利用水稻耐盐品种Pokkali衍生材料选育的高产耐盐新种质的遗传变异

doi:10.3864/j.issn.0578-1752.2025.20.007

Abstract

Abstract:

【Objective】This study aimed to elucidate the genetic basis of high yield and salt tolerance in rice through comparative genomic analysis of the salt-tolerant paternal parent Pokkali-D (Pokkali-Dwarf), the high-yielding maternal parent Huazhan, and their derived line Zhongyandao 16. The findings provide a theoretical foundation and genetic resources for the molecular breeding of salt-tolerant rice. 【Method】A new germplasm named Zhongyandao 16, which combines salt tolerance and high yield, was developed by crossing the salt-tolerant parent Pokkali-D with the high-yielding parent Huazhan. The salt tolerance of Zhongyandao 16 was evaluated based on seedling survival rate under salt stress (120 mmol·L^-¹ NaCl) and yield performance in a saline field (0.4% salinity). To further investigate the genetic basis of its superior traits, whole-genome resequencing of Pokkali-D, Huazhan and Zhongyandao 16 was conducted. Genetic variants inherited from both parents, as well as unique variants present in Zhongyandao 16, were screened through variant detection. High-impact variants (causing frameshifts or premature termination of translation) and moderate-impact variants (resulting in amino acid changes) were annotated for the affected genes. 【Result】Under 120 mmol·L^-1 NaCl stress, the seedling survival rate of Zhongyandao 16 was similar to that of Pokkali-D and significantly higher than that of Huazhan. Under normal field conditions, the yield of Zhongyandao 16 was comparable to Huazhan and significantly higher than Pokkali-D. Under 0.4% salinity field conditions, Zhongyandao 16 exhibited significantly higher yield than both parents, demonstrating a combination of salt tolerance and high yield. Comparative genomic analysis against the Nipponbare reference genome showed that Zhongyandao 16 shared 86 716 identical variants with Huazhan, among which high- and moderate-impact variants were annotated to 1 629 genes. It also shared 21 623 identical variants with Pokkali-D, with high- and moderate-impact variants annotated to 443 genes. Additionally, Zhongyandao 16 carried 372 unique variants, with high- and moderate-impact variants annotated to 11 genes. Functional screening of these 2 083 genes identified 16 involved in salt stress regulation (12 derived from Huazhan, 4 from Pokkali-D), 48 associated with yield-related traits (36 from Huazhan, 12 from Pokkali-D), and 3 modulated both yield and salt tolerance (2 from Huazhan, 1 from Pokkali-D). Notably, salt-tolerance alleles from Pokkali-D including OsPRPL18, OsSTLK, STH1, OsLPR2, and OsLPR5, as well as those from Huazhan, such as OsSAP4, OsY3IP1, OsABI5 and OsHKT1;5, were pyramided in Zhongyandao 16. 【Conclusion】By pyramiding yield-related genes from Huazhan and salt-tolerance alleles from Pokkali-D, Zhongyandao 16 combines high yield and salt tolerance. This demonstrates that introducing key salt-tolerant alleles from Pokkali-D into the high-yielding Huazhan background can effectively enhance salt tolerance without compromising yield.

Key words: rice, new germplasm, salt tolerance, high yield, genetic variants, gene pyramiding

LIU ChunLei, WANG Juan. Genetic Variation Analysis of New Germplasm with Combined High Yield and Salt Tolerance Developed from Derivative Materials of Pokkali[J].Scientia Agricultura Sinica, 2025, 58(20): 4117-4130.

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Figures/Tables 8

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Table 1

Table 2

Table 3

Table 4

Genes annotated from variant sites unique to Huazhan but shared with Zhongyandao16"

基因编号 Gene ID	基因 Gene	具体表型 Phenotype	性状分类 Trait	参考文献 References
Os01g0871700	qSBM1	每穗粒数Grains per panicle（-）	产量性状Yield traits	[8]
Os03g0224200	OsRR21; ORR1	每穗粒数Grains per panicle（+）	产量性状Yield traits	[9]
Os04g0545000	OsWRKY36; sgsd3	每穗粒数Grains per panicle（+）	产量性状Yield traits	[10]
Os05g0141050	WLS5	每穗粒数Grains per panicle（+）	产量性状Yield traits	[11]
Os05g0406100	OsCPN1	每穗粒数Grains per panicle（+）	产量性状Yield traits	[12]
Os11g0157600	OsCCT38; OsPRR59	每穗粒数Grains per panicle（+）	产量性状Yield traits	[13]
Os12g0428600	OsUPL2; LARGE2	每穗粒数Grains per panicle（-）	产量性状Yield traits	[14]
Os12g0553200	GNP12	每穗粒数Grains per panicle（+）	产量性状Yield traits	[15]
Os01g0229300	DFO1; CCP1	结实率Seed-setting rate（+）	产量性状Yield traits	[16]
Os05g0402800	OsPDR2	结实率Seed-setting rate（+）	产量性状Yield traits	[17]
Os09g0551900	OsMLH3; fsv1	结实率Seed-setting rate（+）	产量性状Yield traits	[18]
Os01g0872500	OsNPF5.16	分蘖数Tiller number（+）	产量性状Yield traits	[19]
Os03g0693600	OsIAGLU; OsIAGT1	分蘖数Tiller number（+）	产量性状Yield traits	[20]
Os03g0131900	OscpSRP43; PGL3	分蘖数Tiller number（+）	产量性状Yield traits	[21]
Os06g0717200	FON1	分蘖数Tiller number（+）	产量性状Yield traits	[22]
Os09g0549450	OsNLP4	分蘖数Tiller number（+）	产量性状Yield traits	[23]
Os10g0562700	REL2; OsDLT10	分蘖数Tiller number（-）	产量性状Yield traits	[24]
Os10g0548700	NRRB; OsRLCK306	分蘖数Tiller number（+）	产量性状Yield traits	[25]
Os12g0299700	OsMAB	分蘖数Tiller number（+）	产量性状Yield traits	[26]
Os01g0185400	OsCBE1	单株产量Yield per plant（+）	产量性状Yield traits	[27]
Os03g0609500	OsLBD38	单株产量Yield per plant（+）	产量性状Yield traits	[28]
Os12g0609500	OsHLT1	单株产量Yield per plant（+）	产量性状Yield traits	[29]
Os01g0231000	OsIAA3	粒长Grain length（-）	产量性状Yield traits	[30]
Os09g0410300	TAF2; qCTS-9	籽粒大小Grain size（+）	产量性状Yield traits	[31]
Os01g0276700	OsPK5	千粒重1000-grain weight（+）	产量性状Yield traits	[32]
Os01g0286100	OsPIL15	千粒重1000-grain weight（-）	产量性状Yield traits	[33]
Os01g0286600	OsPPO1; sprl1	千粒重1000-grain weight（+）	产量性状Yield traits	[34]
Os02g0580000	OsFWL3	千粒重1000-grain weight（-）	产量性状Yield traits	[35]
Os02g0180400	HHC2	千粒重1000-grain weight（+）	产量性状Yield traits	[36]
Os03g0696300	OsNF-YA4; OsHAP2D	千粒重1000-grain weight（-）	产量性状Yield traits	[37]
Os05g0136200	OsCIPK17	千粒重1000-grain weight（+）	产量性状Yield traits	[38]
Os05g0119200	OsGPRP3	千粒重1000-grain weight（+）	产量性状Yield traits	[39]
Os06g0675200	LIN1	千粒重1000-grain weight（-）	产量性状Yield traits	[40]
Os07g0464700	OsCYP51H3	千粒重1000-grain weight（+）	产量性状Yield traits	[41]
Os12g0178500	OsSWEET7c	千粒重1000-grain weight（+）	产量性状Yield traits	[42]
Os12g0552600	qTGW12a	千粒重1000-grain weight（+）	产量性状Yield traits	[43]
Os03g0757500	GSA1; UGT83A1	耐盐性Salt tolerance（+）; 千粒重1000-grain weight（+）	耐盐性；产量性状 Salt tolerance; yield traits	[44]
Os04g0464200	OsALDH10A5; OsBADH1	耐盐性Salt tolerance（+）; 千粒重1000-grain weight（+）	耐盐性；产量性状 Salt tolerance; yield traits	[45]
Os01g0798500	OsY3IP1	耐盐性Salt tolerance（+）	耐盐性Salt tolerance	[46]
Os01g0859300	OsABI5; OREB1	耐盐性Salt tolerance（-）	耐盐性Salt tolerance	[47]
Os01g0209700	OsGA2ox7	耐盐性Salt tolerance（-）	耐盐性Salt tolerance	[48]
Os01g0935500	OsHAK2	耐盐性Salt tolerance（-）	耐盐性Salt tolerance	[49]
Os01g0307500	OsHKT1; 5	耐盐性Salt tolerance（+）	耐盐性Salt tolerance	[50]
Os02g0195600	ZFP185; OsSAP4	耐盐性Salt tolerance（+）	耐盐性Salt tolerance	[51]
Os03g0192500	OsPP45; OsBIPP2C1	耐盐性Salt tolerance（+）	耐盐性Salt tolerance	[52]
Os04g0465600	OsMLP423	耐盐性Salt tolerance（+）	耐盐性Salt tolerance	[53]
Os04g0682800	AM1	耐盐性Salt tolerance（+）	耐盐性Salt tolerance	[54]
Os06g0698785	OsCMO	耐盐性Salt tolerance（+）	耐盐性Salt tolerance	[55]
Os08g0206500	OsNF-YC5; OsHAP5F	耐盐性Salt tolerance（+）	耐盐性Salt tolerance	[56]
Os12g0162400	OsCBL6	耐盐性Salt tolerance（-）	耐盐性Salt tolerance	[57]

Table 4

Table 5

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染色体 Chromosome	长度 Length (bp)	Pokkali-D-中盐稻16 Pokkali-D-Zhongyandao 16		华占-中盐稻16 Huazhan-Zhongyandao 16		中盐稻16 Zhongyandao 16
染色体 Chromosome	长度 Length (bp)	变异位点数 Number of variants	变异间隔 Distance between variants (bp/variant)	变异位点数 Number of variants	变异间隔 Distance between variants (bp/variant)	变异位点数 Number of variants	变异间隔 Distance between variants (bp/variant)
1	43270923	1522	28430	12945	3342	34	1272674
2	35937250	531	67678	6094	5897	23	1562489
3	36413819	2664	13668	8092	4499	28	1300493
4	35502694	2330	15237	7796	4553	26	1365488
5	29958434	4152	7215	7914	3785	24	1248268
6	31248787	435	71836	2274	13741	27	1157362
7	29697621	136	218364	8331	3564	41	724332
8	28443022	169	168301	8706	3267	27	1053445
9	23012720	72	319621	8414	2735	28	821882
10	23207287	3463	6701	812	28580	31	748622
11	29021106	6034	4809	1709	16981	37	784354
12	27531856	115	239407	13629	2020	46	598518
总计Total	373245519	21623	17261	86716	4304	372	1003348

类型 Type	Pokkali-D-中盐稻16 Pokkali-D-Zhongyandao 16	华占-中盐稻16 Huazhan-Zhongyandao 16	中盐稻16 Zhongyandao 16
单碱基变异SNP	19500	78394	281
插入INS	836	3110	44
缺失DEL	1287	5212	47
总计Total	21623	86716	372

类型 Type	Pokkali-D-中盐稻16 Pokkali-D-Zhongyandao 16		华占-中盐稻16 Huazhan-Zhongyandao 16		中盐稻16 Zhongyandao 16
类型 Type	数量Count	百分比Percent (%)	数量Count	百分比Percent (%)	数量Count	百分比Percent (%)
HIGH	46	0.08	208	0.10	5	0.60
MODERATE	895	1.60	3143	1.46	11	1.33
LOW	955	1.71	3761	1.75	4	0.48
MODIFIER	54068	96.61	208187	96.70	810	97.59

Genetic Variation Analysis of New Germplasm with Combined High Yield and Salt Tolerance Developed from Derivative Materials of Pokkali

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基因编号 Gene ID	基因 Gene	具体表型 Phenotype	性状分类 Trait	参考文献 References
Os02g0110400	OsCPPR1	结实率Seed-setting rate（+）	产量性状Yield traits	[58]
Os05g0591600	LOGL8	结实率Seed-setting rate（+）	产量性状Yield traits	[59]
Os11g0587000	D27; DWARF27	分蘖数Tiller number（-）	产量性状Yield traits	[60]
Os11g0544600	OsChz1	分蘖数Tiller number（+）	产量性状Yield traits	[61]
Os02g0831500	OsSUS6	单株产量Yield per plant（+）	产量性状Yield traits	[62]
Os05g0591400	OsEBS	单株产量Yield per plant（+）	产量性状Yield traits	[63]
Os10g0498700	SPL38; OsMED16	单株产量Yield per plant（-）	产量性状Yield traits	[64]
Os11g0586300	OsLESV; FLO9	单株产量Yield per plant（+）	产量性状Yield traits	[65]
Os11g0591100	OsGME2	单株产量Yield per plant（+）	产量性状Yield traits	[66]
Os11g0544500	OsPML2	单株产量Yield per plant（+）	产量性状Yield traits	[67]
Os01g0116600	SPL33; LMM5.1	千粒重1000-grain weight（+）	产量性状Yield traits	[68]
Os04g0376300	HTS1; OsPLS4	千粒重1000-grain weight（+）	产量性状Yield traits	[69]
Os01g0127200	OsLPR5; OsLPR1-5	耐盐性Salt tolerance（+）; 单株产量Yield per plant（+）	耐盐性；产量性状 Salt tolerance; yield traits	[70]
Os01g0126200	OsLPR2; OsLPR1-2	耐盐性Salt tolerance（-）	耐盐性Salt tolerance	[71]
Os03g0828100	OsPRPL18; WLP3	耐盐性Salt tolerance（+）	耐盐性Salt tolerance	[72]
Os05g0305900	OsSTLK	耐盐性Salt tolerance（+）	耐盐性Salt tolerance	[73]
Os05g0590300	STH1; D14L2a	耐盐性Salt tolerance（+）	耐盐性Salt tolerance	[74]

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