亚种间杂交对东北粳稻的育种贡献
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摘要
籼稻(indica)和粳稻(japonica)作为亚洲栽培稻的两个亚种,在形态生理特性、遗传分化、地理分布上存在明显差别,亚种间有利基因互相利用,是高产育种的重要途径。从系谱分析近年来北方粳稻区生产上推广的品种绝大多数都是通过籼粳稻杂交育成的,东北粳稻产量日益突破,籼粳杂交的应用对北方粳稻的遗传进展及粮食安全做出了巨大的贡献,但这种贡献产生的分子基础非常复杂。以“日本晴”和“93-11”为代表的粳、籼两亚种的全基因组测序的完成,有力地推动了亚种分化功能位点研究的进展。本研究设计了190个SNPs位点从功能水平上剖析育种行为对北方粳稻遗传结构的影响,47个高遗传效应的亚种特异功能SNPs位点,结合中性亚种特异分化标记InDel和SSILP分子标记,分析东北粳型栽培稻的籼粳血缘比例,通过与日本粳稻与典型籼稻的比较,旨在从功能水平层面验证籼粳杂交对东北粳型水稻基因组的改变,并结合其与产量、品质等性状之间的关系,评价籼粳稻杂交对中国东北水稻育种的贡献,研究结果如下：
1、北方现代粳稻育成品种功能SNPs位点的Shannon-Weiner多样指数极显著低于引入的早期品种和外来粳稻,遗传多样性的趋势表现为外来品种>早期品种>现代品种。育种家通过“选择”将籼粳杂交的优势基因固定,但在淘汰掉不利性状的同时也损失了大量与不利性状相关或相连锁的等位基因,导致了功能基因水平上多样性的狭窄。群体遗传结构和系统进化分析结果表明,籼粳杂交育种与生态环境趋异使中国北方粳稻育成品种基因组结构产生了一定的分化,形成了独特的遗传结构与进化地位。
2、亚种特异功能标记的开发利用为明确粳稻中的籼稻成分和籼型位点提供了便利条件。籼粳分化位点在中性亚种特异标记(InDel, SSILP标记)和高遗传效应亚种特异功能标记(SNPs标记)水平上的表现是一致的,由于人工和自然选择,基因相互渗透,籼稻或粳稻分别导入了另一个亚种的等位基因。东北粳稻栽培品种功能位点上的籼稻基因频率为：辽宁(0.0588)>吉林(0.0514)>黑龙江(0.0368),极显著高于日本粳稻,体现了籼粳杂交优势利用理论对东北粳稻遗传基础的贡献。
3、籼粳稻亚种准确定性,精确定量是亚种分化研究的重要手段和保证。本研究选用的籼粳特异标记、程氏指数法、维管束数目比法三种亚种分类方法之间符合度较高,均能达到90%以上。亚种特性和粳稻型基因频率与产量及穗部性状的相关分析结果表明：育种家在北方粳稻育种过程中有效的利用籼稻品种少孽多花的特性,使东北粳稻育成品种穗数减少,二次枝梗数和二次枝梗粒数、二次粒率、着粒密度、以及每穗粒数增加；同时将一次枝梗数和一次枝梗结实率和千粒重维持在较高水平,使东北粳稻育成品种产量显著提高。
4、亚种特性和粳稻型基因频率与品质性状的相关分析结果表明：籼粳稻杂交使东北粳稻育成品种碾磨品质降低,但保持在优质粳稻范围内；垩白粒率和垩白度降低,长宽比增加,改善了外观品质；食味品质与日本粳稻还有一定差距,籼稻优良基因在粳稻基因组遗传背景下能够发挥增产效应,但同时以高产、高品质为目标的育种却是一个复杂的过程,东北地区水稻品种选育过程中总体上已经较好的解决了高产和优质的矛盾。
5、本研究选用的135个亚种特异功能标记高密度地覆盖了12条染色体。在中性亚种特异功能位点上,第5号、第6号、第10号染色体籼型位点样本较多。在高遗传效应亚种特异功能位点上第2号和第10号染色体的籼型位点样本比例分别高达18.14%和13.38%。统计产量与品质克隆基因附近的籼型位点样本比例：东北粳稻在9号染色体上籼型功能位点样本数为0,而北方粳稻理想株型基因DEP1位于9号染色体上；1号染色体上控制落粒性的基因qSH1两侧位点全部为粳型样本。虽然不能确定哪些基因真正的被利用,但是可以确定东北粳稻选育过程保留了有利基因,淘汰了不利基因。
Indica and japonica are subspecies of Asian cultivated rice (Oryza sativa L.) and possess different biological characteristics.The strategy of breeding high-yielding rice is developing superiority gene of subspecies. In recent years, most cultivated varieties were bred by indica-japonica hybridization in northeast China through seeking pedigree, which realize further increases in rice yieldhave contributed to an improved understanding of the genetic and food security. However, how subspecific hybrid vigor contributes to the high yields of northern japonica rice cultivars is not thoroughly understood. Recent studies of genome-wide sequencing of 'Nipponbare' and '93-11' were developed permit quantitative analysis of indica and japonica components of the rice genome. In this study, we used sinple nucleotide polymorphism (SNP) to analyze genetic diversity and structure of rice cultivars that were cultivated in northern China,47large-effect SNP loci,33subspecies-differentiating InDel and55subspecies-specific intron length polymorphism (SSILP) molecular markers to study genotype frequencies based on subspecies-differentiating loci and detect genomic subspecies lineages compared with Japanese varieties and indica. By combining the relationship between indica or japonica pedigree and yield components, grain quality with correlation analysis to obtain molecular evidence for the contribution of indica-japonica hybridizationto rice breeding in northern China. The major results were as follows:
1The present research showed that genetic diversity of novel rice cultivars bred in northern China were significantly lower than early breeding phase varieties and exotic varieties. Vigor genes of indica-japonica hybridization were fixed through 'selection', at the same time many functional alleles and their genetic linkage blocks to be purified at the population level along with the elimination of negative heterosis traits, which lead the decreased diversity at the functional genome level. Genetic structure and phylogenetic analyse ssuggest that the independent and unique phylogenetic status of modern breeding phase japonica has gradually arisen through the introduction of the indica lineage and natural selection in northern China.
2Subspecies-specific functional molecular markers were developed that permit quantitative analysis of indica and japonica components of the rice genome. The genotype frequencies of subspecies-differentiating InDel, SSILP markers and large-effect SNP loci were significantly positively correlated. Indica and japonica import another subspecies allele respectively through hybridization and natural selection. Indica-type allele frequency of rice cultivars in northeast China, ranked from highest to lowest, was Liaoning (0.0588)> Jilin (0.0514)> Heilongjiang (0.0368), and significantly higher than Japan, which reflect the contribution of indica-japonica hybridization to rice breeding in northeast China.
3The method of researching subspecies differentiation was very important. The consistent degree of classification based on Cheng's index, the vascular bundles characters and subspecies-specific markers was above90%. The correlation analysis of subspecies characters, japonica-type allele frequency and yield components indicated:secondary branches, grains on secondary branches, secondary branches grains rate, spikelets density and spikelets per panicles of novel rice cultivars bred in northeast China has increased and paniclesreduced through indica-japonica hybridization; Primary branches, seed setting rate of primary branches and103-grain weight kept on a higher level, all of these characters lead the yield significantly increased.
4The correlation analysis of subspecies characters, japonica-type allele frequency and grain quality indicated:rice milling quality of novel rice cultivars bred in northeast China had reduced but maintain in the range of high quality standard; Exterior quality had improved since the chalky grain rate and chalkiness dropt, while ratio of grain length to width added; Taste score was not as great as Japanese varieties, breeding of northeast China had perfectly coordinated the relationship of high-yielding and high-quality generally though the process of achieving the objective was very difficult.
5The135subspecies-specific functional markers used in our study were distributed among the12rice chromosomes. Indica-type loci on No.5, No.6and No.10was more than other chromosomes on neutrally-evolving loci; On large phenotypic effects functional loci level, the percentage of indica-type loci on No.2and No.10chromosomes achieved18.14%and13.38%, respectively. The correlation analysis of important cloning genes of agronomic characteristics and sample percentage of indica-type loci indicated:indica-type loci of large phenotypic effects functional loci was0on chromosomes9which hold the erect panicle gene DEP1; Two sides loci of shattering gene qSHl were all japonica-type on chromosomes1. Among these genes controlling agronomic traits, although did not know which gene was utilized, advantageous gene have already reserved in japonica rice and unfavourable gene was eliminated by selection during the process of breeding japonica rice in northeast China.
1、北方现代粳稻育成品种功能SNPs位点的Shannon-Weiner多样指数极显著低于引入的早期品种和外来粳稻,遗传多样性的趋势表现为外来品种>早期品种>现代品种。育种家通过“选择”将籼粳杂交的优势基因固定,但在淘汰掉不利性状的同时也损失了大量与不利性状相关或相连锁的等位基因,导致了功能基因水平上多样性的狭窄。群体遗传结构和系统进化分析结果表明,籼粳杂交育种与生态环境趋异使中国北方粳稻育成品种基因组结构产生了一定的分化,形成了独特的遗传结构与进化地位。
2、亚种特异功能标记的开发利用为明确粳稻中的籼稻成分和籼型位点提供了便利条件。籼粳分化位点在中性亚种特异标记(InDel, SSILP标记)和高遗传效应亚种特异功能标记(SNPs标记)水平上的表现是一致的,由于人工和自然选择,基因相互渗透,籼稻或粳稻分别导入了另一个亚种的等位基因。东北粳稻栽培品种功能位点上的籼稻基因频率为：辽宁(0.0588)>吉林(0.0514)>黑龙江(0.0368),极显著高于日本粳稻,体现了籼粳杂交优势利用理论对东北粳稻遗传基础的贡献。
3、籼粳稻亚种准确定性,精确定量是亚种分化研究的重要手段和保证。本研究选用的籼粳特异标记、程氏指数法、维管束数目比法三种亚种分类方法之间符合度较高,均能达到90%以上。亚种特性和粳稻型基因频率与产量及穗部性状的相关分析结果表明：育种家在北方粳稻育种过程中有效的利用籼稻品种少孽多花的特性,使东北粳稻育成品种穗数减少,二次枝梗数和二次枝梗粒数、二次粒率、着粒密度、以及每穗粒数增加；同时将一次枝梗数和一次枝梗结实率和千粒重维持在较高水平,使东北粳稻育成品种产量显著提高。
4、亚种特性和粳稻型基因频率与品质性状的相关分析结果表明：籼粳稻杂交使东北粳稻育成品种碾磨品质降低,但保持在优质粳稻范围内；垩白粒率和垩白度降低,长宽比增加,改善了外观品质；食味品质与日本粳稻还有一定差距,籼稻优良基因在粳稻基因组遗传背景下能够发挥增产效应,但同时以高产、高品质为目标的育种却是一个复杂的过程,东北地区水稻品种选育过程中总体上已经较好的解决了高产和优质的矛盾。
5、本研究选用的135个亚种特异功能标记高密度地覆盖了12条染色体。在中性亚种特异功能位点上,第5号、第6号、第10号染色体籼型位点样本较多。在高遗传效应亚种特异功能位点上第2号和第10号染色体的籼型位点样本比例分别高达18.14%和13.38%。统计产量与品质克隆基因附近的籼型位点样本比例：东北粳稻在9号染色体上籼型功能位点样本数为0,而北方粳稻理想株型基因DEP1位于9号染色体上；1号染色体上控制落粒性的基因qSH1两侧位点全部为粳型样本。虽然不能确定哪些基因真正的被利用,但是可以确定东北粳稻选育过程保留了有利基因,淘汰了不利基因。
Indica and japonica are subspecies of Asian cultivated rice (Oryza sativa L.) and possess different biological characteristics.The strategy of breeding high-yielding rice is developing superiority gene of subspecies. In recent years, most cultivated varieties were bred by indica-japonica hybridization in northeast China through seeking pedigree, which realize further increases in rice yieldhave contributed to an improved understanding of the genetic and food security. However, how subspecific hybrid vigor contributes to the high yields of northern japonica rice cultivars is not thoroughly understood. Recent studies of genome-wide sequencing of 'Nipponbare' and '93-11' were developed permit quantitative analysis of indica and japonica components of the rice genome. In this study, we used sinple nucleotide polymorphism (SNP) to analyze genetic diversity and structure of rice cultivars that were cultivated in northern China,47large-effect SNP loci,33subspecies-differentiating InDel and55subspecies-specific intron length polymorphism (SSILP) molecular markers to study genotype frequencies based on subspecies-differentiating loci and detect genomic subspecies lineages compared with Japanese varieties and indica. By combining the relationship between indica or japonica pedigree and yield components, grain quality with correlation analysis to obtain molecular evidence for the contribution of indica-japonica hybridizationto rice breeding in northern China. The major results were as follows:
1The present research showed that genetic diversity of novel rice cultivars bred in northern China were significantly lower than early breeding phase varieties and exotic varieties. Vigor genes of indica-japonica hybridization were fixed through 'selection', at the same time many functional alleles and their genetic linkage blocks to be purified at the population level along with the elimination of negative heterosis traits, which lead the decreased diversity at the functional genome level. Genetic structure and phylogenetic analyse ssuggest that the independent and unique phylogenetic status of modern breeding phase japonica has gradually arisen through the introduction of the indica lineage and natural selection in northern China.
2Subspecies-specific functional molecular markers were developed that permit quantitative analysis of indica and japonica components of the rice genome. The genotype frequencies of subspecies-differentiating InDel, SSILP markers and large-effect SNP loci were significantly positively correlated. Indica and japonica import another subspecies allele respectively through hybridization and natural selection. Indica-type allele frequency of rice cultivars in northeast China, ranked from highest to lowest, was Liaoning (0.0588)> Jilin (0.0514)> Heilongjiang (0.0368), and significantly higher than Japan, which reflect the contribution of indica-japonica hybridization to rice breeding in northeast China.
3The method of researching subspecies differentiation was very important. The consistent degree of classification based on Cheng's index, the vascular bundles characters and subspecies-specific markers was above90%. The correlation analysis of subspecies characters, japonica-type allele frequency and yield components indicated:secondary branches, grains on secondary branches, secondary branches grains rate, spikelets density and spikelets per panicles of novel rice cultivars bred in northeast China has increased and paniclesreduced through indica-japonica hybridization; Primary branches, seed setting rate of primary branches and103-grain weight kept on a higher level, all of these characters lead the yield significantly increased.
4The correlation analysis of subspecies characters, japonica-type allele frequency and grain quality indicated:rice milling quality of novel rice cultivars bred in northeast China had reduced but maintain in the range of high quality standard; Exterior quality had improved since the chalky grain rate and chalkiness dropt, while ratio of grain length to width added; Taste score was not as great as Japanese varieties, breeding of northeast China had perfectly coordinated the relationship of high-yielding and high-quality generally though the process of achieving the objective was very difficult.
5The135subspecies-specific functional markers used in our study were distributed among the12rice chromosomes. Indica-type loci on No.5, No.6and No.10was more than other chromosomes on neutrally-evolving loci; On large phenotypic effects functional loci level, the percentage of indica-type loci on No.2and No.10chromosomes achieved18.14%and13.38%, respectively. The correlation analysis of important cloning genes of agronomic characteristics and sample percentage of indica-type loci indicated:indica-type loci of large phenotypic effects functional loci was0on chromosomes9which hold the erect panicle gene DEP1; Two sides loci of shattering gene qSHl were all japonica-type on chromosomes1. Among these genes controlling agronomic traits, although did not know which gene was utilized, advantageous gene have already reserved in japonica rice and unfavourable gene was eliminated by selection during the process of breeding japonica rice in northeast China.
引文
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