0.0173

Fig. 3. Validation of function of qPn1.1/qBM1.1/qDBM1.1. A, Comparison of genotypic structure of qPn1.1/qBM1.1/qDBM1.1 locus in different backcross inbred lines (BILs). Black bar and blank bar represent fragments from O. longistaminata and 9311, respectively. B, Photosynthetic rate of corresponding BILs. Different lowercase letters at the top of the bar indicate significant differences among different BILs by the Duncan’s multiple range test at P < 0.05.

Fig. 4. Validation of function of qPn8.1. A, Comparison of genotypic structure of qPn8.1 locus in different backcross inbred lines (BILs). Black bar and blank bar represent fragments from O. longistaminata and 9311, respectively. Gray bar represents heterozygote genotype. B, Photosynthetic rate of corresponding BILs. Different lowercase letters at the top of the bar indicate significant differences among different BILs at P < 0.05 by the Duncan’s multiple range test. C, Means of Pn of BILs with qPn8.1. ***, Significant difference at P < 0.001 by the Duncan’s multiple range test. D, Relative expression levels of candidate gene ARE1 in different BILs and 9311. In A, B and D, BIL1763, BIL1781, BIL1728, BIL1731 and BIL1787 harbor qPn8.1 from O. longistaminata; BIL1702 does not harbor qPn8.1 as 9311; and BIL1711 is the heterozygote genotype.

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