Whole-genome Analysis and Precision Breeding Strategies for a Novel Japonica Rice Variety Jiru Dao 1

doi:10.13560/j.cnki.biotech.bull.1985.2025-1293

Abstract

Abstract:

Objective This study aimed to systematically elucidate the genetic basis of the novel Japonica rice variety Jiru Dao 1, evaluate its production potential and risks, and formulate precise molecular design breeding strategies. Method Agronomic traits, grain quality, and disease resistance data from the Shandong Provincial Regional Trials and Production Trials (2019-2021) were integrated. Whole-genome resequencing of Jiru Dao 1 was performed using the Illumina HiSeq platform. Genotyping of 319 important agronomic trait-associated quantitative trait nucleotides (QTNs) was conducted based on the RiceNavi system, followed by genotype-phenotype association analysis. Result The average yield of Jiru Dao 1 was 10 437.0 kg/hm², 8.1% higher than the control. Its grain quality met the Level 3 standard of the national “High-Quality Paddy” (GB/T 17891-1999) specification, and it was recognized as a superior-tasting variety by Jiangsu province in 2023. Genotype analysis revealed that its high yield and lodging resistance originated from the pyramiding of favorable alleles such as sd1 and Ghd8; its excellent tasting quality was controlled by key genes including Waxy (low amylose content) and ALK (low gelatinization temperature). For disease resistance, it carried multiple blast resistance genes (pi35, Pita, Pib, Pid2, Pid3, and Pi21) and genes (Xa3, xa25) resisting to bacterial blight. Both OsCd1 and OsNRAMP5 were superior “non-cadmium-accumulating” alleles. Meanwhile, Gn1a and NOG1 were identified as “to-be-improved” alleles limiting yield potential. Chalk5 was a “chalkiness-increasing” allele affecting appearance quality; and NRT1.1B, OsNR2, and PSTOL1 were mostly “neutral” alleles, constraining nutrient use efficiency. Conclusion Jiru Dao 1 represents a successful example of traditional breeding by pyramiding multiple favorable alleles for high yield, good quality, multiple disease resistance, and low cadmium accumulation. However, its yield potential, appearance stability, and disease resistance breadth are limited by inferior alleles such as Gn1a and Chalk5 and the absence of broad-spectrum resistance genes. Whole-genome dissection precisely identified these genetic strengths and weaknesses, providing a scientific basis to overcome the empirical limitations of conventional breeding. Therefore, a precision breeding strategy is proposed: using Jiru Dao 1 as the recipient, key favorable alleles (Gn1a, Chalk5, Pi2/Pi9,and Xa23) are introduced via marker-assisted selection, while whole-genome background selection preserves its elite genetic background, enabling targeted variety improvement.

Key words: Japonica rice, Jiru Dao 1, whole-genome resequencing, RiceNavi, genotype analysis, molecular design breeding

GAO Guo-liang, ZHANG Qiao-ling, FENG Wen-jie, GAO Fa-rui, GAO Bo, ZONG Ke-dong, GE Lin, LI Shang-xian, WANG Qiu-yun, HUANG Xin-cheng. Whole-genome Analysis and Precision Breeding Strategies for a Novel Japonica Rice Variety Jiru Dao 1[J]. Biotechnology Bulletin, doi: 10.13560/j.cnki.biotech.bull.1985.2025-1293.

Figures/Tables 4

References 26

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试验类型 Test type	全生育期 Growth period （d）	株高 Plant height （cm）	有效穗 Panicles （×10⁴/hm²）	每穗总粒数 Spikelets per panicle	结实率 Seed setting rate （%）	千粒重 1 000-grain weight （g）	产量 Yield （kg/hm²）	较对照增产 Yield increase over CK （%）
2019年区域试验	157	100.5	360.0	133.5	79.9	26.2	10 983.0	10.7
2020年区域试验	156	103.0	336.0	124.0	92.6	26.6	9 889.5	5.4
2021年生产试验	155	101.3	348.0	104.9	86.1	26.4	9 129.0	9.4
平均 Average	156	101.6	348.0	128.7	86.2	26.4	10 437.0	8.1

试验类型 Test type	全生育期 Growth period （d）	株高 Plant height （cm）	有效穗 Panicles （×10⁴/hm²）	每穗总粒数 Spikelets per panicle	结实率 Seed setting rate （%）	千粒重 1 000-grain weight （g）	产量 Yield （kg/hm²）	较对照增产 Yield increase over CK （%）
2019年区域试验	157	100.5	360.0	133.5	79.9	26.2	10 983.0	10.7
2020年区域试验	156	103.0	336.0	124.0	92.6	26.6	9 889.5	5.4
2021年生产试验	155	101.3	348.0	104.9	86.1	26.4	9 129.0	9.4
平均 Average	156	101.6	348.0	128.7	86.2	26.4	10 437.0	8.1

性状类别 Trait category	基因 Gene	等位类型 Allele type	遗传效应 Genetic effect	与表型的关联分析及风险评估 Association with phenotype and risk assessment
株高/株型 Plant height/Plant architecture	sd1	有利	半矮秆	是理想株高和强抗倒伏性的基础
	Ghd8	有利	株高降低	与sd1协同作用，共同贡献于理想的株高与抗倒伏能力
	TAC1	有利	分蘖角度小	贡献于其紧凑株型
产量构成 Yield components	LAX1	有利	产量提高	高产的遗传基础之一，促进穗型发育
	Gn1a	待改良	穗粒数少	限制了每穗粒数的进一步提升，是制约产量潜力的关键位点
	NOG1	待改良	穗粒数低	与Gn1a共同限制穗粒数，是制约产量的遗传短板
	GNP1	待改良	穗粒数一般	进一步限制了穗粒数的遗传潜力
稻米品质 Rice quality	Waxy	有利	直链淀粉含量降低	决定适中直链淀粉含量，是优良食味的关键
	ALK	有利	糊化温度降低	塑造了其软米特性与优良蒸煮食味品质
	Chalk5	待改良	垩白率提高	在灌浆期遭遇逆境时外观品质易波动，垩白度易升高，是外观品质不稳定及提升至更高优质等级（如部标1级）的主要障碍
	Badh2	中性	米粒无香味	解释其无香味的特性
抗病性 Disease resistance	pi35， Pita	有利	稻瘟病抗性	经KASP验证，是其稻瘟病中抗表现的基础，符合区域抗性分布特征
	Pib， Pid2， Pid3， Pi21	有利	稻瘟病抗性	多位点中效抗性基因的聚合，增强了抗性谱。是其对稻瘟病表现中抗的重要支持
	Pi9， Pi2， Pigm	缺失	广谱高抗	导致其对稻瘟病的抗性不够持久和全面，是抗病体系中的薄弱环节
	Xa3， Xa25	有利	白叶枯病抗性	解释了其对白叶枯病的抗性
	Xa23	缺失	广谱高抗	缺乏最有效的广谱基因Xa23，存在抗性丧失风险
环境安全 Environmental safety	OsCd1， OsNRAMP5	有利	不富集镉	为其在轻中度镉污染地区的安全生产提供了核心遗传保障
养分利用 Nutrient utilization	NRT1.1B， OsNR2	中性	氮肥利用效率一般	解释了其对氮肥需求较高的现象，有改良空间
养分利用 Nutrient utilization	PSTOL1	中性	磷吸收效率一般	磷吸收效率有待提升

性状类别 Trait category	基因 Gene	等位类型 Allele type	遗传效应 Genetic effect	与表型的关联分析及风险评估 Association with phenotype and risk assessment
株高/株型 Plant height/Plant architecture	sd1	有利	半矮秆	是理想株高和强抗倒伏性的基础
	Ghd8	有利	株高降低	与sd1协同作用，共同贡献于理想的株高与抗倒伏能力
	TAC1	有利	分蘖角度小	贡献于其紧凑株型
产量构成 Yield components	LAX1	有利	产量提高	高产的遗传基础之一，促进穗型发育
	Gn1a	待改良	穗粒数少	限制了每穗粒数的进一步提升，是制约产量潜力的关键位点
	NOG1	待改良	穗粒数低	与Gn1a共同限制穗粒数，是制约产量的遗传短板
	GNP1	待改良	穗粒数一般	进一步限制了穗粒数的遗传潜力
稻米品质 Rice quality	Waxy	有利	直链淀粉含量降低	决定适中直链淀粉含量，是优良食味的关键
	ALK	有利	糊化温度降低	塑造了其软米特性与优良蒸煮食味品质
	Chalk5	待改良	垩白率提高	在灌浆期遭遇逆境时外观品质易波动，垩白度易升高，是外观品质不稳定及提升至更高优质等级（如部标1级）的主要障碍
	Badh2	中性	米粒无香味	解释其无香味的特性
抗病性 Disease resistance	pi35， Pita	有利	稻瘟病抗性	经KASP验证，是其稻瘟病中抗表现的基础，符合区域抗性分布特征
	Pib， Pid2， Pid3， Pi21	有利	稻瘟病抗性	多位点中效抗性基因的聚合，增强了抗性谱。是其对稻瘟病表现中抗的重要支持
	Pi9， Pi2， Pigm	缺失	广谱高抗	导致其对稻瘟病的抗性不够持久和全面，是抗病体系中的薄弱环节
	Xa3， Xa25	有利	白叶枯病抗性	解释了其对白叶枯病的抗性
	Xa23	缺失	广谱高抗	缺乏最有效的广谱基因Xa23，存在抗性丧失风险
环境安全 Environmental safety	OsCd1， OsNRAMP5	有利	不富集镉	为其在轻中度镉污染地区的安全生产提供了核心遗传保障
养分利用 Nutrient utilization	NRT1.1B， OsNR2	中性	氮肥利用效率一般	解释了其对氮肥需求较高的现象，有改良空间
养分利用 Nutrient utilization	PSTOL1	中性	磷吸收效率一般	磷吸收效率有待提升