Dissecting Genetic Basis of Deep Rooting in Dongxiang Wild Rice

doi:10.1016/j.rsci.2021.11.002

Abstract

Abstract:

Deep rooting is an important trait in rice drought resistance. Genetic resources of deep-rooting varieties are valuable in breeding of water-saving and drought-resistant rice. In the present study, 234 BC₂F₇ backcross introgression lines were derived from a cross of Dongye 80 (an accession of Dongxiang wild rice as the donor parent) and R974 (an indica restorer line as the recurrent parent). A genetic linkage map containing 1 977 bin markers was constructed by ddRADSeq for QTL analysis. Thirty-one QTLs for four root traits (the number of deep roots, the number of shallow roots, the total number of deep roots and the ratio of deep roots) were assessed on six rice chromosomes in two environments (2020 Shanghai and 2021 Hainan). Two of the QTLs, qDR5.1 and qTR5.2, were located on chromosome 5 in a 70-kb interval. They were detected in both environments. qDR5.1 explained 13.35% of the phenotypic variance in 2020 Shanghai and 12.01% of the phenotypic variance in 2021 Hainan. qTR5.2 accounted for 10.88% and 10.93% of the phenotypic variance, respectively. One QTL (qRDR2.2) for the ratio of deep roots was detected on chromosome 2 in a 210-kb interval and accounted for 6.72% of the phenotypic variance in 2020. The positive effects of these three QTLs were all from Dongxiang wild rice. Furthermore, nine and four putative candidate genes were identified in qRDR2.2 and qDR5.1/qTR5.2, respectively. These findings added to our knowledge of the genetic control of root traits in rice. In addition, this study will facilitate the future isolation of candidate genes of the deep-rooting trait and the utilization of Dongxiang wild rice in the improvement of rice drought resistance.

Key words: Dongxiang wild rice, backcross introgression line, deep rooting, genetic analysis, QTL

Nie Yuanyuan, Xia Hui, Ma Xiaosong, Lou Qiaojun, Liu Yi, Zhang Anling, Cheng Liang, Yan Longan, Luo Lijun. Dissecting Genetic Basis of Deep Rooting in Dongxiang Wild Rice[J]. Rice Science, 2022, 29(3): 277-287.

Figures/Tables 8

Table 1. Performances of DR, SR, TR and RDR in parents and backcross introgression lines in 2020 and 2021.

Trait	Environment	Year	R974	Dongye 80	Backcross introgression line
Trait	Environment	Year	R974	Dongye 80	Minimum	Maximum	Average	SD	CV (%)
DR	Shanghai	2020	63.2 ± 39.7	113.0 ± 68.7	19.8	227.8	67.5	36.1	53.6
	Hainan	2021	79.5 ± 43.7	129.3 ± 32.8*	27.8	194.8	104.6	32.4	31.0
SR	Shanghai	2020	270.5 ± 105.0	156.3 ± 44.5	55.5	595.8	233.1	77.4	33.2
	Hainan	2021	224.0 ± 83.4	95.0 ± 27.1*	23.0	335.7	183.0	49.7	27.2
TR	Shanghai	2020	333.7 ± 135.2	269.3 ± 110.8	77.8	734.0	298.9	100.6	33.7
	Hainan	2021	303.5 ± 105.1	224.3 ± 38.8	67.3	519.0	287.6	73.5	25.6
RDR	Shanghai	2020	0.19 ± 0.07	0.40 ± 0.08**	0.07	0.52	0.22	0.08	36.6
	Hainan	2021	0.26 ± 0.11	0.58 ± 0.10**	0.17	0.66	0.36	0.07	19.2

Fig. 1. Distribution frequencies of four root-related traits in 234 Dongye 80/R974 backcross introgression lines under two environments. A?D, Distribution frequencies of the number of deep roots (A), the number of shallow roots (B), the total number of roots (C) and the ratio of deep roots (D).

Table 2. Correlations among DR, SR, TR and RDR in backcross introgression lines measured in 2020 and 2021.

Parameter	20DR	20SR	20TR	20RDR	21DR	21SR	21TR
20SR	0.501**
20TR	0.749**	0.941**
20RDR	0.713**	-0.175**	0.133*
21DR	0.358**	0.157*	0.253**	0.269**
21SR	0.211**	0.396**	0.388**	-0.110	0.585**
21TR	0.300**	0.337**	0.374**	0.044	0.836**	0.934**
21RDR	0.175*	-0.255**	-0.137	0.466**	0.491**	-0.348**	-0.019

Table 3. QTLs for root traits in backcross introgression lines.

Fig 2. Distribution of QTLs related to DR, SR, TR and RDR derived from Dongxiang wild rice (Dongye 80). The black shapes show QTLs that were detected in Shanghai (SH), and the white shapes represent QTLs that were identified in Hainan (HN). The red shapes represent QTLs mapped in both environments. DR, The number of deep roots; SR, The number of shallow roots; TR, The total number of roots; RDR, Ratio of deep roots.

Fig. 3. Confirmation of QTLs qRDR2.2 (A) and qDR5.1 (B). Data are Mean ± SD (n = 6). **, Significant differences between backcross introgression lines (BILs) and recurrent parent R974 at P < 0.01.

Fig. 4. Validation of QTLs for ratio of deep roots (RDR) (A) and number of deep roots (DR) (B), and their pyramiding effects. SD, Standard deviation. **, Significant difference between the lines pyramided with different QTLs at P < 0.01.

Table 4. Putative genes at two QTL regions under hormone treatment and association analysis in rice.

QTL	Chromosome	Interval	Putative gene	Cloned symbol
qRDR2.2	2	c02b009‒c02b015	LOC_Os02g01355
			LOC_Os02g03410	OsCPK4
			LOC_Os02g03710
			LOC_Os02g03900	Nrat1
			LOC_Os02g04160	OsTEF1
			LOC_Os02g04270
			LOC_Os02g04520	RGG2
			LOC_Os02g04640	OsPHR3
			LOC_Os02g04680	OsSPL3
qDR5.1	5	c05b004‒c05b005	LOC_Os05g01030
			LOC_Os05g01040
			LOC_Os05g02070	OsMT2b
			LOC_Os05g02140

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