Comprehensive Evaluation and Comparative Analysis of Jiahe Series Long-Grain japonica Rice with High Eating Quality Based on Gene Chip Technology

doi:10.16819/j.1001-7216.2024.231216

Abstract

Abstract:

【Objective】 The Jiahe series long-grain japonica rice is renowned for its slender grain shape, exceptional appearance quality, superior eating quality, high yield, and high disease resistance. This study aimed to elucidate the distinctive characteristics and challenges of these rice varieties, analyze the genetic foundation for the development of high-quality traits in these varieties, and lay a foundation for the innovation and utilization of long-grain japonica rice varieties. 【Method】 We utilized the GSR40K high-density rice chip to ascertain the indica-japonica identity and variety similarity of five long-grain japonica rice varieties (lines) of Jiahe series, and identified breeding-related functional genes. Furthermore, the genetic basis of the Jiahe series long-grain japonica rice was compared with that of the long-grain japonica rice Daohuaxiang 2 from Northeast China. 【Result】 The japonica segments in the genome of the Jiahe series long-grain japonica rice accounted for 84.20% to 88.38%, indicating the classification of these varieties into typical japonica rice types. The genetic similarity of Jiahe series japonica rice varieties (lines) exceeded 92%, with genomic identity ranging from 77.59% to 91.73%, while the similarity with Daohuaxiang 2 was lower, averaging 84.55% genetic similarity and 49.52% to 53.68% genome identity. Jiahe series japonica rice contains functional alleles for long grain genes gs3 and GW7, as well as the large grain type gene qSW5/GW5 and the multi-spikelet number gene LAX1 in Jiahexiang 1. The development of fine quality traits is mainly attributed to the combination of ALK^c/Wx^b/OsAAP6 and other major functional alleles. The fragrance in Jiahexiang 1 resulted from the exon 2 mutation type of the Badh2 gene. Jiahe series long-grain japonica rice varieties (lines) harbor numerous blast resistance genes, such as the combinations Pizt+Pii/HIT7/pi5-1, Pizt+Pii/HIT7/pi5-1, Pizt+Pi-ta, and Pizt+Pii/HIT7/pi5-1+Pi-d2/Pid2+Pid3+Pi-ta. In contrast, Jiahe series japonica rice only possesses Xa26/Xa3 genes for white leaf blight resistance. 【Conclusion】 The exceptional advantages of Jiahe series long-grain japonica rice stem from the comprehensive impact of multiple favorable allelic gene variations on yield, quality, resistance, and agronomic traits. Nonetheless, there are drawbacks of high variety similarity and a solitary gene for white leaf blight resistance. The findings of this study also furnish a scientific basis for the genetic enhancement of Jiahe series long-grain japonica rice varieties.

Key words: long-grain japonica rice, grain shape, functional gene, haplotype, indica-japonica identity, gene chip

摘要：

【目的】 嘉禾系列长粒粳稻粒型（细）长，外观品质突出，食味优良，丰产性与主栽品种相近，抗病性较好。本研究旨在明确嘉禾系列长粒粳稻品种的特点与存在问题，解析嘉禾系列长粒粳稻品种优质性状形成的遗传基础，为长粒粳稻品种创新利用提供依据。【方法】 以5份嘉禾系列长粒粳稻品种（系）为材料，利用GSR40K水稻高密度芯片分析品种籼粳属性、相似度，鉴定育种相关功能基因，同时比较嘉禾系列长粒粳稻品种（系）与东北长粒粳稻稻花香2号遗传基础差异。【结果】 嘉禾系列长粒粳稻品种（系）和稻花香2号基因组中，粳稻区段数占比84.20%~88.38%，均为典型粳稻类型；嘉禾系列长粒粳稻品种（系）间遗传相似度超过92%，基因组相似度为77.59%~91.73%，与稻花香2号遗传相似度为84.55%，基因组相似度为49.52%~53.68%；嘉禾系列长粒粳稻含有长粒优势功能基因gs3和GW7，嘉禾香1号还含有大粒型基因qSW5/GW5和多穗粒数基因LAX1；嘉禾系列品种的品质性状形成主要是ALK^c/Wx^b/OsAAP6等优势功能基因组合所致，嘉禾香1号香味是由Badh2第2外显子突变所致；嘉禾系列长粒粳稻品种（系）含有较多的抗稻瘟病基因，如抗病基因组合Pizt+Pii/HIT7/pi5-1、Pizt+Pi-ta、Pizt+Pii/HIT7/pi5-1+Pi-d2/Pid2+Pid3+Pi-ta，抗白叶枯基因只有Xa26/Xa3。【结论】 嘉禾系列长粒粳稻食味优、丰产稳产、抗病抗逆的突出优点，是品种含有较多的产量、品质、抗性、株型、生育期等优势等位基因变异综合影响的结果，但也存在品种相似度较高、白叶枯抗性基因单一的不足。本研究结果也为后续嘉禾系列长粒粳稻品种遗传改良提供了依据。

关键词: 长粒粳稻, 粒型, 功能基因, 单倍型, 籼粳属性, 基因芯片

DING Zhengquan, PAN Yueyun, SHI Yang, HUANG Haixiang. Comprehensive Evaluation and Comparative Analysis of Jiahe Series Long-Grain japonica Rice with High Eating Quality Based on Gene Chip Technology[J]. Chinese Journal OF Rice Science, 2024, 38(4): 397-408.

丁正权, 潘月云, 施扬, 黄海祥. 基于基因芯片的嘉禾系列长粒优质食味粳稻综合评价与比较[J]. 中国水稻科学, 2024, 38(4): 397-408.

Figures/Tables 9

References 31

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类别 Category	基因 Gene	数量 Number	功能 Function
产量 Yield component	Gn1a/OsCKX2, NOG1, LAX1, GNP1, APO1; GW2, GS3, qLGY3/OsMADS1/GW3p6/OsLG3b, GL3.1/qGL3, GL3.3/qTGW3, OsCYP704A3, qSW5/GW5, GW6a/OsglHAT1, OsSNB, OsSPL13/GLW7, GW7, GW8/OsSPL16, GE/CYP78A13/BG2, GL3.2/CYP78A5, GS5, qNGR2/GRF4; PTB1; OsSPL14(IPA1); LSCHL4/NAL1	24	增加穗粒数; 粒型; 提高结实率; 理想株型和高产; 减产
品质 Taste quality	OsAAP6; LOX-3; OsACS6/SSG6; Wx; ALK; Badh2	6	提高种子蛋白质含量; 降低陈化气味的产生; 提高L-天冬酰胺含量; 直链淀粉含量; 糊化温度; 香味
抽穗期 Heading date	OsCOL4, Hd16, Hd3a, Hd1, Ghd7/Hd4, Ghd8, DTH8, OsPRR37/Hd2/Ghd7.1; DTH2/Hd7, OsMADS51, OsMADS50/Hd9/OsSOC1/DTH3, Hd17/Hd3b, RFT1, Ehd1, RCN1	15	抽穗期提前; 抽穗期延迟
株型 Plant architecture	D2/CYP90D2/SMG11, TAC3, TAC1; TIG1; SCM3/OsTB1; OsOTUB1/WTG1; OsTb2; D61/OsBRI1, OsbHLH174, ILI3/OsbHLH153; sd1; SLR1/OsGAI/Slr1-d; OsSPY; OsLG1; OsGSK2	15	分蘖角度增大; 分蘖角度减小; 少蘖抗倒伏; 少蘖增加穗粒数; 多蘖; 剑叶角度增大; 半矮秆; 高秆; 增加株高; 散穗型; 中胚轴长度增大
非生物逆境抗性Abiotic Stress resistance	NRAT1; BET1; OsHMA4; Os-MOT1;1; OsHKT1;1; OsHMA3, qGMN7.1/OsNRAMP5; qSE3/OsHAK21, Os-HKT1;5/SKC1; OsALS; bZIP73, HAN1, qLTG3-1; OsPP15, OsLG3, DROT1, Nced; TT1; OsNPF6.1, NRT1.1B; OsHKT2;1; DRO1; OsJAZ1; qUVR-10; psr1	25	铝敏感; 耐硼; 铜敏感; 减少钼积累; 根部钠含量增加; 高镉积累; 耐盐; 抗除草剂; 冷敏感; 抗旱; 耐热; 氮高效; 降低钾利用率; 浅根; 根部长度与重量减小; 光修复; 提高再生能力
生物逆境抗性Biological stress resistance	Bph3, Bph14, Bph15, Bph18, Bph26, Bph6, Bph9; bsr-d1, Pi9, Pi50, Pi-d2/Pid2, Pizt, Pii/HIT7/pi5-1, Pi56, Pi-CO39/RGA4, LHCB5, Pi54/Pi-kh, Pi-ta, Ptr, Pi1, Pi2, Pi5, Pia, Pid3, Pigm, pikh; Xa1, Xa13, Xa21, Xa23, Xa26/Xa3, xa5, Xa7; Rymv1; OsSAP16	35	增强褐飞虱的抗性; 增强稻瘟病抗性; 增强白叶枯病抗性; 抗黄色斑驳病毒病; 抗水稻东格鲁病毒
育性与恢复性Fertility and restoration	Rf3/OsMADS3, Rf2; HSA1b, ESA1, DPL2, S5-3/ORF3, S5-4/ORF4; S5-5/ORF5, S7; Pms1/PMS1T, tms5	11	育性恢复; 籼粳杂种不育; 杂交亲和; 光敏雄性不育; 温敏雄性不育
其他 Others	BOC1; sh4, qSH1; OsPME1, OsTSD2, OsUGT706D1, OsUGT707A2, OsUGT707A2, OsAT4c; Rd/DFR/OsDfr, Rc, An-2/OsLOGL6/LABA1, OsC1, Hairy Leaf 6/HL6	14	愈伤组织褐化; 非落粒; 次生代谢物; 种子形态

类别 Category	基因 Gene	数量 Number	功能 Function
产量 Yield component	Gn1a/OsCKX2, NOG1, LAX1, GNP1, APO1; GW2, GS3, qLGY3/OsMADS1/GW3p6/OsLG3b, GL3.1/qGL3, GL3.3/qTGW3, OsCYP704A3, qSW5/GW5, GW6a/OsglHAT1, OsSNB, OsSPL13/GLW7, GW7, GW8/OsSPL16, GE/CYP78A13/BG2, GL3.2/CYP78A5, GS5, qNGR2/GRF4; PTB1; OsSPL14(IPA1); LSCHL4/NAL1	24	增加穗粒数; 粒型; 提高结实率; 理想株型和高产; 减产
品质 Taste quality	OsAAP6; LOX-3; OsACS6/SSG6; Wx; ALK; Badh2	6	提高种子蛋白质含量; 降低陈化气味的产生; 提高L-天冬酰胺含量; 直链淀粉含量; 糊化温度; 香味
抽穗期 Heading date	OsCOL4, Hd16, Hd3a, Hd1, Ghd7/Hd4, Ghd8, DTH8, OsPRR37/Hd2/Ghd7.1; DTH2/Hd7, OsMADS51, OsMADS50/Hd9/OsSOC1/DTH3, Hd17/Hd3b, RFT1, Ehd1, RCN1	15	抽穗期提前; 抽穗期延迟
株型 Plant architecture	D2/CYP90D2/SMG11, TAC3, TAC1; TIG1; SCM3/OsTB1; OsOTUB1/WTG1; OsTb2; D61/OsBRI1, OsbHLH174, ILI3/OsbHLH153; sd1; SLR1/OsGAI/Slr1-d; OsSPY; OsLG1; OsGSK2	15	分蘖角度增大; 分蘖角度减小; 少蘖抗倒伏; 少蘖增加穗粒数; 多蘖; 剑叶角度增大; 半矮秆; 高秆; 增加株高; 散穗型; 中胚轴长度增大
非生物逆境抗性Abiotic Stress resistance	NRAT1; BET1; OsHMA4; Os-MOT1;1; OsHKT1;1; OsHMA3, qGMN7.1/OsNRAMP5; qSE3/OsHAK21, Os-HKT1;5/SKC1; OsALS; bZIP73, HAN1, qLTG3-1; OsPP15, OsLG3, DROT1, Nced; TT1; OsNPF6.1, NRT1.1B; OsHKT2;1; DRO1; OsJAZ1; qUVR-10; psr1	25	铝敏感; 耐硼; 铜敏感; 减少钼积累; 根部钠含量增加; 高镉积累; 耐盐; 抗除草剂; 冷敏感; 抗旱; 耐热; 氮高效; 降低钾利用率; 浅根; 根部长度与重量减小; 光修复; 提高再生能力
生物逆境抗性Biological stress resistance	Bph3, Bph14, Bph15, Bph18, Bph26, Bph6, Bph9; bsr-d1, Pi9, Pi50, Pi-d2/Pid2, Pizt, Pii/HIT7/pi5-1, Pi56, Pi-CO39/RGA4, LHCB5, Pi54/Pi-kh, Pi-ta, Ptr, Pi1, Pi2, Pi5, Pia, Pid3, Pigm, pikh; Xa1, Xa13, Xa21, Xa23, Xa26/Xa3, xa5, Xa7; Rymv1; OsSAP16	35	增强褐飞虱的抗性; 增强稻瘟病抗性; 增强白叶枯病抗性; 抗黄色斑驳病毒病; 抗水稻东格鲁病毒
育性与恢复性Fertility and restoration	Rf3/OsMADS3, Rf2; HSA1b, ESA1, DPL2, S5-3/ORF3, S5-4/ORF4; S5-5/ORF5, S7; Pms1/PMS1T, tms5	11	育性恢复; 籼粳杂种不育; 杂交亲和; 光敏雄性不育; 温敏雄性不育
其他 Others	BOC1; sh4, qSH1; OsPME1, OsTSD2, OsUGT706D1, OsUGT707A2, OsUGT707A2, OsAT4c; Rd/DFR/OsDfr, Rc, An-2/OsLOGL6/LABA1, OsC1, Hairy Leaf 6/HL6	14	愈伤组织褐化; 非落粒; 次生代谢物; 种子形态

品种 Cultivar	株高 PH (cm)	生育期 GD(d)	有效穗数 PPN (×10⁴/hm²)	每穗粒数GNP	结实率 SSR (%)	千粒重 KGW (g)	长宽比 LR	产量 Yield (kg/hm²)	增幅 Increase rate (%)
JH212	95.0	151.5	20.0	103.3	93.3	27.9	2.9	7524.00	1.8
JHX 1	103.5	157.5	19.0	120.7	91.4	30.7	2.7	9808.50	2.4
JH549	86.3	155.0	23.4	126.8	96.1	21.1	2.7	9051.00	−0.6
JH276	89.6	129.5	20.0	121.3	88.7	27.6	3.0	8253.00	−3.9
JH6426	99.8	152.0	22.1	136.6	96.1	23.5	2.7	9927.00	−1.0
秀水134 Xiushui 134	91.6	153.0	20.9	135.5	89.0	27.0	1.8	9456.75	—

品种 Cultivar	株高 PH (cm)	生育期 GD(d)	有效穗数 PPN (×10⁴/hm²)	每穗粒数GNP	结实率 SSR (%)	千粒重 KGW (g)	长宽比 LR	产量 Yield (kg/hm²)	增幅 Increase rate (%)
JH212	95.0	151.5	20.0	103.3	93.3	27.9	2.9	7524.00	1.8
JHX 1	103.5	157.5	19.0	120.7	91.4	30.7	2.7	9808.50	2.4
JH549	86.3	155.0	23.4	126.8	96.1	21.1	2.7	9051.00	−0.6
JH276	89.6	129.5	20.0	121.3	88.7	27.6	3.0	8253.00	−3.9
JH6426	99.8	152.0	22.1	136.6	96.1	23.5	2.7	9927.00	−1.0
秀水134 Xiushui 134	91.6	153.0	20.9	135.5	89.0	27.0	1.8	9456.75	—

品种Cultivar	整精米率HMR(%)	垩白粒率CR(%)	垩白度CD(%)	透明度Transparency	碱消值ASV	胶稠度GC(mm)	直链淀粉含量AAC (%)	稻瘟病抗性BR	白叶枯病抗性BBR	褐飞虱抗性BphR
JH212	71.6	10.0	1.0	1.0	7.0	78.0	16.6	中抗MR	感S	—
JHX 1	57.8	16.5	2.4	1.5	6.6	70.5	17.5	中感MS	中感MS	高感HS
JH276	66.2	8.0	1.3	1.0	7.0	68.0	17.7	中抗MR	感S	高感HS
JH549	68.1	2.0	0.3	1.0	7.0	60.0	14.5	抗R	感S	—
Ⅰ^*	69.0		1.0	1.0	7.0	70.0	13.0~18.0
Ⅱ^*	66.0		3.0	2.0	7.0	60.0	13.0~19.0
Ⅲ^*	63.0		5.0	2.0	6.0	60.0	13.0~20.0