亚洲栽培稻籼—粳遗传分化及其与地理分布的关系
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摘要
籼-粳分化代表亚洲栽培稻(Oryza sativa L.)遗传分化中主要的分化类型,长期以来也是栽培稻遗传分化及其利用研究的焦点。由于籼稻和粳稻之间在形态、生理、遗传以及对应的生境存在一系列差异,有些极端分化的籼稻和粳稻类型在杂交时存在显著的生殖隔离,因此,栽培稻被划分为籼稻亚种(O.sativa L. subsp. indica Kato)和粳稻亚种(O. sativa L. subsp. japonica Kato)。本研究首次采用高效精确鉴定籼-粳分化的插入-缺失分子标记(Insertion/Deletion, InDel),系统阐明栽培品种的籼-粳遗传分化,并定量地确定籼-粳遗传分化的程度。本研究根据不同类型栽培稻品种的地域适应性,分析其地理分布规律,并分析海拔和纬度怎样影响这一分布,为进一步理解籼稻和粳稻种植区的划分提供依据；同时,籼稻和粳稻类型的精确鉴定,为其在育种中的合理应用提供科学依据,特别是籼-粳杂种优势的利用和在分子辅助育种中有效地选择亲本的种质资源提供依据。本研究的主要结果如下：
1.栽培稻品种沿着海拔梯度的籼-粳分化及其分布：采用34对能够特异区分籼粳的InDel分子标记,分析了来自中国云南省的203份亚洲栽培稻品种和14份野生稻种,海拔梯度在450m到2350m之间。研究结果表明：(1)云南栽培稻品种发生了显著的遗传分化,分成籼稻和粳稻两大类群,其中只有极少数的栽培稻和几乎所有的野生稻种表现为中间类型,没有发生分化；(2)籼稻适应区几乎覆盖了所有的采样区域,而粳稻更适应于海拔高于1400m的区域,表明籼稻对海拔具有很宽的适应范围,而粳稻则更适应于高海拔地区；(3)云南的栽培稻品种未出现大量的中间类型,表明在云南分化程度较高的籼稻和粳稻可能由其它地方引种而来,因此云南可能不是栽培稻的起源中心之一,而是栽培稻的遗传多样性中心之一。
2.栽培稻品种沿纬度梯度的籼-粳分化及其分布：采用34对InDel分子标记,对分布于亚洲南纬3°到北纬45°的纬度区间内的387个品种以及5个不同来源的非洲栽培稻品种和52个野生稻种群作为研究材料进行实验分析。结果表明：(1)亚洲栽培稻聚类为两个相对独立的群体,表明亚洲栽培稻发生了显著的遗传分化,而非洲栽培稻和野生稻则没有相应的遗传分化；(2)籼稻和粳稻沿纬度梯度的地理分布呈现不同的模式：籼稻在南纬2°到北纬40°的广大范围内具有广泛的适应性；粳稻则明显集中分布在高于北纬15°的地区；大部分的中间类型则分布在低于北纬27°的地区；(3)对取样区间的栽培稻类型的种植比例和各纬度梯度30年年均温的相关分析表明：籼稻的分布对温度变化不敏感,粳稻的分布则对温差变化反应敏感；同样中间类型对温度变化反应敏感。因此,栽培稻沿着不同纬度梯度的籼-粳遗传分化以及地理分布与其所在环境的生态因子——温度紧密相关。
3.为了进一步了解能够特异区分籼-粳的InDel分子标记与籼-粳遗传分化功能基因的关系,本文分析了与InDel分子标记紧密连锁的基因序列,发现有50条基因序列具有一定的功能结构域。比对日本晴和93-11中获得序列结果发现：(1)与标记R2M10紧密相邻的基因序列存在90个变异；(2)与标记R4M43紧密相邻的基因序列存在19个变异；(3)与标记R8M46紧密相邻的基因序列存在18个变异；(4)与标记R3M10紧密相邻的基因序列存在1个变异,在420bp位置日本晴有一个缺失突变,93-1l在此位置插入碱基T,造成蛋白序列发生移码突变,且93-11中该基因在609bp位置提前终止。深入研究这些基因序列并进行进一步验证其功能,将有助于深入了解栽培稻籼-粳遗传分化过程中所受到的选择作用,为栽培稻籼-粳分化的起源和形成机理提供生物信息学和分子生物学支持。
Indica-japonica variation represents the most significant genetic differentiation in Asian cultivated rice, and it has also been the focus of how to use genetic differentiation of cultivated rice. Based on the differentiation in characteristics of morphology, physiology, genetics and their habitat, especially when significant differentiated varieties shows obvious reproductive isolation and sterility in F1 hybrids, Asian cultivated rice was classified into two sub-species Oryza sativa L. subsp. indica Kato and subsp. japonica Kato. In this study Insertion/Deletion molecular markers (InDel) was first used in indica-japonica genetic differentiation of cultivated rice and identification of the degree of indica-japonica differentiation. Based on that indica rice and japonica rice adapt to different environmental conditions we analyzed the differentiation and distribution patterns of cultivated rice along altitude and latitude gradients, and also accurately identified the type of rice. In order to exploring the difference in genome of typical indica and typical japonica, we analyzed gene sequence which is located near to the InDel molecular markers. This research will facilitate indica-japonica differentiation theoretical research, strategic utilization and conservation of rice germplasm, and provide scientific data for introducing different type of rice to certain place to achieve better agronomic characteristics. The mainly results of this study are:
1. In this study, we analyzed 203 varieties and 14 wild accessions of rice collected from localities across an altitude gradient between 450 and 2,350 m above sea level in Yunnan, China, applying the "InDel molecular index" developed recently. Results from PCA of the InDel data demonstrated significant genetic differentiation of rice varieties from Yunnan into indica and japonica types. A few cultivars and nearly all wild rice accessions showed only moderate or no differentiation. Further analyses demonstrated a clear distribution pattern of the rice varieties in the mountainous region:indica varieties were grown across the entire altitude gradient in the sampling areas, but most japonica varieties were found above 1,400 m. These results clearly indicated that indica rice could be cultivated in areas at much higher altitudes than those categorized by the traditional methods. The knowledge opens a new dimension for introducing indica rice varieties to mountainous regions at higher altitudes and for selecting rice germplasm in these regions. In addition, the pattern of significant indica-japonica differentiation in rice varieties from Yunnan suggested the exotic origin of cultivated rice, which did not support the hypothesis that Yunnan is a part of the center of origin of rice, although it is certainly one of the centers of genetic diversity for rice.
2. Asian cultivated rice has significantly differentiated into indica and japonica subspecies that have extensive distribution worldwide. To determine genetic differentiation of Asian cultivated rice across a latitudinal gradient, a total of 387 Asian cultivated rice varieties, five African rice varieties, and 52 wild rice accessions collected from a wide range of Asian countries and other regions were analyzed applying the InDel molecular index. The principal component analysis classified Asian cultivated rice into two distinct groups, which demonstrated significant molecular genetic differentiation of Asia cultivated rice, while all wild rice and African cultivated rice showed no evident differentiation. The results clearly indicated that Asian cultivated rice has differentiated profoundly since its domestication and during its adaptation to various environments, contrasting with wild rice and African rice. Analysis of the geographic distribution indicated a clear pattern for the different types of rice, in which indica rice varieties were found across a wide range of latitudes from -2°S to 40°N and japonica varieties were mostly focused in the high latitude areas greater than 15°N. Most intermediate types of rice originated in regions at latitudes lower than 27°N. Correlation patterns between rice types and temperature along the latitude gradients suggested that indica rice was considerably less sensitive to temperature along the latitude ranges, but japonica rice was highly sensitive to the temperature at different latitudes. The molecular genetic intermediate type of rice was also sensitive to temperature. We conclude that the distribution pattern of different types of Asian rice across large latitudinal ranges is the consequence of their adaptation in relation to ecological factors of the environment, especially temperature. This has an important implication in breeding of hybrid rice by selecting properly differentiated indica and japonica parents.
3. In order to understand the indica-japonica differentiation information in genome which linked with InDel molecular marker and to learn the molecular mechanism of indica-japonica differentiation, in this study we analyzed sequence approached closely to 34 InDel molecular markers and found:there are 50 sequences have functional domain which means these sequence could be real gene. Based on the PCR we get these sequences separately from typical indica and typical japonica. Further alignment of sequencing result showed that there are molecular variation between the sequence from typical indica 93-11 and typical japonica niponbare:Near the molecular marker R2M10, the sequences from 93-11 and niponbare have 90 bases change; R4M43, there are 19 bases change; R8M46, there are 18 variation in sequence; R3M10, there is one variation in sequence, there is one deletion mutation in japonica at the position of 420bp which make one shift mutation in related protein sequence; it was a termination beforehand in indica at the position of 609bp. Understanding these predicted gene sequences and further analysis of their domain and function, will help us to understand the selection process of indica-japonica variation. This study has very important implication in indicating the origin, differentiation and dimension of indica-japonica variation, and also in providing the genetic information for the mechanism of indica-japonica variation.
1.栽培稻品种沿着海拔梯度的籼-粳分化及其分布：采用34对能够特异区分籼粳的InDel分子标记,分析了来自中国云南省的203份亚洲栽培稻品种和14份野生稻种,海拔梯度在450m到2350m之间。研究结果表明：(1)云南栽培稻品种发生了显著的遗传分化,分成籼稻和粳稻两大类群,其中只有极少数的栽培稻和几乎所有的野生稻种表现为中间类型,没有发生分化；(2)籼稻适应区几乎覆盖了所有的采样区域,而粳稻更适应于海拔高于1400m的区域,表明籼稻对海拔具有很宽的适应范围,而粳稻则更适应于高海拔地区；(3)云南的栽培稻品种未出现大量的中间类型,表明在云南分化程度较高的籼稻和粳稻可能由其它地方引种而来,因此云南可能不是栽培稻的起源中心之一,而是栽培稻的遗传多样性中心之一。
2.栽培稻品种沿纬度梯度的籼-粳分化及其分布：采用34对InDel分子标记,对分布于亚洲南纬3°到北纬45°的纬度区间内的387个品种以及5个不同来源的非洲栽培稻品种和52个野生稻种群作为研究材料进行实验分析。结果表明：(1)亚洲栽培稻聚类为两个相对独立的群体,表明亚洲栽培稻发生了显著的遗传分化,而非洲栽培稻和野生稻则没有相应的遗传分化；(2)籼稻和粳稻沿纬度梯度的地理分布呈现不同的模式：籼稻在南纬2°到北纬40°的广大范围内具有广泛的适应性；粳稻则明显集中分布在高于北纬15°的地区；大部分的中间类型则分布在低于北纬27°的地区；(3)对取样区间的栽培稻类型的种植比例和各纬度梯度30年年均温的相关分析表明：籼稻的分布对温度变化不敏感,粳稻的分布则对温差变化反应敏感；同样中间类型对温度变化反应敏感。因此,栽培稻沿着不同纬度梯度的籼-粳遗传分化以及地理分布与其所在环境的生态因子——温度紧密相关。
3.为了进一步了解能够特异区分籼-粳的InDel分子标记与籼-粳遗传分化功能基因的关系,本文分析了与InDel分子标记紧密连锁的基因序列,发现有50条基因序列具有一定的功能结构域。比对日本晴和93-11中获得序列结果发现：(1)与标记R2M10紧密相邻的基因序列存在90个变异；(2)与标记R4M43紧密相邻的基因序列存在19个变异；(3)与标记R8M46紧密相邻的基因序列存在18个变异；(4)与标记R3M10紧密相邻的基因序列存在1个变异,在420bp位置日本晴有一个缺失突变,93-1l在此位置插入碱基T,造成蛋白序列发生移码突变,且93-11中该基因在609bp位置提前终止。深入研究这些基因序列并进行进一步验证其功能,将有助于深入了解栽培稻籼-粳遗传分化过程中所受到的选择作用,为栽培稻籼-粳分化的起源和形成机理提供生物信息学和分子生物学支持。
Indica-japonica variation represents the most significant genetic differentiation in Asian cultivated rice, and it has also been the focus of how to use genetic differentiation of cultivated rice. Based on the differentiation in characteristics of morphology, physiology, genetics and their habitat, especially when significant differentiated varieties shows obvious reproductive isolation and sterility in F1 hybrids, Asian cultivated rice was classified into two sub-species Oryza sativa L. subsp. indica Kato and subsp. japonica Kato. In this study Insertion/Deletion molecular markers (InDel) was first used in indica-japonica genetic differentiation of cultivated rice and identification of the degree of indica-japonica differentiation. Based on that indica rice and japonica rice adapt to different environmental conditions we analyzed the differentiation and distribution patterns of cultivated rice along altitude and latitude gradients, and also accurately identified the type of rice. In order to exploring the difference in genome of typical indica and typical japonica, we analyzed gene sequence which is located near to the InDel molecular markers. This research will facilitate indica-japonica differentiation theoretical research, strategic utilization and conservation of rice germplasm, and provide scientific data for introducing different type of rice to certain place to achieve better agronomic characteristics. The mainly results of this study are:
1. In this study, we analyzed 203 varieties and 14 wild accessions of rice collected from localities across an altitude gradient between 450 and 2,350 m above sea level in Yunnan, China, applying the "InDel molecular index" developed recently. Results from PCA of the InDel data demonstrated significant genetic differentiation of rice varieties from Yunnan into indica and japonica types. A few cultivars and nearly all wild rice accessions showed only moderate or no differentiation. Further analyses demonstrated a clear distribution pattern of the rice varieties in the mountainous region:indica varieties were grown across the entire altitude gradient in the sampling areas, but most japonica varieties were found above 1,400 m. These results clearly indicated that indica rice could be cultivated in areas at much higher altitudes than those categorized by the traditional methods. The knowledge opens a new dimension for introducing indica rice varieties to mountainous regions at higher altitudes and for selecting rice germplasm in these regions. In addition, the pattern of significant indica-japonica differentiation in rice varieties from Yunnan suggested the exotic origin of cultivated rice, which did not support the hypothesis that Yunnan is a part of the center of origin of rice, although it is certainly one of the centers of genetic diversity for rice.
2. Asian cultivated rice has significantly differentiated into indica and japonica subspecies that have extensive distribution worldwide. To determine genetic differentiation of Asian cultivated rice across a latitudinal gradient, a total of 387 Asian cultivated rice varieties, five African rice varieties, and 52 wild rice accessions collected from a wide range of Asian countries and other regions were analyzed applying the InDel molecular index. The principal component analysis classified Asian cultivated rice into two distinct groups, which demonstrated significant molecular genetic differentiation of Asia cultivated rice, while all wild rice and African cultivated rice showed no evident differentiation. The results clearly indicated that Asian cultivated rice has differentiated profoundly since its domestication and during its adaptation to various environments, contrasting with wild rice and African rice. Analysis of the geographic distribution indicated a clear pattern for the different types of rice, in which indica rice varieties were found across a wide range of latitudes from -2°S to 40°N and japonica varieties were mostly focused in the high latitude areas greater than 15°N. Most intermediate types of rice originated in regions at latitudes lower than 27°N. Correlation patterns between rice types and temperature along the latitude gradients suggested that indica rice was considerably less sensitive to temperature along the latitude ranges, but japonica rice was highly sensitive to the temperature at different latitudes. The molecular genetic intermediate type of rice was also sensitive to temperature. We conclude that the distribution pattern of different types of Asian rice across large latitudinal ranges is the consequence of their adaptation in relation to ecological factors of the environment, especially temperature. This has an important implication in breeding of hybrid rice by selecting properly differentiated indica and japonica parents.
3. In order to understand the indica-japonica differentiation information in genome which linked with InDel molecular marker and to learn the molecular mechanism of indica-japonica differentiation, in this study we analyzed sequence approached closely to 34 InDel molecular markers and found:there are 50 sequences have functional domain which means these sequence could be real gene. Based on the PCR we get these sequences separately from typical indica and typical japonica. Further alignment of sequencing result showed that there are molecular variation between the sequence from typical indica 93-11 and typical japonica niponbare:Near the molecular marker R2M10, the sequences from 93-11 and niponbare have 90 bases change; R4M43, there are 19 bases change; R8M46, there are 18 variation in sequence; R3M10, there is one variation in sequence, there is one deletion mutation in japonica at the position of 420bp which make one shift mutation in related protein sequence; it was a termination beforehand in indica at the position of 609bp. Understanding these predicted gene sequences and further analysis of their domain and function, will help us to understand the selection process of indica-japonica variation. This study has very important implication in indicating the origin, differentiation and dimension of indica-japonica variation, and also in providing the genetic information for the mechanism of indica-japonica variation.
引文
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